Nucleotide Excision Repair Pathway Research Articles

Abstract B021: Targeting nucleotide excision repair in non-muscle invasive bladder cancer

Abstract Background: Previous studies demonstrated that nucleotide excision repair (NER) plays a critical role in cisplatin-based chemotherapy response in muscle-invasive bladder cancer (MIBC), and that spironolactone (SP) is a potent NER inhibitor. We sought to investigate the role of SP in enhancing the response to mitomycin chemotherapy in non-muscle invasive bladder cancer (NMIBC). Materials and Methods: KU1919 cells (NER proficient) were used for chemotherapy response to mitomycin. Cell viability was examined using CellTiter-Glo. IC50 concentrations were calculated using a four-parameter sigmoidal model and plots generated by GraphPad Prism 9. Drug combination indexes (CI) of chemotherapy and SP were calculated using Chou-Talalay method. Cell cycle and apoptosis analysis were measured by assay and Annexin V apoptosis detection kit. DNA damage response and apoptosis signaling were examined by Western blot of gamma-H2AX, cleaved Caspase-3, and cleaved PARP. Results: Combinations of mitomycin and SP (2 μM: 40 μM, CI = 0.09) resulted in strong synergies in KU1919 cells. Mitomycin combined with SP led to more cells with a sub-G1 phase DNA content (9.43% vs. 4.69%, P < 0.01) and apoptosis (55.85% vs. 13.11% P < 0.01) than treatment with mitomycin alone. Western blot analyses showed that the addition of SP to mitomycin treatment induced increased protein expression of DNA damage response genes (gamma-H2AX) and activation of apoptosis (cleaved Caspase-3 and cleaved PARP). Conclusion: Targeting the NER pathway with SP in NMIBC enhances mitomycin-induced DNA damage signaling and subsequent cell apoptosis. These findings offer proof of concept and rationale for combining NER inhibitors with intravesical chemotherapy in NMIBC. Citation Format: Dongbo Xu, Li Wang, Kyle Wieczorekl, Zhiyu Tian, Qiang Li. Targeting nucleotide excision repair in non-muscle invasive bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B021.

Mutagenesis and Repair of γ-Radiation- and Radical-Induced Tandem DNA Lesions

Ionizing radiation induces many different types of DNA lesions. But one of its characteristics is to produce complex DNA damage, of which tandem DNA damage has received much attention, owing to its promise of distinctive biological properties. Oxidative stresses in response to inflammation in tissues and metal-catalyzed reactions that result in generation of radicals also form these DNA lesions. In this minireview, we have summarized the formation of the tandem lesions as well as the replication and repair studies carried out on them after site-specific synthesis. Many of these lesions are resistant to the traditional base excision repair, so that they can only be repaired by the nucleotide excision repair pathway. They also block DNA replication and, when lesion bypass occurs, it may be significantly error-prone. Some of these tandem DNA lesions may contribute to ageing, neurological diseases, and cancer.

Exploring the Mechanisms of Yishen Tongluo Decoction on Repairing DNA Damage in Mouse Spermatogonia Cells Based on Whole Transcriptome Sequencing.

The aim of this study was to investigate the potential mechanism through which Yishen Tongluo decoction (YSTL) repairs DNA damage caused by benzo(a)pyrene diol epoxide (BPDE) in mouse spermatocytes (GC-2). The GC-2 cells were divided randomly into the control group, BPDE group, and low-, medium-, and high-dose YSTL groups of YSTL decoction. A comet assay was used to detect the DNA fragment index (DFI) of cells in each group. Based on the DFI results, whole transcriptome sequencing was conducted, followed by trend analysis, gene ontology (GO) enrichment analysis, kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, and ceRNA network analysis. Compared with the control group, the BPDE group reported a significant increase in the DNA fragmentation index (DFI) (p < .05). Compared with the BPDE group, the low-, high- and medium-dose YSTL groups had a significantly reduced DFI (p < .05). Whole-transcriptome sequencing revealed seven differentially expressed circRNAs, 203 differentially expressed miRNAs, and 3,662 differentially expressed mRNAs between the control group and the BPDE group. There was a total of 12 differentially expressed circRNAs, 204 miRNAs, and 2150 mRNAs between the BPDE group and the traditional Chinese medicine group. The pathways involved include DNA repair pathway, nucleotide excision repair pathway, base excision repair pathway, etc. The ceRNA network reported that Hmga2 was the core protein involved, novel_cir_000117 and mmu-miR-466c-3p were located upstream of Hmga2, and they were regulatory factors associated with Hmga2. Finally, we conclude that YSTL decoction may repair sperm DNA damage caused by BPDE through the novel_cir_000117-mmu-miR-466c-3p-Hmga2 pathway.

