Regulation Of DNA Repair Research Articles

Prognostic value of iron metabolism-related genes in bladder urothelial carcinoma

Abstract Objectives Iron metabolism-related genes (IMRGs) play important roles in the prognostic assessment of many tumours. However, IMRGs have not been reported as prognostic biomarkers in bladder urothelial carcinoma (BLCA). Methods Gene expression profiles and clinical data from BLCA patients were obtained from The Cancer Genome Atlas (TCGA) database. We used the DESeq2 package to screen for differentially expressed genes (DEGs). The predictive values of the differentially expressed IMRGs in BLCA patients were further evaluated using univariate Cox regression analysis. The risk-scoring model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm. The performance of this model for predicting the prognosis of BLCA patients in TCGA-BLCA cohort was assessed using Kaplan–Meier (K–M) and receiver operating characteristic (ROC) curves. This risk-scoring model was combined with the clinicopathological characteristics of BLCA patients in a multiple regression analysis, and a nomogram was constructed using the independent predictors identified. ROC analysis and calibration curves were adapted to test the predictive ability of the nomogram. Gene set enrichment analysis (GSEA) was used to identify potential molecular pathways and processes enriched by differential expression genes between risk groups. Finally, we explored the ability of the risk-scoring model to assess immune cell infiltration levels through a correlation analysis. Results Fourteen identified IMRGs with prognostic value were incorporated into the risk-scoring model. The ROC and K–M survival curves indicated that the model could effectively predict the overall survival (OS) outcomes of BLCA patients. The multiple regression analysis revealed that the risk-scoring model could be used as an independent prognostic factor for BLCA patients, and the associated nomogram could effectively predict the OS outcomes of BLCA patients. GSEA revealed that the DEGs between the risk groups were mainly involved in biological processes such as developmental process, cell cycle, mitosis, RHO GTPase reaction, DNA repair, and extracellular matrix regulation. The immune infiltration analysis showed that the infiltration levels of immune cells such as natural killer cells, memory T cells, effector T cells, Th2 cells, and macrophages differed significantly between the risk groups. Conclusions IMRGs screening revealed prognosis-associated genes. The prognostic model constructed could effectively predict the prognosis of BLCA patients, and the identified genes represent potential targets for BLCA treatment.

Multi-Omic Analysis of CIC's Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity.

CIC encodes a transcriptional repressor and MAPK signalling effector that is inactivated by loss-of-function mutations in several cancer types, consistent with a role as a tumour suppressor. Here, we used bioinformatic, genomic, and proteomic approaches to investigate CIC's interaction networks. We observed both previously identified and novel candidate interactions between CIC and SWI/SNF complex members, as well as novel interactions between CIC and cell cycle regulators and RNA processing factors. We found that CIC loss is associated with an increased frequency of mitotic defects in human cell lines and an in vivo mouse model and with dysregulated expression of mitotic regulators. We also observed aberrant splicing in CIC-deficient cell lines, predominantly at 3' and 5' untranslated regions of genes, including genes involved in MAPK signalling, DNA repair, and cell cycle regulation. Our study thus characterises the complexity of CIC's functional network and describes the effect of its loss on cell cycle regulation, mitotic integrity, and transcriptional splicing, thereby expanding our understanding of CIC's potential roles in cancer. In addition, our work exemplifies how multi-omic, network-based analyses can be used to uncover novel insights into the interconnected functions of pleiotropic genes/proteins across cellular contexts.

Kaempferol inhibits non-homologous end joining repair via regulating Ku80 stability in glioma cancer

