Hallmarks of DNA replication stress

Transcription-Replication Conflicts: Unlocking New Frontiers in Cancer

Genome instability (GIN) is a cell pathology linked to cancer promotion and tumor evolution. Transcription is an essential cellular process but also a potential source of DNA damage and GIN. Transcription-replication conflicts (TRCs) are a predominant source of GIN, and defective TRC resolution may seriously compromise genome integrity. Importantly, chromatin dynamics helps orchestrate the response to TRCs to preserve genome integrity. Multiple epigenetic deficiencies have been shown to cause transcription-induced replication stress, resulting in DNA breaks and mutations. Consistently, chromatin alterations are frequent in cancer and correlate with increased mutation burden at TRC sites in tumors. Here, we review our current knowledge of TRC processing, the consequences of its dysfunction, and its relevance in cancer. We focus on the interplay between the DNA damage response (DDR) and chromatin dynamics and discuss the clinical potential of targeting TRCs as anticancer strategies and drugging the associated epigenetic signatures.

Co-inhibition of Notch1 and ChK1 triggers genomic instability and melanoma cell death increasing the lifespan of mice bearing melanoma brain metastasis

BACKGROUND

Melanoma brain metastases (MBM) are a leading cause of death in patients with advanced disease. MBM treatment relay on targeted and immunotherapy and on stereotactic radiosurgery as gold standard. Life expectancy has improved significantly with these therapies however, targeted therapy is short lived and only about half of the patients respond to immunotherapy, while radiation is limited by melanoma cells intrinsic resistance to DNA damage. New therapeutic approaches are therefore needed to treat MBM. Here we investigate a new role of Notch1 in genomic instability and demonstrate that blockade of both Notch1 and the DNA repair factor ChK1 causes extensive DNA damage and tumor cell death increasing survival in MBM bearing mice.

METHODS

Anti-Notch1 (anti-N1) was previously described. Prexaserib, a ChK1 inhibitor, is currently in clinical trials. K457 and A375 melanoma cells were used. RNA sequencing was performed in K457 cells treated with anti-N1 and Gene Set Enrichment Analysis performed. DNA damage was evaluated by a DNA fiber assay to assess replication fork speed; and γH2AX foci count and neutral comet assay to quantify double strand breaks. Cell survival was evaluated by trypan blue and a colony formation assay. Luciferase expressing A375 cells were orthotopically inoculated in the right cerebral cortex of athymic nude mice, for in vivo evaluation of a therapy with anti-N1 and prexasertib. Survival was assessed by Kaplan-Meyer survival curves and significance assessed by a Log-rank test.

RESULTS

Notch1 blockade caused genomic instability by reducing histone availability, leading to DNA replication stress and DNA damage. This in turn, resulted in the activation of the DNA Damage Response pathway ATR/ChK1 to counter the damage. Co-inhibition of Notch1, via anti-N1, and ChK1, via prexasertib (prex), exacerbated DNA damage increasing melanoma cell death. Importantly, combination anti-N1/prex significantly improved survival of mice bearing MBMs.

CONCLUSIONS

A therapy with anti-N1/prexasertib could represent a novel treatment strategy, alone or in combination with current treatment regimens, for melanoma brain metastases.

DNA repair and the contribution to chemotherapy resistance

The DNA damage response comprises a set of imperfect pathways that maintain cell survival following exposure to DNA damaging agents. Cancers frequently exhibit DNA repair pathway alterations that contribute to their intrinsic genome instability. This, in part, facilitates a therapeutic window for many chemotherapeutic agents whose mechanisms of action often converge at the generation of a double-strand DNA break. The development of therapy resistance occurs through countless molecular mechanisms that promote tolerance to DNA damage, often by preventing break formation or increasing repair capacity. This review broadly discusses the DNA damaging mechanisms of action for different classes of chemotherapeutics, how avoidance and repair of double-strand breaks can promote resistance, and strategic directions for counteracting therapy resistance.

ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent transcription replication conflicts in triple negative breast cancer

Oncogene-induced replicative stress (RS) drives tumor progression by disrupting genome stability, primarily through transcription-replication conflicts (TRCs), which promote R-loop accumulation and trigger the DNA damage response (DDR). In this study, we investigate the role of chromatin regulators in exacerbating TRCs and R-loop accumulation in cancer. We find that in breast cancer patients, the simultaneous upregulation of MYC and the H2A.Z-specific chaperone ANP32E correlates with increased genomic instability. Genome-wide analyses reveal that ANP32E-driven H2A.Z turnover alters RNA polymerase II processivity, leading to the accumulation of long R-loops at TRC sites. Furthermore, we show that ANP32E overexpression enhances TRC formation and activates an ATR-dependent DDR, predisposing cancer cells to R-loop-mediated genomic fragility. By exploiting the vulnerability of ANP32E-expressing cancer cells to ATR inhibitors, we find that tumors relied on this DDR pathway, whose inhibition halts their pro-metastatic capacity. These findings identify ANP32E as a key driver of TRC-induced genomic instability, indicating ATR inhibition as a potential therapeutic strategy for ANP32E-overexpressing tumors.

Acorus calamus L. Essential Oil Induces Oxidative Stress and DNA Replication Disruptions in Root Meristem Cells of Two Fabaceae and Two Brassicaceae Species

Environmental concerns regarding synthetic herbicides have sparked interest in plant-derived bioactive compounds as eco-friendly alternatives. This study investigated the cellular targets of sweet flag essential oil (Acorus calamus L., SEO at IC50 concentration) in root meristem cells of Fabaceae (Vicia faba, Lupinus luteus) and Brassicaceae (Brassica napus, Arabidopsis thaliana), focusing on reactive oxygen species (ROS) accumulation (DAB, NBT staining), DNA replication dynamics (EdU labeling), and genome integrity (γ-H2AX immunocytochemistry, TUNEL assay, and DNA electrophoresis). SEO induced oxidative stress (200-250% of control depending on the species) and replication stress, causing DNA double-strand breaks in 50% of proliferating cells, confirmed by γ-H2AX/TUNEL. Consequently, cells were prolonged in the G1 phase, replication activity dropped to 70% of control in Fabaceae and 80% in Brassicaceae, and EdU incorporation intensity decreased to 80% and 70% of control, respectively. An increased proportion of cells replicating heterochromatin indicated slowed S-phase progression. Despite genotoxic effects, SEO did not trigger endoreplication, apoptotic DNA fragmentation, or extensive cell death. All species exhibited a uniform stress response, although sensitivity varied, which previously enabled the establishment of selective SEO doses between Fabaceae and Brassicaceae. These findings suggest that SEO exerts phytotoxicity by disrupting S-phase progression, supporting its potential as a selective bioherbicide.

Genetic modeling of ELP1-associated Sonic hedgehog medulloblastoma identifies MDM2 as a selective therapeutic target

Germline loss-of-function (LOF) variants in Elongator acetyltransferase complex subunit 1 (ELP1) are the most prevalent predisposing genetic events in childhood medulloblastoma (MB), accounting for ∼30% of the Sonic hedgehog (SHH) 3 subtype. The mechanism(s) by which germline ELP1 deficiency provokes SHH-MB pathogenesis remain unknown. Genetically engineered mice mimicking heterozygous Elp1 LOF (Elp1HET) seen in affected germline carriers exhibit hallmark features of premalignancy in cerebellar granule neuron progenitors (GNPs), including increased DNA replication stress, genomic instability, accelerated cell cycle, and stalled differentiation. Orthotopic transplantation of Elp1HET GNPs harboring somatic Ptch1 inactivation yields SHH-MB-like tumors with compromised p53 signaling, providing a plausible explanation for the exclusivity of ELP1-associated MBs in the SHH-3 subtype. Preclinical treatment of ELP1-mutant patient-derived xenografts with an FDA-approved MDM2 inhibitor reactivates p53-dependent apoptosis and extends survival. Our findings functionally substantiate the role of ELP1 deficiency in SHH-MB predisposition and nominate therapeutics targeting MDM2 as a rational treatment option.