Evidence for persistent UV-induced DNA damage and altered DNA damage response in xeroderma pigmentosa patient corneas

Xeroderma pigmentosum (XP) is a rare genetic disorder characterized by injury to the ocular surface due to exposure to ultraviolet (UV) radiation. UV-induced damage in the cells leads to the formation of cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidone photoproducts that are repaired by the NER (Nucleotide Excision Repair) pathway. Mutations in the genes coding for NER proteins, as reported in XP patients, would lead to sub-optimal damage repair resulting in clinical signs varying from photo-keratitis to cancerous lesions on the ocular surface. Here, we aimed to provide evidence for the accumulation of DNA damage and activation of DNA repair pathway proteins in the corneal cells of patients with XP. Corneal buttons of patients who underwent penetrating keratoplasty were stained to quantify DNA damage and the presence of activated DNA damage response proteins (DDR) using specific antibodies. Positive staining for pH2A.X and thymidine dimers confirmed the presence of DNA damage in the corneal cells. Positive cells were found in both control corneas and XP samples however, unlike normal tissues, positive cells were found in all cell layers of XP samples indicating that these cells were sensitive to very low levels of UV. pH2A.X-positive cells were significantly more in XP corneas (p < 0.05) indicating the presence of double strand breaks in these tissues. A positive expression of phosphorylated-forms of DDR proteins was noted in XP corneas (unlike controls) such as ataxia telangiectasia mutated/Rad-3 related proteins (ATM/ATR), breast cancer-1 and checkpoint kinases-1 and -2. Nuclear localization of XPA was noted in XP samples which co-localized (calculated using Pearson's correlation) with pATM (0.9 ± 0.007) and pATR (0.6 ± 0.053). The increased presence of these in the nucleus confirms that unresolved DNA damage was accumulating in these cells thereby leading to prolonged activation of the damage response proteins. An increase in pp53 and TUNEL positive cells in the XP corneas indicated cell death likely driven by the p53 pathway. For comparison, cultured normal corneal epithelial cells were exposed to UV-radiation and stained for DDR proteins at 3, 6 and 24 h after irradiation to quantify the time taken by cells with intact DDR pathway to repair damage. These cells, when exposed to UV showed nuclear translocation of DDR proteins at 3 and 6 h which reduced significantly by 24 h confirming that the damaged DNA was being actively repaired leading to cell survival. The persistent presence of the DDR proteins in XP corneas indicates that damage is being actively recognized and DNA replication is stalled, thereby causing accumulation of damaged DNA leading to cell death, which would explain the cancer incidence and cell loss reported in these patients.

Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress.

Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in humans affecting immunocompromised and elderly populations. Adaptation of pathogens in hostile environments is crucial in establishing infection and persistence within the host. However, the sophisticated cellular and molecular mechanisms of stress response in M. intracellulare still need to be fully explored. We aimed to elucidate the transcriptional response of M. intracellulare under acidic and oxidative stress conditions. At the transcriptome level, 80 genes were shown [FC] ≥ 2.0 and p < 0.05 under oxidative stress with 10mM hydrogen peroxide. Specifically, 77 genes were upregulated, while 3 genes were downregulated. In functional analysis, oxidative stress conditions activate DNA replication, nucleotide excision repair, mismatch repair, homologous recombination, and tuberculosis pathways. Additionally, our results demonstrate that DNA replication and repair system genes, such as dnaB, dinG, urvB, uvrD2, and recA, are indispensable for resistance to oxidative stress. On the contrary, 878 genes were shown [FC] ≥ 2.0 and p < 0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis highlighted nitrogen and sulfur metabolism pathways as the primary responses to acidic stress. Our findings provide evidence of the critical role played by nitrogen and sulfur metabolism genes in the response to acidic stress, including narGHIJ, nirBD, narU, narK3, cysND, cysC, cysH, ferredoxin 1 and 2, and formate dehydrogenase. Our results suggest the activation of several pathways potentially critical for the survival of M. intracellulare under a hostile microenvironment within the host. This study indicates the importance of stress responses in M. intracellulare infection and identifies promising therapeutic targets.