BackgroundTargeting DNA damage response and DNA repair proficiency of cancers is an important anticancer strategy. Kaempferol (Kae), a natural flavonoid, displays potent antitumor properties in some cancers. However, the precise underlying mechanism of Kae regulates DNA repair system are poorly understood. PurposeWe aim to evaluate the efficacy of Kae in the treatment of human glioma as well as the molecular mechanism regarding DNA repair. Study designEffects of Kae on glioma cells were detected using CCK-8 and EdU labeling assays. The molecular mechanism of Kae on glioma was determined using RNAseq. The inhibition effects of Kae on DNA repair were verified using Immunoprecipitation, immunofluorescence, and pimEJ5-GFP report assays. For in vivo study, orthotopic xenograft models were established and treated with Kae or vehicle. Glioma development was monitored by bioluminescence imaging, Magnetic Resonance Imaging (MRI), and brain sections Hematoxylin/Eosin (HE) staining. Immunohistochemical (IHC) analysis was used to detect expression of Ku80, Ki67 and γH2AX in engrafted glioma tissue. ResultsWe found that Kae remarkably inhibits viability of glioma cells and decreases its proliferation. Mechanistically, Kae regulates multiple functional pathways associated with cancer, including non-homologous end joining (NHEJ) repair. Further studies revealed that Kae inhibits release of Ku80 from the double-strand breaks (DSBs) sites via reducing ubiquitylation and degradation of Ku80. Therefore, Kae significantly suppresses NHEJ repair and induces accumulation of DSBs in glioma cells. Moreover, Kae displays a dramatic inhibition effects on glioma growth in an orthotopic transplantation model. These data demonstrate that Kae can induce deubiquitination of Ku80, suppress NHEJ repair and inhibit glioma growth. ConclusionOur findings indicate that inhibiting release of Ku80 from the DSBs by Kae may be a potential effective approach for glioma treatment.

Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway

Congenital heart disease (CHD) is the most common type of birth defect and the main noninfectious cause of death during the neonatal stage. The non-POU domain containing, octamer-binding gene, NONO, performs a variety of roles involved in DNA repair, RNA synthesis, transcriptional and post-transcriptional regulation. Currently, hemizygous loss-of-function mutation of NONO have been described as the genetic origin of CHD. However, essential effects of NONO during cardiac development have not been fully elucidated. In this study, we aim to understand role of Nono in cardiomyocytes during development by utilizing the CRISPR/Cas9 gene editing system to deplete Nono in the rat cardiomyocytes H9c2. Functional comparison of H9c2 control and knockout cells showed that Nono deficiency suppressed cell proliferation and adhesion. Furthermore, Nono depletion significantly affected the mitochondrial oxidative phosphorylation (OXPHOS) and glycolysis, resulting in H9c2 overall metabolic deficits. Mechanistically we demonstrated that the Nono knockout impeded the cardiomyocyte function by attenuating phosphatidyl inositol 3 kinase-serine/threonine kinase (Pi3k/Akt) signaling via the assay for transposase-accessible chromatin using sequencing in combination with RNA sequencing. From these results we propose a novel molecular mechanism of Nono to influence cardiomyocytes differentiation and proliferation during the development of embryonic heart. We conclude that NONO may represent an emerging possible biomarkers and targets for the diagnosis and treatment of human cardiac development defects.

Pan-Cancer Analysis of the Tumorigenic Effect and Prognostic Diagnostic Value of FAM111B in Human Carcinomas.

FAM111B (FAM111 trypsin-like peptidase B) gene mutations have been linked to a hereditary fibrosing poikiloderma disorder known to cause poikiloderma, tendon contracture, myopathy, and pulmonary fibrosis (POIKTMP). Overexpression of FAM111B has been associated with an increased risk of certain cancers with a poor prognosis, although the relationship between FAM111B and other tumors is still unclear, and the molecular mechanism of its action is not fully understood. We investigated the biological functions of FAM111B in 33 solid tumors using multi-omics data. We further recruited 109 gastric cancer (GC) patients for a clinical cohort study to confirm the effect of FAM111B on early tumor recurrence. Furthermore, we assessed the role of FAM111B in GC cell proliferation and migration via EdU incorporation, CCK8 and transwell assays in vitro. We found that FAM111B can enhance oncogenesis and progression in multiple tumor types. The clinical cohort of GC showed that upregulation of FAM111B is associated with early recurrence of GC, and knockdown of the FAM111B gene can inhibit the proliferation and migration of GC cells. Gene enrichment analysis indicates that FAM111B promotes cancer through immune system process, chromosome instability, DNA repair, and apoptosis regulation. Mechanistically, FAM111B appears to promote the growth cycle of malignant tumor cells while inhibiting apoptosis. FAM111B may serve as a potential pan-cancer biomarker for predicting the prognosis and survival of malignant tumor patients. Our study elucidates the role of FAM111B in the occurrence and development of various cancers, and highlights the need for future research on FAM111B in cancers.

A vast evolutionarily transient translatome contributes to phenotype and fitness.

