DNA Repair Activity Research Articles

Interaction with single-stranded DNA-binding protein modulates Escherichia coli RadD DNA repair activities

The bacterial RadD enzyme is important for multiple genome maintenance pathways, including RecA DNA strand exchange and RecA-independent suppression of DNA crossover template switching. However, much remains unknown about the precise roles of RadD. One potential clue into RadD mechanisms is its direct interaction with the single-stranded DNA binding protein (SSB), which coats single-stranded DNA exposed during genome maintenance reactions in cells. Interaction with SSB stimulates the ATPase activity of RadD. To probe the mechanism and importance of RadD:SSB complex formation, we identified a pocket on RadD that is essential for binding SSB. In a mechanism shared with many other SSB-interacting proteins, RadD uses a hydrophobic pocket framed by basic residues to bind the C-terminal end of SSB. We found that RadD variants that substitute acidic residues for basic residues in the SSB binding site impair RadD:SSB complex formation and eliminate SSB stimulation of RadD ATPase activity in vitro. Additionally, mutant E. coli strains carrying charge reversal radD changes display increased sensitivity to DNA damaging agents synergistically with deletions of radA and recG, although the phenotypes of the SSB-binding radD mutants are not as severe as a full radD deletion. This suggests that cellular RadD requires an intact the interaction with SSB for full RadD function.

Classification of triple-negative breast cancer based on pathway enrichment levels.

Triple-negative breast cancer (TNBC) is highly heterogeneous in the stromal and immune microenvironment, genome integrity, oncogenic signatures, and metabolic processes. However, a classification of TNBC by combining these features remains lacking. Here we classified TNBC based on the enrichment levels of 14 pathways related to immune, stromal, oncogenic and metabolic signatures by unsupervised clustering. In three bulk tumor transcriptome datasets and a single cell RNA-Seq (scRNA-seq) dataset, we consistently identified four TNBC subtypes: Imm-E, Str-E, DR-E, and Met-E. Imm-E displayed the strongest immune signatures, the lowest intratumor heterogeneity (ITH), the highest global methylation levels, the lowest tumor purity, and the best prognosis. Str-E showed the strongest stromal signatures and TGF-β signaling. DR-E had the highest DNA repair activity, cell cycle activity, and genomic instability. Met-E demonstrated the strongest hormone metabolism and signaling, the highest ITH, the lowest genomic instability, and the worst prognosis. The subtyping of TNBC provides novel insights into tumor biology and clinical implications for this disease.

Abstract 1647: In vivo efficacy and metabolism of a new synthetized dual EGFR-DNA targeting combi-molecule in a human stem cells-derived model of glioblastoma implanted intracranially in mice