Disrupting glycolysis and DNA repair in anaplastic thyroid cancer with nucleus-targeting platinum nanoclusters

Cancer cells rely on aerobic glycolysis and DNA repair signals to drive tumor growth and develop drug resistance. Yet, fine-tuning aerobic glycolysis with the assist of nanotechnology, for example, dampening lactate dehydrogenase (LDH) for cancer cell metabolic reprograming remains to be investigated. Here we focus on anaplastic thyroid cancer (ATC) as an extremely malignant cancer with the high expression of LDH, and develop a pH-responsive and nucleus-targeting platinum nanocluster (Pt@TAT/sPEG) to simultaneously targets LDH and exacerbates DNA damage. Pt@TAT/sPEG effectively disrupts LDH activity, reducing lactate production and ATP levels, and meanwhile induces ROS production, DNA damage, and apoptosis in ATC tumor cells. We found Pt@TAT/sPEG also blocks nucleotide excision repair pathway and achieves effective tumor cell killing. In an orthotopic ATC xenograft model, Pt@TAT/sPEG demonstrates superior tumor growth suppression compared to Pt@sPEG and cisplatin. This nanostrategy offers a feasible approach to simultaneously inhibit glycolysis and DNA repair for metabolic reprogramming and enhanced tumor chemotherapy.

Genetic variations in DNA excision repair pathway contribute to the chemosensitivity and prognosis of acute myeloid leukemia

Acute myeloid leukemia (AML) is a hematologic malignancy with a high recurrence rate and poor long-term prognosis. DNA excision repair systems, such as base excision repair (BER) and nucleotide excision repair (NER), play a major role in maintaining genomic stability and integrity. Further intensive investigations are necessary to uncover additional AML prognosis loci. In this study, we analyzed 16 candidate SNPs within NER and BER pathways in AML patients. Our results showed the GT/GG genotype of the XPC rs2228001 polymorphism was significantly associated with WBC count in dominant models (OR = 0.41, 95 % CI = 0.18–0.96, p = 0.039). Additionally, the rs25487 and rs3213245 SNPs in the XRCC1 gene, in both co-dominant and dominant models, were significantly associated with PLT count in AML (p < 0.05). The GG genotype of rs1130409 in APEX1 was more prone to adverse cytogenetics in both the codominant and recessive models (p < 0.05). Furthermore, the GA genotypes of ERCC8 rs158572 in codominant model was significantly correlated with refractory group (p < 0.05). ERCC8 rs158572 and XRCC1 rs3213245 in both codominant and dominant models were significantly correlated with the MRD positivity (p < 0.05). Kaplan-Meier analysis revealed an link between overall survival (OS) and the co-dominant, dominant, and recessive models of rs2228001 in XPC. Additionally, patients with the GG and GT/GG genotype in the co-dominant, dominant model and recessive model in XPC rs2228001 exhibited significantly longer survival (p < 0.05). Multivariate Cox analyses indicated that rs2228001 in both co-dominant and dominant models were independent favorable factors impacting patient OS (OR < 1). Our findings suggest that genetic polymorphisms in DNA excision repair pathway genetic polymorphisms contribute to the chemosensitivity and prognosis of acute myeloid leukemia.

A recombinant fungal photolyase autonomously enters human cell nuclei to fix UV-induced DNA lesions.

Solar ultraviolet radiations induced DNA damages in human skin cells with cyclobutane pyrimidine dimers (CPD) and (6-4) photoproducts (6-4PPs) as the most frequent lesions. CPDs are repaired much slower than 6-4PPs by the nucleotide excision repair pathway, which are thus the major lesions that interfere with key cellular processes and give rise to gene mutations, possibly resulting in skin cancer. In prokaryotes and multicellular eukaryotes other than placental mammals, CPDs can be rapidly repaired by CPD photolyases in one simple enzymatic reaction using the energy of blue light. In this study, we aim to construct recombinant CPD photolyases that can autonomously enter human cell nuclei to fix UV-induced CPDs. A fly cell penetration peptide and a viral nucleus localization signal peptide were recombined with a fungal CPD photolyase to construct a recombinant protein. This engineered CPD photolyase autonomously crosses cytoplasm and nuclear membrane of human cell nuclei, which then efficiently photo-repairs UV-induced CPD lesions in the genomic DNA. This further protects the cells by increasing SOD activity, and decreasing cellular ROSs, malondialdehyde and apoptosis.

