Double-strand Breaks Research Articles

RECQL4 requires PARP1 for recruitment to DNA damage, and PARG dePARylation facilitates its associated role in end joining.

RecQ helicases, highly conserved proteins with pivotal roles in DNA replication, DNA repair and homologous recombination, are crucial for maintaining genomic integrity. Mutations in RECQL4 have been associated with various human diseases, including Rothmund-Thomson syndrome. RECQL4 is involved in regulating major DNA repair pathways, such as homologous recombination and nonhomologous end joining (NHEJ). RECQL4 has more prominent single-strand DNA annealing activity than helicase activity. Its ability to promote DNA damage repair and the precise role of its DNA annealing activity in DNA repair are unclear. Here we demonstrate that PARP1 interacts with RECQL4, increasing its single-stranded DNA strand annealing activity. PARP1 specifically promoted RECQL4 PARylation at both its N- and C-terminal regions, promoting RECQL4 recruitment to DNA double-strand breaks (DSBs). Inhibition or depletion of PARP1 significantly diminished RECQL4 recruitment and occupancy at specific DSB sites on chromosomes. After DNA damage, PARG dePARylated RECQL4 and stimulated its end-joining activity. RECQL4 actively displaced replication protein A from single-stranded DNA, promoting microhomology annealing in vitro. Furthermore, depletion of PARP1 or RECQL4 substantially impacted classical-NHEJ- and alternative-NHEJ-mediated DSB repair. Consequently, the combined activities of PARP1, PARG and RECQL4 modulate DNA repair.

Phosphorylation-dependent WRN-RPA interaction promotes recovery of stalled forks at secondary DNA structure

The WRN protein is vital for managing perturbed replication forks. Replication Protein A strongly enhances WRN helicase activity in specific in vitro assays. However, the in vivo significance of RPA binding to WRN has largely remained unexplored. We identify several conserved phosphorylation sites in the acidic domain of WRN targeted by Casein Kinase 2. These phosphorylation sites are crucial for WRN-RPA interaction. Using an unphosphorylable WRN mutant, which lacks the ability to bind RPA, we determine that the WRN-RPA complex plays a critical role in fork recovery after replication stress countering the persistence of G4 structures after fork stalling. However, the interaction between WRN and RPA is not necessary for the processing of replication forks when they collapse. The absence of WRN-RPA binding hampers fork recovery, causing single-strand DNA gaps, enlarged by MRE11, and triggering MUS81-dependent double-strand breaks, which require repair by RAD51 to prevent excessive DNA damage.

M6A -mediated lncRNA SCIRT stability promotes NSCLC progression through binding to SFPQ and activating the PI3K/Akt pathway

Non-small cell lung cancer (NSCLC) has emerged as one of the most prevalent malignancies worldwide. N6-methyladenosine (m6A) methylation, a pervasive epigenetic modification in long noncoding RNAs (lncRNAs), plays a crucial role in NSCLC progression. Here, we report that m6A modification and the expression of the lncRNA stem cell inhibitory RNA transcript (SCIRT) was significantly upregulated in NSCLC tissues and cells. Functional analysis revealed that SCIRT enhanced NSCLC cell proliferation, migration, invasion, and epithelial‒mesenchymal transition. The m6A modification of SCIRT can be installed by METTL3, which enhanced the stability of this lncRNA. Notably, SCIRT overexpression in response to DNA double-strand breaks (DSBs) sensitized cells to camptothecin (CPT) and impairs DNA homologous recombination repair. SCIRT directly interacted with SFPQ in vitro and was primarily localized in the nucleus. Furthermore, ectopic SCIRT expression upregulated SFPQ and activated the PI3K/Akt pathway following CPT treatment, suggesting an unexpected role of SCIRT in facilitating SFPQ-mediated DSB repair. In brief, our findings highlight the oncogenic role of SCIRT in NSCLC by binding SFPQ and activating PI3K/Akt signaling, presenting a promising therapeutic target for personalized NSCLC treatment.

Mangiferin Protects Mesenchymal Stem Cells Against DNA Damage and Cellular Aging via SIRT1 Activation.

