DNA damage and the balance between survival and death in cancer biology

High-throughput 3D spheroid screens identify microRNA sensitizers for improved thermoradiotherapy in locally advanced cancers

Chemoradiotherapy is the standard of care for many locally advanced cancers, including cervical and head and neck cancers, but many patients cannot tolerate chemotherapy. Clinical trials have shown that radiotherapy combined with hyperthermia (thermoradiotherapy) may be equally effective, yet it yields a suboptimal overall survival of patients, emphasizing the need for improvement. MicroRNAs (miRNAs), short non-coding RNA sequences, are often dysregulated in cancer and exhibit significant potential as radiosensitizers by targeting genes associated with the DNA damage response. In this study, high-throughput miRNA screening of four cervical cancer cell lines identified 55 miRNAs with significant sensitizing potential, with 18 validated across 10 additional cancer cell lines (6 cervical and 4 head and neck). Functional studies of 6 miRNAs, including miR-16, miR-27a, miR-181c, miR-221, miR-224, and miR-1293, showed that they reduced DNA damage repair by downregulating ATM, DNA-PKcs, Ku70/80, and RAD51. Additionally, differential expression of miR-27a, miR-221, and miR-224 in treatment-sensitive versus treatment-resistant patients indicated their predictive biomarker potential for treatment response of cervical cancer patients. Conclusively, this study has identified 18 promising miRNAs for the development of sensitizers for thermoradiotherapy and may provide potential biomarkers for predicting treatment response in locally advanced cancers.

Flavonoids and their role in oxidative stress, inflammation, and human diseases

Oxidative stress and chronic inflammation are important drivers in the pathogenesis and progression of many chronic diseases, such as cancers of the breast, kidney, lung, and others, autoimmune diseases (rheumatoid arthritis), cardiovascular diseases (hypertension, atherosclerosis, arrhythmia), neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, Huntington's disease), mental disorders (depression, schizophrenia, bipolar disorder), gastrointestinal disorders (inflammatory bowel disease, colorectal cancer), and other disorders. With the increasing demand for less toxic and more tolerable therapies, flavonoids have the potential to effectively modulate the responsiveness to conventional therapy and radiotherapy. Flavonoids are polyphenolic compounds found in fruits, vegetables, grains, and plant-derived beverages. Six of the twelve structurally different flavonoid subgroups are of dietary significance and include anthocyanidins (e.g. pelargonidin, cyanidin), flavan-3-ols (e.g. epicatechin, epigallocatechin), flavonols (e.g. quercetin, kaempferol), flavones (e.g. luteolin, baicalein), flavanones (e.g. hesperetin, naringenin), and isoflavones (daidzein, genistein). The health benefits of flavonoids are related to their structural characteristics, such as the number and position of hydroxyl groups and the presence of C2C3 double bonds, which predetermine their ability to chelate metal ions, terminate ROS (e.g. hydroxyl radicals formed by the Fenton reaction), and interact with biological targets to trigger a biological response. Based on these structural characteristics, flavonoids can exert both antioxidant or prooxidant properties, modulate the activity of ROS-scavenging enzymes and the expression and activation of proinflammatory cytokines (e.g., interleukin-1beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α)), induce apoptosis and autophagy, and target key signaling pathways, such as the nuclear factor erythroid 2-related factor 2 (Nrf2) and Bcl-2 family of proteins. This review aims to briefly discuss the mutually interconnected aspects of oxidative and inflammatory mechanisms, such as lipid peroxidation, protein oxidation, DNA damage, and the mechanism and resolution of inflammation. The major part of this article discusses the role of flavonoids in alleviating oxidative stress and inflammation, two common components of many human diseases. The results of epidemiological studies on flavonoids are also presented.

Integrated spatial and single cell transcriptomics identifies PRKDC as a dual prognostic biomarker and therapeutic target in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality, with a pressing need for effective biomarkers and therapeutic targets. Despite the clinical use of alpha-fetoprotein (AFP) as a diagnostic biomarker, its limitations in sensitivity and specificity necessitate the identification of novel markers. In this study, we investigated the role of Protein Kinase, DNA-Activated, Catalytic Subunit (PRKDC) in HCC prognosis and its potential as a therapeutic target. Utilizing spatial transcriptomics and single-cell RNA sequencing (scRNA-seq), we dissected the cellular composition of PRKDC in HCC tissue samples, revealing its high expression in malignant cell subpopulations and its association with the tumor immune microenvironment. Through clinical signature analysis, we observed widespread PRKDC expression in HCC tissues, particularly in immune cells, highlighting its link to immune cell infiltration. Further analyses confirmed high PRKDC expression in malignant cells and its inhibitory effect on immune cell infiltration. Copy number variation (CNV) analysis revealed significant genomic instability, with PRKDC exhibiting both amplifications and deletions across chromosomal regions, underscoring its role in tumorigenesis. Functional overexpression of PRKDC in HCC cell lines enhanced cell proliferation, migration, and altered cell cycle dynamics, with a notable increase in the G2/S phase. Taken together, we first to integrate spatial transcriptomics and single-cell transcriptomics and bulk RNA-seq to reveal that PRKDC is a reliable prognostic biomarker and a potential therapeutic target. High PRKDC expression is associated with shorter survival times and an abnormal tumor microenvironment, highlighting its impact on immune cell infiltration and HCC prognosis. Targeting PRKDC could selectively inhibit its expression in tumor cells, providing new strategies for HCC treatment.

Tylophora yunnanensis extract inhibits cholesterol biosynthesis to suppress triple negative breast cancer

ETHNOPHARMACOLOGICAL RELEVANCE

Female breast cancer ranks second in incidence rate and fourth in mortality globally. Tylophora yunnanensis Schlechter (Asclepiadaceae) is frequently used in folk medicine to treat irregular menses, falls caused injuries, rheumatoid arthritis, hepatitis, gastric ulcers, and gynecological tumors.

AIMS OF THE STUDY

To explore the molecular mechanism of T. yunnanensis against breast cancer.

MATERIALS AND METHODS

Numerous experiments were implemented for detection of cell proliferation, death, toxicity, MMP, cycle, apoptosis, DNA damage, and cholesterol levels. Transcriptomic analysis, proteomic analysis, exogenous cholesterol antagonism, gene overexpression and Western blot were performed to explore the mechanism of action. A tumor-bearing animal model was utilized. The chemical composition of T. yunnanensis extract (TYE) was analyzed using LC-MS/MS.

RESULTS

TYE repressed the proliferation of BT549 and 4T1 cells, with IC50 values of 4.88, 2.98 μg/mL for 24 h and 4.70, 1.87 μg/mL for 48 h, respectively. Cell cycle arrest was also induced. The multi-omics analysis displayed that TYE suppressed cholesterol biosynthesis and interfered with DNA damage repair in TNBC cells. Exogenous cholesterol reversed these effects, counteracted the elevated intracellular TC, FC, γ-H2AX, and tail moment. TYE downregulated the expression of SQLE, MVK, FDPS, TM7SF2, and DHCR24 proteins, which was offset by addition of cholesterol. Overexpression of SQLE reduced the inhibition effects of TYE on cell viability but was not responsible for the expression inhibition of MVK, FDPS and DHCR24 proteins. TYE decreased the tumor growth, serum TC and TG, and in situ expression of ki67 and SQLE in tumor-bearing mice and had no acute toxicity to mice. No chemical components of TYE were identified.

CONCLUSION

TYE inhibits SQLE transcription to decrease its protein expression, reduces cholesterol biosynthesis and accumulation, impedes DNA damage repair, leading to cell cycle arrest, and thus elicits cell death, followed by obstruction of breast cancer progression. T. yunnanensis may be a novel anti-breast cancer agent owing to its inhibitory effects on cholesterol biosynthesis.