Translation is the process by which ribosomes synthesize proteins. Ribosome profiling recently revealed that many short sequences previously thought to be noncoding are pervasively translated. To identify protein-coding genes in this noncanonical translatome, we combine an integrative framework for extremely sensitive ribosome profiling analysis, iRibo, with high-powered selection inferences tailored for short sequences. We construct a reference translatome for Saccharomyces cerevisiae comprising 5,400 canonical and almost 19,000 noncanonical translated elements. Only 14 noncanonical elements were evolving under detectable purifying selection. A representative subset of translated elements lacking signatures of selection demonstrated involvement in processes including DNA repair, stress response, and post-transcriptional regulation. Our results suggest that most translated elements are not conserved protein-coding genes and contribute to genotype-phenotype relationships through fast-evolving molecular mechanisms.

Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli.

Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix rosea (LrAgo) are active in heterologous Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin, depending on the host double-strand break repair machinery. Both pAgos are preferentially loaded with small guide DNAs (smDNAs) derived from the sites of replication termination. Ciprofloxacin increases the amounts of smDNAs from the termination region and from the sites of genomic DNA cleavage by gyrase, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin enhances asymmetry in the distribution of smDNAs around Chi sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases may help to complete replication of chromosomal DNA by promoting chromosome decatenation or participating in the processing of gyrase cleavage sites, and may switch their functional activities depending on the host species. IMPORTANCE Prokaryotic Argonautes (pAgos) are programmable nucleases with incompletely understood functions in vivo. In contrast to eukaryotic Argonautes, most studied pAgos recognize DNA targets. Recent studies suggested that pAgos can protect bacteria from invader DNA and counteract phage infection and may also have other functions including possible roles in DNA replication, repair, and gene regulation. Here, we have demonstrated that two cyanobacterial pAgos, SeAgo and LrAgo, can assist DNA replication and facilitate cell division in the presence of topoisomerase inhibitors in Escherichia coli. They are specifically loaded with small guide DNAs from the region of replication termination and protect the cells from the action of the gyrase inhibitor ciprofloxacin, suggesting that they help to complete DNA replication and/or repair gyrase-induced breaks. The results show that pAgo proteins may serve as a backup to topoisomerases under conditions unfavorable for DNA replication and may modulate the resistance of host bacterial strains to antibiotics.

Wee1 epigenetically modulates H2B mono-ubiquitination at K120 lysine and DNA double-strand break repair through phosphorylation of H2BY37-dependent manner in small-cell lung cancer.

DNA damage repair is a crucial mechanism highly related to therapy resistance for various therapeutic strategies. Our previous results have shown that the degree of drug resistance in small-cell lung cancer (SCLC) cell lines was proportional to both the transcription and expression levels of Wee1, indicating that Wee1, an evolutionarily highly conserved kinase, plays a vital role in the therapeutic resistance of SCLC. In the present study, we aim to determine the nonclassical mechanism of Wee1 on DNA repair regulation. Western blot was conducted to determine the mono-ubiquitination level of H2Bub. Comet assay was used to evaluate the degree of DNA damage. Immunofluorescence was conducted to determine the DNA repair markers. Co-immunoprecipitation was utilized to assess the potential interactions with H2BY37ph. MTT assays were used to evaluate the survival rates of SCLC cells. Overexpression of Wee1 increases the level of H2BK120ub and alleviates ionizing radiation (IR)-induced DNA damage in SCLC cells. Moreover, H2BK120ub is a crucial molecule in Wee1-mediated double-strain break (DSB) repair in SCLC cells. Mechanisms study indicated that H2BY37ph is involved in Wee1-mediated H2BK120ub through interaction with the E3 ubiquitin ligase RNF20-RNF40 complex and upregulates its phosphorylation, mutation of H2BY37 phosphorylation sites attenuated DSB repair and enhanced the sensitivity of IR-induced SCLC cell death. H2BY37ph produces crosstalk with H2BK120ub in an E3 ubiquitin ligase-dependent manner, promoting Wee1-mediated DSB repair in SCLC cells. This study clarifies the nonclassical mechanism of Wee1 regulation of DSB repair, which provides a theoretical basis for the clinical understanding of the regulatory network of Wee1 and its use as a target for overcoming multiple types of therapeutic resistance.