Loss of protein phosphatase 4 inhibitory protein leads to genomic instability and heightens vulnerability to replication stress

Protein phosphatase 4 inhibitory protein (PP4IP) has recently emerged as a key player in cellular processes, particularly in DNA double-strand break repair and telomere maintenance, although research on its functions remains limited. To further investigate the cellular pathways involving PP4IP, we conducted transcriptomic analysis via RNA sequencing in PP4IP-knockout cells and observed an upregulation of p21 expression. This upregulation was linked to an increased population of p21-positive G1-phase cells in the absence of PP4IP. Prior studies have suggested that unresolved under-replicated DNA in mother cells, transmitted to daughter cells, can trigger a quiescent G1 phase characterized by p21 expression and the formation of p53-binding protein 1 (53BP1) nuclear bodies. Consistent with this, we found a higher proportion of 53BP1 nuclear bodies-positive G1 cells in PP4IP-knockout cells compared to controls. Additionally, PP4IP-deficient cells displayed an increased occurrence of anaphase bridges-indicative of incomplete DNA replication-without a corresponding increase in lagging chromosomes. Furthermore, PP4IP-knockout cells exhibited a heightened susceptibility to replication stress, as evidenced by an elevated frequency of replication stress-induced chromatid breaks and increased sensitivity to such stress. Collectively, these results suggest that PP4IP plays a critical role in safeguarding cells from replication stress and ensuring genomic stability.

SMARCA4 deficiency: implications for non-small cell lung cancer and management strategies, with relevance to and distinctions from thoracic undifferentiated tumor

In 2021, the fifth edition of the World Health Organization (WHO) classification of thoracic tumors introduced a new category, "Thoracic SMARCA4-deficient undifferentiated tumor", highlighting SMARCA4 deficiency as a key molecular marker for classifying as "other pulmonary epithelial tumors". SMARCA4 is a gene encoding a protein involved in chromatin remodeling, and approximately 8% of non-small cell lung cancer (NSCLC) patients exhibit SMARCA4 deletions. These patients are more prone to drug resistance, early recurrence, and unfavorable clinical outcomes. Moreover, NSCLC patients with concomitant SMARCA4 mutations may not benefit from currently available treatments, underscoring the distinctiveness of this subgroup. Thoracic SMARCA4-deficient undifferentiated tumors (SMARCA4-UT) represent distinct entities from SMARCA4-deficient non-small cell lung cancer (SMARCA4-dNSCLC). This distinction is supported by their divergent pathological characteristics, demographic profiles, and survival outcomes. NSCLC cases deficient in SMARCA4 exhibit high malignancy, yet the precise biological mechanisms underlying this phenomenon remain under intensive investigation. Pathological examination and immunohistochemistry can effectively differentiate SMARCA4-UT from SMARCA4-dNSCLC. SMARCA4-UT typically manifests as adenocarcinoma or, more rarely, as squamous cell carcinoma with undifferentiated rhabdomyoblastic morphology. Therefore, elucidating the mechanisms underlying SMARCA4 alterations in NSCLC and their regulatory roles in tumorigenesis and the microenvironment is crucial. This article aims to discuss the structure, biological functions, significance in NSCLC development, and emerging potential therapeutic strategies related to SMARCA4 while providing clinical practice guidance for NSCLC patients with SMARCA4 deletions.

NUDT16 enhances the resistance of cancer cells to DNA-damaging agents by regulating replication fork stability via reversing HMGA1 ADP-ribosylation

Precise DNA replication is the basis for maintaining cell proliferation and genome stability. Current chemotherapy drugs and radiotherapy induce cell death by aggravating replication stress, albeit with poor efficacy. The replication stress response has been shown to play fundamental roles in resistance to radiotherapy and chemotherapy. High mobility group A1 (HMGA1) promotes tumor progression by regulating autophagy, angiogenesis, and chemoresistance; however, its role in coordinating replication stress and cell cycle progression remains elusive. Our results indicated that HMGA1 recruited FANCD2 to promote DNA replication and cell cycle progression both by attenuating R-loop-induced replication stress and by protecting stalled replication forks from degradation, ultimately enhancing tumor resistance to chemotherapy and irradiation treatment. We also identified HMGA1 as a novel substrate for the dePARylase NUDT16. NUDT16 was found to suppress the binding of HMGA1 to the E3 ubiquitin ligase CHFR by removing its PARylation at Glu 50, thereby reducing its ubiquitin-proteasome pathway-mediated degradation and enhancing HMGA1 protein stability. NUDT16-HMGA1 inhibition can significantly improve the sensitivity of tumor cells to chemotherapy and irradiation treatment. Collectively, these data suggest that NUDT16 enhances the ability of tumor cells to cope with replication stress by reversing the PARylation and positively regulating the protein expression of HMGA1. Therefore, targeting the NUDT16-HMGA1 pathway may be a novel strategy to enhance the sensitivity of radiotherapy and chemotherapy.

Mechanism of DNA replication fork breakage and PARP1 hyperactivation during replication catastrophe

Ataxia telangiectasia and Rad3-related (ATR) inhibition triggers a surge in origin firing, resulting in increased levels of single-stranded DNA (ssDNA) that rapidly deplete all available RPA. This leaves ssDNA unprotected and susceptible to breakage, a phenomenon known as replication catastrophe. However, the mechanism by which unprotected ssDNA breaks remains unclear. Here, we reveal that APOBEC3B is the key enzyme targeting unprotected ssDNA at replication forks, initiating a reaction cascade that induces fork collapse and poly(ADP-ribose) polymerase 1 (PARP1) hyperactivation. Mechanistically, we demonstrate that uracils generated by APOBEC3B at replication forks are removed by UNG2, resulting in abasic sites that are subsequently cleaved by APE1 endonuclease. Moreover, we show that APE1-mediated DNA cleavage is the critical enzymatic step for PARP1 hyperactivation in cells, regardless of how abasic sites are generated on DNA. Last, we demonstrate that APOBEC3B-induced PARP1 trapping and DNA double-strand breaks drive cell sensitivity to ATR inhibition, creating a context of synthetic lethality when coupled with PARP inhibitors.

Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets

Cancer progression and therapeutic resistance are closely linked to a stemness phenotype. Here, we introduce a protein-expression-based stemness index (PROTsi) to evaluate oncogenic dedifferentiation in relation to histopathology, molecular features, and clinical outcomes. Utilizing datasets from the Clinical Proteomic Tumor Analysis Consortium across 11 tumor types, we validate PROTsi's effectiveness in accurately quantifying stem-like features. Through integration of PROTsi with multi-omics, including protein post-translational modifications, we identify molecular features associated with stemness and proteins that act as active nodes within transcriptional networks, driving tumor aggressiveness. Proteins highly correlated with stemness were identified as potential drug targets, both shared and tumor specific. These stemness-associated proteins demonstrate predictive value for clinical outcomes, as confirmed by immunohistochemistry in multiple samples. The findings emphasize PROTsi's efficacy as a valuable tool for selecting predictive protein targets, a crucial step in customizing anti-cancer therapy and advancing the clinical development of cures for cancer patients.

hTERT and SV40LgT Renal Cell Lines Adjust Their Transcriptional Responses After Copy Number Changes from the Parent Proximal Tubule Cells

Primary mouse renal proximal tubule epithelial cells (moRPTECs) were immortalized by lentivirus transduction to create hTERT or SV40LgT (LgT) cell lines. Prior work showed a more pronounced injury and repair response in LgT versus hTERT cells after chemical challenge. We hypothesized that unique genomic changes occurred after immortalization, altering critical genes and pathways. RNA-seq profiling and whole-genome sequencing (WGS) of parent, hTERT, and LgT cells showed that 92.5% of the annotated transcripts were shared, suggesting a conserved proximal tubule expression pattern. However, the cell lines exhibited unique transcriptomic and genomic profiles different from the parent cells. Three transcript classes were quite relevant for chemical challenge response-Cyps, ion channels, and metabolic transporters-each important for renal function. A pathway analysis of the hTERT cells suggested alterations in intermediary and energy metabolism. LgT cells exhibited pathway activation in cell cycle and DNA repair that was consistent with replication stress. Genomic karyotyping by combining WGS and RNA-seq data showed increased gene copy numbers in chromosome 5 for LgT cells, while hTERT cells displayed gene copy losses in chromosomes 4 and 9. These data suggest that the exaggerated transcriptional responses of LgT cells versus hTERT cells result from differences in gene copy numbers, replication stress, and the unique selection processes underlying LgT or hTERT immortalization.