The protective effects of mangiferin (MAG) against etoposide- and high glucose (HG)-induced DNA damage and aging were investigated in human bone marrow-mesenchymal stem cells (hBM-MSCs). Etoposide, a topoisomerase II inhibitor, was used to induce double-strand breaks (DSBs) in hBM-MSCs, resulting in increased genotoxicity, elevated levels of the DNA damage sensor ATM and CDKN1A, and decreased levels of the aging markers H3 and H4. MAG activated AMPK and SIRT1, thus protecting against DSB-induced damage. Following long-term exposure to HG, MAG significantly mitigated DNA damage and delayed cellular aging, as evidenced by the preservation of H3, H4, LMNB1, and SIRT1 mRNA levels and reduction in γ-H2AX foci and DSBs. Furthermore, MAG improved genome stability, as indicated by decreased LINE1 expression and increased levels of the heterochromatin marker TRIM28, thereby maintaining H3K9me3 levels. MAG and metformin treatment enhanced cell proliferation, reduced senescence-associated β-galactosidase staining, and lowered the levels of the senescence-associated secretory phenotype factors IL-1A, IL-1B, IL-6, IL-8, CCL2, and CCL20 and senescence marker CDKN1A, CDKN2A and p53. MAG may reduce DNA damage and delay aging in hBM-MSCs under HG conditions, highlighting their potential as therapeutic agents for aging-related diseases.

Abstract P011: STN1 (OBFC1) promotes DNA double-strand break repair in a potentially CTC1-STN1-TEN1 (CST) complex-independent role in pancreatic cancer

Abstract Purpose: Pancreatic cancer (PC) is an aggressive lethal tumor with an unmet need for novel therapeutic approaches. KRAS activating mutations occur in 90-95% of PC and contribute to tumor progression and resistance to therapy, including radiation. The mechanisms by which oncogenic KRAS promotes radiation resistance are critical to understand in order to identify novel therapies. Methods: We first analyzed the expression levels of DNA damage response and repair genes using Affymetrix RNA expression microarray in isogenic HCT116 and SW48 cells with KRAS wide-type and KRASG13D activating mutations to identify novel targets by which KRAS mutations may confer radiation resistance. We analyzed the expression of STN1 in pancreas normal and cancer tissues and assessed the correlation with PC clinical outcomes using TCGA dataset. Human tumor xenografts were generated to explore the role of STN1 on tumor growth in vivo. Radiation response was assessed through clonogenicity and gH2AX foci assays. Homologous recombination (HR) and non-homologous end joining (NHEJ) repair reporter assays, chromatin spreading assay, cell cycle analysis, mitotic catastrophe, Annexin-V assays were performed to investigate the mechanisms of radiation-induced cell death. Mass spectrometry analysis was performed to identify STN1 interacting proteins important in DNA damage response and further validated by immunoprecipitation and immunoblotting. Results: We find that KRAS activation increases STN1 expression to enhance DNA double strand break repair capacity in PC. STN1 is a component of the CST complex normally important for telomere duplication and maintenance. We find that STN1 is significantly upregulated in PC, especially in aggressive subtypes of PC, associates with KRAS oncogenic mutations, and correlates with poor patient clinical outcomes. Genetic silencing or pharmacologic inhibition of KRAS signaling decreases STN1 expression in PC cells, suggesting KRAS signaling positively regulates STN1 expression. Interestingly, STN1 depletion reduces tumor growth in a heterotopic model of KRAS mutant PC. Mechanistically, depletion of STN1 potentiates DNA damage, replication stress, and sensitizes PC cells to ionizing radiation independent of CTC1 and TEN1. In support of this finding, STN1 silencing reduces both HR and NHEJ repair of DSBs. Furthermore, knockdown of STN1 impairs cell cycle arrest at the G2/M phase in response to ionizing radiation, which is accompanied with increased mitotic catastrophe, radiation-induced apoptosis. Proteomic analysis reveals that STN1 physically interacts with many proteins important for DNA repair, replication and cell cycle progression, including ATM, DICER1, CEP164, and CEP250. Conclusion: Our findings have revealed a novel, potentially CST complex-independent role of STN1 in DSB repair after radiation. STN1 may function at one of the apical nodes in the DNA damage response pathway by interacting with ATM. Our findings suggest STN1 may be a promising target for improving genotoxic therapies in KRAS mutant cancers, including PC. Citation Format: Tiantian Cui, Changxian Shen, Linlin Yang, Ling Gui, Sergio Corrales-Guerrero, Sindhu Nair, Joanna M. Karasinska, James T. Topham, Xiaoli Ping, Jeremy M. Stark, Terence M. Williams.STN1 (OBFC1) promotes DNA double-strand break repair in a potentially CTC1-STN1-TEN1 (CST) complex-independent role in pancreatic cancer.[abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr P011