Abstract 2034: The NAE1 inhibitor MLN4924 sensitizes both BRCA1 wild type and mutant triple negative breast cancers to cisplatin by reducing the nucleotide excision repair protein XPC level

Abstract Background: Triple-negative breast cancer (TNBC) shows poor survival and prognosis, high recurrence, and poor response to conventional therapeutics. To develop novel therapeutics for TNBC, we explored the efficacy of the neddylation inhibitor, MLN4924. We showed that MLN4924 displayed increased sensitivity against TNBC compared to non-TNBC subtypes. Mechanistically, MLN4924 induced extensive re-replication and DNA damage leading to cell death. Furthermore, MLN4924 improved cisplatin efficacy by elevating the DNA damage levels. To demonstrate the mechanisms of MLN4924+cisplatin-mediated enhanced cell death, we examined the XPC level, a key factor in the nucleotide excision repair (NER) pathway, playing a central role in cisplatin damage repair. Neddylation of CUL4A promotes XPC ubiquitination which influences XPC binding to the DNA damage sites for NER. Methods: We examined the XPC protein level by Western blot assay and RNA level by Real Time PCR using both BRCA1-wild type (MDA-MB-231) and BRCA1-mutated (MDA-MB-436) cell lines and mouse xenograft tumor samples. We evaluated if the proteosome inhibitor MG132 stabilizes XPC ubiquitination and protein levels by treating these cells with MG132 for various times. We also overexpressed XPC in these cell lines and examined the effect on survival upon MLN4924 and MLN4924+cisplatin treatments. Results: Our results demonstrate that MLN4924 reduces XPC ubiquitination upon shorter drug treatment but reduces the protein level upon longer drug treatment in both BRCA1-wild type and BRCA1-mutated cell lines. MG132 treatment did not stabilize the XPC ubiquitination level upon shorter drug treatment but stabilized the protein level upon longer drug treatment. We also observed a reduction in the XPC protein level in tumor samples which correlated with the increase in the DNA damage level. Surprisingly, XPC overexpression improved the cell survival in both MLN4924- and MLN4924+cisplatin-treated BRCA1-wild type and mutated TNBC cells. Conclusion: We hypothesize that a reduction in the XPC ubiquitination and protein levels plays a role in cisplatin-induced DNA damage repair reducing NER efficiency and consequently increasing the DNA damage upon MLN4924+cisplatin treatment. Since overexpression of XPC results in improved survival of both MLN4924-and MLN4924+cisplatin-treated cells, we anticipate that XPC not only regulates cisplatin damage repair through NER but may have a broader role in MLN4924 sensitization beyond the NER pathway. Importantly, MLN4924 treatment does not affect the XPC mRNA level emphasizing that neddylation influences the XPC protein level. In summary, our research uncovers novel insights into the role of XPC in both MLN4924 and MLN4924+cisplatin sensitization, shedding light on potential avenues for innovative therapeutic strategies for TNBC patients. Citation Format: Shrilekha Misra, Mateusz Opyrchal, Alo Ray. The NAE1 inhibitor MLN4924 sensitizes both BRCA1 wild type and mutant triple negative breast cancers to cisplatin by reducing the nucleotide excision repair protein XPC level [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2034.

Abstract 6013: VIO-01, a pan-DDR DNA decoy mediating DNA repair abrogation and unleashing the anti-tumor immune response