Abstract Introduction. Glioblastoma multiforme (GBM) is the most aggressive form of primary brain tumours with an average survival rate of 12-18 months. The existing treatment (chemotherapy with temozolomide (TMZ)+radiotherapy) increases the median survival by 2-3 months. One protein, the epidermal growth factor receptor (EGFR) is expressed in 57.4% of GBM and half of them expresses its aggressive mutant, EGFRvIII, whose expression is associated with resistance to apoptosis, activation of DNA repair and ultimately resistance to chemotherapy. In the context of a strategy termed “combi-targeting”, we developed molecules designed to block EGFRvIII while being capable of inducing DNA damage. In vivo analysis suggests that the first prototype of such a class ZR2002 loses its DNA damaging function through metabolic oxidation. Recently, we surmised that a molecule designed to be metabolically stable may require a lower dose to be active in vivo. To test this hypothesis, we measured the cytotoxicity of the new combi-molecule, called "AF143", in a panel of glioblastoma cell lines and then we determined its efficacy and drug metabolism in an in vivo model of glioblastoma derived from human glioblastoma stem cells (GSC) with known resistance to TMZ. Material and Methods. Three glioblastoma cells line (U87-wt, U87-EGFR and U87-EGFRvIII) and the human GSC (1123IC7R) were used to determine IC50 of AF143 and ZR2002 with SRB or alamarBlue assay. Xenograft of tumors were obtained by intracranial injection of 1123IC7R-Luc GSC into the head of NSG female mice. One group of mice was treated with ZR2002 (N=8), the other with AF143 (N=7), the last with vehicle (N=8). Mice received 10 total doses: 2 cycles of 1 dose (100mg/kg) daily for 5 consecutive days followed by 2 days off, by oral gavage. The tumour burden was measured by bioluminescent imaging and drug metabolism by LC-MS. Body weights, mortality and toxicity were monitored. Survival curves and statistical analysis calculated. Results. In vitro growth inhibitory analysis showed that AF143 was 2-fold more potent than ZR2002 in U87-EGFR and 1123IC7R GSC and 3-fold more potent in U87-EGFRvIII. In vivo analysis of AF143 given alone showed significant antitumor activity (p<0.05) after 5 doses treatment, while ZR2002 induced an apparent tumour delay (p>0.05). Remarkably, AF143 and ZR2002 treatment significantly prolonged the overall survival of mice compared with the control group (p= 0.0004 for AF143 and p=0.04 for ZR2002). Analysis of drug metabolism revealed that in contrast to ZR2002, AF143 remained intact after 2h treatment, with moderate levels of N-acetyl and N6-dealkylated metabolites. Conclusion. The results in toto suggest that the intact structure of AF143 is stable to metabolism, can cross the blood brain barrier and induce antitumour activity in a EGFRvIII expressing glioblastoma stem cell model. Citation Format: Caterina Facchin, Ana Belen Fraga Timiraos, Brian Meehan, Nadia Babaa, Lata Adnani, Anne-Laure Larroque, Janusz Rak, Bertrand J Jean-Claude. In vivo efficacy and metabolism of a new synthetized dual EGFR-DNA targeting combi-molecule in a human stem cells-derived model of glioblastoma implanted intracranially in mice [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 1647.

Abstract 6106: Epigenetic-miRNA regulatory circuit confers ovarian cancer chemoresistance through RAD18-mediated DNA damage tolerance and repair signaling

Abstract Epithelial ovarian cancer (EOC) is the deadliest gynecological malignancy. This cancer typically is not detected, 70-80% of patients, until an advanced stage (stage III-IV). The standard of care OC entails complete surgical resection of all visible abdominal-pelvic tumors, followed by platinum-based chemotherapy combined with a taxane. New recommendations for patients responding to adjuvant therapy is to include a PARP inhibitor with or without bevacizumab for maintenance therapy. Despite initial responses, the majority of stage 3 & 4 more than 70% of OC patients experience recurrent disease. Frequently, individuals become resistant to these treatments. This dreadful circumstance highlights the pressing need to identify the molecular mechanisms underlying the disease's aggressive nature upon recurrence and the development of treatment resistance. Several genetic and epigenetic factors have been linked to the reprogramming of tumor cells by controlling the pattern of transcriptional and post-transcriptional gene expression. Particularly, the miRNA-mediated regulatory circuit plays a significant role in tumor progression and therapeutic responses. Our analysis of miRNA expression signature in human ovarian cancer cell line panel showed little to no expression of miR221_5p and a corresponding increase in DNA damage response and repair gene RAD18 expression. RAD18 plays a critical role in cellular DNA damage tolerance and repair activity against chemotherapeutics, including platinum drugs. Similarly, loss of miRNA221_5p is associated with aggressive tumor cell growth, stemness, chemoresistance to platinum drugs, and poor prognosis in several cancers. Based on this information, we have hypothesized that miR221_5p regulates RAD18-mediated DNA damage tolerance and repair and may offer novel therapeutic intervention to overcome EOC chemoresistance. Our experimental data confers that miR221_5p post-transcriptionally regulates RAD18 by binding to its 3’-UTR region and restores OC cell sensitivity to platinum drugs. Mechanistically, our results demonstrate that miRNA221_5p epigenetically regulates RAD18-mediated DNA damage tolerance and homologous recombination repair and could be a novel therapeutic to overcome OC chemoresistance. Collectively, our studies identify a novel chemotherapy-induced epigenetic modulator in OC therapeutic resistance and offer novel miRNA 221-5p-mediated therapeutic intervention for the treatment of chemoresistant OC and to prevent disease recurrence. Citation Format: Tasmin Rahman Omy, Chinnadurai Mani, Komaraiah Palle, Mark Reedy. Epigenetic-miRNA regulatory circuit confers ovarian cancer chemoresistance through RAD18-mediated DNA damage tolerance and repair signaling. [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 6106.