Abstract B027: Investigating NRF2-mediated radioresistance in HPV-negative head and neck squamous cell carcinoma preclinical models

Abstract Background: Head and neck squamous cell carcinomas (HNSCC) that are not driven by human papillomavirus (HPV) are associated with a higher likelihood of treatment resistance and recurrence compared to HPV-positive HNSCC. There are currently no genomic-guided treatments for HPV-negative HNSCC, meaning that patients do not benefit from precision medicine approaches. Thus, it is critical to understand the mechanisms underlying HNSCC progression to identify molecular targets and better stratify therapeutic options for patients. NFE2L2 encodes for nuclear erythroid 2-related factor 2 (NRF2), a transcription factor that plays a crucial role in responding to oxidative stress by regulating the expression of genes associated with cellular defense mechanisms. Mutations in NFE2L2 and its negative regulator, KEAP1, make up approximately 25% of HPV-negative HNSCCs. Additionally, constitutive activation of NRF2 confers a growth advantage and causes resistance to chemotherapy and radiotherapy. We will elucidate the role of NRF2, identifying novel radiosensitizers to better guide therapeutic strategies for HPV-negative HNSCC patients. Methods: Using clonogenic and long-term viability assays measuring radiation response, we identified radioresistant and radiosensitive cells in a panel of 19 HPV-negative SCC cell lines. An area-under-the-curve (AUC) metric was used to measure cellular response to multiple doses of ionizing radiation. Reactive oxygen species (ROS) and DNA double strand breaks (DSBs) were quantified using DCFDA and γH2AX assays, respectively. Radiosensitization was measured using the ∆AUC of varying drug doses of NRF2 inhibitor, ML385. NFE2L2 and KEAP1 were knocked down using RNA interference in radioresistant and radiosensitive cells, respectively. Results: We identified 13 radiosensitive and 6 radioresistant cell lines out of the 19 HPV-negative SCC cell lines. There was a strong correlation between AUCs of the clonogenic and long-term viability assays (Pearson r=0.74, p=3.0×10–4). Six cell lines were consistently radioresistant (AUC>3.5) in both assays. None of the cell lines contained mutations in the NRF2 pathway, and only 1/6 were radiosensitized by ML385 (∆AUC=2); this effect was not correlated with ROS or DSBs, yet was abrogated by NFE2L2 knockdown. KEAP1 knockdown cell lines were generated for ongoing functional characterization and for genetic screens to identify radiosensitizers in HPV-negative HNSCC. Conclusions: We aim to identify the role of NRF2 in the treatment response of HPV-negative HNSCC. Although NRF2 is an important pathway in driving a radioresistant phenotype, the majority of radioresistant cell lines were not sensitized by NRF2 inhibition. Therefore, elucidating the molecular underpinnings of NRF2-mediated therapeutic resistance will be critical to identifying novel radiosensitizers with activity in HPV-negative HNSCC. Citation Format: Aakshi Puri, Meghan Lambie, Scott V. Bratman. Investigating NRF2-mediated radioresistance in HPV-negative head and neck squamous cell carcinoma preclinical models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr B027.