Impact of radiation therapy on the immunological tumor microenvironment

External beam radiation therapy (RT) is a cornerstone of modern cancer management, being utilized in both curative and palliative settings due to its safety, efficacy, and widespread availability. A primary biological effect of RT is DNA damage, which leads to significant cytostatic and cytotoxic effects. Importantly, malignant cells possess a limited capacity for DNA repair compared to normal cells, and when combined with irradiation techniques that minimize damage to healthy tissues, this creates an advantageous therapeutic window. However, the clinical effectiveness of RT also appears to involve both direct and indirect interactions between RT and non-transformed components of the tumoral ecosystem, particularly immune cells. In this review, we describe the molecular and cellular mechanisms by which irradiated cancer cells modify the immunological tumor microenvironment and how such changes ultimately impact tumor growth.

Multifunctional Janus Nanoparticles Capable of Anchoring to the Cell Membrane and Serving as "Cellular Backpacks" for Advanced Theranostics

A cell-based theranostic system can be fabricated by attaching nanomedicines to the surface of carrier cells, but it remains a challenge to achieve the attachment without involving endocytosis. Herein, we address this challenge by developing multifunctional Janus nanoparticles with orthogonal surface properties for the two opposite halves. When incubated with carrier cells, the hydrophobic half made of polystyrene readily inserts into the plasma membrane, whereas the hydrophilic SiO2 half grafted with poly(ethylene glycol) protrudes away from the cell surface. Additionally, the SiO2 half can be made with a cavity to hold theranostic agents and thus serves as a "backpack" for the carrier cell. By confining the theranostic agents in the SiO2 compartment and outside the carrier cell during the delivery process, their adverse impact on the cell is minimized. Upon release in an in vitro spheroid model, the agents quickly eradicate cancer cells. Moreover, the polystyrene half can be loaded with superparamagnetic nanoparticles to enhance magnetic resonance imaging contrast and enable magnetic manipulation, facilitating image-guided and target-directed treatments. By further optimizing the interactions between the multifunctional Janus nanoparticles and carrier cells, this system can be developed into a robust platform for cell-based theranostics.

Sequential metabolic probes illuminate nuclear DNA for discrimination of cancerous and normal cells

Elucidating the timing and spatial distribution of DNA synthesis within cancer cells is vital for cancer diagnosis and targeted therapy. However, current probes for staining nucleic acids rely on electrostatic interactions and hydrogen bonds with the nucleic acid, resulting in "static" DNA staining and the inability to distinguish cell types. Here, we present a proof-of-concept study of sequential metabolic probes, for the first time allowing for cancer-cell-specific illumination of DNA. This breakthrough is achieved by the combination of a "dual-locked" nucleoside analog VdU-Lys, and a new tetrazine-based bioorthogonal probe. Specifically, 5-vinyl-2'-deoxyuridine (VdU) release is only conducted in programmatically triggered histone deacetylases (HDACs) and cathepsin L (CTSL) as "sequential keys", enabling the modification of vinyl groups into the nuclear DNA of cancerous cells rather than normal cells. Subsequently, tetrazine-based Et-PT-Tz could in situ light-up DNA containing VdUs with significant fluorescence illumination (120-fold enhancement) through rapid bioorthogonal reaction. We demonstrated the compatibility of our probe in cancer-specific sensing of DNA with a high signal-to-noise ratio ranging from in vitro multiple cell lines to whole-organism scale. This approach would serve as a benchmark for the development of cell-specific metabolic reporters for DNA labelling, to characterize DNA metabolism in various types of cell lines.

Perspectives on cancer therapy-synthetic lethal precision medicine strategies, molecular mechanisms, therapeutic targets and current technical challenges

In recent years, synthetic lethality has become an important theme in the field of targeted cancer therapy. Synthetic lethality refers to simultaneous defects in two or more genes leading to cell death, whereas defects in any single gene do not lead to cell death. Taking advantage of the genetic vulnerability that exists within cancer cells, it theoretically has no negative impact on healthy cells and has fewer side effects than non-specific chemotherapy. Currently, targeted cancer therapies focus on inhibiting key pathways in cancer. However, it has been found that over-activation of oncogenic-related signaling pathways can also induce cancer cell death, which is a major breakthrough in the new field of targeted therapies. In this review, we summarize the conventional gene targets in synthetic lethality (PARP, ATR, ATM, WEE1, PRMT) and provide an in-depth analysis of their latest potential mechanisms. We explore the impact of over-activation of pathways such as PI3K/AKT, MAPK, and WNT on cancer cell survival, and present the technical challenges of current research. Important theoretical foundations and insights are provided for the application of synthetic lethal strategies in cancer therapy, as well as future research directions.

Triple-negative breast cancer molecular subtypes and potential detection targets for biological therapy indications

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer associated with poor prognosis. While chemotherapy remains the conventional treatment approach, its efficacy is limited and often accompanied by significant toxicity. Advances in precision-targeted therapies have expanded treatment options for TNBC, including immunotherapy, poly (ADP-ribose) polymerase inhibitors, androgen receptor inhibitors, cell cycle-dependent kinase inhibitors, and signaling pathway inhibitors. However, the heterogeneous nature of TNBC contributes to variations in treatment outcomes, underscoring the importance of identifying intrinsic molecular subtypes for personalized therapy. Additionally, due to patient-specific variability, the therapeutic response to targeted treatments is inconsistent. This highlights the need to strategize patients based on potential therapeutic targets for targeted drugs to optimize treatment strategies. This review summarizes the classification strategies and immunohistochemical (IHC) biomarkers for TNBC subtypes, along with potential targets for identifying indications for targeted drug therapy. These insights aim to support the development of personalized treatment approaches for TNBC patients.

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.

Discovery of novel quinazoline derivatives containing trifluoromethyl against cell proliferation by targeting werner helicase

A series of novel 2-trifluoromethyl-4-aminoquinazoline derivatives were designed and synthesized, and their antitumor activities were evaluated. Among them, several target compounds exhibited nanomolar inhibitory activities against K562 and LNCaP. Meanwhile, the results of in vitro and in vivo activity evaluation showed that compound 9 had the significant selective anticancer activity and the lower toxicity. The target prediction and pathway analysis showed that the mechanism of compound 9 on the proliferation inhibitory activity of K562 and PC3 cells may be via inhibiting werner helicase (WRN) activity and affecting DNA damage repair. As expected, biological evaluation showed that compound 9 bind to WRN, significantly downregulated the expression of WRN, inhibited the MDM2/p53 pathway, to render the damaged DNA unrepaired, eventually causing mitotic arrest and cell death. Our findings provide a foundation for further research of trifluoromethyl-quinazoline-4-amines as WRN-dependent anticancer agents that targeting DNA damage repair pathway.

β-Catenin Drives the FOXC2-Mediated Epithelial-Mesenchymal Transition and Acquisition of Stem Cell Properties

Background: Aggressive forms of breast cancer, such as triple-negative breast cancer (TNBC), are associated with an increase in cancer cells that exhibit stem cell properties. The activation of the epithelial-mesenchymal transition (EMT) program, mediated by the transcription factor FOXC2, generates these stem-like cells. FOXC2 is linked to poor prognoses across various cancer types and is notably upregulated in TNBC, where it establishes and sustains these stem-like cells within the tumor population. Methods: Here, we decode the pathways regulating FOXC2 activation using EMT-enriched cell line models. Stemness was assessed using mammosphere assays and mesenchymal markers by western blot. Expression correlations with clinical data was examined using the EMTome. Results: We demonstrate that β-catenin serves as a critical mediator of mesenchymal and stemness characteristics through FOXC2 upregulation. By disrupting β-catenin, we find that FOXC2 expression, mesenchymal properties, and stemness are reduced; however, the introduction of exogenous FOXC2 expression in β-catenin deficient cells is enough to restore the mesenchymal and stemness phenotype. These findings support the idea that FOXC2 acts as the downstream regulator of β-catenin and influences both mesenchymal and stemness properties. Moreover, there is a positive correlation between the expression of β-catenin and FOXC2 in various cancer subtypes observed in clinical patient samples. Conclusions: Our study clarifies the role of the β-catenin/FOXC2 signaling axis in maintaining stemness properties, suggesting potential targets for TNBC and other cancers driven by EMT-related mesenchymal and stemness characteristics.

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.