Abstract 3379: Comprehensive circulating tumor DNA and CTC profiling of treatment naïve early-stage head and neck cancer patients reveals early signature of disease progression

Abstract Comprehensive CtDNA and CTC profiling of treatment naïve early-stage head and neck cancer patients reveals early signatures of disease progressionBackground: We performed comprehensive ctDNA analysis on early-stage HNC patients in a pilot study to determine the mutational landscape in HNC patients with a known tobacco history. Methods: We analysed ctDNA of 18 early-stage HNC patients for genomic landscapes using the illumina NextSeq 2000 NGS. A custom-designed OncoIndex gene panel was used for the hybrid capture target-enrichment of critical cancer genes. Panel was designed to detect cancer targeting exonic sequence of 600 genes reporting SNVs and indels along fusions and copy number amplification. The gene panel detected genome-wide signatures including bTMB, MSI (microsatellite instability), HRD (homologous recombination deficiency) prediction and calculate cfDNA tumor fraction. Results: 80 % patients showed presence of at least one CTC in peripheral blood, possibly indicating the progressive disease at the time of presentation. Comprehensive genomic profile obtained from plasma cfDNA of early-stage HNC cancer patients predominantly had low bTMB and MSI Scores (99 % patients). However, HRD and LOH matrix was high for 60 % patients indicating highly dysregulated DNA repair activities. Concurring to these observations, 98 % patients had mutations in key tumor suppressor and DNA damage response (DDR) genes possibly resulting in their loss of function. Besides DNA damage pathway, 60% patients harboured alterations in RTK genes including FGFR, EGFR and PDEGFR family and 32% patients showed activating mutations in Erk1 and its upstream regulators. MSH2 was the most prominently mutated gene (37%) followed by FGFR (32%). Surprisingly, unlike HPV positive advanced HNC cases, TP53 mutations were not detected in any patient, though alterations in TS genes were most prevalent in the study population. 51% alterations resulted into truncated proteins possibly impairing their functions, while 42% alterations were point mutations, 6 % were frameshift and 1 % indels. Presence of mutations in BRAF, PDGFR, FGFR and KIT genes suggested for the potential therapy resistance. Tumor fraction representing ctDNA showed elevated range from 20 % to 45 % with a corresponding ploidy between 2 to 4. Conclusions: Comprehensive ctDNA profile showed major gene alterations in TS and DDR response pathway genes besides mutations in proliferative signaling members. TP53 mutation was not detected, although critical tumor suppressor and DDR genes were predominantly mutated, suggesting for a unique mutation pattern associated with early-stage HNC due to tobacco etiology. Our results suggest that comprehensive ctDNA analysis along CTC profiling can predict the disease progression beforehand and may offer new treatment options to early-stage HNC patients. Citation Format: Gowhar Shafi, Atul Bharde, Fauzul Moubeen, Kanchan Hariramani, Alain D’Souza, Trupti Kad, Bhagwat Jadhav, Sangita Prajapati, Aditi Rani, Madhura Basavalingegowda, Mohan Uttarwar, Gourishankar Aland, Sreeja Jayant, Aravindan Vasudevan, Pankaj Chaturvedi, Jayant Khandare. Comprehensive circulating tumor DNA and CTC profiling of treatment naïve early-stage head and neck cancer patients reveals early signature of disease progression [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 3379.

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.

Sex-biased molecular differences in lung adenocarcinoma are ethnic and smoking specific