Abstract A009: Targeting DNA damage responsive pathways in cancer therapy

Abstract DNA double strand breaks (DSBs) result in activation of several key DNA damage response (DDR) kinases including ATM, ATR, and DNA-PK. These protein kinases not only promote DNA damage-induced checkpoint control, but also facilitate DSB repair in humans. Thus, these DDR kinases have become promising drug targets for cancer therapy. However, the benefits of targeting DDR kinases remain to be realized, in part due to the lack of predictive biomarkers. By undertaking CRISPR screens with inhibitors targeting key DDR kinases, we obtained a global and unbiased view of genetic interactions with DDR inhibition. Additionally, we compared the synergistic effects of combining different DDR inhibitors and found that ATM and PARP inhibitors showed remarkable synergy, which depends on the dominant negative function of ATM inhibition. Moreover, to provide comprehensive and unbiased perspective of DDR signaling pathways, we performed 30 fluorescence-activated cell sorting–based genome-wide CRISPR screens with antibodies recognizing distinct endogenous DNA damage–signaling proteins to identify new regulators involved in DNA damage response (DDR). We discovered that proteasome-mediated processing is an early and prerequisite event for cells to trigger camptothecin- and etoposide-induced DDR signaling. Furthermore, we identified PRMT1 and PRMT5 as new modulators that regulate ATM protein level. Additionally, we discovered that GNB1L is a master regulator of DDR signaling via its role as a co-chaperone for PIKK proteins. Collectively, these screens offer a rich resource for further investigation of DDR, which may provide insight into strategies of targeting these DDR pathways to improve therapeutic outcomes. More recently, we have adopted dTAG technology for the investigation of many essential DDR and replication proteins, which provide mechanistic insights into the roles of these essential proteins in genome maintenance. Additionally, we have expanded FACS-based screens for the studies of other cancer-associated pathways and explored key biological processes critical for cancer progression in vivo. These studies will facilitate the development of better therapies for cancer patients. Citation Format: Junjie Chen. Targeting DNA damage responsive pathways in cancer therapy. [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Targeted Therapies in Combination with Radiotherapy; 2025 Jan 26-29; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(2_Suppl):Abstract nr A009.

Contribution of Nuclear Fragmentation to Dose and RBE in Carbon-Ion Radiotherapy.

Variable relative biological effectiveness (RBE) of carbon radiotherapy may be calculated using several models, including the microdosimetric kinetic model (MKM), stochastic MKM (SMKM), repair-misrepair-fixation (RMF) model, and local effect model I (LEM), which have not been thoroughly compared. In this work, we compared how these four models handle carbon beam fragmentation, providing insight into where model differences arise. Monoenergetic and spread-out Bragg peak carbon beams incident on a water phantom were simulated using Monte Carlo. Using these beams, input parameters for each model (microdosimetric spectra, DNA double-strand break yield, kinetic energy spectra, physical dose fragment contributions) were calculated for each contributing carbon beam fragment (hydrogen, helium, lithium, beryllium, boron, secondary carbon, primary carbon, electrons, and "other"). Scored input parameters for each fragment were used to calculate linear (α) and quadratic (β) parameters according to each model, which were combined with reference α and β values and absorbed physical dose to calculate RBE. Contributions from secondary fragments were found to exceed 30% of the total physical dose. Using identical beam parameters, the four models produced not only different RBE values but also different RBE trends. In all models, RBE was highest for secondary carbon ions. Beyond secondary carbons, the RBE magnitude typically increased with the atomic number of the fragment, but RBE trends differed dramatically by model and beamline region (entrance, spread-out Bragg peak, and tail). Variations in fragment RBE were large enough to be apparent in biological dose predictions. This study demonstrated that fragmentation is a nonnegligible consideration in carbon radiotherapy. Our findings identified differences in RBE among specific fragments and the four models, contributing to variability in the total biological dose across models. Because these findings emphasize differences in how various models handle carbon beam fragments, greater care should be taken in characterization of secondary fragments in particle therapy.

CHD6 has poly(ADP-ribose)- and DNA-binding domains and regulates PARP1/2-trapping inhibitor sensitivity via abasic site repair

To tolerate oxidative stress, cells enable DNA repair responses often sensitive to poly(ADP-ribose) (PAR) polymerase 1 and 2 (PARP1/2) inhibition—an intervention effective against cancers lacking BRCA1/2. Here, we demonstrate that mutating the CHD6 chromatin remodeler sensitizes cells to PARP1/2 inhibitors in a manner distinct from BRCA1, and that CHD6 recruitment to DNA damage requires cooperation between PAR- and DNA-binding domains essential for nucleosome sliding activity. CHD6 displays direct PAR-binding, interacts with PARP-1 and other PAR-associated proteins, and combined DNA- and PAR-binding loss eliminates CHD6 relocalization to DNA damage. While CHD6 loss does not impair RAD51 foci formation or DNA double-strand break repair, it causes sensitivity to replication stress, and PARP1/2-trapping or Pol ζ inhibitor-induced γH2AX foci accumulation in S-phase. DNA repair pathway screening reveals that CHD6 loss elicits insufficiency in apurinic-apyrimidinic endonuclease (APEX1) activity and genomic abasic site accumulation. We reveal APEX1-linked roles for CHD6 important for understanding PARP1/2-trapping inhibitor sensitivity.