Abstract Background: Targeting specific DNA Damage Response (DDR) proteins has been worldwide studied and developed, with the example of PARP inhibitors being the only approved treatments in this field. Here, we describe the antineoplastic and immunomodulatory effects of VIO-01, a first-in-class DNA decoy-cholesterol conjugate, that operates as a pan repair proteins decoy, resulting in constitutive exhaustion of the DNA damage response. Methods: VIO-01-induced DDR proteins trapping and cell cytotoxicity were examined in both homologous recombination proficient (HRP) and deficient (HRD) cancer cells. DNA repair efficacy was monitored by analyzing repair protein recruitment to damage sites. RNAseq analysis in HRP/HRD ovarian cancer cells was employed to uncover the molecular mechanisms underlying VIO-01 effects. Effects on the innate and adaptive immune responses were assessed by following T-cell mediated anti-tumor cytotoxicity. VIO-01 antitumor efficacy and biodistribution were also assessed. Additionally, the interest of cholesterol as a vector for VIO-01 was analyzed compared to other ligands like the folate receptor ligand. Results: VIO-01 bounds to several DDR proteins, such as PARP1, KU70/80, MRN complex and MSH2/MSH3 with high affinity, resulting in an abrogation of single- and double-strand break repair. In line with this, and through global transcriptome analysis, VIO-01 treatment resulted in notable downregulation of Base Excision Repair, NHEJ and Nucleotide Excision Repair pathways in both HRP/HRD cell lines. Additionally, VIO-01 elicited the activation of the immune system and inflammatory responses in ovarian cancer cells. Conjointly, VIO-01 treatment induced a significant differentiation of monocytes into non-classical monocytes, leading to a shaping of the tumor microenvironment via CD8+ T cell recruitment in early stage of activation. The activity of VIO-01 was specific to tumor cells, while sparing healthy and immune cells, at odds with PARP inhibitors. In line with in vitro results, VIO-01 mediated antitumor efficacy in vivo coupled to tumor-targeting T-cell responses. These interesting effects were driven by a favorable ADME/PK profile, showing a long-lasting VIO-01 residence time VIO-01 into tumors (at least 3 days post treatment), coupled to a clear hijacking from the liver and a rapid blood clearance, ensuring a minimal toxicity. Moreover, regulatory toxicology studies demonstrated a favorable safety profile of VIO-01 in non-human primate with the major findings being a transient increase in complement factors induced by the binding of VIO-01 to factor H, which was not observed in human serum, predicting favorable safety profile in humans. Conclusions: Our results provide a preclinical rationale for using VIO-01 to trigger DNA damage exhaustion and an antitumor immune response, paving the way for rapid clinical application in patients bearing HRD or HRP tumors. Citation Format: Vlada Zakharova, Chloe Doizelet, Nicolas Babault, Marie-Christine Lienafa, Fetta Mazed, Megane Debiais, Pierre Vilela, Emilie Perroud, Wael Jdey. VIO-01, a pan-DDR DNA decoy mediating DNA repair abrogation and unleashing the anti-tumor immune response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6013.

Identification of expression profiles and prognostic value of RFCs in colorectal cancer

Colorectal cancer (CRC) ranks among the most prevalent cancers globally, with its incidence closely tied to DNA damage. The Replication Factor C (RFC) complexes comprises five protein subunits: RFC1, RFC2, RFC3, RFC4, and RFC5. These RFC complexes play crucial roles in DNA replication, repair pathways, activities post DNA damage, and ATP-dependent processes during DNA synthesis. However, the impact of RFC complexes proteins on CRC prognosis remains unclear. To explore this, we employed a computational analysis approach, utilizing platforms such as the DepMap portal, GEPIA, DAVID Bioinformatics for KEGG pathway analysis, Human Protein Atlas (HPA), STRING, and TIMER. Our results indicate that the mRNA levels of RFC1 and RFC5 were the least expressed among CRC cell lines compared to other RFC complex subunits. Notably, low RFC1 and RFC5 expression was correlated with poor prognosis in terms of CRC patients' overall survival (OS). Immunohistochemical results from the Human Protein Atlas demonstrated medium staining for RFC1, RFC2, and RFC5 in CRC tissues. Furthermore, the low expression of RFC1 and RFC5 showed a significant correlation with high expression levels of miR-26a-5p and miR-636, impacting cell proliferation through mismatch repair, DNA replication, and the nucleotide excision repair pathway. Although the precise functions of RFC1 in cancer are still unknown, our findings suggest that the small-molecule single target, CHEMBL430483, and multiple target molecules could be potential treatments for CRC. In conclusion, the elevated expression of miR-26a-5p and miR-636 targeting RFC1 and RFC5 expression holds promise as a potential biomarker for early-stage CRC detection. These insights provide novel directions and strategies for CRC therapies.

ERCC4: a potential regulatory factor in inflammatory bowel disease and inflammation-associated colorectal cancer.