BackgroundSex-related differences in cancer epidemiology, tumor biology, immune system activity, and pharmacogenomics have been suggested to be important considerations for precision cancer control. Here we elucidated systematically sex biases in genetic variants, gene expression profiles, and immunological landscapes of lung adenocarcinoma patients (LUADs) with different ancestry and smoking status.MethodsSomatic mutation and mRNA expression data of Asian and Non-Asian LUADs were obtained from public databases. Sex-biased genetic mutations, gene expression, biological pathways, and immune infiltration were identified in the context of smoking status and race.ResultsAmong nonsmokers, male-biased mutations were prevalent in Asian LUADs, while few sex-biased mutations were detected in Non-Asian LUADs. EGFR was the only mutation whose frequency was significantly higher in females than males in both Asian and Non-Asian nonsmokers. More genes exhibited sex-biased expression in Non-Asian LUADs compared to Asian LUADs. Moreover, genes distinctly expressed in females were mainly related to immune-related pathways, whereas those in males were more involved in activation of DNA repair, E2F_targets, and MYC_targets pathways. We also detected sex-specific immune infiltration in the context of genetic variation. In EGFR-mutant LUADs, males had a significantly increased infiltration of CD8 + T cells, whereas resting CD4 + memory T cells were more abundant in females. Additionally, in KRAS-mutant LUADs, CD8 + and CD4 + T cells were more abundant in females than males. In addition, we detected all female patients with high SCGB3A2 expression were exclusively sensitive to immunotherapy, while this phenomenon was not observed in male patients.ConclusionsOur findings provided evidence that sex-related molecular and cellular components are involved in shaping tumor distinct genetic and immune features, which might have important impact on personalized targeted and immune therapy.

Possible repair of UV-damaged Spodoptera littoralis nucleopolyhedrovirus DNA via generation of mutant carrying photolyase gene with DNA repair activity

BackgroundBaculoviruses can be inactivated by ultraviolet (UV) light, which limits their application as an efficient biopesticide. In an attempt to enhance virus resistance to UV inactivation, a photolyase gene, isolated from Spodoptera litura granulovirus (SpliGV), was expressed in a photolyase deficient Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) and the infectivity of recombinant virus expressing phr gene was determined after exposure to UV irradiation.ResultsExpression of the photolyase resulted in a fivefold resistance of virus occlusion bodies of the recombinant virus (vSpli-phr) compared to the wild type SpliNPV upon exposure to UV irradiation as measured by LC50 value when fed on S. littoralis neonate. Furthermore, the recombinant virus expressing phr showed a significant decrease in the time required for lethality than the control virus with about 22 h, as measured by ST50 value. Hence, expression of photolyase via vSpli-phr relatively may rescue the viral DNA damage caused by UV irradiation.ConclusionsThis study provided the evidence that the generated recombinant virus encoding a functioning photolyase, which may have implications for the development of a new generation of baculoviruses with enhanced insect pest management capabilities.

Causes of Mutation Rate Variability in Plant Genomes.

Mutation is the source of all heritable diversity, the essential material of evolution and breeding. While mutation rates are often regarded as constant, variability in mutation rates has been observed at nearly every level-varying across mutation types, genome locations, gene functions, epigenomic contexts, environmental conditions, genotypes, and species. This mutation rate variation arises from differential rates of DNA damage, repair, and transposable element activation and insertion that together produce what is measured by DNA mutation rates. We review historical and recent investigations into the causes and consequences of mutation rate variability in plants by focusing on the mechanisms shaping this variation. Emerging mechanistic models point to the evolvability of mutation rate variation across genomes via mechanisms that target DNA repair, shaping the diversification of plants at phenotypic and genomic scales.

The Complex Roles of DNA Repair Pathways, Inhibitors, Hyperthermia, and Contact Inhibition in Cell Cycle Halts.

The cell cycle has the capacity to safeguard the cell's DNA from damage. Thus, cell cycle arrest can allow tumor cells to investigate their own DNA repair processes. Cancer cells become extremely reliant on G1-phase cyclin-dependent kinases due to mutated oncogenes and deactivated tumor suppressors, producing replication stress and DNA damage during the S phase and destroying checkpoints that facilitate progression through the S/G2/M phase. DNA damage checkpoints activate DNA repair pathways to prevent cell proliferation, which occurs when the genome is damaged. However, research on how cells recommence division after a DNA lesion-induced arrest is insufficient which is merely the result of cancer cells' susceptibility to cell cycle arrest. For example, defects in the G1 arrest checkpoint may cause a cancer cell to proliferate more aggressively, and attempts to fix these complications may cause the cell to grow more slowly and eventually die. Defects in the G2-M arrest checkpoint may enable a damaged cell to enter mitosis and suffer apoptosis, and attempts to boost the effectiveness of chemotherapy may increase its cytotoxicity. Alternatively, attempts to promote G2-M arrest have also been linked to increased apoptosis in the laboratory. Furthermore, variables, such as hyperthermia, contact inhibition, nucleotide shortage, mitotic spindle damage, and resting phase effects, and DNA replication inhibitors add together to halt the cell cycle. In this review, we look at how nucleotide excision repair, MMR, and other variables, such as DNA replication inhibitors, hyperthermia, and contact inhibition, contribute to the outlined processes and functional capacities that cause cell cycle arrest.