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.

DNA2 and MSH2 activity collectively mediate chemically stabilized G4 for efficient telomere replication

G-quadruplexes (G4s) are widely existing stable DNA secondary structures in mammalian cells. A long-standing hypothesis is that timely resolution of G4s is needed for efficient and faithful DNA replication. In vitro , G4s may be unwound by helicases or alternatively resolved via DNA2 nuclease mediated G4 cleavage. However, little is known about the biological significance and regulatory mechanism of the DNA2-mediated G4 removal pathway. Here, we report that DNA2 deficiency or its chemical inhibition leads to a significant accumulation of G4s and stalled replication forks at telomeres, which is demonstrated by a high-resolution technology: Single molecular analysis of replicating DNA (SMARD). We further identify that the DNA repair complex MutSα (MSH2-MSH6) binds G4s and stimulates G4 resolution via DNA2-mediated G4 excision. MSH2 deficiency, like DNA2 deficiency or inhibition, causes G4 accumulation and defective telomere replication. Meanwhile, G4-stabilizing environmental compounds block G4 unwinding by helicases but not G4 cleavage by DNA2. Consequently, G4 stabilizers impair telomere replication and cause telomere instabilities, especially in cells deficient in DNA2 or MSH2.

A noncanonical role of SAT1 enables anchorage independence and peritoneal metastasis in ovarian cancer

Anchorage-independent survival of ovarian tumor cells in ascites is the initial and critical step for peritoneal metastasis. How ovarian tumor cells achieve anchorage independence remains unclear. Here we show that a noncanonical role of spermidine/spermine N1-acetyltransferase 1 (SAT1) dictates anchorage-independent cell survival and potentiates metastatic dissemination in ovarian cancer. SAT1-high cancer cells are prevalent in ascitic tumors, and high SAT1 expression in primary tumors is linked to increased peritoneal metastasis rates in ovarian cancer patients. Mechanistically, SAT1 noncanonically acetylates H3K27 domains in multiple mitosis-regulating genes, increasing their transcriptional levels and protecting disseminating cells from aberrant mitosis and mitotic cell death. Notably, the acetylation of H3K27 by SAT1 depends on the reductive carboxylation of glutamine to supply acetyl-CoA in the nucleus. SAT1 inhibition with the small-molecule inhibitor ginkgolide B attenuates the metastatic tumor burden in mouse models. We conclude that SAT1 inhibition is a promising therapeutic strategy for metastatic ovarian cancer.

Strain diversity and host specificity of the gut symbiont Gilliamella in Apis mellifera, Apis cerana and Bombus terrestris

Social bees, with their specialized gut microbiota and societal transmission between individuals, provide an ideal model for studying host-gut microbiota interactions. While the functional disparities arising from strain-level diversity of gut symbionts and their effects on host health have been studied in Apis mellifera and bumblebees, studies focusing on host-specific investigations of individual strains across different honeybee hosts remain relatively unexplored. In this study, the complete genomic sequences of 17 strains of Gilliamella from A. mellifera, Apis cerana and Bombus terrestris were analyzed. The analysis revealed that the strains of A. mellifera display a more expansive genomic and functional content compared to the strains of A. cerana and B. terrestris. Phylogenetic analysis showed a deep divergence among the Gilliamella strains from different hosts. Additionally, biochemistry tests and antibiotic susceptibility tests revealed that gut strains from A. mellifera exhibited a more extensive pathway for carbohydrate metabolism and a greater resistance to antibiotics than gut strains from A. cerana and B. terrestris. Strains from A. mellifera and A. cerana showed higher colonization efficiency and competitive ability whithin their respective host species, indicating a higher degree of host-specific adaptation of local gut microbiota. In addition, colonization by A. mellifera-derived strain triggers a stronger transcriptional response in the host than A. cerana-derived strain. The variation in the number of differentially expressed genes and the involvement of distinct signaling pathways across these two host species suggest species-specific adaptations to Gilliamella strains. These findings suggest that despite occupying similar niches in the bee gut, strain-level variations can influence microbial functions, and their impact on host physiological functions may vary across different strains.

Pericytes Promote More Vascularization than Stromal Cells via an Interleukin-6-Dependent Mechanism in Microfluidic Chips

Pericytes are a key player in vascularization, protecting endothelial cells from external harm and promoting the formation of new vessels when necessary. However, pericytic identity and its relationship with other cell types, such as mesenchymal stromal/stem cells, is highly debated. This study compares the role of pericytes and unselected stromal cells in vascularization using multichannel microfluidic chips. In both angiogenesis and vasculogenesis, pericytes promote more vessel formation than stromal cells. Pericytes can wrap around endothelial vessels acting as mural cells, while stromal cells remain separated. Whole-transcriptome sequencing confirms an upregulation of pro-vascularization genes in endothelial cell-pericyte co-cultures, while metabolism increases and inflammation decreases in stromal cell co-cultures. Treatment of stromal-endothelial cell co-cultures with either conditioned media or isolated extracellular vesicles from pericytes replicates the increase in vasculogenesis of the direct co-cultures. Cytokine quantification reveals that interleukin 6 (IL-6) is significantly increased in pericyte conditions. Blocking it with siltuximab results in a reduction of pericyte vasculogenic potential comparable to stromal cell levels, revealing that pericyte pro-vascularization is mediated by IL-6. This study provides new insights into the relationship between pericytes and endothelial cells and the elusive identity of mesenchymal stromal cells. These findings are relevant for both vascular biology and tissue engineering.

Mutations in tumor suppressor genes Vhl and Rassf1a cause DNA damage, chromosomal instability and induce gene expression changes characteristic of clear cell renal cell carcinoma

RASSF1A is frequently biallelically inactivated in clear cell renal cell carcinoma (ccRCC) due to loss of chromosome 3p and promoter hypermethylation. Here we investigated the cellular and molecular consequences of single and combined deletion of the Rassf1a and Vhl tumor suppressor genes to model the common ccRCC genotype of combined loss of function of RASSF1A and VHL. In mouse embryonic fibroblasts and in primary kidney epithelial cells, double deletion of Rassf1a and Vhl caused chromosomal segregation defects and increased formation of micronuclei, demonstrating that pVHL and RASSF1A function to maintain genomic integrity. Combined Rassf1a and Vhl deletion in kidney epithelial cells in vivo increased proliferation and caused mild tubular disorganization, but did not lead to the development of kidney tumors. Single cell RNA-sequencing unexpectedly revealed that Rassf1a or Vhl deletion both induce the expression of an overlapping set of genes in a sub-population of proximal tubule cells. Many of these genes are also upregulated in the Vhl/Trp53/Rb1 deficient mouse model of ccRCC. In other subsets of proximal tubule cells, combined Vhl/Rassf1a deletion induced the expression of additional genes that were not upregulated in each of the single knockouts. The expression of the human homologues of Rassf1a-regulated genes correlate negatively with RASSF1 expression levels in human ccRCC. Our results suggest that the loss of RASSF1A function establishes a ccRCC-characteristic gene expression pattern.