Suppression of USP7 negatively regulates the stability of ETS proto-oncogene 2 protein

Ubiquitin-specific protease 7 (USP7) is one of the deubiquitinating enzymes (DUBs) that remove mono or polyubiquitin chains from target proteins. Depending on cancer types, USP7 has two opposing roles: oncogene or tumor suppressor. Moreover, it also known that USP7 functions in the cell cycle, apoptosis, DNA repair, chromatin remodeling, and epigenetic regulation through deubiquitination of several substrates including p53, mouse double minute 2 homolog (MDM2), Myc, and phosphatase and tensin homolog (PTEN). The [P/A/E]-X-X-S and K-X-X-X-K motifs of target proteins are necessary elements for the binding of USP7. In a previous study, we identified a novel substrate of USP7 through bioinformatics analysis using the binding motifs for USP7, and suggested that it can be an effective tool for finding new substrates for USP7. In the current study, gene ontology (GO) analysis revealed that putative target proteins having the [P/A/E]-X-X-S and K-X-X-K motifs are involved in transcriptional regulation. Moreover, through protein-protein interaction (PPI) analysis, we discovered that USP7 binds to the AVMS motif of ETS proto-oncogene 2 (ETS2) and deubiquitinates M1-, K11-, K27-, and K29-linked polyubiquitination of ETS2. Furthermore, we determined that suppression of USP7 decreases the protein stability of ETS2 and inhibits the transcriptional activity of ETS2 by disrupting the binding between the GGAA/T core motif and ETS2. Therefore, we propose that USP7 can be a novel target in cancers related to the dysregulation of ETS2.

The RUNX Family of Proteins, DNA Repair, and Cancer.

The RUNX family of transcription factors, including RUNX1, RUNX2, and RUNX3, are key regulators of development and can function as either tumor suppressors or oncogenes in cancer. Emerging evidence suggests that the dysregulation of RUNX genes can promote genomic instability in both leukemia and solid cancers by impairing DNA repair mechanisms. RUNX proteins control the cellular response to DNA damage by regulating the p53, Fanconi anemia, and oxidative stress repair pathways through transcriptional or non-transcriptional mechanisms. This review highlights the importance of RUNX-dependent DNA repair regulation in human cancers.

Atorvastatin Can Modulate DNA Damage Repair in Endothelial Cells Exposed to Mitomycin C

HMG-CoA reductase inhibitors (statins) are widely used in the therapy of atherosclerosis and have a number of pleiotropic effects, including DNA repair regulation. We studied the cytogenetic damage and the expression of DNA repair genes (DDB1, ERCC4, and ERCC5) in human coronary artery (HCAEC) and internal thoracic artery endothelial cells (HITAEC) in vitro exposed to mitomycin C (MMC) (positive control), MMC and atorvastatin (MMC+Atv), MMC followed by atorvastatin treatment (MMC/Atv) and 0.9% NaCl (negative control). MMC/Atv treated HCAEC were characterized by significantly decreased micronuclei (MN) frequency compared to the MMC+Atv group and increased nucleoplasmic bridges (NPBs) frequency compared to both MMC+Atv treated cells and positive control; DDB1, ERCC4, and ERCC5 genes were upregulated in MMC+Atv and MMC/Atv treated HCAEC in comparison with the positive control. MMC+Atv treated HITAEC were characterized by reduced MN frequency compared to positive control and decreased NPBs frequency in comparison with both the positive control and MMC/Atv group. Nuclear buds (NBUDs) frequency was significantly lower in MMC/Atv treated cells than in the positive control. The DDB1 gene was downregulated in the MMC+Atv group compared to the positive control, and the ERCC5 gene was upregulated in MMC/Atv group compared to both the positive control and MMC+Atv group. We propose that atorvastatin can modulate the DNA damage repair response in primary human endothelial cells exposed to MMC in a cell line- and incubation scheme-dependent manner that can be extremely important for understanding the fundamental aspects of pleoitropic action of atorvastatin and can also be used to correct the therapy of patients with atherosclerosis characterized by a high genotoxic load.

Abstract 3677: DNA damage signaling activates de novo GTP synthesis to promote chemoradiation resistance in glioblastoma