Structural and Functional Analysis of a Prokaryotic (6-4) Photolyase from the Aquatic Pathogen Vibrio Cholerae†.

Photolyases are flavoproteins, which are able to repair UV-induced DNA lesions in a light-dependent manner. According to their substrate, they can be distinguished as CPD- and (6-4) photolyases. While CPD-photolyases repair the predominantly occurring cyclobutane pyrimidine dimer lesion, (6-4) photolyases catalyze the repair of the less prominent (6-4) photoproduct. The subgroup of prokaryotic (6-4) photolyases/FeS-BCP is one of the most ancient types of flavoproteins in the ubiquitously occurring photolyase & cryptochrome superfamily (PCSf). In contrast to canonical photolyases, prokaryotic (6-4) photolyases possess a few particular characteristics, including a lumazine derivative as antenna chromophore besides the catalytically essential flavin adenine dinucleotide as well as an elongated linker region between the N-terminal α/β-domain and the C-terminal all-α-helical domain. Furthermore, they can harbor an additional short subdomain, located at the C-terminus, with a binding site for a [4Fe-4S] cluster. So far, two crystal structures of prokaryotic (6-4) photolyases have been reported. Within this study, we present the high-resolution structure of the prokaryotic (6-4) photolyase from Vibrio cholerae and its spectroscopic characterization in terms of invitro photoreduction and DNA-repair activity.

Distinct Profiles of DNA Repair Activity Define Favorable-risk Prostate Cancer Subtypes With Divergent Outcome.

Understanding if divergent molecular profiles of DNA damage and repair (DDR) pathway activity, a biomarker of disease progression, exist in prostate tumors with favorable-risk features is an unmet need, which this study aim to unearth. This was a multicenter registry genome-wide expression profiling study of prospectively collected radical prostatectomy (RP) tumor samples from 2014 to 2016. DDR activity was calculated from average expression of 372 DDR genes. Consensus hierarchical clustering was used to arrive at a robust clustering solution based on DDR gene expression patterns. Genome-wide differential expression between clusters was performed, and outcomes were evaluated across expression patterns. Of 5239 patients from the prospective registry, 376 had favorable-risk disease (Grade group [GG] 1 to 2, PSA prior to RP <10ng/ml, pT2 or less). DDR activity score was correlated with prognostic genomic signatures that predict for metastatic risk (r=0.37, P < 2e-16) and high grade groups (P < .001). High DDR activity (top-quartile) was observed in 28% of patients with favorable-risk disease. In favorable-risk disease, 3 distinct clusters with varied DDR activity emerged with consensus clustering. Cluster I (compared with cluster II-III and GG3-GG5 disease) had the highest expression of all DDR sub-pathways, MYC, PAPR1, AR, and AR activity (P < .001 for all). Furthermore, cluster I was associated with poorer metastasis-free survival (MFS) and Overall survival (OS) compared with other clusters (MFS; HR: 2.43, 95%CI, [1.22-4.83], P = .01; OS; HR: 2.77, 95%CI, [1.18-6.5], P = .01). Cluster I is a novel subgroup of favorable-risk disease with high DDR activity, AR activity, PARP1 and chr8q/MYC expression, and poorer MFS and OS.

SPRTN-dependent DPC degradation precedes repair of damaged DNA: a proof of concept revealed by the STAR assay.

DNA-protein crosslinks (DPCs), formed by the covalent conjugation of proteins to DNA, are toxic lesions that interfere with DNA metabolic processing and transcription. The development of an accurate biochemical assay for DPC isolation is a priority for the mechanistic understanding of their repair. Here, we propose the STAR assay for the direct quantification of DPCs, sensitive to physiologically relevant treatment conditions. Implementing the STAR assay revealed the formation of small cross-linked peptides on DNA, created by the proteolytic degradation of DPCs by SPRTN. The initial proteolytic degradation of DPCs is required for the downstream activation of DNA repair, which is mediated through the phosphorylation of H2Ax. This leads to the accumulation of DNA repair factors on chromatin and the subsequent complete removal of the cross-linked peptides. These results confirmed that the repair of DPCs is a two-step process, starting with proteolytic resection by SPRTN, followed by the repair of the underlying damage to the DNA.