Graphene oxide-chloroquine conjugate induces DNA damage in A549 lung cancer cells through autophagy modulation

Autophagy is a highly regulated catabolic process by which unnecessary, dysfunctional, or damaged proteins and other cellular components are degraded and recycled to promote cellular differentiation, survival, and development. In response to endogenous or exogenous stresses, cancer cells use autophagy pathways for survival through activation of complex DNA damage repair (DDR) mechanisms. In the present study, we demonstrated the genotoxicity induced in A549 lung cancer cells by exposure to the GO-Chl nanoconjugate and elucidated the role of autophagy modulation in harnessing the DNA-damage response. GO-Chl causes loss of plasma membrane integrity, cell cycle arrest, and significant genotoxicity in A549 cells. Further, elevated expression of key autophagy proteins beclin-1, ATG-7, LC-3-I/II, and SQSTM1/p62 reveal that inhibition of autophagy plays a crucial role in regulating DDR capabilities of cancer cells. The results indicate that the interplay between DDR and autophagy pathways may open new paradigms for developing effective combinatorial nanoscale drug systems against multidrug-resistance cancers.

DNA damage-induced YTHDC1 O-GlcNAcylation promotes homologous recombination by enhancing m6A binding

N6-methyladenosine (m6A) is the most prevalent internal RNA modification, and its regulators include writers, readers and erasers. m6A is under stringent control and takes part in many biological events, but it is not known whether there is an interplay between m6A and glycosylation. Here we investigated an m6A reader, YTHDC1, which has been shown to be recruited to the DNA-RNA hybrid at DNA damage sites and regulate homologous recombination (HR) during DNA damage repair. We found that YTHDC1 is subject to O-linked β-N-acetylglucosamine (O-GlcNAc) modification at Ser396 upon DNA damage, which is pivotal for YTHDC1 chromatin binding and ionization radiation induced focus (IRIF) formation. RNA immunoprecipitation (RIP) and molecular dynamics (MD) simulations indicate that O-GlcNAcylation is vital for YTHDC1 to bind with m6A RNA. Fluorescence recovery after photo bleaching (FRAP) analysis revealed that YTHDC1 O-GlcNAcylation is essential for DNA damage-induced YTHDC1-m6A condensate formation. We further demonstrate that YTHDC1 O-GlcNAcylation promotes HR-mediated DNA damage repair and cell survival, probably through recruitment of Rad51 to the damage sites. We propose that YTHDC1 O-GlcNAcylation is instrumental for HR.

Wavelength-dependency of the impact of light on proliferation and DNA damage of corneal cells in vitro

The wavelength-dependent impact of light has been mainly studied focusing on retina. In particular, an opposite effect of the two ends of the visible spectrum was observed, with blue wavelengths being harmful and red wavelengths being protective. However, few studies on the cornea indicate that the increasing exposition to artificial light due to digital devices is linked to an increase in computer vision syndrome affecting the cornea. In this study, we aim at deciphering the impact of blue and red LED light on a primary culture of corneal endothelial cells, by looking at cell death and proliferation, and at DNA replication and DNA breaks. Our results show that exposure to blue light at 5.35 J/cm2 (455 nm) induces the inhibition of DNA replication and cell proliferation, and the formation of DNA breaks, highlighted by the formation of γH2AX foci and DNA fragmentation. Addition of red light at 0.3 J/cm2 (630 nm) to blue light mitigates the formation of DNA damage and delays the kinetics of formation and repair of the damage. Interestingly, exposure of the corneal cells to red light alone induces the formation of γH2AX foci that do not correspond to DNA breaks, but to DNA replication forks in proliferative cells. Our results highlight the wavelength-dependent effect of light on the cornea, and point out that the formation of γH2AX foci is not always representative of DNA breaks. This emphasizes the importance of light spectrum in eye health, an important issue in today's changing light environment.

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.

HDGF Knockout Suppresses Colorectal Cancer Progression and Drug Resistance by Modulating the DNA Damage Response

Colorectal cancer (CRC) is a highly heterogeneous gastrointestinal malignancy. Despite significant advances in molecular targeted therapies for CRC in recent years, the increase in the overall survival rates for CRC patients remains limited. Therefore, there is an urgent need to explore novel drug targets. Herein, we show that heparin binding growth factor (HDGF) is highly expressed in CRC, and that its overexpression is associated with a poor disease-free interval. Additionally, we reveal that HDGF knockout reduces proliferation, migration, and invasion, while enhancing apoptosis in CRC cells, thereby validating HDGF as a potential therapeutic target for CRC. Mechanistically, we found that HDGF modulates DNA damage response and, by recruiting C-terminal binding protein-interacting protein (CtIP), it facilitates homologous recombination repair to influence CRC drug sensitivity. Furthermore, we propose that HDGF may serve as a recognition protein for H3K36me3, participating in the repair of damaged transcriptionally active genes, thus maintaining genomic stability in CRC.

The Evolutionary Forest of Pancreatic Cancer

SIGNIFICANCE

Although the pancreatic cancer genome has been described, it has not been explored with respect to stages of diagnosis or treatment bottlenecks. We now describe and quantify the genomic features of PDAC in the context of evolutionary metrics and in doing so have identified a novel prognostic biomarker.

Mechanistic investigation and the optimal dose based on baicalin in the treatment of ulcerative colitis-A preclinical systematic review and meta-analysis

BACKGROUND

Ulcerative colitis (UC) is a type of inflammatory bowel disease, and current treatments often fall short, necessitating new therapeutic options. Baicalin shows therapeutic promise in UC animal models, but a systematic review is needed.

METHODS

A systematic search was conducted across databases including PubMed, EBSCO, Web of Science, and Science Direct, up to March 2024, identifying randomized controlled trials (RCTs) examining baicalin's impact on UC in animal models. Seventeen studies were selected through manual screening. Meta-analyses and subgroup analyses utilized Rev Man 5.3 and Stata 15.0 software to assess symptom improvement.

RESULTS

From 1304 citations, 17 were analyzed. Baicalin significantly modulated various biomarkers: HCS (SMD = -3.91), DAI (MD = -2.75), spleen index (MD = -12.76), MDA (SMD = -3.88), IL-6 (SMD = -10.59), IL-1β (SMD = -3.98), TNF-α (SMD = -8.05), NF-κB (SMD = -5.46), TLR4 (MD = -0.38), RORγ (MD = -0.89), MCP-1 (MD = -153.25), MPO (SMD = -7.34), Caspase-9 (MD = -0.93), Caspase-3 (MD = -0.45), FasL (MD = -1.20)) and enhanced BWC (MD = 0.06), CL (MD = 1.39), ZO-1 (MD = 0.44), SOD (SMD = 3.04), IL-10 mRNA (MD = 3.14), and FOXP3 (MD = 0.45) levels. Baicalin's actions may involve the PI3K/AKT, TLR4/NF-κB, IKK/IKB, Bcl-2/Bax, Th17/Treg, and TLRs/MyD88 pathways. Optimal therapeutic outcomes were predicted at dosages of 60-150 mg/kg over 10-14 weeks.

CONCLUSION

Baicalin demonstrates a multifaceted therapeutic potential in UC, attributed to its anti-inflammatory, antioxidant, anti-apoptotic, and intestinal barrier repair properties. While higher doses and longer treatments appear beneficial, further research, particularly human clinical trials, is necessary to verify its effectiveness and safety in people.

Transcription factors, nucleotide excision repair, and cancer: A review of molecular interplay

Bulky DNA adducts are mostly formed by external factors such as UV irradiation, smoking or treatment with DNA crosslinking agents. If such DNA adducts are not removed by nucleotide excision repair, they can lead to formation of driver mutations that contribute to cancer formation. Transcription factors (TFs) may critically affect both DNA adduct formation and repair efficiency at the binding site to DNA. For example, "hotspot" mutations in melanoma coincide with UV-induced accumulated cyclobutane pyrimidine dimer (CPD) adducts and/or inhibited repair at the binding sites of some TFs. Similarly, anticancer treatment with DNA cross-linkers may additionally generate DNA adducts leading to secondary mutations and the formation of malignant subclones. In addition, some TFs are overexpressed in response to UV irradiation or chemotherapeutic treatment, activating oncogenic and anti-oncogenic pathways independently of nucleotide excision repair itself. This review focuses on the interplay between TFs and nucleotide excision repair during cancer development and progression.