The pathogenesis of inflammatory bowel disease (IBD) remains unclear and is associated with an increased risk of developing colitis-associated cancer (CAC). Under sustained inflammatory stimulation in the intestines, loss of early DNA damage response genes can lead to tumor formation. Many proteins are involved in the pathways of DNA damage response and play critical roles in protecting genes from various potential damages that DNA may undergo. ERCC4 is a structure-specific endonuclease that participates in the nucleotide excision repair (NER) pathway. The catalytic site of ERCC4 determines the activity of NER and is an indispensable gene in the NER pathway. ERCC4 may be involved in the imbalanced process of DNA damage and repair in IBD-related inflammation and CAC. This article primarily reviews the function of ERCC4 in the DNA repair pathway and discusses its potential role in the processes of IBD-related inflammation and carcinogenesis. Finally, we explore how this knowledge may open novel avenues for the treatment of IBD and IBD-related cancer.

The effect of mesenchymal stem cells administration on DNA repair gene expressions in critically ill COVID-19 patients: prospective controlled study

When the studies are evaluated, immunomodulatory effect of MSCs, administration in critically ill patients, obstacle situations in use and side effects, pulmonary fibrosis prevention, which stem cells and their products, regeneration effect, administration route, and dosage are listed under the main heading like. The effect of MSC administration on DNA repair genes in COVID-19 infection is unknown. Our aim is to determine the effect of mesenchymal stem cells (MSCs) therapy applied in critically ill patients with coronavirus infection on DNA repair pathways and genes associated with those pathways. Patients (n = 30) divided into two equal groups. Group-1: Patients in a critically ill condition, Group-2: Patients in critically ill condition and transplanted MSCs. The mechanism was investigated in eleven genes of five different pathways; Base excision repair: PARP1, Nucleotide excision repair (NER): RAD23B and ERCC1, Homologous recombinational repair (HR): ATM, RAD51, RAD52 and WRN, Mismatch repair (MMR): MLH1, MSH2, and MSH6, Direct reversal repair pathway: MGMT. It was found that MSCs application had a significant effect on 6 genes located in 3 different DNA damage response pathways. These are NER pathway genes; RAD23 and ERCC1, HR pathway genes; ATM and RAD51, MMR pathway genes; MSH2 and MSH6 (p < 0.05). Two main points were shown. First, as a result of cellular damage in critical patients with COVID-19, DNA damage occurs and then DNA repair pathways and genes are activated in reaction to this situation. Second, administration of MSC to patients with COVID-19 infection plays a positive role by increasing the expression of DNA repair genes located in DNA damage pathways.

Abstract A035: Genome-wide CRISPRi screening reveals determinants of platinum sensitivity and resistance in high-grade serous ovarian cancer

Abstract A035: Genome-wide CRISPRi screening reveals determinants of platinum sensitivity and resistance in high-grade serous ovarian cancer

STK19 is a DNA/RNA-binding protein critical for DNA damage repair and cell proliferation.

STK19 was originally identified as a manganese-dependent serine/threonine-specific protein kinase, but its function has been highly debated. Here, the crystal structure of STK19 revealed that it does not contain a kinase domain, but three intimately packed winged helix (WH) domains. The third WH domain mediated homodimerization and double-stranded DNA binding, both being important for its nuclear localization. STK19 participated in the nucleotide excision repair (NER) and mismatch repair (MMR) pathways by recruiting damage repair factors such as RPA2 and PCNA. STK19 also bound double-stranded RNA through the DNA-binding interface and regulated the expression levels of many mRNAs. Furthermore, STK19 knockdown cells exhibited very slow cell proliferation, which cannot be rescued by dimerization or DNA-binding mutants. Therefore, this work concludes that STK19 is highly unlikely to be a kinase but a DNA/RNA-binding protein critical for DNA damage repair (DDR) and cell proliferation. To prevent further confusions, we renamed this protein as TWH19 (Tandem Winged Helix protein formerly known as STK19).