Abstract Glioblastoma (GBM) is uniformly fatal due to inherent radiation (RT) and chemotherapy resistance. We have found this therapeutic resistance is mediated by alterations in tumor cellular metabolic activity. Our group and others have found that metabolites can regulate DNA repair and RT resistance in brain tumors, but little is known about how DNA damage regulates metabolic pathway activity in cancer. Here, we show that DNA damage acutely increases guanine-containing purine metabolites in multiple in vitro and intracranial GBM models. By interrogating metabolic fluxes in vitro using a variety of stable isotope tracers, we confirmed RT-induced elevation in guanylates was due to increased de novo purine synthesis (DNPS) rather than activation of purine salvage. By developing and using novel stable isotope tracing methods to directly measure DNPS in awake, unrestrained mice, we confirmed that orthotopic GBMs have higher DNPS rates than adjacent cortical tissue that further increase after treatment with RT. Neither salvage synthesis of purines nor pyrimidine synthesis were impacted by RT in any intracranial tissues. With these findings, we opened a clinical study to directly measure purine synthesis in patients, and we found that human GBMs have similarly high purine synthesis rates compared to normal brain tissue. Because DNA damage activated DNPS without affecting purine salvage or pyrimidine synthesis, we reasoned that active signaling may be involved. Indeed, therapy-induced DNPS increases are lost in vitro and in vivo upon pharmacological or genomic inhibition of the DNA-damage sensing kinase DNA-PK. Moreover, RT and DNA-PK have direct influence over the spatial organization of DNPS enzymes, including IMPDH, the rate-limiting step in guanylate synthesis. Because purines can promote DNA repair, these findings suggest that DNA-PK signaling helps promote DNA repair in part by causing the spatial reorganization of DNPS enzymes, thereby activating purine synthesis. To determine if disrupting this regulation can augment GBM treatment efficacy, we combined an FDA-approved inhibitor of purine synthesis with chemoradiation in a variety of mouse models of GBM. Critically, targeting GTP synthesis improved the efficacy of both RT alone and chemoradiation in multiple patient-derived and syngeneic intracranial models, suggesting a potential therapeutic targeting opportunity in patients. In this study, we have developed novel methodology to directly measure purine synthesis in brain tumors in mice and humans. With these tools, we discovered that after DNA damage, DNA-PK mediates a novel pathway controlling the spatial reorganization of purine synthesis enzymes and subsequent DNPS increases. The resulting elevation of GTP levels promotes therapy resistance in tumors, and we are now directly measuring and inhibiting this molecular activity in patients with GBM in an effort to improve standard therapy. Citation Format: Andrew J. Scott, Alexandra M. O'Brien, Weihua Zhou, Vidhi Pareek, Zhou Sha, Sravya Palavalasa, Ayesha U. Kothari, Kari Wilder-Romans, Li Zhang, Anthony C. Andren, Sriram Chandrasekaran, Jason Heth, Yoshie Umemura, Nathan Qi, John Woulfe, Sriram Venneti, Meredith A. Morgan, Theodore S. Lawrence, Wajd N. Al-Holou, Costas A. Lyssiotis, Daniel R. Wahl. DNA damage signaling activates de novo GTP synthesis to promote chemoradiation resistance in glioblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3677.

Abstract 5367: Deep neural networks using protein-protein network information predict multiple myeloma survival

Abstract The modern development of sequencing technologies provides a comprehensive molecular portrait of human cancers. There is a strong need to develop methods to not only improve patient prognosis predictions but also to understand the driving factors for treatment. However, the high-dimension, low-sample size nature of the genomic data poses challenges for typical machine learning algorithms. The systematic understanding of genes with respect to a network (protein-protein interaction (PPI) network) is a way to handle the limit and the nonparametric analysis of geometric properties such as Ollivier-Ricci curvature and associated invariant measure developed by our group have proven to be successful for the prediction of survival in multiple cancers. In this work, we propose a novel supervised deep learning approach combining the aforementioned geometric methods, which benefit from the flexibility provided by deep learning techniques while still preserving much of the interpretability of the geometric analysis. We take advantage of a state-of-the-art graph neural network approach. Sparse connections between layers were inspired by the known biology of the PPI network from the Human Protein Reference Database (HPRD) and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, supplemented with geometric network features which are fed into the network in corresponding layers. The prediction is based on a local-global principle, where highly predictive features are selected from early layers of the network and fed directly to the final layer to produce a multivariable Cox regression. We applied our method to RNA-Seq gene expression data from the CoMMpass study of multiple myeloma (MM). More specifically, 657 patients in the data set were randomly divided into training, validation and set-aside testing sets by a ratio of 6:2:2. We obtained an average C-index 0.66 of the prediction in the testing set from a 10-fold data split. Dichotomizing the testing set by its mean value to define high-risk vs. low-risk yielded a significant p-value of the log-rank test in the set-aside data (p-value =3e-4). We observed that geometric protein network information not only improved the outcome prediction (vs. 6% worse without geometric feature inputs), but was also more robust to fold splitting. From our model, we identified WEE1, CENPE and CENPF as top genes driving survival differences (higher expression of WEE1 increased risk and lower negative curvature between CENPE and CENPF increased risk). WEE1 is a cell cycle-related gene that regulates DNA repair and CENPE and CENPF are components of a fibrous layer of mitotic kinetochores, which have been indicated in the literature to be related to the prognosis as well as possible targets for treatment. While it is therefore logical that these genes would be implicated in the natural history of MM, they were identified entirely on the basis of network analysis. Citation Format: Jiening Zhu, Jung Hun Oh, Anish K. Simhal, Rena Elkin, Larry Norton, Joseph O. Deasy, Allen R. Tannenbaum. Deep neural networks using protein-protein network information predict multiple myeloma survival. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5367.