The role of Box A of HMGB1 in producing γH2AX associated DNA breaks in lung cancer

An ideal chemotherapeutic agent damages DNA, specifically in cancer cells, without harming normal cells. Recently, we used Box A of HMGB1 plasmid as molecular scissors to produce DNA gaps in normal cells. The DNA gap relieves DNA tension and increases DNA strength, preventing DNA double-strand breaks (DSBs). Since the formation of HMGB1-produced DNA gaps in cancers may differ from normal cells, the outcome of introducing Box A into cancer cells may be different. We demonstrated that in lung cancer cells, γH2AX foci and histone modification associating DSBs were produced by Box A. We transfected Box A plasmid into lung cancer cell lines to overexpress Box A and evaluated the expression levels of γH2AX foci and other DNA damage response (DDR) signaling cascade markers, including ATM, ATR, and p53. Then, we demonstrated the downstream effects of DSBs on lung cancer, lowering cell proliferation, decreasing cell migration, and promoting apoptosis. Thus, Box A in lung cancer promoted the opposite outcome to normal cells by breaking cancer DNA.

ParSite is a multicolor DNA labeling system that allows for simultaneous imaging of triple genomic loci in living cells.

The organization of the human genome in space and time is critical for transcriptional regulation and cell fate determination. However, robust methods for tracking genome organization or genomic interactions over time in living cells are lacking. Here, we developed a multicolor DNA labeling system, ParSite, to simultaneously track triple genomic loci in the U2OS cells. The tricolor ParSite system is derived from the T. thermophilus ParB/ParSc (TtParB/ParSc) system by rational design. We mutated the interface between TtParB and ParSc and generated a new pair of TtParBm and ParSm for genomic DNA labeling. The insertions of 16 base-pair palindromic ParSc and ParSm into genomic loci allow dual-color DNA imaging in living cells. A pair of genomic loci labeled by ParSite could be colocalized with p53-binding protein 1 (53BP1) in response to CRISPR/Cas9-mediated double-strand breaks (DSBs). The ParSite permits tracking promoter and terminator dynamics of the APP gene, which spans 290 kilobases in length. Intriguingly, the hybrid ParS (ParSh) of half-ParSc and half-ParSm enables for the visualization of a third locus independent of ParSc or ParSm. We simultaneously labeled 3 loci with a genomic distance of 36, 89, and 352 kilobases downstream the C3 repeat locus, respectively. In sum, the ParSite is a robust DNA labeling system for tracking multiple genomic loci in space and time in living cells.

Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes.

DNA copy number changes via chromosomal rearrangements or the production of extrachromosomal circular DNA. Here, we demonstrate that the histone deacetylase Sir2 maintains the copy number of budding yeast ribosomal RNA gene [ribosomal DNA (rDNA)] by suppressing end resection of DNA double-strand breaks (DSBs) formed upon DNA replication fork arrest in the rDNA and their subsequent homologous recombination (HR)-mediated rDNA copy number changes during DSB repair. Sir2 represses transcription from the regulatory promoter E-pro located near the fork arresting site. When Sir2 is absent, this transcription is stimulated but terminated by arrested replication forks. This transcription-replication collision induces DSB formation, DSB end resection and the Mre11-Rad50-Xrs2 complex-dependent DSB repair that is prone to chromosomal rDNA copy number changes and the production of extrachromosomal rDNA circles. Therefore, repression of transcription near arrested replication forks is critical for the maintenance of rDNA stability by directing DSB repair into the HR-independent, rearrangement-free pathway.