Ingenane Diterpenoids from Euphorbia peplus as Potential New CHK1 Inhibitors That Sensitize Cancer Cells to Chemotherapy

Phosphorylation of checkpoint kinase 1 at Ser-345 (p-CHK1(S345)) mediates the replication stress response in cancer cells, leading to chemotherapy resistance. Therefore, finding inhibitors of p-CHK1(S345) is currently a promising strategy to prevent acquired drug resistance. In this study, 14 ingenane diterpenoids (1-14), involving two undescribed compounds possessing an unprecedented exocyclic double bond Δ6(20), were identified from Euphorbia peplus. The inhibitory effects of the isolated compounds on p-CHK1(S345) and their structure-activity relationship (SAR) were investigated. Compounds 7 and 8 presented the strongest inhibitory effects, abrogated cell cycle arrest, and caused the accumulation of DNA damage, improving the sensitivity of cancer cells to chemotherapeutic drugs. An in vivo assay confirmed the enhancement of 8 on the anticancer effect of topotecan via blocking of p-CHK1(S345). Mechanistically, 8 increased CHK1 ubiquitination to inhibit p-CHK1(S345) via activation of protein kinase C (PKC). PKC activation was first found to enhance CHK1 ubiquitination to block p-CHK1(S345). Above all, this finding not only indicates that compound 8 could be developed as a novel CHK1 inhibitor but also reveals a previously unrecognized role of PKC in regulating cancer chemotherapy sensitivity.

Uracil processing by SMUG1 in the absence of UNG triggers homologous recombination and selectively kills BRCA1/2-deficient tumors

Resistance to poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) is the major obstacle to their effectiveness in the treatment of homologous recombination (HR)-deficient (HRD) tumors. Hence, developing alternative treatments for HRD tumors is critical. Here, we show that targeting the uracil excision pathway kills HRD tumors, including those with PARPi resistance. We found that the interplay between the two major uracil DNA glycosylases UNG and SMUG1 is regulated by nuclear nicotinamide adenine dinucleotide (NAD+), which maintains UNG at replication forks (RFs) and restrains SMUG1 chromatin binding. In the absence of UNG, SMUG1 retention on chromatin leads to persistent abasic sites, which incision by APE1 results in PARP1 hyperactivation, stalled RFs, and RAD51 foci. In HRD cells (i.e., BRCA1/2-deficient), this leads to under-replicated DNA that, when propagated throughout mitosis, results in chromosome fragmentation and cell death. Our findings open up unique possibilities for targeted therapies for HRD tumors based on UNG inhibition and uracil accumulation in the genome.

An enzymatic-independent function of palmitoyl hydrolase in cohesin loading onto chromosome

Sister chromatid cohesion is mediated by a conserved multiprotein complex called cohesin. The loading of cohesin onto chromosomes involves the RSC (remodels the structure of chromatin) chromatin remodeling complex. Here, we demonstrate that the fission yeast Phi1, a palmitoyl hydrolase inactive protein 1, serves to bridge the interaction between cohesin and the RSC complex. Phi1 interacts with Rad21 in cohesin and Snf21, the RSC complex ATPase, to promote chromosome loading of cohesin. The identified characteristic features of Phi1 are conserved in the human homologues Apt1 and Apt2, which interact with Rad21 and Brg1, the human homologue of Snf21, in an enzymatic-independent manner. Intriguingly, the cohesin-Apt1-Brg1 complex is upregulated in C4-2B prostate cancer cells, and co-depletion of Apt1 and Apt2 by small interfering RNA triggers mitotic catastrophe in these cells. In addition, Apt1 nuclear localization is associated with poor clinical outcomes in prostate cancer. These results suggest a pro-survival function against mitotic stress for the complex.

Control of Replication Stress Response by Cytosolic Fe-S Cluster Assembly (CIA) Machinery

Accurate DNA replication is essential for the maintenance of genome stability and the generation of healthy offspring. When DNA replication is challenged, signals accumulate at blocked replication forks that elicit a multifaceted cellular response, orchestrating DNA replication, DNA repair and cell cycle progression. This replication stress response promotes the recovery of DNA replication, maintaining chromosome integrity and preventing mutations. Defects in this response are linked to heightened genetic instability, which contributes to tumorigenesis and genetic disorders. Iron-sulfur (Fe-S) clusters are emerging as important cofactors in supporting the response to replication stress. These clusters are assembled and delivered to target proteins that function in the cytosol and nucleus via the conserved cytosolic Fe-S cluster assembly (CIA) machinery and the CIA targeting complex. This review summarizes recent advances in understanding the structure and function of the CIA machinery in yeast and mammals, emphasizing the critical role of Fe-S clusters in the replication stress response.

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.

Dynamics of replication timing during mammalian development

Recent developments in low-input genomics techniques have greatly advanced the analysis of the order in which DNA is replicated in the genome - that is, replication timing (RT) - and its interrelationships with other processes. RT correlates or anticorrelates with genomic-specific parameters such as gene expression, chromatin accessibility, histone modifications, and the 3D structure of the genome, but the significance of how they influence each other and how they relate to biological processes remains unclear. In this review I discuss the results of recent analyses of RT, the time at which it is remodeled and consolidated during embryogenesis, how it influences development and differentiation, and the regulatory mechanisms and factors involved.

G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation

DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork collisions with preformed G4s in the parental DNA using reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by arresting the CMG helicase. Cryo-electron microscopy structures of stalled yeast and human CMG complexes reveal that the folded G4 is lodged inside the central CMG channel, arresting translocation. The G4 stabilizes the CMG at distinct translocation intermediates, suggesting an unprecedented helical inchworm mechanism for DNA translocation. These findings illuminate the eukaryotic replication fork mechanism under normal and perturbed conditions.

Inhibition of DEK restores hematopoietic stem cell function in Fanconi anemia

Hematopoietic stem cells (HSCs) are susceptible to replication stress, which is a major contributor to HSC defects in Fanconi anemia (FA). Here, we report that HSCs relax the global chromatin by downregulating the expression of a chromatin architectural protein, DEK, in response to replication stress. DEK is abnormally accumulated in bone marrow (BM) CD34+ cells from patients with FA and in Fancd2-deficient HSCs. DEK haploinsufficiency promotes chromatin relaxation, replication stress relief, and function recovery of Fancd2-deficient HSCs. Furthermore, inhibition of DEK restores the proliferation of FA CD34+ cells in vitro and enhances their engraftment in vivo. Mechanistically, the activating transcription factor 2 (ATF2), specifically phosphorylated ATF2 at Thr69/71, was identified as a promoter of DEK transcription. Fancd2 deficiency results in p38 hyperphosphorylation, which in turn phosphorylates ATF2 at Thr69/71, leading to DEK accumulation in HSCs. In conclusion, our findings establish a functional link between chromatin relaxation and replication stress tolerance in HSCs and highlight DEK as a target for FA.

The end of the genetic paradigm of cancer

Genome sequencing of cancer and normal tissues, alongside single-cell transcriptomics, continues to produce findings that challenge the idea that cancer is a 'genetic disease', as posited by the somatic mutation theory (SMT). In this prevailing paradigm, tumorigenesis is caused by cancer-driving somatic mutations and clonal expansion. However, results from tumor sequencing, motivated by the genetic paradigm itself, create apparent 'paradoxes' that are not conducive to a pure SMT. But beyond genetic causation, the new results lend credence to old ideas from organismal biology. To resolve inconsistencies between the genetic paradigm of cancer and biological reality, we must complement deep sequencing with deep thinking: embrace formal theory and historicity of biological entities, and (re)consider non-genetic plasticity of cells and tissues. In this Essay, we discuss the concepts of cell state dynamics and tissue fields that emerge from the collective action of genes and of cells in their morphogenetic context, respectively, and how they help explain inconsistencies in the data in the context of SMT.