Differential requirement for BRCA1-BARD1 E3 ubiquitin ligase activity in DNA damage repair and meiosis in the Caenorhabditis elegans germ line.

The tumor suppressor BRCA1-BARD1 complex regulates many cellular processes; of critical importance to its tumor suppressor function is its role in genome integrity. Although RING E3 ubiquitin ligase activity is the only known enzymatic activity of the complex, the in vivo requirement for BRCA1-BARD1 E3 ubiquitin ligase activity has been controversial. Here we probe the role of BRCA1-BARD1 E3 ubiquitin ligase activity in vivo using C. elegans. Genetic, cell biological, and biochemical analyses of mutants defective for E3 ligase activity suggest there is both E3 ligase-dependent and independent functions of the complex in the context of DNA damage repair and meiosis. We show that E3 ligase activity is important for nuclear accumulation of the complex and specifically to concentrate at meiotic recombination sites but not at DNA damage sites in proliferating germ cells. While BRCA1 alone is capable of monoubiquitylation, BARD1 is required with BRCA1 to promote polyubiquitylation. We find that the requirement for E3 ligase activity and BARD1 in DNA damage signaling and repair can be partially alleviated by driving the nuclear accumulation and self-association of BRCA1. Our data suggest that in addition to E3 ligase activity, BRCA1 may serve a structural role for DNA damage signaling and repair while BARD1 plays an accessory role to enhance BRCA1 function.

Mycobacterial helicase Lhr abets resistance to DNA crosslinking agents mitomycin C and cisplatin.

Mycobacterium smegmatis Lhr exemplifies a novel clade of helicases composed of an N-terminal ATPase/helicase domain (Lhr-Core) and a large C-terminal domain (Lhr-CTD) that nucleates a unique homo-tetrameric quaternary structure. Expression of Lhr, and its operonic neighbor Nei2, is induced in mycobacteria exposed to mitomycin C (MMC). Here we report that lhr deletion sensitizes M. smegmatis to killing by DNA crosslinkers MMC and cisplatin but not to killing by monoadduct-forming alkylating agent methyl methanesulfonate or UV irradiation. Testing complementation of MMC and cisplatin sensitivity by expression of Lhr mutants in Δlhr cells established that: (i) Lhr-CTD is essential for DNA repair activity, such that Lhr-Core does not suffice; (ii) ATPase-defective mutant D170A/E171A fails to complement; (iii) ATPase-active, helicase-defective mutant W597A fails to complementand (iv) alanine mutations at the CTD-CTD interface that interdict homo-tetramer formation result in failure to complement. Our results instate Lhr's ATP-driven motor as an agent of inter-strand crosslink repair in vivo, contingent on Lhr's tetrameric quaternary structure. We characterize M. smegmatis Nei2 as a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Counter to previous reports, we find Nei2 is inactive as a lyase at a THF abasic site and has feeble uracil glycosylase activity.