Abstract 6124: Recombinant apurinic/apyrimidinic endonuclease-1/redox factor-1 plus acetylsalicylic acid combination therapy inhibits tumorigenesis in an orthotopic xenograft murine model of triple-negative breast cancer

Abstract Triple-negative breast cancer (TNBC) is characterized with hormone receptor negative and frequently exhibits inherently aggressive clinical behavior, resulting in poor prognoses. TNBCs are highly heterogenic, leading to obstacles in identifying new therapeutic targets and performing targeted therapy. Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1), a multifunctional protein, is mainly involved in DNA repair and redox regulation; it is upregulated in various cancers and is extracellularly secreted because of hyperacetylation. We previously reported that hyperacetylation induced APE1/Ref-1 release causes apoptosis in TNBCs. In the current study, we aimed to assess the therapeutic efficacy of combination treatment involving recombinant human APE1/Ref-1 (rhAPE1/Ref-1) plus acetylsalicylic acid (ASA) in TNBC xenograft mice. ASA co-treatment was used to induce and lasting acetylation of rhAPE1/Ref-1. For in vivo analysis, we constructed an orthotopic xenograft in vivo model of TNBC by using MDA-MB-231 cells. We performed combination therapy involving intravenous injection of purified rhAPE1/Ref-1 (1 mg/kg) and oral administration of ASA (20 mg/kg) thrice a week for 6 weeks in TNBC xenograft mice. This rhAPE1/Ref-1 plus ASA combination therapy inhibited tumor formation and growth, without damaging liver or kidney tissue, and decreased plasma levels of the cancer marker CEA and breast cancer-specific markers CA27-29 and CA15-3 in the TNBC xenograft mice. The TNBC group, which underwent combination therapy, had more apoptotic cells and greater inflammatory cell infiltration in tumor tissues than the vehicle group did. Additionally, in tumor tissue of TNBC with combination therapy exhibits increased apoptosis following upregulation of Bax, cleaved-caspase-3, and cleaved-PARP. Thus, we found that rhAPE1/Ref-1 plus ASA combination therapy enhanced antitumor effects in TNBCs via inflammatory cell infiltration and apoptosis signaling pathways. Our findings indicate the therapeutic potential of rhAPE1/Ref-1 plus ASA combination therapy for TNBC. Citation Format: Yu Ran Lee, Hee Kyoung Joo, Eun-Ok Lee, Sungmin Kim, Hao Jin, Yeon Hee Choi, Eun Ju Choi, Byeong Hwa Jeon. Recombinant apurinic/apyrimidinic endonuclease-1/redox factor-1 plus acetylsalicylic acid combination therapy inhibits tumorigenesis in an orthotopic xenograft murine model of triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6124.

Abstract 3716: RNA N6-methyladenosine binding protein, YTHDF1 regulates DNA repair and cancer immunity in protein synthesis levels

Abstract N6-methyladenosine RNA methylation is one of the most abundant post transcriptional modifications in eukaryotic messenger RNAs and plays crucial roles in cancer development and progression. YTHDF1 is an m6A reader protein and has been reported to increase the translation of mRNAs in cooperation with YTHDF3. In gastric cancer, YTHDF1 was reported to be overexpressed in cancer tissues, but detailed effects of YTHDF1 in cancer immunity have not been fully elucidated. In RNA sequencing data from a TGCA gastric cancer cohort, the expression of YTHDF1 was inversely correlated with the cytotoxic T cell markers, such as CD8A, GZMA, and GZMB. To investigate the effect of YTHDF1 overexpression on gene expression regulation in protein levels, we performed the proteomic analysis for newly synthesized proteins using non-canonical amino acid azidohomoalanine and click chemistry tagging reaction in the presence of interferon-γ (IFN-γ). Protein synthesis of genes in ‘DNA damage response’ and ‘DNA repair’ gene sets increased in YTHDF1-overexpressed samples. On the contrary, protein synthesis of genes in ‘Allograph rejection’, ‘NK cell mediated cytotoxicity’, and ‘NF-κB signaling’ gene sets decreased in YTHDF1-overexpressed samples. Especially, YTHDF1 reduced basal expression of DNA damage marker, γH2AX, suggesting that DNA damage repair was enhanced by YTHDF1 overexpression. Our study suggests that YTHDF1 plays pervasive roles in DNA repair and cancer immunity by regulating gene expression in protein levels. Citation Format: Dongjun Jang, Hae Rim Jung, Jaeik Oh, Sung-Yup Cho. RNA N6-methyladenosine binding protein, YTHDF1 regulates DNA repair and cancer immunity in protein synthesis levels. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3716.