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.

Conventional chemotherapy: millions of cures, unresolved therapeutic index

In recent decades, millions of patients with cancer have been cured by chemotherapy alone. By 'cure', we mean that patients with cancers that would be fatal if left untreated receive a time-limited course of chemotherapy and their cancer disappears, never to return. In an era when hundreds of thousands of cancer genomes have been sequenced, a remarkable fact persists: in most patients who have been cured, we still do not fully understand the mechanisms underlying the therapeutic index by which the tumour cells are killed, but normal cells are somehow spared. In contrast, in more recent years, patients with cancer have benefited from targeted therapies that usually do not cure but whose mechanisms of therapeutic index are, at least superficially, understood. In this Perspective, we will explore the various and sometimes contradictory models that have attempted to explain why chemotherapy can cure some patients with cancer, and what gaps in our understanding of the therapeutic index of chemotherapy remain to be filled. We will summarize principles which have benefited curative conventional chemotherapy regimens in the past, principles which might be deployed in constructing combinations that include modern targeted therapies.

Cell cycle dysregulation in cancer

Cancer is a systemic manifestation of aberrant cell cycle activity and dysregulated cell growth. Genetic mutations can determine tumor onset by either augmenting cell division rates or restraining normal controls such as cell cycle arrest or apoptosis. As a result, tumor cells not only undergo uncontrolled cell division but also become compromised in their ability to exit the cell cycle accurately. Regulation of cell cycle progression is enabled by specific surveillance mechanisms known as cell cycle checkpoints, and aberrations in these signaling pathways often culminate in cancer. For instance, DNA damage checkpoints, which preclude the generation and augmentation of DNA damage in the G1, S, and G2 cell cycle phases, are often defective in cancer cells, allowing cell division in spite of the accumulation of genetic errors. Notably, tumors have evolved to become dependent on checkpoints for their survival. For example, checkpoint pathways such as the DNA replication stress checkpoint and the mitotic checkpoint rarely undergo mutations and remain intact because any aberrant activity could result in irreparable damage or catastrophic chromosomal missegregation leading to cell death. In this review, we initially focus on cell cycle control pathways and specific functions of checkpoint signaling involved in normal and cancer cells and then proceed to examine how cell cycle control and checkpoint mechanisms can provide new therapeutic windows that can be exploited for cancer therapy. SIGNIFICANCE STATEMENT: DNA damage checkpoints are often defective in cancer cells, allowing cell division in spite of the accumulation of genetic errors. Conversely, DNA replication stress and mitotic checkpoints rarely undergo mutations because any aberrant activity could result in irreparable damage or catastrophic chromosomal missegregation, leading to cancer cell death. This review focuses on the checkpoint signaling mechanisms involved in cancer cells and how an emerging understanding of these pathways can provide new therapeutic opportunities for cancer therapy.

Radiotherapy-resistant prostate cancer cells escape immune checkpoint blockade through the senescence-related ataxia telangiectasia and Rad3-related protein

BACKGROUND

The majority of patients with prostate cancer (PCa) exhibit intrinsic resistance to immune checkpoint blockade (ICB) following radiotherapy (RT). This resistance is generally attributed to the limited antigen presentation of heterogeneous cells within tumors. Here, we aimed to isolate and characterize these diverse subgroups of tumor post-RT to understand the molecular mechanisms of their resistance to ICB.

METHODS

Single-cell RNA-sequencing (scRNA-seq) was used to profile senescent cancer cell clusters induced by RT in LNCaP cells. The expression and phosphorylation levels of ataxia telangiectasia and Rad3-related protein (ATR) were assessed by immunohistochemistry in clinical samples from patients with or without RT. Co-immunoprecipitation, mutagenesis, and Western blotting were used to measure the interactions between proteins. Xenograft experiments were performed to assess the tumor immune response in the mice.

RESULTS

We identified a subset of PCa cells that exhibited resistance to RT, characterized by a reduced antigen presentation capability, which enhanced their ability to evade immune detection and resist cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) blockade. scRNA-seq revealed that the senescent state was a transient phase of PCa cells post-RT, particularly in CTLA-4 blockade treatment-resistant cells. This state was marked by increased cytosolic ATR level. Cytosolic ATR phosphorylated CD86 in its cytosolic domain and enhanced the interaction between CD86 and its E3 ligase MARCH1 through electrostatic attraction. Depletion or inhibition of Atr increased the sensitivity to immune attack and improved responses to anti-Ctla-4 antibody treatment in a mouse model.

CONCLUSIONS

Our findings indicate that the activation of cytosolic ATR, which is associated with cellular senescence, impedes the effectiveness of combined RT and ICB treatments. This discovery may provide valuable insights for improving the efficacy of combined RT and ICB therapies in PCa.

Comprehensive multi-omics analyses expose a precision therapy strategy that targets replication stress in hepatocellular carcinoma using WEE1 inhibition

INTRODUCTION

Hepatocellular carcinoma (HCC) is an extremely heterogeneous malignancy with a poor prognosis, highlighting the need to target specific vulnerabilities within the tumor during treatment.

OBJECTIVES

This study employs multi-omics analysis techniques to provide novel insights into personalized therapeutic strategies for HCC patients.

METHODS

We performed proteomic and transcriptomic sequencing on 178 and 94 clinical samples of primary HCC without prior treatment, respectively. We employed an unbiased Kinome CRISPR-Cas9 library screening approach to systematically evaluate and identify novel therapeutic strategies that specifically target replication stress (RS). The synergy between oxaliplatin and adavosertib was verified using in vitro and in vivo models, including hydrodynamic injection, patient-derived organoids, and patient-derived xenografts.

RESULTS

In both proteomic- and transcriptomic-based subtyping analyses, subtypes characterized by hyperproliferative features demonstrated the poorest prognosis and the highest levels of RS. Among all first-line chemotherapeutic agents in these analyses, oxaliplatin accumulated the highest RS levels in HCC, while resistance remained a major challenge. With unbiased Kinome CRISPR loss-of-function gene screening, WEE1 was identified as a synthetic lethal target of oxaliplatin. The synergy between the WEE1 inhibitor adavosertib and oxaliplatin has been demonstrated in multiple in vitro and in vivo models. Mechanistically, adavosertib inhibits oxaliplatin-induced homologous recombination repair and G2/M checkpoint activation, leading to the accumulation of lethal DNA damage. Furthermore, patients with HCC showing high RS levels had poor prognoses and responded well to adavosertib and oxaliplatin combination treatments. This was validated by preclinical models and unsupervised clustering analysis.

CONCLUSIONS

Our findings provide promising insights into the precise therapeutic targeting of RS in HCC at both the proteomic and transcriptomic levels. Furthermore, our study highlights the potential of combining oxaliplatin with adavosertib as a treatment approach for HCC. In this study, we analyzed 178 and 94 pairs of clinical HCC samples using proteomic and transcriptomic sequencing, respectively. We discovered that the subtype characterized by high proliferation had the worst prognosis and highest RS level. Drug screening revealed that oxaliplatin promotes RS accumulation in HCC, but its resistance remains a challenge. Through unbiased CRISPR deletion-gene screening, WEE1 was identified as a lethal target of oxaliplatin. The WEE1 inhibitor adavosertib inhibits oxaliplatin-induced DNA repair, leading to lethal DNA damage accumulation. Furthermore, our clustering analysis based on RS levels demonstrated that HCC patients with high RS levels have poorer prognoses and be more beneficial from adavosertib and oxaliplatin combination therapy. These findings support an individualized treatment approach for HCC targeting RS based on WEE1 Inhibition.