PS-B08-6: ROLE OF THE HMGB-1/RAGE AXIS AND MINERALOCORTICOID RECEPTOR IN THE PATHOGENESIS OF ACUTE KIDNEY INJURY

Background: Endothelial dysfunction plays a central role in the pathogenesis of cardio-renal syndrome. High mobility group box-1 (HMGB-1) is a protein with various roles in different cellular compartments, and indirectly regulates the activity of transcription and DNA repair in the nucleus. On the other hand, during tissue damage, it is released into the extracellular environment as damage-associated molecular patterns (DAMPs). HMGB-1 is elevated in the pathogenesis of acute kidney injury (AKI) and be involved in endothelial dysfunction through binding to toll like receptor (TLR) and receptor for advanced glycation end products (RAGE). In addition, we recently demonstrated that RAGE-mediated Rac1 activated mineralocorticoid receptor (MR) and subsequently resulted in podocytes damage. In the present study, we hypothesized that crosstalk between HMGB-1/ RAGE and Rac1-MR pathways could contribute to endothelial dysfunction in AKI. Methods: In the present study, we performed a renal ischemia-reperfusion model (I/R group) on C57BL/6J mice to evaluate the expression of Rac1-MR pathway and organ damage. In addition, the I/R group was pretreated with MR blocker (esaxerenone) and evaluated in the same way. In vitro study, we investigated whether HMGB-1 could activate Rac1-MR axis and thus induce endothelial injury in cultured human umbilical vein endothelial cells (HUVECs) by assessing expression levels of genes for MCP-1 and NF-κB with or without administration of RAGE aptamer or MR blocker. Results: In the I/R group, MR activation assessed by translocation into the nucleus and enhanced RAGE expression were observed along with HMGB-1 and RAGE elevation, and pretreatment with MR blocker suppressed the elevation of serum creatinine levels as well as tubular necrosis. Further, the loss of peritubular capillaries observed in I/R kidney was markedly suppressed by MR blocker. In vitro study, HMGB-1 supplementation significantly increased RAGE expression, GTP-bound Rac1 and enhanced MR translocation into the nucleus in HUVECs as well. We also found that HMGB-1 upregulated MCP-1 and NF-κB, all of which were significantly blocked by pretreatment of RAGE aptamer and MR blocker. Conclusion: These results suggest that there may be a close relationship between HMGB-1/ RAGE axis and Rac1/ MR activation, thus contributing endothelial injury. Using RAGE aptamer or MR blocker could be novel therapeutic strategies against endothelial dysfunction in patients with AKI.

Age- and Microbiota-Dependent Cell Stemness Plasticity Revealed by Cattle Cell Landscape.

Newborn ruminants are considered functionally monogastric animals. The poor understanding of cellular differences between newborn and mature ruminants prevents the improvement of health and performance of domestic ruminants. Here, we performed the single-cell RNA sequencing on the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, rectum, liver, salivary gland, and mammary gland from newborn and adult cattle. A comprehensive single-cell transcriptomic atlas covering 235,941 high-quality single cells and 78 cell types was deciphered. A Cattle Cell Landscape database (http://cattlecelllandscape.zju.edu.cn) was established to elaborately display the data and facilitate effective annotation of cattle cell types and subtypes for the broad research community. By measuring stemness states of epithelial cells in each tissue type, we revealed that the epithelial cells from newborn forestomach (rumen, reticulum, and omasum) were more transcriptionally indistinct and stochastic compared with the adult stage, which was in contrast to those of abomasum and intestinal tissues. The rapid forestomach development during the early life of calves was driven by epithelial progenitor-like cells with high DNA repair activities and methylation. Moreover, in the forestomach tissues of newborn calves, the Megasphaera genus was involved in regulating the transcriptional plasticity of the epithelial progenitor-like cells by DNA methylation regulation. A novel cell type, the STOML3+ cell, was found to be newborn-specific. It apparently plays a crucial role in stemness maintenance of its own and cholangiocytes in the hepatic microenvironment. Our results reveal that the age- and microbiota-dependent cell stemness plasticity drives the postnatal functional maturity of ruminants.

DNA Repair Gene OGG1 Ser326Cys Polymorphism and DNA Damage in Patients with Type 2 Diabetes

8-hydroxydeoxyguanosine (8-OHdG) is the most frequent oxidative DNA damage. 8-oxo-deoxyguanosine DNA glycosylase 1 (OGG1) is involved in the repair of 8-OHdG. Many studies indicated that DNA repair is decreased in type 2 diabetes (T2DM). Single nucleotide polymorphisms in DNA repair genes may be linked to a decrease in DNA repair activity. The main objective of this study was to see how the OGG1 Ser326Cys gene polymorphism affected OGG1 expression and urinary excretion of 8-OHdG in T2DM patients. OGG1 expression and OGG1 genotyping in lymphocytes were detected by immunocytochemical staining and Polymerase Chain Reaction-Restriction Fragment Length Polymorphism assay, respectively. Urinary 8-OHdG levels were measured by using ELISA kit in patients with T2DM. Compared with control cases, patients with T2DM had lower OGG1 immunopositivity and higher urinary 8-OHdG levels. No significant difference was found in OGG1 immunopositivity or urinary 8-OHdG levels between subjects with different OGG1 genotypes in both groups. In conclusion, The OGG1 Ser326Cys gene polymorphism has no effect on neither OGG1 expression nor urinary 8-OHdG levels. Increased urinary 8-OHdG levels despite low OGG1 immunopositivity may be derived from the action of other DNA repair enzymes.