Abstract 3498: GTP-dependent signaling links metabolism, non-homologous end joining and treatment responses in cancer and normal tissues

Abstract Introduction/Objectives: Purines regulate DNA repair in brain tumors through uncertain mechanisms. We sought to define the mechanisms by which purines regulate DNA repair and therapy response. Methods: Crispr/Cas9, siRNA, and CDNA overexpression and immunoblot were used to modulate and confirm protein levels. γ-H2AX and Rad51 foci were enumerated using immunofluorescence. Fluorescent reporter assays were performed to detect DNA repair activity. Phosphoproteomics was used to identify GTP-dependent (de)phosphorylation events after RT and antibodies generated against novel sites. Celltiter-glo or clonogenic assay were performed to evaluate drug/RT responses. IHC was used to detect protein expression. Animal models of glioblastoma and normal tissue (irradiation of GI system) were used to assess DNA repair and treatment responses in vivo. Results: Pharmacogenomic inhibition of GTP (but not ATP) synthesis sensitized GBM cells to RT, slowed the repair of RT-induced DSBs and inhibited the activity of non-homologous end joining (NHEJ), but not homologous recombination (HR). These effects could be rescued by GTP (but not ATP) supplementation. We found a GTP-dependent RT-induced dephosphorylation event on Abl interactor 1 (Abi-1) serine 323 (S323) using phosphoproteomics. We generated a new antibody for p-Abi-1 (S323), validated its specificity, and confirmed that RT causes a GTP-dependent dephosphorylation of Abi-1 (S323). Knockout of Abi-1 slowed RT-induced DSB repair and this was rescued by re-expression of dephosphomimetic Abi-1 (S323A) but not phosphomimetic Abi-1 (S323D). Abi-1 canonically binds to the small GTP-activated protein Rac1. Expression of constitutively active Rac1 promoted the dephosphorylation of Abi-1 (S323) and DSB repair while these effects were blocked by dominant negative Rac1. Pharmacogenomic inhibition of protein phosphatase 5 reversed the GTP- and Rac1-mediated dephosphorylation of Abi-1 and DSB repair. These findings have therapeutic relevance. In GBM PDX samples, levels of p-Abi-1 (S323) negatively correlated with Rac1 activity and predicted favorable efficacy of genotoxic treatments. In orthotopic GBM mouse models, inhibition of Rac1 enhanced RT responses and suppressed Abi-1 S323 dephosphorylation. Abi-1 knockout enhanced efficacy of numerous genotoxic treatments and could be rescued by Abi-1 S323A (but not Abi-1 S323D) re-expression. This regulation is generalizable beyond brain cancer, as GTP supplementation promoted DNA repair and p-Abi1 (S323) dephosphorylation in normal astrocytes and enteroids and protected mice from RT-mediated gastrointestinal injury. Conclusions: GTP promotes DNA repair by activating Rac1 and PP5 to dephosphorylate Abi-1 and stimulate NHEJ. Disrupting this regulation could improve brain tumor treatment responses while augmenting it could help protect normal tissues from genotoxic injury. Citation Format: Weihua Zhou, Angelica Lin, Zitong Zhao, John Yang, Kari Wilder-Romans, Jie Xu, Sumeet Solanki, Jing Li, Annabel Yang, Andrew Scott, Ayesha Kothari, Erik Peterson, Navyateja Korimerla, Jessica Liang, Janna Jacobson, Sravya Palavalasa, Alexandra Obrien, Sean Ferris, Shuang Zhao, Jann N. Sarkaria, Meredith Morgan, Theodore S. Lawrence, Costas A. Lyssiotis, Yatrik Shah, Daniel R. Wahl. GTP-dependent signaling links metabolism, non-homologous end joining and treatment responses in cancer and normal tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3498.