Salt-inducible kinase 2 confers radioresistance in colorectal cancer by facilitating homologous recombination repair

Resistance to radiotherapy remains a critical barrier in treating colorectal cancer (CRC), particularly in cases of locally advanced rectal cancer (LARC). To identify key kinases involved in CRC radioresistance, we employed a kinase-targeted CRISPR-Cas9 library screen. This approach aimed to identify potential kinase inhibitors as radiosensitizers. Our screening identified salt-inducible kinase 2 (SIK2) as a critical factor in CRC radioresistance. Increased SIK2 expression correlated with reduced tumor regression and poorer outcomes in LARC patients undergoing neoadjuvant chemoradiotherapy. The depletion of SIK2 significantly enhanced radiation-induced apoptosis and tumor regression. Mechanistically, SIK2 interacts with valosin-containing protein (VCP), promoting its hyperphosphorylation. This modification improves VCP's capacity to extract K48-linked ubiquitin-conjugated proteins from chromatin, thus aiding the recruitment of RPA and RAD51 to DNA damage sites. This mechanism strengthens homologous recombination-mediated DNA repair, which contributes to radioresistance. Importantly, ARN-3236, a SIK2 inhibitor, markedly sensitized CRC cells to radiation both in vivo and in vitro, providing a potential strategy to overcome radioresistance. In summary, our findings reveal a novel mechanism by which SIK2 contributes to the radioresistance of CRC, proposing SIK2 as a potential therapeutic target with its inhibitor significantly enhancing CRC radiotherapy efficacy.

Metabolic Rewiring in the Face of Genomic Assault: Integrating DNA Damage Response and Cellular Metabolism

The DNA damage response (DDR) and cellular metabolism exhibit a complex, bidirectional relationship crucial for maintaining genomic integrity. Studies across multiple organisms, from yeast to humans, have revealed how cells rewire their metabolism in response to DNA damage, supporting repair processes and cellular homeostasis. We discuss immediate metabolic shifts upon damage detection and long-term reprogramming for sustained genomic stability, highlighting key signaling pathways and participating molecules. Importantly, we examine how DNA repair processes can conversely induce metabolic changes and oxidative stress through specific mechanisms, including the histone H2A variant X (H2AX)/ataxia telangiectasia mutated (ATM)/NADPH oxidase 1 (Nox1) pathway and repair-specific ROS signatures. The review covers organelle-specific responses and metabolic adaptations associated with different DNA repair mechanisms, with a primary focus on human cells. We explore the implications of this DDR-metabolism crosstalk in cancer, aging, and neurodegenerative diseases, and discuss emerging therapeutic opportunities. By integrating recent findings, this review provides a comprehensive overview of the intricate interplay between DDR and cellular metabolism, offering new perspectives on cellular resilience and potential avenues for therapeutic intervention.

Targeting Ataxia Telangiectasia-Mutated and Rad3-Related for Anaplastic Thyroid Cancer

BACKGROUND

Anaplastic thyroid cancer (ATC) is one of the most aggressive human malignancies and has a poor prognosis. Ataxia telangiectasia mutated and Rad3 related (ATR) is a key regulator for the DNA damage response and a potential target to treat cancer.

METHODS

We assessed the efficacy of BAY 1895344, an ATR inhibitor, in three ATC cell lines.

RESULTS

BAY 1895344 caused dose-response cytotoxicity in three ATC cell lines. BAY 1895344 induced S-phase and G2-phase arrest, activated caspase-3 activity and induced apoptosis in ATC cells. BAY 1895344 meaningfully retarded the tumor growth of an ATC xenograft model. BAY 1895344 therapy, combined with dabrafenib and trametinib, had synergism in vitro and revealed robust tumor growth suppression in vivo in two xenograft models of ATC harboring mutant BRAFV600E. Furthermore, the combination of BAY 1895344 with lenvatinib was more effective than either agent alone in a xenograft model of ATC.

CONCLUSIONS

These results reveal that BAY 1895344 has potential in treating ATC.

The functional regulation between extracellular vesicles and the DNA damage responses

The DNA damage response (DDR) is a crucial regulatory mechanism for the survival of organisms, and irregularity of DDR may contribute to the development of various diseases, including tumors, making it is a prominent topic in therapeutic research. Extracellular vesicles (EVs), as important mediators of intercellular communication, have been extensively studied in recent years. Notably, an increasing number of studies have revealed a strong connection between DDR and EVs. On one hand, DNA damage affects the release of EVs and their compositional content; on the other hand, EVs can dictate cell survival or death by modulating DDR in both the parental and the recipient cells. This review outlines current progress in the inter-regulatory relationship between EVs and DDR, with special emphasis on the effects of EVs derived from various sources on DDR in recipient cells. In addition, the potential applications of EVs in research and tumor therapy are discussed.

AZD1390, an Ataxia telangiectasia mutated inhibitor, enhances cisplatin mediated apoptosis in breast cancer cells

Genomic instability is often caused by deficiencies in DNA damage repair pathways, making therapeutic targeting of DDR beneficial for cancer patients with specific DDR functions. ATM kinase plays a critical role in various cellular processes and its deficiency increases sensitivity to DDR-targeted agents in different cancers. Recent studies highlight ATM inhibition as a potential clinical target, with AZD1390 being a notable ATM inhibitor due to its potent and selective inhibition, ability to accumulate at DNA breaks. The study aimed to evaluate the potential anti-cancer effects of AZD1390, a key component of the DNA damage response, in breast cancer cells. The impact of the combination of AZD1390 and cisplatin on various parameters such as cell viability, proliferation, colony formation capacity, DNA damage, reactive oxygen species (ROS) levels, mitochondrial membrane potential, cell cycle progression, and cell death in breast cancer cells was evaluated using several methodologies, including WST-1 assays, real-time cell analysis, colony formation assays, comet assays, DCF-DA, MMP/JC-1 staining assays, flow cytometry along with Western blot analysis. We found that AZD1390 and cisplatin displayed synergistic antitumor effects in breast cancer cells at low doses. Addinationaly exhibited significant anti-proliferative effects in colony formation and real-time cell proliferation experiments, increasing intracellular ROS levels and mitochondrial membrane potential.The combined treatment also arrested the cell cycle at the G2-M point. Furthermore, combination of AZD1390 with cisplatin enhances its apoptotic effects in MCF-7 and MDA-MB-231 cells. These findings could aid in developing new treatments for breast cancer that exploit the genomic instability of cancer cells.

Combined inhibition of RAD51 and CHK1 causes synergistic toxicity in cisplatin resistant cancer cells by triggering replication fork collapse

The therapeutic efficacy of the anticancer drug cisplatin is limited by acquired drug resistance. Cisplatin forms DNA crosslinks, that, if not removed, lead to replication stress. Due to this, the DNA damage response (DDR) gets activated regulating cell cycle arrest, DNA repair, cell death or survival. This makes DDR components promising targets for the development of new therapeutic approaches aiming to overcome acquired drug resistance. To this end, cisplatin-resistant bladder cancer cells were analyzed regarding their sensitivity to combination treatments with selected pharmacological DDR inhibitors. Synergistic cytolethal effects were achieved after combined treatment with low to moderate doses of the non-genotoxic RAD51-inhibitor (RAD51i) B02 and CHK1-inhibitor (CHK1i) PF477736. This effect was also found in cisplatin resistant tumor cells of other origin as well as with other RAD51i and CHK1i. Combined treatments promoted decelerated replication, S-phase blockage, accumulation of DNA strand breaks, DDR activation and stimulation of apoptotic cell death as compared to mono-treatment, which is independent of the expression of RAD51, CHK1, and PrimPol. Based on these data, we suggest combined inhibition of RAD51 and CHK1 to overcome acquired cisplatin resistance of malignant cells. We propose that the molecular mechanism of this synergistic toxicity relies on a simultaneous inactivation of two key DNA damage tolerance pathways regulating replication fork restart, thereby circumventing the activation of alternative compensatory mechanisms and, in consequence, eventually effectively triggering apoptotic cell death by replication fork collapse.