BMP signaling promotes zebrafish heart regeneration via alleviation of replication stress

In contrast to mammals, adult zebrafish achieve complete heart regeneration via proliferation of cardiomyocytes. Surprisingly, we found that regenerating cardiomyocytes experience DNA replication stress, which represents one reason for declining tissue regeneration during aging in mammals. Pharmacological inhibition of ATM and ATR kinases revealed that DNA damage response signaling is essential for zebrafish heart regeneration. Manipulation of Bone Morphogenetic Protein (BMP)-Smad signaling using transgenics and mutants showed that BMP signaling alleviates cardiomyocyte replication stress. BMP signaling also rescues neonatal mouse cardiomyocytes, human fibroblasts and human hematopoietic stem and progenitor cells (HSPCs) from replication stress. DNA fiber spreading assays indicate that BMP signaling facilitates re-start of replication forks after replication stress-induced stalling. Our results identify the ability to overcome replication stress as key factor for the elevated zebrafish heart regeneration capacity and reveal a conserved role for BMP signaling in promotion of stress-free DNA replication.

Combined inhibition of ribonucleotide reductase and WEE1 induces synergistic anticancer activity in Ewing's sarcoma cells

BACKGROUND

Ewing's sarcoma is a childhood bone and soft tissue cancer with poor prognosis. Treatment outcomes for Ewing's sarcoma patients have improved only modestly over the past decades, making the development of new treatment strategies paramount. In this study, the combined targeting of ribonucleotide reductase (RNR) and WEE1 was explored for its effectiveness against Ewing's sarcoma cells.

METHODS

The RNR inhibitor triapine and the WEE1 inhibitors adavosertib and ZN-c3 were tested in p53 wild-type and p53 mutant Ewing's sarcoma cells. The combination of adavosertib with the PARP inhibitors olaparib and veliparib was tested for comparison. Combinatorial effects were determined by flow cytometric analyses of cell death, loss of mitochondrial membrane potential and DNA fragmentation as well as by caspase 3/7 activity assay, immunoblotting and real-time RT-PCR. The drug interactions were assessed using combination index analysis.

RESULTS

RNR and WEE1 inhibitors were weakly to moderately effective on their own, but highly effective in combination. The combination treatments were similarly effective in p53 wild-type and p53 mutant cells. They synergistically induced cell death and cooperated to elicit mitochondrial membrane potential decay, to activate caspase 3/7 and to trigger DNA fragmentation, evidencing the induction of the apoptotic cell death cascade. They also cooperated to boost CHK1 phosphorylation, indicating augmented replication stress after combination treatment. In comparison, the combination of adavosertib with PARP inhibitors produced weaker synergistic effects.

CONCLUSION

Our findings show that combined inhibition of RNR and WEE1 was effective against Ewing's sarcoma in vitro. They thus provide a rationale for the evaluation of the potential of combined targeting of RNR and WEE1 in Ewing's sarcoma in vivo.

PICH, A protein that maintains genomic stability, can promote tumor growth

Genomic instability is regardedas a hallmark of cancer cells. It can be presented in many ways, among which chromosome instability has received attention. Ultrafine anaphase bridges are a typeof chromatin bridges, the untimely resolution of which can also lead to chromosome instability. PICH can play a role in maintaining chromosome stability by regulating chromosome morphologyand resolving ultrafine anaphase bridges. Recently, PICH has been found to be overexpressed in various cancers. Overexpression of PICH is related to the proliferation of tumors and poor prognosis. In this article, we consider that PICH can maintain genomic stability by regulating appropriate chromosome structure, ensuring proper chromosome segregation, and facilitating replication fork reversal. We summarize how PICH regulates chromosome stability, how PICH resolves Ultrafine anaphase bridges with other proteins, and how PICH promotes tumor progression.

PARP inhibition-associated heterochromatin confers increased DNA replication stress and vulnerability to ATR inhibition in SMARCA4-deficient cells

DNA replication stress (RS), a prevalent feature of various malignancies, arises from both genetic mutations and genotoxic exposure. Elevated RS levels increase the vulnerability of cancer cells to ataxia telangiectasia and Rad3-related kinase inhibitors (ATRis). Here, we screened for DNA damage response inhibitors that enhance ATRi-induced cytotoxicity using SWI/SNF complex-deficient cells and identified a potent synergy between ATRi and poly(ADP-ribose) polymerase inhibitor (PARPi), particularly in SMARCA4-deficient cells. PARP inhibition triggers chromatin changes, namely elevated histone H3 at lysine 9 di-methylation (H3K9me2), a hallmark of facultative heterochromatin, increasing dependence on ATR activity for replication fork progression and cell survival. Interestingly, SMARCA4 deficient cells, intrinsically vulnerable to replication stress, exhibited exacerbated DNA damage upon combined ATRi and PARPi treatment in a Mre11- and Mus81-mediated manner. In vivo, combined treatment with intermittent ATRi and continuous PARPi showed greater inhibition of tumor growth than ATRi alone in SMARCA4-deficient lung adenocarcinoma xenograft models. These findings demonstrate that PARPi-induced heterochromatin amplifies RS and ATRi susceptibility, providing a potential rationale for therapeutic strategies targeting SMARCA4-deficient tumors.

Origin of Chromosome 12 Trisomy Surge in Human Induced Pluripotent Stem Cells (iPSCs)

Cultured pluripotent stem cells are unique in being the only fully diploid immortal human cell lines. However, during continued culture, they acquire significant chromosome abnormalities. Chromosome 12 trisomy is the most common whole-chromosome abnormality found during culture of human induced pluripotent stem cells (iPSCs). The conventional paradigm is that trisomy 12 occurs very rarely but provides a proliferative advantage, enabling these cells to outcompete the diploid. Here, we challenge this prevailing model by demonstrating that trisomy 12 arises simultaneously in a very high percentage of diploid cells. Using a single cell line that reproducibly undergoes transition from diploid to trisomy 12, we found that proliferation differences alone do not account for the rapid dominance of trisomic cells. Through careful mapping by fluorescent in-situ hybridization, we identified critical transition passages where trisomic cells first appeared and swiftly gained dominance. Remarkably, single trisomic cells repeatedly emerged de novo from diploid parents. Delving deeper, we discovered an extremely high incidence of chromosome 12 anaphase bridging exclusively during transition passages, along with overrepresentation of chromosome 12 chromatids in micronuclei. These micronuclei fail to replicate during S phase. Subsequently, when these micronucleated cells enter mitosis they contain an unreplicated chromosome 12 chromatids. We also found that nearly 20% of the shorter p arms of chromosome 12 but not the longer q arms exhibited loss of subtelomeric repeats during transition passages. Chromosome 12p arms were exclusively responsible for the bridging observed in anaphase cells. Our findings unveil a novel mechanism of whole-chromosome instability in human stem cells, where chromosome 12p arm-specific segregation errors occur simultaneously in a high percentage of cells. The slight yet significant growth advantage of trisomy 12 cells allows them to persist and eventually dominate the population. Our findings detailing this novel interpretation of the origin of chromosome instability in cultured of human stem cells may have broad implications for understanding the genesis of aneuploidy across diverse biological systems.