WT1 regulates expression of DNA repair gene Neil3 during nephrogenesis.

Mammalian nephrons arise from a population of nephron progenitor cells (NPCs) expressing the master transcription factor Wilms tumor-1 (WT1), which is crucial for NPC proliferation, migration, and differentiation. In humans, biallelic loss of WT1 precludes nephrogenesis and leads to the formation of Wilms tumor precursor lesions. We hypothesize that WT1 normally primes the NPC for nephrogenesis by inducing expression of NPC-specific DNA repair genes that protect the genome. We analyzed transcript levels for a panel of DNA repair genes in embryonic day 17.5 (E17.5) versus adult mouse kidneys and noted seven genes that were increased >20-fold. We then isolated Cited1+ NPCs from E17.5 kidneys and found that only one gene, nei-like DNA glycosylase 3 (Neil3), was enriched. RNAscope in situ hybridization of E17.5 mouse kidneys showed increased Neil3 expression in the nephrogenic zone versus mature nephron structures. To determine whether Neil3 expression is WT1 dependent, we knocked down Wt1 in Cited1+ NPCs (60% knockdown efficiency) and noted a 58% reduction in Neil3 transcript levels. We showed that WT1 interacts with the Neil3 promoter and that activity of a Neil3 promoter-reporter vector was increased twofold in WT1+ versus WT1- cells. We propose that Neil3 is a WT1-dependent DNA repair gene expressed at high levels in Cited1+ NPCs, where it repairs mutational injury to the genome during nephrogenesis. NEIL3 is likely just one of many such lineage-specific repair mechanisms that respond to genomic injury during kidney development.NEW & NOTEWORTHY We studied the molecular events leading to Wilms tumors as a model for the repair of genomic injury. Specifically, we showed that WT1 activates DNA repair gene Neil3 in nephron progenitor cells. However, our observations offer a much broader principle, demonstrating that the embryonic kidney invests in lineage-specific expression of DNA repair enzymes. Thus, it is conceivable that failure of these mechanisms could lead to a variety of "sporadic" congenital renal malformations and human disease.

Integrating single-cell RNA sequencing and prognostic model revealed the carcinogenicity and clinical significance of FAM83D in ovarian cancer.

Ovarian cancer (OC) is a fatal gynecological tumor with high mortality and poor prognosis. Yet, its molecular mechanism is still not fully explored, and early prognostic markers are still missing. In this study, we assessed carcinogenicity and clinical significance of family with sequence similarity 83 member D (FAM83D) in ovarian cancer by integrating single-cell RNA sequencing (scRNA-seq) and a prognostic model. A 10x scRNA-seq analysis was performed on cells from normal ovary and high-grade serous ovarian cancer (HGSOC) tissue. The prognostic model was constructed by Lasso-Cox regression analysis. The biological function of FAM83D on cell growth, invasion, migration, and drug sensitivity was examined in vitro in OC cell lines. Luciferase reporter assay was performed for binding analysis between FAM83D and microRNA-138-5p (miR-138-5p). Our integrative analysis identified a subset of malignant epithelial cells (C1) with epithelial-mesenchymal transition (EMT) and potential hyperproliferation gene signature. A FAM83D+ malignant epithelial subcluster (FAM83D+ MEC) was associated with cell cycle regulation, apoptosis, DNA repair, and EMT activation. FAM83D resulted as a viable prognostic marker in a prognostic model that efficiently predict the overall survival of OC patients. FAM83D downregulation in SKOV3 and A2780 cells increased cisplatin sensitivity, reducing OC cell proliferation, migration, and invasion. MiR-138-5p was identified to regulate FAM83D's carcinogenic effect in OC cells. Our findings highlight the importance of miR-138 -5p/FAM83D/EMT signaling and may provide new insights into therapeutic strategies for OC.