The Anti-Cancer Stem Cell Properties of Copper(II)-Terpyridine Complexes with Attached Salicylaldehyde Moieties

We report the synthesis, characterisation, and anti-breast cancer stem cell (CSC) properties of two copper(II)-terpyridine complexes with bidentate salicylaldehyde moieties (2-hydroxybenzaldehyde for 1 and 2-hydroxy-1-naphthaldehyde for 2). The copper(II)-terpyridine complexes 1 and 2 are stable in biologically relevant aqueous solutions and display micromolar potency towards breast CSCs. The most effective complex 1 is 5-fold and 6.6-fold more potent towards breast CSCs than salinomycin and cisplatin, respectively. The copper(II)-terpyridine complexes 1 and 2 also decrease the formation and viability of three-dimensionally cultured mammospheres within the micromolar range. Notably complex 1 is up to 7-fold more potent towards mammospheres than salinomycin or cisplatin. Mechanistic studies suggest that the copper(II)-terpyridine complexes 1 and 2 are able to readily enter breast CSCs, elevate intracellular reactive oxygen species levels, induce DNA damage (presumably by oxidative DNA cleavage), and evoke apoptosis that is independent of caspases. This study shows that the copper(II)-terpyridine motif is a useful building block for the design of anti-breast CSC agents and reinforces the therapeutic potential of copper coordination complexes.

The Photodynamic Agent Designed by Involvement of Hydrogen Atom Transfer for Enhancing Photodynamic Therapy

Although Type-I photodynamic therapy has attracted increasingly growing interest due to its reduced dependence on oxygen, the design of effective Type-I photosensitizers remains a challenge. In this work, we report a design strategy for Type-I photosensitizers by the involvement of hydrogen atom transfer (HAT). As a proof of concept, a HAT-involved Type-I PS, which simultaneously generates superoxide and carbon-centered radicals under light-irradiation, was synthesized. This photosensitizer is comprised of a fluorene-substituted BODIPY unit as an electron acceptor covalently linked with a triphenylamine moiety as an electron donor. Under light-irradiation, photo-induced intramolecular electron transfer occurs to generate the BODIPY anion radical and triphenylamine cation radical. The former transfers electrons to oxygen to generate O2 -⋅, while the latter loses a proton to produce a benzyl carbon-centered radical which is well characterized. The resulting carbon-centered radicals efficiently oxidize NADH by HAT reaction. This photosensitizer demonstrates remarkable photocytotoxicity even under hypoxic conditions, along with outstanding in vivo antitumor efficacy in mouse models bearing HeLa tumors. This work offers a novel strategy for the design of Type-I photosensitizers by involvement of HAT.

DNA damage of peripheral blood lymphocytes as a dual biomarker: Diagnostic and treatment response in woman breast cancer patients

BackgroundBreast cancer is the leading malignancy among women and the lack of ideal early biomarkers hampers diagnosis and treatment monitoring. Genomic instability, central to breast cancer development, makes DNA damage a potential biomarker for these purposes.ObjectiveThis study aims to evaluate the predictive value of DNA damage for diagnosis, and treatment monitoring in breast cancer, with CA 15-3, a conventional cancer biomarker, included for comparison to assess the added value of DNA damage measurement.MethodsDNA damage was measured in peripheral blood lymphocytes of 58 breast cancer patients, and 31 healthy controls, employing comet assay, both before and after treatment. Serum CA 15-3 levels were assessed at the same time points for comparison.ResultsDNA damage levels were significantly higher in cancer patients compared to healthy controls, with the most elevated levels observed in patients with advanced-stage disease, irrespective of age, sex, lifestyle, or genetic status. Post-treatment assessments showed a significant rise in DNA damage. In comparison, CA 15-3 showed less consistent relevance for diagnostic and monitoring.ConclusionsThis study underscores the greater potential of DNA damage as a consistent and reliable biomarker for breast cancer, with CA 15-3 providing complementary but less consistent data for clinical decision-making.

Quercetin exhibits cytotoxicity in cancer cells by inducing two-ended DNA double-strand breaks

Quercetin, a flavonoid, is involved in the induction of DNA double-strand breaks (DSBs), in addition to its antioxidant properties. Although DNA topoisomerase II (Top2) and reactive oxygen species (ROS) have been suggested as possible mechanisms through which quercetin induces DSBs, the exact mechanism remains unclear. In this study, we examined the mechanism of DSB induction by quercetin and its repair using HeLa cells and gene-knockout cell lines generated from human Nalm-6 cells. Immunofluorescence staining for γH2AX, a DSB marker, and analysis of the frequency of random integration of foreign DNA, which correlates with the number of DSBs and DSB repair pathways, indicated that quercetin induces DSBs in a concentration-dependent manner. The sensitivity assay suggested that the factor involved in quercetin-induced DSBs was not Top2. However, ROS was found to accumulate transiently in quercetin-treated HeLa cells. Furthermore, the addition of ascorbic acid increased the survival of quercetin-treated HeLa cells, suggesting that quercetin induces a transient accumulation of ROS, which in turn induces DSBs. The resulting DSBs were repaired primarily by non-homologous end-joining and homologous recombination, similar to X-ray-induced DSBs. Taken together, quercetin, used as a radiomimetic agent, has the potential to produce effects equivalent to those of an X ray-dose at a relatively low risk.

Transcriptomic clustering of chronic lymphocytic leukemia: molecular subtypes based on Bruton's tyrosine kinase expression levels

Historically, CLL prognostication relied on disease burden, reflected in clinical stage. Later, chromosome abnormalities and genomics suggested several CLL subtypes which were aligned with response to therapy. Gene expression profiling data identified pathways associated with CLL progression. We hypothesized that transcriptome and proteome may identify functional omics associated with CLL nosology. As a test cohort, we utilized publicly available treatment-naïve CLL transcriptomics data (n = 130) and did consensus clustering that identified BTK-expression-based clusters. The BTK-High and BTK-Low clusters were validated in public and our in-house databases (n = >550 CLL patients). To associate with functional relevance, we took samples from 151 previously treated patient with CLL and analyzed them using RNA sequencing and reverse-phase protein array. Transcript levels were strongly correlated with BTK protein levels. BTK-High subtype showed increased CCL3/CCL4 levels and disease burden such as high WBC. BTK-Low subtype showed down-regulated mRNA/proteins of DNA-repair pathway and increased DNA-damage-response, which may have contributed to enrichment of inflammatory pathway. BTK-Low subtype was rich in proapoptotic gene and protein expression and relied less on BCR pathway. High-BTK subgroup was enriched in replication/repair pathway and transcription machinery. In conclusion, profiling of 5 datasets of ~700 patients revealed unique BTK-associated expression clusters in CLL.

CO2 protects cells from iron-Fenton oxidative DNA damage in Escherichia coli and humans

While hydroxyl radical is commonly named as the Fenton product responsible for DNA and RNA damage in cells, here we demonstrate that the cellular reaction generates carbonate radical anion due to physiological bicarbonate levels. In human and Escherichia coli models, their transcriptomes were analyzed by RNA direct nanopore sequencing of ribosomal RNA and chromatography coupled to electrochemical detection to quantify oxidation products in order to follow the bicarbonate dependency in H2O2-induced oxidation. These transcriptomic studies identified physiologically relevant levels of bicarbonate focused oxidation on the guanine base favorably yielding 8-oxo-7,8-dihydroguanine (OG). In human cells, the bicarbonate-dependent oxidation was further analyzed in the metabolome by mass spectrometry, and a glycosylase-dependent qPCR assay to quantify oxidation sites in telomeres. These analyses further identify guanine as the site of oxidation when bicarbonate is present upon H2O2 exposure. Labile iron as the catalyst for forming carbonate radical anion was demonstrated by repeating the bicarbonate-dependent oxidations in cells experiencing ferroptosis, which had a >fivefold increase in redox-active iron, to find enhanced overall guanine-specific oxidation when bicarbonate was present. The complete profiling of nucleic acid oxidation in the genome, transcriptome, and metabolome supports the conclusion that a cellular Fe(II)-carbonate complex redirects the Fenton reaction to yield carbonate radical anion. Focusing H2O2-induced oxidative modification on one pathway is consistent with the highly evolved base excision repair suite of enzymes to locate G-oxidation sites for repair and gene regulation in response to oxidative stress.