Defective homologous recombination and genomic instability predict increased responsiveness to carbon ion radiotherapy in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is notably resistant to conventional chemotherapy and radiation treatment. However, clinical trials indicate that carbon ion radiotherapy (CIRT) with concurrent gemcitabine is effective for unresectable locally advanced PDAC. This study aimed to identify patient characteristics predictive of CIRT response. We utilized a panel of human PDAC cell lines with diverse genetic profiles to determine their sensitivity to CIRT compared to γ-rays, assessing relative biological effectiveness (RBE) at 10% survival, which ranged from 1.96 to 3.04. Increased radiosensitivity was linked to impaired DNA double-strand break (DSB) repair, particularly in cell lines with deficiencies in the homologous recombination (HR) repair pathway and/or elevated genomic instability from replication stress. Furthermore, pretreatment with the HR inhibitor B02 significantly enhanced CIRT sensitivity in a radioresistant PDAC cell line when irradiated in the spread-out Bragg peak but not at the entry position of the beam. These findings suggest that PDAC tumors with HR pathway mutations or high replication stress are more likely to benefit from CIRT while minimizing normal tissue toxicity.

Role of Oxidative Stress in the Occurrence, Development, and Treatment of Breast Cancer

Breast cancer is one of the most prevalent cancers worldwide. Recent studies have increasingly emphasized the role of oxidative stress in the initiation and progression of breast cancer. This article reviews how oxidative stress imbalance influences the occurrence and advancement of breast cancer, elucidating the intricate mechanisms through which reactive oxygen species (ROS) operate in this context and their potential therapeutic applications. By highlighting these critical insights, this review aims to enhance our understanding of oxidative stress as a potential target for innovative therapeutic strategies in the management of breast cancer.

A tale of two strands: Decoding chromatin replication through strand-specific sequencing

DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells.

Synergistic protection of nascent DNA at stalled forks by MSANTD4 and BRCA1/2-RAD51

The regressed arms of reversed replication forks exhibit structural similarities to one-ended double-stranded breaks and need to be protected against uncontrolled nucleolytic degradation. Here, we identify MSANTD4 (Myb/SANT-like DNA-binding domain-containing protein 4), a functionally uncharacterized protein that uniquely counters the replication protein A (RPA)-Bloom (BLM)/Werner syndrome helicase (WRN)-DNA replication helicase/nuclease 2 (DNA2) complex to safeguard reversed replication forks from detrimental degradation, independently of the breast cancer susceptibility proteins (BRCA1/2)-DNA repair protein RAD51 pathway. MSANTD4 specifically interacts with the junctions between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) in DNA substrates harboring a 3' overhang, which resemble the structural features of regressed arms processed by WRN-DNA2. This DNA-binding capability allows MSANTD4 to accumulate at reversed forks, strategically antagonizing the RPA-BLM/WRN-DNA2 complex by impeding its access to the ssDNA-dsDNA junction of the regressed arms. Loss of MSANTD4 exacerbates genome instability induced by replication stress in BRCA1/2-deficient cells. Our findings unveil a collaborative defense mechanism orchestrated by MSANTD4 and BRCA1/2-RAD51, effectively counteracting nucleolytic attacks on the regressed arms and synergistically preserving the integrity of reversed forks.

DNA replication stress underpins the vulnerability to oxidative phosphorylation inhibition in colorectal cancer

Mitochondrial oxidative phosphorylation (OXPHOS) is a therapeutic vulnerability in glycolysis-deficient cancers. Here we show that inhibiting OXPHOS similarly suppresses the proliferation and tumorigenicity of glycolytically competent colorectal cancer (CRC) cells in vitro and in patient-derived CRC xenografts. While the increased glycolytic activity rapidly replenished the ATP pool, it did not restore the reduced production of aspartate upon OXPHOS inhibition. This shortage in aspartate, in turn, caused nucleotide deficiencies, leading to S phase cell cycle arrest, replication fork stalling, and enrichment of the p53 pathway, manifestations of replication stress. The addition of purine nucleobases adenine and guanine along with the pyrimidine nucleoside uridine restored replication fork progression and cell proliferation, whereas the supplementation of exogenous aspartate recovered the nucleotide pool, demonstrating a causal role of the aspartate shortage in OXPHOS inhibition-induced nucleotide deficiencies and consequently replication stress and reductions in proliferation. Moreover, we demonstrate that glutamic-oxaloacetic transaminase 1 (GOT1) is critical for maintaining the minimum aspartate pool when OXPHOS is inhibited, as knockdown of GOT1 further reduced aspartate levels and rendered CRC cells more sensitive to OXPHOS inhibition both in vitro and in vivo. These results propose GOT1 targeting as a potential avenue to sensitize cancer cells to OXPHOS inhibitors, thus lowering the necessary doses to efficiently inhibit cancer growth while alleviating their adverse effects.

The RING Finger E3 Ligase RNF25 Protects DNA Replication Forks Independently of its Canonical Roles in Ubiquitin Signaling

The DNA damage response (DDR) mechanisms that allow cells to tolerate DNA replication stress are critically important for genome stability and cell viability. Using an unbiased genetic screen we identify a role for the RING finger E3 ubiquitin ligase RNF25 in promoting DNA replication stress tolerance. In response to DNA replication stress, RNF25-deficient cells generate aberrantly high levels of single-stranded DNA (ssDNA), accumulate in S-phase and show reduced mitotic entry. Using single-molecule DNA fiber analysis, we show that RNF25 protects reversed DNA replication forks generated by the fork remodeler HLTF from nucleolytic degradation by MRE11 and CtIP. Mechanistically, RNF25 interacts with the replication fork protection factor REV7 and recruits REV7 to nascent DNA after replication stress. The role of RNF25 in protecting replication forks is fully separable from its canonical functions in ubiquitin conjugation. This work reveals the RNF25-REV7 signaling axis as an important protective mechanism in cells experiencing replication stress.

Pesticide avermectin B1a exerts cytotoxicity by blocking the interaction between mini-chromosome maintenance 6 protein (MCM6) and chromatin licensing and DNA replication factor 1 (CDT1)

Avermectin B1a, a widely used pesticide, has recently raised safety concerns since it possesses potential cytotoxicity toward mammalian cells. Nevertheless, the exact mechanisms that underlie the cytotoxicity induced by avermectin B1a remain elusive. The loading of the mini-chromosome maintenance 6 protein (MCM6) onto chromatin at replication origins by chromatin licensing and DNA replication factor 1 (CDT1) is an essential step for licensing DNA for replication. Here, we first report that avermectin B1a occupies the CDT1-binding domain (CBD) of MCM6 to block the interaction between MCM6 and CDT1 and thus inhibits the licensing for DNA replication. Avermectin B1a inhibits the proliferation with IC50 being 15.1 μM and induces cell cycle arrest at the G0/G1 phase in MEF cells. Moreover, abnormal replication licensing induced by avermectin B1a causes replication stress and DNA double strand breaks, which in turn leads to apoptosis in MEF cells. Further molecular docking uncovers that four residues Glu763, Ile760, Arg771, and Glu774 are vital for the formation of hydrogen bonds in avermectin B1a-CBD interaction. Furthermore, the upregulation of MCM6 or/and CDT1 reverses the avermectin B1a-induced decrease in cell viability and normalizes the cell cycle, indicating that the blockage of MCM6-CDT1 interaction is one of the mechanisms underlying avermectin B1a-induced cytotoxicity. This study not only provides new insights into the mechanism of avermectin B1a-induced cytotoxicity but also offers a useful molecular tool for the investigation of MCM6-CDT1 interaction.