ATM Expression and Activation in Ataxia Telangiectasia Patients with and without Class Switch Recombination Defects

BackgroundAtaxia telangiectasia mutated (ATM) kinase plays a critical role in DNA double-strand break (DSB) repair. Ataxia telangiectasia (A-T) patients exhibit abnormalities in immunoglobulin isotype expression and class switch recombination (CSR). This study investigates the role of residual ATM kinase expression and activity in the severity of A-T disease.MethodsA-T patients with defined genetic diagnoses were classified based on CSR and based on the severity of their medical complications. Isolated peripheral blood mononuclear cells from any patient were evaluated before and after exposure to 0.5 Gy ionizing radiation for one minute. Western blotting was performed to identify the expression of ATM and phosphorylated ATM (p-ATM) proteins compared to age-sex-matched healthy controls.ResultsIn severe A-T patients (n = 6), the majority (66.7%) had frameshift mutations, while 33.3% had nonsense mutations in the ATM gene. The mild group (n = 3) had two cases of splice errors and one missense mutation. All patients with CSR defect had elevated IgM serum levels, whereas all switched immunoglobulins were reduced in them. Expression of ATM and p-ATM proteins was significantly lower (p = 0.01) in all patients compared to healthy controls, both pre-and post- and post-radiation. Additionally, low ATM and p-ATM protein expression levels were linked with the clinical severity of patients but were not correlated with CSR defects.ConclusionExpression and activation of ATM protein were defective in A-T patients compared to healthy controls. Altered expression of ATM and p-ATM proteins may have potential clinical implications for prognostic evaluation and symptom severity assessment in individuals with A-T.

The LIM-domain-only protein LMO2 and its binding partner LDB1 are differentially required for class switch recombination

The LIM-domain-only protein LMO2 interacts with LDB1 in context-dependent multiprotein complexes and plays key roles in erythropoiesis and T cell leukemogenesis, but whether they have any roles in B cells is unclear. Through a CRISPR/Cas9-based loss-of-function screening, we identified LMO2 and LDB1 as factors for class switch recombination (CSR) in murine B cells. LMO2 contributes to CSR at least in part by promoting end joining of DNA double-strand breaks (DSBs) and inhibiting end resection. Although LDB1 stabilizes LMO2 proteins, it is not required for end joining but functions as a positive regulator of AID transcription independent of LMO2, and this function of LDB1 requires its dimerization domain. Moreover, LDB1 directly binds to and promotes the looping of the AID promoter to upstream enhancers through dimerization. Our study revealed the mechanistically separated roles of LMO2 and LDB1 in different steps of CSR for antibody diversification.

DOP024 Transport of pks+ E. coli derived genotoxin colibactin from bacteria into host cell

Abstract Background Colorectal cancer (CRC) is among the most prevalent cancer worldwide with a rapidly increasing frequency. Many studies have highlighted a close association between CRC, inflammatory bowel diseases (IBD), and alterations in gut microbial composition. Among these, particular attention has been drawn to B2 serotype Escherichia coli and other pks-positive Enterobacteriaceae. These bacteria carry a genetic island encoding a multi-enzyme assembly line responsible for the non-ribosomal synthesis of colibactin, a peptide-polyketide hybrid molecule that acts as a potent genotoxin. Colibactin alkylates double-stranded DNA, causing inter-strand crosslinks, double-strand breaks (DSB), and a specific mutational signature commonly found in CRC. Despite the growing knowledge about colibactin synthesis and its mode of action, the mechanism by which it is delivered from bacteria to the host epithelium remains unclear. Here, we hypothesize a small-particle carriage system to overcome the instability of colibactin and the physical obstacle posed by the mucus layer. Methods Conditioned media (CM) from pks+ and isogenic pks- bacteria were harvested, filtered, and ultracentrifuged to isolate distinct fractions, including vesicle and soluble portions. These fractions were tested for their ability to induce DNA DSBs in patient-derived colon organoids, which were detected by γH2AX staining. To more closely match in vivo exposure conditions, we created apical-out converted organoids in addition to classical basal-out growth. This approach allowed us to simulate and compare exposure to surfaces accessible before and only after the loss of barrier integrity, a typical hallmark of IBD. Results Our experiments demonstrated that basal application of bacterial isolates caused increased signs of cellular stress and genetic damage, independent of colibactin. In apical-out organoids, several fractions of the cell-free bacterial supernatant, but only those derived from pks+ E. coli, were able to reliably induce double-strand breaks. Conclusion Even though the genotoxic effect following CM treatment was substantially less pronounced than in co-culture experiments, our results suggest that the transfer of colibactin between bacteria and epithelium might not depend exclusively on direct physical contact, as suspected by other studies. The data support the presence of a mid-distance carriage system that is not limited by the size of bacteria and can therefore cross the intestinal barrier. Beyond that, we demonstrated that intestinal organoids are overall more susceptible to immunological stress by bacterial components when exposed at their basal surface, which indicates a significant bias in studies relying solely on classical organoid culture as an experimental system.