A model for Scc2p stimulation of cohesin's ATPase and its inhibition by acetylation of Smc3p.

The evolutionarily conserved cohesin complex mediates sister chromatid cohesion and facilitates mitotic chromosome condensation, DNA repair, and transcription regulation. These biological functions require cohesin's two ATPases, formed by the Smc1p and Smc3p subunits. Cohesin's ATPase activity is stimulated by the Scc2p auxiliary factor. This stimulation is inhibited by Eco1p acetylation of Smc3p at an interface with Scc2p. It was unclear how cohesin's ATPase activity is stimulated by Scc2p or how acetylation inhibits Scc2p, given that the acetylation site is distal to cohesin's ATPase active sites. Here, we identify mutations in budding yeast that suppressed the in vivo defects caused by Smc3p acetyl-mimic and acetyl-defective mutations. We provide compelling evidence that Scc2p activation of cohesin ATPase depends on an interface between Scc2p and a region of Smc1p proximal to cohesin's Smc3p ATPase active site. Furthermore, substitutions at this interface increase or decrease ATPase activity to overcome ATPase modulation by acetyl-mimic and acetyl-null mutations. Using these observations and an existing cryo-EM structure, we propose a model for regulating cohesin ATPase activity. We suggest that Scc2p binding to Smc1p causes the adjacent Smc1p residues and ATP to shift, stimulating Smc3p's ATPase. This stimulatory shift is inhibited through acetylation of the distal Scc2p-Smc3p interface.

Effect of low temperature on the resistance of Listeria monocytogenes and Escherichia coli O157:H7 to acid electrolyzed water

Low temperature can affect the resistance of pathogenic bacteria to other external stress. The present study was envisaged to assess the tolerance of L. monocytogenes and E. coli O157:H7 to acidic electrolyzed water (AEW) under low temperature stress. AEW treatment caused a damage to cell membrane of the pathogenic bacteria, which led to protein leakage and DNA damage. Compared with the pathogenic bacteria cultured at 37 °C (pure culture), the L. monocytogenes and E. coli O157:H7 cells cultivated at low temperature presented a less damage and had a higher survival rate when exposed to AEW. Therefore, 4 °C or 10 °C grown bacteria were less susceptible to AEW than those cultured at 37 °C. And this phenomenon was verified when AEW was used to treat the pathogenic bacteria inoculated in salmon. In addition, transcriptomic sequencing technology (RNA-seq) was used to reveal the mechanism of AEW tolerance of L. monocytogenes under low temperature stress. Transcriptomic analysis showed the expression of the cold shock protein, regulation of DNA-templated transcription, ribosome pathway, phosphotransferase system (PTS), bacteria chemotaxis, SOS response and DNA repair were involved in the resistance of L. monocytogenes to AEW. We speculated that the direct modulation of the expression of cold shock protein CspD, the indirect effect on the expression of cspD by inhibiting the expression of Crp/Fnr family transcriptional regulator or enhancing the level of cAMP by regulating PTS could reduce the resistance of L. monocytogenes cultivated at 4 °C to AEW. Our study contributes to solving the problem of the reduced bacteriostatic effect in cold storage environment.

M6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis

SF3B1 is the most mutated splicing factor (SF) in myelodysplastic syndromes (MDSs), which are clonal hematopoietic disorders with variable risk of leukemic transformation. Although tumorigenic SF3B1 mutations have been extensively characterized, the role of "non-mutated" wild-type SF3B1 in cancer remains largely unresolved. Here, we identify a conserved epitranscriptomic program that steers SF3B1 levels to counteract leukemogenesis. Our analysis of human and murine pre-leukemic MDS cells reveals dynamic regulation of SF3B1 protein abundance, which affects MDS-to-leukemia progression invivo. Mechanistically, ALKBH5-driven 5' UTR m6A demethylation fine-tunes SF3B1 translation directing splicing of central DNA repair and epigenetic regulators during transformation. This impacts genome stability and leukemia progression invivo, supporting an integrative analysis in humans that SF3B1 molecular signatures may predict mutational variability and poor prognosis. These findings highlight a post-transcriptional gene expression nexus that unveils unanticipated SF3B1-dependent cancer vulnerabilities.

The role of demethylase AlkB homologs in cancer.

The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms' most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers' biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.