Fetal hepatocytes protect the HSPC genome via fetuin-A

The maintenance of genomic integrity in rapidly proliferating cells is a substantial challenge during embryonic development1-3. Although numerous cell-intrinsic mechanisms have been revealed4-7, little is known about genome-protective effects and influences of developmental tissue microenvironments on tissue-forming cells. Here we show that fetal liver hepatocytes provide protection to haematopoietic stem and progenitor cell (HSPC) genomes. Lineage tracing and depletion in mice demonstrated that delayed hepatocyte development in early fetal livers increased the chromosomal instability of newly colonizing HSPCs. In addition, HSPCs developed tolerance to genotoxins in hepatocyte-conditioned medium, suggesting that hepatocytes protect the HSPC genome in a paracrine manner. Proteomic analyses demonstrated the enrichment of fetuin-A in hepatocyte-conditioned medium but not in early fetal livers. Fetuin-A activates a Toll-like receptor pathway to prevent pathogenic R-loop accumulation in HSPCs undergoing DNA replication and gene transcription in the fetal liver. Numerous haematopoietic regulatory genes frequently involved in leukaemogenic mutations are associated with R-loop-enriched regions. In Fetua-knockout mice, HSPCs showed increased genome instability and susceptibility to malignancy induction. Moreover, low concentrations of fetuin-A correlated with the oncogenesis of childhood leukaemia. Therefore, we uncover a mechanism operating in developmental tissues that offers tissue-forming cell genome protection and is implicated in developmental-related diseases.

Modern biology of extrachromosomal DNA: A decade-long voyage of discovery

Genomic instability is a hallmark of cancer and is a major driving force of tumorigenesis. A key manifestation of genomic instability is the formation of extrachromosomal DNAs (ecDNAs) - acentric, circular DNA molecules ranging from 50 kb to 5 Mb in size, distinct from chromosomes. Ontological studies have revealed that ecDNA serves as a carrier of oncogenes, immunoregulatory genes, and enhancers, capable of driving elevated transcription of its cargo genes and cancer heterogeneity, leading to rapid tumor evolution and therapy resistance. Although ecDNA was documented over half a century ago, the past decade has witnessed a surge in breakthrough discoveries about its biological functions. Here, we systematically review the modern biology of ecDNA uncovered over the last ten years, focusing on how discoveries during this pioneering stage have illuminated our understanding of ecDNA-driven transcription, heterogeneity, and cancer progression. Furthermore, we discuss ongoing efforts to target ecDNA as a novel approach to cancer therapy. This burgeoning field is entering a new phase, poised to reshape our knowledge of cancer biology and therapeutic strategies.

Replication stress increases de novo CNVs across the malaria parasite genome

Changes in the copy number of large genomic regions, termed copy number variations (CNVs), contribute to important phenotypes in many organisms. CNVs are readily identified using conventional approaches when present in a large fraction of the cell population. However, CNVs that are present in only a few genomes across a population are often overlooked but important; if beneficial under specific conditions, a de novo CNV that arises in a single genome can expand during selection to create a larger population of cells with novel characteristics. While the reach of single cell methods to study de novo CNVs is increasing, we continue to lack information about CNV dynamics in rapidly evolving microbial populations. Here, we investigated de novo CNVs in the genome of the Plasmodium parasite that causes human malaria. The highly AT-rich P. falciparum genome readily accumulates CNVs that facilitate rapid adaptation to new drugs and host environments. We employed a low-input genomics approach optimized for this unique genome as well as specialized computational tools to evaluate the de novo CNV rate both before and after the application of stress. We observed a significant increase in genomewide de novo CNVs following treatment with a replication inhibitor. These stress-induced de novo CNVs encompassed genes that contribute to various cellular pathways and tended to be altered in clinical parasite genomes. This snapshot of CNV dynamics emphasizes the connection between replication stress, DNA repair, and CNV generation in this important microbial pathogen.

Integrated pan-cancer analysis and experimental verification of the roles of meiotic nuclear divisions 1 in breast cancer

INTRODUCTION

The aberrant up-regulation of meiotic nuclear division 1 (MND1) in somatic cells is considered as one of the driving factors of oncogenesis, whereas its expression and role in breast invasive cancer (BRCA) remain unclear. Hence, this study embarked on a comprehensive evaluation of MND1 across various cancers and identified its roles in BRCA.

METHODS

Based on publicly available databases, including but not limited to UCSC Xena, TCGA, GTEx, GEO, STRING, GeneMANIA, and CancerSEA, we evaluated the expression patterns, genomic features, and biological functions of MND1 from a pan-cancer viewpoint and delved into the implications of MND1 in the prognosis and treatment of BRCA. Further molecular biology experiments were undertaken to identify the role of MND1 in proliferation, migration, and apoptosis in BRCA cells.

RESULTS

Elevated levels of MND1 were notably observed in a wide array of tumor types, especially in BRCA, COAD, HNSC, LIHC, LUAD, LUSC, STAD, and UCEC. Elevated MND1 expression was markedly associated with shortened OS in several tumors, including BRCA (HR = 1.52 [95%CI, 1.10-2.09], P = 0.011). The up-regulation of MND1 in BRCA was validated in external cohorts and clinical samples. Survival analyses demonstrated that elevated MND1 expression was associated with decreased survival for patients with BRCA. Co-expressed genes of MND1 were identified, and subsequent pathway analyses based on significantly associated genes indicated that MND1 plays key roles in DNA replication, cell cycle regulation, and DNA damage repair. The observed abnormal elevation and activation of MND1 led to increased proliferation and migration, along with decreased apoptosis in BRCA cells.

CONCLUSIONS

MND1 emerges as a promising biomarker for diagnostic and therapeutic targeting in various cancers, including BRCA. The abnormal up-regulation and activation of MND1 are linked to carcinogenesis and poor prognosis among BRCA patients, which may be attributed to its involvement in HR-dependent ALT, warranting further scrutiny.

Biphasic DNA damage and non-canonical replication stress response govern radiation-induced senescence in glioblastoma

Therapy-induced senescence (TIS) in glioblastoma (GBM) residual disease and escape from TIS account for resistance and recurrence, but the mechanism of TIS manifestation remains obscure. Here, we demonstrate that replication stress (RS) is critical for the induction of TIS in residual cells by employing an in vitro GBM therapy-resistance cellular model. Interestingly, we found a 'biphasic' mode of DNA damage after radiation treatment and reveal that the second phase of DNA damage arises majorly in the S phase of residual cells due to RS. Mechanistically, we show that persistent phosphorylated ATR is a safeguard for radiation resilience, whereas the other canonical RS molecules remain unaltered during the second phase of DNA damage. Importantly, RS preceded the induction of senescence, and ATR inhibition resulted in TIS reduction, leading to apoptosis. Moreover, ATR inhibition sensitized PARP-1 inhibitor-induced enhanced TIS-mediated resistance, leading to cell death. Our study demonstrates the crucial role of RS in TIS induction and maintenance in GBM residual cells, and targeting ATR alone or in combination with a PARP-1 inhibitor will be an effective strategy to eliminate TIS for better treatment outcomes.

HROB Is Implicated in DNA Replication

DNA replication represents a series of precisely regulated events performed by a complex protein machinery that guarantees accurate duplication of the genetic information. Since DNA replication is permanently faced by a variety of exogenous and endogenous stressors, DNA damage response, repair and replication must be closely coordinated to maintain genomic integrity. HROB has been identified recently as a binding partner and activator of the Mcm8/9 helicase involved in DNA interstrand crosslink (ICL) repair. We identified HROB independently as a nuclear protein whose expression is co-regulated with various DNA replication factors. Accordingly, the HROB protein level showed a maximum in S phase and a downregulation in quiescence. Structural prediction and homology searches revealed that HROB is a largely intrinsically disordered protein bearing a helix-rich region and a canonical oligonucleotide/oligosaccharide-binding-fold motif that originated early in eukaryotic evolution. Employing a flow cytometry Förster resonance energy transfer (FRET) assay, we detected associations between HROB and proteins of the DNA replication machinery. Moreover, ectopic expression of HROB protein led to an almost complete shutdown of DNA replication. The available data imply a function for HROB during DNA replication across barriers such as ICLs.