Chrysophanol: A promising natural compound in cancer therapy - Mechanistic insights and future perspectives

Cancer continues to be a leading cause of death worldwide, highlighting the urgent need for the development of new therapeutic strategies. Chrysophanol, a naturally occurring anthraquinone compound, has demonstrated significant potential in cancer treatment due to its diverse biological activities. This review delves into the mechanisms through which chrysophanol exerts its anti-cancer effects, including the induction of cell cycle arrest, promotion of apoptosis, regulation of autophagy, and initiation of necrosis across various cancer cell lines. Additionally, the review discusses chrysophanol's impact on inhibiting cancer cell invasion and metastasis and its role in modulating chemotherapy sensitivity. Despite the promising therapeutic potential of chrysophanol, challenges such as poor water solubility, low bioavailability, and safety concerns remain. Comprehensive clinical trials are essential to validate its efficacy and safety. This review emphasizes chrysophanol as a promising candidate for cancer therapy and underscores the necessity for further research to fully harness its therapeutic potential.

Synergy trap for guardian angels of DNA: Unraveling the anticancer potential of phthalazinone-thiosemicarbazone hybrids through dual PARP-1 and TOPO-I inhibition

Targeting DNA repair, like PARP-1 and TOPO-I, shows promise in cancer therapy. However, resistance to single agents requires complex and costly combination strategies with significant side effects. Thus, there's an urgent need for single agents with dual inhibition. Current dual inhibitors focusing on the C-4 position of the phthalazinone core for PARP inhibition often have high molecular weights. Clinical use of PARP inhibitors is limited by hematological and other toxicities from concurrent PARP-2 inhibition. They're mainly effective in gynecological cancers, despite high PARP-1 and TOPO-I expression in various cancers. Moreover, their efficacy is limited to BRCA1-expressing breast cancer. In this study, we synthesized 27 dual inhibitors for PARP-1 and TOPO-I with molecular weights below 500 g/mol through hybridizing a phthalazinone core with a thiosemicarbazone linker. Among these, 6c demonstrated exceptional broad spectrum and potency against the NCI 60 cancer cell lines, with GI50 values from 1.65 to 5.63 µM. Notably, 6c exposed the highest PARP-1 inhibition (IC50 = 32.2 ± 3.26 nM) and a selectivity over PARP-2 (IC50 = 2844 ± 111 nM). Furthermore, 6c's inhibition of TOPO-I (IC50 = 46.2 ± 3.3 nM) surpassed the control camptothecin by eleven-fold. Mechanistically, 6c disrupted the cell cycle at the S phase, induced apoptosis, and displayed a favorable safety profile against normal cells. Compound 6c induced PARP trapping and synthetic lethality and showed high efficacy on BRCA1-expressing cell lines. So, decreasing the likelihood of cancer cell resistance to chemotherapy. Drug-likeness predictions and molecular modeling were also performed.

Cellular responses to developmental exposure to pyriproxyfen in chicken model: Contrasting embryos with and without exencephaly

The insecticide pyriproxyfen (PPF), commonly used in drinking water, has already been described as a potential neurotoxic agent in non-target organisms, particularly during embryonic development. Consequently, exposure to PPF can lead to congenital anomalies in the central nervous system. Therefore, understanding the impact of this insecticide on developing neural cells is a relevant concern that requires attention. Thus, this study aimed to investigate the effects of PPF on the proliferation, differentiation, migration, and cell death of neural cells by comparing embryos that develop exencephaly with normal embryos, after exposure to this insecticide. Chicken embryos, used as a study model, were exposed to concentrations of 0.01 and 10 mg/L PPF on embryonic day E1 and analyzed on embryonic day E10. Exposed embryos received 50 μL of PPF diluted in vehicle solution, and control embryos received exclusively 50 μL of vehicle solution. After exposure, embryos were categorized into control embryos, embryos with exencephaly exposed to PPF, and embryos without exencephaly exposed to PPF. The results showed that although the impact was differentiated in the forebrain and midbrain, both brain vesicles were affected by PPF exposure, and this was observed in embryos with and without exencephaly. The most evident changes observed in embryos with exencephaly were DNA damage accompanied by alterations in cell proliferation, increased apoptosis, and reduced neural differentiation and migration. Embryos without exencephaly showed DNA damage and reduced cell proliferation and migration. These cellular events directly interfered with the density and thickness of neural cell layers. Together, these results suggest that PPF exposure causes cellular damage during neurogenesis, regardless of whether embryos display or do not display external normal morphology. This nuanced understanding provides important insights into the neurotoxicity of PPF and its potential effects on inherent events in neurogenesis.

A Nucleophilicity-Engineered DNA Ligation Blockade Nanoradiosensitizer Induces Irreversible DNA Damage to Overcome Cancer Radioresistance

During fractionated radiotherapy, DNA damage repair intensifies in tumor cells, culminating in cancer radioresistance and subsequent radiotherapy failure. Despite the recent development of nanoradiosensitizers targeting specific DNA damage repair pathways, the persistence of repair mechanisms involving multiple pathways remains inevitable. To address this challenge, a nucleophilicity-engineered DNA ligation blockade nanoradiosensitizer (DLBN) comprising Au/CeO2 heteronanostructure modified with trans-acting activator of transcription peptides is reported, which targets and inhibits the DNA ligation inside cancer cell nuclei via heterointerface-mediated dephosphorylation of DNA, a crucial step in overcoming cancer radioresistance. First, the Schottky-type heteronanostructure of cancer cell nucleus-targeting DLBN effectively intensifies radiation-induced DNA damage via catalase-mimetic activity and radiation-triggered catalytic reactions. Notably, by leveraging Au/CeO2 heterointerface, DLBN spontaneously dissociates H2O to hydroxide, a nucleophile with higher nucleophilicity, thereby exhibiting remarkable dephosphorylation capability at DNA nicks through facilitated nucleophilic attack. This enables the blockade of DNA ligation, a pivotal step in all DNA damage repair pathways, effectively interrupting the repair process. Consequently, DLBN resensitizes radioresistant cells by overcoming therapy-induced radioresistance, leading to a substantial accumulation of unrepaired DNA damage. These findings offer insight into the dephosphorylation of DNA within nuclei, and underscore the potential of heteronanostructure-based nanoradiosensitizer to block DNA ligation against therapy-induced radioresistance.

Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade

Tardigrades are captivating organisms known for their resilience in extreme environments, including ultra-high-dose radiation, but the underlying mechanisms of this resilience remain largely unknown. Using genome, transcriptome, and proteome analysis of Hypsibius henanensis sp. nov., we explored the molecular basis contributing to radiotolerance in this organism. A putatively horizontally transferred gene, DOPA dioxygenase 1 (DODA1), responds to radiation and confers radiotolerance by synthesizing betalains-a type of plant pigment with free radical-scavenging properties. A tardigrade-specific radiation-induced disordered protein, TRID1, facilitates DNA damage repair through a mechanism involving phase separation. Two mitochondrial respiratory chain complex assembly proteins, BCS1 and NDUFB8, accumulate to accelerate nicotinamide adenine dinucleotide (NAD+) regeneration for poly(adenosine diphosphate-ribosyl)ation (PARylation) and subsequent poly(adenosine diphosphate-ribose) polymerase 1 (PARP1)-mediated DNA damage repair. These three observations expand our understanding of mechanisms of tardigrade radiotolerance.