P0212 Non-canonical STING signaling in intestinal epithelial cells guides DNA damage-driven stem cell function and protects from intestinal carcinogenesis

Abstract Background RNaseH2 plays a critical role in removing mis-bounded RNA from the DNA double strand helix1. Absence of RNaseH2 results in spontaneous double-stranded DNA breaks and cytosolic release of dsDNA2. We have previously shown that epithelial deficiency of RNaseH2b (H2bΔIEC) leads to a p53-dependent stem cell suppression and additional deficiency of p53 results in spontaneous intestinal carcinogenesis3. Due to the central role of cGAS/STING in sensing dsDNA, we aim to investigate the role of epithelial STING in a mouse model of chronic epithelial DNA damage and tumor prevention in this study. Methods DNA damage was assessed using comet assay in ModeK cell line with cGAS and STING knock out. Protein kinase activity were assessed by Pamgene Kinase Assay. Intestinal organoids were generated from H2bΔIEC and H2bΔIEC/Tmem173-/-mice. Colony forming assay and EdU staining were performed in all genotypes to assess the impact of STING on epithelial stem cell function and proliferation were assessed by CellTiter Glo assay. RNA sequencing was performed in intestinal organoids. Spontaneous carcinogenesis was assessed in 1-year aged mice. Results Loss of RNaseH2b results in activation of cGAS/STING pathway and subsequent upregulation of IFN-I signature. Deficiency of cGAS/STING lead to impaired IFN-I independent DNA damage repair which were accessed by WB and comet assay. During the DNA damage response, STING but not cGAS mediates the P53 pathway and the P21-CDK axis. Organoid EdU stanning displayed restored proliferation in H2bΔIEC/Tmem173-/- compared to H2bΔIEC. RNA sequencing from H2bΔIEC/Tmem173-/-organoid further confirmed decreased G2/M DNA damage checkpoint and P53 signature compared to H2bΔIEC. In vivo, we show that H2bΔIEC/Tmem173-/- mice have downregulated DNA damage repair and developed spontaneous small bowel adenocarcinoma after 53 weeks. Tumor derived from H2bΔIEC/Tmem173-/- mice show sensitivity to CDK inhibitor consistent with in vitro validation. Conclusion We provide evidence that non-canonical role of epithelial STING mediates DNA damage response and guides P21-CDK1 axis in preventing tumor genesis. Our research provided evidence understand the role of STING in DNA damage response and intestine carcinogenesis.

Repurposing Linezolid in Conjunction with Histone Deacetylase Inhibitor Access in the Realm of Glioblastoma Therapies.

Since decades after temozolomide was approved, no effective drugs have been developed. Undoubtedly, blood-brain barrier (BBB) penetration is a severe issue that should be overcome in glioblastoma multiforme (GBM) drug development. In this research, we were inspired by linezolid through structural modification with several bioactive moieties to achieve the desired brain delivery. The results indicated that the histone deacetylase modification, referred to as compound 1, demonstrated promising cytotoxic effects in various brain tumor cell lines. Further comprehensive mechanism studies indicated that compound 1 induced acetylation, leading to DNA double-strand breaks, and induced the ubiquitination of RAD51, disrupting the DNA repair process. Furthermore, compound 1 also exhibited dramatic improvement in the orthotopic GBM mouse model, demonstrating its efficacy and satisfying BBB penetration. Therefore, the reported compound 1, provided with an independent therapeutic pathway, satisfying elongation in survival and tumor size reduction, and the ability to penetrate the BBB, was potent to achieve further development.