Abstract A031: ZEB2 induced EMT drives therapy resistance by activating nucleotide excision repair I gene ERCC1 And ERCC4 n colorectal cancer

Abstract Resistance to adjuvant chemotherapy is a major clinical problem in the treatment of colorectal cancer (CRC). The aim of this study was to elucidate the role of an epithelial to mesenchymal transition (EMT)-inducing protein, ZEB2, in chemoresistance of CRC, and to uncover the underlying mechanism. We performed IHC for ZEB2 and association analyses with clinical outcomes on primary CRC and matched CRC liver metastases in compliance with observational biomarker study guidelines. ZEB2 expression in primary tumors was an independent prognostic marker of reduced overall survival and disease-free survival in patients who received adjuvant FOLFOX chemotherapy. ZEB2 expression was retained in 96% of liver metastases. The ZEB2-dependent EMT transcriptional program activated nucleotide excision repair (NER) pathway largely via upregulation of the ERCC1 gene and other components in NER pathway, leading to enhanced viability of CRC cells upon oxaliplatin treatment. ERCC1-overexpressing CRC cells did not respond to oxaliplatin in vivo, as assessed using a murine orthotopic model in a randomized and blinded preclinical study. Our findings show that ZEB2 is a biomarker of tumor response to chemotherapy and risk of recurrence in CRC patients. We propose that the ZEB2-ERCC1 axis is a key determinant of chemoresistance in CRC. Citation Format: Hajir Al Saihati. ZEB2 induced EMT drives therapy resistance by activating nucleotide excision repair I gene ERCC1 And ERCC4 n colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A031.

Transcription factor E2F3 activates CDC25B to regulate DNA damage and promote mitoxantrone resistance in stomach adenocarcinoma.

CDC25B, as a member of the cell cycle regulating protein family, is located in the cytoplasm and is involved in the transition of the cell cycle and mitosis. CDC25B is highly expressed in various tumors and is a newly discovered oncogene. This study aimed to investigate the impact of CDC25B on mitoxantrone resistance in stomach adenocarcinoma (STAD) and its possible mechanisms. This study analyzed the expression of CDC25B and its potential transcription factor E2F3 in STAD, as well as the IC50 values of tumor tissues by bioinformatics analysis. Expression levels of CDC25B and E2F3 in STAD cells were measured by qRT-PCR. MTT was utilized to evaluate cell viability and IC50 values of STAD cells, and comet assay was utilized to analyze the level of DNA damage in STAD cells. Western blot was used to analyze the expression of DNA damage-related proteins. The targeting relationship between E2F3 and CDC25B was validated by dual-luciferase and ChIP assays. Bioinformatics analysis and molecular experiments showed that CDC25B and E2F3 were highly expressed in STAD, and CDC25B was enriched in the mismatch repair and nucleotide excision repair pathways. The IC50 values of tumor tissues with high expression of CDC25B were relatively high. Dual-luciferase and ChIP assays confirmed that CDC25B could be transcriptionally activated by E2F3. Cell experiments revealed that CDC25B promoted mitoxantrone resistance in STAD cells by regulating DNA damage. Further research found that low expression of E2F3 inhibited mitoxantrone resistance in STAD cells by DNA damage, but overexpression of CDC25B reversed the impact of E2F3 knockdown on mitoxantrone resistance in STAD cells. This study confirmed a novel mechanism by which E2F3/CDC25B mediated DNA damage to promote mitoxantrone resistance in STAD cells, providing a new therapeutic target for STAD treatment.

Abstract B012: Pedigree and multi-omics analyses implicate nucleotide excision repair genes, XPA, ERCC6, and ERCC8, in susceptibility to breast cancer