The PPP2R1A cancer hotspot mutant p.R183W increases clofarabine resistance in uterine serous carcinoma cells by a gain-of-function mechanism

PURPOSE

Uterine serous carcinoma (USC) is generally associated with poor prognosis due to a high recurrence rate and frequent treatment resistance; hence, there is a need for improved therapeutic strategies. Molecular analysis of USC identified several molecular markers, useful to improve current treatments or identify new druggable targets. PPP2R1A, encoding the Aα subunit of the tumor suppressive Ser/Thr phosphatase PP2A, is mutated in up to 40% of USCs. Here, we investigated the effect of the p.R183W PPP2R1A hotspot variant on treatment response to the nucleoside analogue clofarabine.

METHODS AND RESULTS

USC cells stably expressing p.R183W Aα showed increased resistance to clofarabine treatment in vitro and, corroborated by decreased clofarabine-induced apoptosis, G1 phase arrest, DNA-damage (γH2AX) and activation of ATM and Chk1/2 kinases. Phenotypic rescue by pharmacologic PP2A inhibition or dicer-substrate siRNA (dsiRNA)-mediated B56δ subunit knockdown supported a gain-of-function mechanism of Aα p.R183W, promoting dephosphorylation and inactivation of deoxycytidine kinase (dCK), the cellular enzyme responsible for the conversion of clofarabine into its bioactive form. Therapeutic assessment of related nucleoside analogues (gemcitabine, cladribine) revealed similar effects, but in a cell line-dependent manner. Expression of two other PPP2R1A USC mutants (p.P179R or p.S256F) did not affect clofarabine response in our cell models, arguing for mutant-specific effects on treatment outcome as well.

CONCLUSIONS

While our results call for PPP2R1A mutant and context-dependent effects upon clofarabine/nucleoside analogue monotherapy, combining clofarabine with a pharmacologic PP2A inhibitor proved synergistically in all tested conditions, highlighting a new generally applicable strategy to improve treatment outcome in USC.

Plant‐Derived Phytochemicals and Their Nanoformulations for Inducing Programed Cell Death in Cancer

Phytochemicals are a diverse class of compounds found in various plant‐based foods and beverages that have displayed the capacity to exert powerful anticancer effects through the induction of programed cell death (PCD) in malignancies. PCD is a sophisticated process that maintains in upholding tissue homeostasis and eliminating injured or neoplastic cells. Phytochemicals have shown the potential to induce PCD in malignant cells through various mechanisms, including modulation of cell signaling pathways, regulation of reactive oxygen species (ROS), and interaction with critical targets in cells such as DNA. Moreover, recent studies have suggested that nanomaterials loaded with phytochemicals may enhance cell death in tumors, which can also stimulate antitumor immunity. In this review, a comprehensive overview of the current understanding of the anticancer effects of phytochemicals and their potential as a promising approach to cancer therapy, is provided. The impacts of phytochemicals such as resveratrol, curcumin, apigenin, quercetin, and some approved plant‐derived drugs, such as taxanes on the regulation of some types of PCD, including apoptosis, pyroptosis, anoikis, autophagic cell death, ferroptosis, and necroptosis, are discussed. The underlying mechanisms and the potential of nanomaterials loaded with phytochemicals to enhance PCD in tumors are also explained.

Isolation and comparative genotoxicity screening of trichokonins VI and VIII on CHO-K1 cells

Peptaibols are fungal peptides that exhibit efficacy against pathogen microorganisms. Trichokonin VI (TK-VI) and trichokonin VIII (TK-VIII) are known peptaibols isolated from the endolichenic fungi Hypocrea sp. Previous investigations reported that trichokonin VI presents antiproliferative effects on tumor cells. This study is pioneering in elucidating the genotoxic effects of TK-VI and TK-VIII, contributing to the thorough assessment of their safety as potential therapeutic agents. The present investigation aimed to evaluate the genotoxicity of TK-VI and TK-VIII on CHO-K1 cells. Cytotoxicity was evaluated using the XTT assay and clonogenic survival assays, followed by evaluation of DNA damage using the comet assay and micronucleus test conducted in vitro. The XTT assay results indicated IC50 values of 10.30 µM and 9.89 µM for TK-VI and TK-VIII, respectively. The clonogenic survival assay indicated that concentrations of 10 µM or higher completely inhibited the cell colony formation. In the comet assay, both TK-VI and TK-VIII increased the DNA damage score and the frequency of comet nuclei in all tested concentrations. In the micronucleus assay, TK-VI and TK-VIII at 10 µM increased the frequency of MN in CHO-K1 cells. Both TK-VI and TK-VIII exhibited genotoxic effects. Our findings underscore the importance of considering the genotoxicological safety of peptaibols, particularly when assessing their potential for other biological activities.

Cannabidiol and fluorinated derivative anti-cancer properties against glioblastoma multiforme cell lines, and synergy with imidazotetrazine agents

BACKGROUND

Glioblastoma multiforme (GBM) is an aggressive cancer with poor prognosis, partly due to resistance to the standard chemotherapy treatment, temozolomide (TMZ). Phytocannabinoid cannabidiol (CBD) has exhibited anti-cancer effects against GBM, however, CBD's ability to overcome common resistance mechanisms to TMZ have not yet been investigated. 4'-Fluoro-cannabidiol (4'-F-CBD, or HUF-101/PECS-101) is a derivative of CBD, that exhibits increased activity compared to CBD during in vivo behavioural studies.

METHODS

This anti-cancer activity of cannabinoids against GBM cells sensitive to and representing major resistance mechanisms to TMZ was investigated. Cannabinoids were also studied in combination with imidazotetrazine agents, and advanced mass spectrometry with the 3D OrbiSIMS was used to investigate the mechanism of action of CBD.

RESULTS

CBD and 4'-F-CBD were found to overcome two major resistance mechanisms (methylguanine DNA-methyltransferase (MGMT) overexpression and DNA mismatch repair (MMR)-deficiency). Synergistic responses were observed when cells were exposed to cannabinoids and imidazotetrazine agents. Synergy increased with T25 and 4'-F-CBD. 3D OrbiSIMS analysis highlighted the presence of methylated-DNA, a previously unknown anti-cancer mechanism of action of CBD.

CONCLUSIONS

This work demonstrates the anti-cancer activity of 4'-F-CBD and the synergy of cannabinoids with imidazotetrazine agents for the first time and expands understanding of CBD mechanism of action.

PTPRT loss enhances anti-PD-1 therapy efficacy by regulation of STING pathway in non-small cell lung cancer

With the revolutionary progress of immune checkpoint inhibitors (ICIs) in non-small cell lung cancer, identifying patients with cancer who would benefit from ICIs has become critical and urgent. Here, we report protein tyrosine phosphatase receptor type T (PTPRT) loss as a precise and convenient predictive marker independent of PD-L1 expression for anti-PD-1/PD-L1 axis therapy. Anti-PD-1/PD-L1 axis treatment markedly increased progression-free survival in patients with PTPRT-deficient tumors. PTPRT-deficient tumors displayed cumulative DNA damage, increased cytosolic DNA release, and higher tumor mutation burden. Moreover, the tyrosine residue 240 of STING was identified as a direct substrate of PTPRT. PTPRT loss elevated phosphorylation of STING at Y240 and thus inhibited its proteasome-mediated degradation. PTPRT-deficient tumors released more IFN-β, CCL5, and CXCL10 by activation of STING pathway and increased immune cell infiltration, especially of CD8 T cells and natural killer cells, ultimately enhancing the efficacy of anti-PD-1 therapy in multiple subcutaneous and orthotopic tumor mouse models. The response of PTPRT-deficient tumors to anti-PD-1 therapy depends on the tumor-intrinsic STING pathway. In summary, our findings reveal the mechanism of how PTPRT-deficient tumors become sensitive to anti-PD-1 therapy and highlight the biological function of PTPRT in innate immunity. Considering the prevalence of PTPRT mutations and negative expression, this study has great value for patient stratification and clinical decision-making.