HP1 Promotes the Centromeric Localization of ATRX and Protects Cohesion by Interfering Wapl Activity in Mitosis.

α thalassemia/mental retardation syndrome X-linked (ATRX) serves as a part of the sucrose nonfermenting 2 (SNF2) chromatin-remodeling complex. In interphase, ATRX localizes to pericentromeric heterochromatin, contributing to DNA double-strand break repair, DNA replication, and telomere maintenance. During mitosis, most ATRX proteins are removed from chromosomal arms, leaving a pool near the centromere region in mammalian cells, which is critical for accurate chromosome congression and sister chromatid cohesion protection. However, the function and localization mechanisms of ATRX at mitotic centromeres remain largely unresolved. The clustered regularly interspaced short palindromic repeats with CRISPR-associated protein 9 (CRISPR-Cas9) system and overexpression approaches were employed alongside immunofluorescence to investigate the mechanism of ATRX localization at the centromere. To study the binding mechanism between ATRX and heterochromatin protein 1 (HP1), both full-length and truncated mutants of hemagglutinin (HA)-ATRX were generated for co-immunoprecipitation and glutathione S-transferase (GST)-pull assays. Wild-type ATRX and HP1 binding-deficient mutants were created to investigate the role of ATRX binding to HP1 during mitosis, with the Z-Leu-Leu-Leu-al (MG132) maintenance assay, cohesion function assay, and kinetochore distance measurement. Our research demonstrated that HP1α, HP1β, and HP1γ facilitate the positioning of ATRX within the mitotic centromere area through their interaction with the first two [P/L]-X-V-X-[M/L/V] (PxVxL)motifs at the N-terminus of ATRX. ATRX deficiency causes aberrant mitosis and decreased centromeric cohesion. Furthermore, reducing Wapl activity can bypass the need for ATRX to protect centromeric cohesion. These results provide insights into the mechanism of ATRX's centromeric localization and its critical function in preserving centromeric cohesion by reducing Wapl activity in human cells.

Obesity increases DNA damage in the breast epithelium

Obesity is a modifiable risk factor for breast cancer. Yet, how obesity contributes to cancer initiation is not fully understood. The goal of this study was to determine if the body mass index (BMI) and metabolic hallmarks of obesity are related to DNA damage in normal breast tissue. In a mouse model of diet-induced obesity, weight gain was associated with elevated levels of DNA double-strand breaks in the mammary gland. We also found a positive correlation between BMI and DNA breaks in the breast epithelium of premenopausal women (but not postmenopausal women). High BMI was associated with elevated systemic and tissue-level oxidative DNA damage across the lifespan, and we propose that the breast epithelium undergoing menstruous proliferation waves is particularly prone to the generation of DNA breaks from oxidative lesions. Ancestry was an important modulator of the obesity-DNA break connection. Compared to non-Hispanic Whites, women identifying as African Americans had higher levels of DNA breaks, as well as elevated leptin and IGF-1. In 3D cultures of breast acini, both leptin and IGF-1 caused an accumulation of DNA damage. The results highlight a connection between premalignant genomic alterations in the breast epithelium and metabolic health modulated by obesity and ancestry. They call for attention on biological determinants of breast cancer risk disparities.

A dual role of Cohesin in DNA DSB repair

Cells undergo tens of thousands of DNA-damaging events each day. Defects in repairing double-stranded breaks (DSBs) can lead to genomic instability, contributing to cancer, genetic disorders, immunological diseases, and developmental defects. Cohesin, a multi-subunit protein complex, plays a crucial role in both chromosome organization and DNA repair by creating architectural loops through chromatin extrusion. However, the mechanisms by which cohesin regulates these distinct processes are not fully understood. In this study, we identify two separate roles for cohesin in DNA repair within mammalian cells. First, cohesin serves as an intrinsic architectural factor that normally prevents interactions between damaged chromatin. Second, cohesin has an architecture-independent role triggered by ATM phosphorylation of SMC1, which enhances the efficiency of repair. Our findings suggest that these two functions work together to reduce the occurrence of translocations and deletions associated with non-homologous end joining, thereby maintaining genomic stability.