The iron maiden: Oligodendroglial metabolic dysfunction in multiple sclerosis and mitochondrial signaling

Multiple sclerosis (MS) is an autoimmune disease, governed by oligodendrocyte (OL) dystrophy and central nervous system (CNS) demyelination manifesting variable neurological impairments. Mitochondrial mechanisms may drive myelin biogenesis maintaining the axo-glial unit according to dynamic requisite demands imposed by the axons they ensheath. The promotion of OL maturation and myelination by actively transporting thyroid hormone (TH) into the CNS and thereby facilitating key transcriptional and metabolic pathways that regulate myelin biogenesis is fundamental to sustain the profound energy demands at each axo-glial interface. Deficits in regulatory functions exerted through TH for these physiological roles to be orchestrated by mature OLs, can occur in genetic and acquired myelin disorders, whereby mitochondrial efficiency and eventual dysfunction can lead to profound oligodendrocytopathy, demyelination and neurodegenerative sequelae. TH-dependent transcriptional and metabolic pathways can be dysregulated during acute and chronic MS lesion activity depriving OLs from critical acetyl-CoA biochemical mechanisms governing myelin lipid biosynthesis and at the same time altering the generation of iron metabolism that may drive ferroptotic mechanisms, leading to advancing neurodegeneration.

Leveraging diverse cellular stress patterns for predicting clinical outcomes and therapeutic responses in patients with multiple myeloma

Tumour microenvironment harbours diverse stress factors that affect the progression of multiple myeloma (MM), and the survival of MM cells heavily relies on crucial stress pathways. However, the impact of cellular stress on clinical prognosis of MM patients remains largely unknown. This study aimed to provide a cell stress-related model for survival and treatment prediction in MM. We incorporated five cell stress patterns including heat, oxidative, hypoxic, genotoxic, and endoplasmic reticulum stresses, to develop a comprehensive cellular stress index (CSI). Then we systematically analysed the effects of CSI on survival outcomes, clinical characteristics, immune microenvironment, and treatment sensitivity in MM. Molecular subtypes were identified using consensus clustering analysis based on CSI gene profiles. Moreover, a prognostic nomogram incorporating CSI was constructed and validated to aid in personalised risk stratification. After screening from five stress models, a CSI signature containing nine genes was established by Cox regression analyses and validated in three independent datasets. High CSI was significantly correlated with cell division pathways and poor clinical prognosis. Two distinct MM subtypes were identified through unsupervised clustering, showing significant differences in prognostic outcomes. The nomogram that combined CSI with clinical features exhibited good predictive performances in both training and validation cohorts. Meanwhile, CSI was closely associated with immune cell infiltration level and immune checkpoint gene expression. Therapeutically, patients with high CSI were more sensitive to bortezomib and antimitotic agents, while their response to immunotherapy was less favourable. Furthermore, in vitro experiments using cell lines and clinical samples verified the expression and function of key genes from CSI. The CSI signature could be a clinically applicable indicator of disease evaluation, demonstrating potential in predicting prognosis and guiding therapy for patients with MM.

Mechanisms of cytotoxicity in six classes of ionic liquids: Evaluating cell cycle impact and genotoxic and apoptotic effects

Ionic liquids (ILs), earlier praised for their eco-friendliness, have emerged as key chemicals in advancing green chemistry, catalysis, solvent development, and more. However, the discovery of their notable toxicity has led to a controversial reputation of ILs and has shifted the research landscape towards understanding their biological impacts. The present study examines the mechanism of cytotoxicity of 32 ILs across six classes, highlighting their effects on the cell cycle of the Jurkat cell line. Focusing on five ILs with pronounced cytotoxicity, we uncover their genotoxic effects and their role in inducing apoptosis. Our findings suggest intricate interplay between the extrinsic and intrinsic apoptotic pathways at different time points after exposure to ILs. Moreover, the ILs studied displayed marked genotoxicity, likely stemming from the accumulation of double-strand DNA breaks in the Jurkat cells. This investigation offers a comprehensive view on interactions of ILs with eukaryotic cells, thereby providing new guidelines for developing safer pharmaceutical and industrial applications of these chemicals. The results not only broaden and enhance the previous perceptions but also open new avenues in research, emphasizing the dual potential of ILs in innovation and safety, and marking a significant step towards integrating chemical innovations with biological safety.

Premalignant Progression in the Lung: Knowledge Gaps and Novel Opportunities for Interception of Non-Small Cell Lung Cancer. An Official American Thoracic Society Research Statement

Rationale: Despite significant advances in precision treatments and immunotherapy, lung cancer is the most common cause of cancer death worldwide. To reduce incidence and improve survival rates, a deeper understanding of lung premalignancy and the multistep process of tumorigenesis is essential, allowing timely and effective intervention before cancer development. Objectives: To summarize existing information, identify knowledge gaps, formulate research questions, prioritize potential research topics, and propose strategies for future investigations into the premalignant progression in the lung. Methods: An international multidisciplinary team of basic, translational, and clinical scientists reviewed available data to develop and refine research questions pertaining to the transformation of premalignant lung lesions to advanced lung cancer. Results: This research statement identifies significant gaps in knowledge and proposes potential research questions aimed at expanding our understanding of the mechanisms underlying the progression of premalignant lung lesions to lung cancer in an effort to explore potential innovative modalities to intercept lung cancer at its nascent stages. Conclusions: The identified gaps in knowledge about the biological mechanisms of premalignant progression in the lung, together with ongoing challenges in screening, detection, and early intervention, highlight the critical need to prioritize research in this domain. Such focused investigations are essential to devise effective preventive strategies that may ultimately decrease lung cancer incidence and improve patient outcomes.

Development and therapeutic potential of DNA-dependent protein kinase inhibitors

The deployment of DNA damage response (DDR) combats various forms of DNA damage, ensuring genomic stability. Cancer cells' propensity for genomic instability offers therapeutic opportunities to selectively kill cancer cells by suppressing the DDR pathway. DNA-dependent protein kinase (DNA-PK), a nuclear serine/threonine kinase, is crucial for the non-homologous end joining (NHEJ) pathway in the repair of DNA double-strand breaks (DSBs). Therefore, targeting DNA-PK is a promising cancer treatment strategy. This review elaborates on the structures of DNA-PK and its related large protein, as well as the development process of DNA-PK inhibitors, and recent advancements in their clinical application. We emphasize our analysis of the development process and structure-activity relationships (SARs) of DNA-PK inhibitors based on different scaffolds. We hope this review will provide practical information for researchers seeking to develop novel DNA-PK inhibitors in the future.

CO2 protects cells from iron-Fenton oxidative DNA damage in E. coli and humans

Whereas hydroxyl radical is commonly named as the Fenton product responsible for DNA and RNA damage in cells, here we demonstrate that the cellular reaction generates carbonate radical anion due to physiological levels of bicarbonate. Analysis of the metabolome, transcriptome and, in human cells, the nuclear genome shows a consistent buffering of H2O2-induced oxidative stress leading to one common pathway, namely guanine oxidation. Particularly revealing are nanopore-based studies of direct RNA sequencing of cytosolic and mitochondrial ribosomal RNA along with glycosylase-dependent qPCR studies of oxidative DNA damage in telomeres. The focusing of oxidative modification on one pathway is consistent with the highly evolved base excision repair suite of enzymes and their involvement in gene regulation in response to oxidative stress.

Oxidative stress-mediated epigenetic remodeling, metastatic progression and cell signaling in cancer

Cancer is a serious public health issue and cases are rising at a high rate around the world. Altered production of reactive oxygen species (ROS) causes oxidative stress (OS) which plays a vital role in cancer development by disrupting signaling pathways and genomic integrity in the cellular microenvironment. In this study, we reviewed the regulation of noncoding RNAs, histone modifications, and DNA methylation which OS is involved in. These mechanisms promote cancer growth, metastasis, and resistance to chemotherapeutic agents. There is significant potential to improve patient outcomes through the development of customized medications and interventions that precisely address the role of OS in the onset and progression of cancer. Redox-modulating drugs, antioxidant-based therapies, and measures to restore regular cellular activity and OS-modulated signaling pathways are some examples of these strategies. One other hypothesis rationalizes the cancer-suppressing effect of OS, which acts as a two-edged condition that warns against the use of antioxidants for cancer treatment and management. The present study was executed to review the impact of OS on epigenetic machinery, the evolution of metastatic cancer, and how OS mediates cellular signaling. Along with, insights into the potential of targeting OS-mediated mechanisms for cancer therapy.