Abstract Background: The majority of low- and moderate-risk [odds ratios (OR) ≤ 3] susceptibility genes for peri- and post-menopausal breast cancer (≥50 years of age), particularly those with minor allele frequency (MAF) of &amp;lt;30%, have not yet been identified and/or validated. We used a hypothesis-driven integrative approach to identify breast cancer susceptibility genes by analyzing pedigree and multi-omics (genomics, transcriptomics, mutation landscape) data. Methods: We conducted pedigree analysis in 31 families with DNA repair disorders, xeroderma pigmentosum (XP), trichothiodystrophy (TTD), Cockayne syndrome (CS), XP/TTD and XP/CS. These disorders can be caused by mutations in genes involved in the nucleotide excision repair (NER) pathway such as XPA-XPG, ERCC6 and ERCC8. We estimated the frequency of hereditary breast cancer, defined as the presence of at least two cases of premenopausal breast cancer (diagnosed &amp;lt;50 years of age) or one case of premenopausal breast cancer and one case of ovarian cancer in one side of the family, in our study. Furthermore, we conducted individual analysis of four genome-wide association studies (GWAS) datasets (totaling 2961 cases and 4335 controls), individual and meta-analysis of two gene expression microarray datasets (98 cases and 163 controls), and targeted analysis of The Cancer Genome Atlas (TCGA) (522 breast cancers). All analyses involved invasive ductal breast carcinoma in women diagnosed at ≥50 years of age. Results: In an XP family with causative mutations in XPA, there were four cases of premenopausal breast cancer (including heterozygote mutation carriers), one case of ovarian cancer, and one case of prostate cancer. Comprehensive sequencing failed to identify a BRCA1 or BRCA2 mutation in this family. Overall, 7 of 31 (22.6%) families with DNA repair disorders had a family history that was compatible with hereditary breast cancer. Hence, we selected a panel of NER genes as candidates for association studies with breast cancer. Our candidate-gene association analysis of GWAS datasets suggested an increased risk of breast cancer with ERCC6 (main effect:1.29 ≤ OR ≤ 2.91, 0.005 ≤ p ≤ 0.04, 11.8 ≤ MAF ≤ 29.7%) and implicated its interaction with ERCC8 (joint effect:3.03 ≤ OR ≤ 5.31, 0.01 ≤ pinteraction ≤ 0.03). Our transcriptomics analysis identified significant upregulation of ERCC6 (p=7.95 × 10–6) and ERCC8 (p=4.67 × 10–6) in breast cancer. Our analysis of TCGA breast tumor data showed similar mutation frequency of ERCC6 (1.8%) and ERCC8 (0.3%) as known breast cancer susceptibility genes such as BLM (1.9%) and LSP1 (0.3%). Conclusion: Our integrative analyses suggest that ERCC6 may be a previously unreported low- to moderate-risk breast cancer susceptibility gene, which may also interact with ERCC8. ERCC6 and ERCC8 code for the main components of the transcription-coupled (TC) repair sub-pathway of the NER. TC-NER protects against genotoxic agents, such as free radicals and reactive oxygen species. Our results provide a deeper biologic insight and leads for prevention of common breast cancer. Citation Format: Roxana Moslehi, Amiran Dzutsev. Pedigree and multi-omics analyses implicate nucleotide excision repair genes, XPA, ERCC6, and ERCC8, in susceptibility to breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr B012.

Clinicopathological Study of Xeroderma Pigmentosa: A Series of Eight Cases

Abstract Background: Xeroderma pigmentosa (XP) is a rare inherited (autosomal recessive) disease, resulting from impairment in DNA repair that involves recognition and repair of ultraviolet radiation (UVR)-induced DNA damage in the nucleotide excision repair pathway. This results in increased photosensitivity, UVR-induced damage to skin and eye, increased susceptibility to cutaneous and ocular cancers, and progressive neurodegeneration in some patients. Aims and Objective: The objective of the study was to describe the clinicopathological spectrum of eight cases of XP. Materials and Methods: An ambispective case series was conducted in a pediatric tertiary care hospital in eastern India during a 10-year period from 2013 to 2022. Results: All the children of our cohort were born of consanguineous marriage. The mean age of presentation was 1.2 years (range: 7 months–3 years), whereas three children presented during their infancy. The male-to-female ratio was 5:3. The most common findings were cutaneous (100%), followed by ophthalmic (75%) and/or neurological symptoms (25%). Patients had normal skin at birth but soon developed extreme photosensitivity followed by abnormal skin pigmentation and subsequently progressive xerosis, atrophy, wrinkling, and poikiloderma over time. Six patients had varied degrees of ocular involvement, whereas three of them had severe manifestations including madarosis, tylosis, ectropion, lagophthalmos, phthisis bulbi, clouding and scarring of the cornea with complete or partial loss of vision, and ophthalmic malignancies. Fifty percent (n = 4) of cases had cutaneous and ocular premalignant (actinic keratosis) and malignant lesions including melanoma and nonmelanoma skin cancer such as squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) in their early childhood. One patient had simultaneous occurrence of multiple malignancies together (SCC, BCC, and melanoma). Neurological abnormalities (subnormal intelligence) were found in two cases. There was no evidence of sensory neural hearing loss, microcephaly, neuroregression, or neurodeficits. Conclusion: Although XP is associated with increased mortality and morbidity, early diagnosis followed by persistent vigorous photoprotection and regular screening for early detection of malignancies along with psychological support can drastically improve patients’ quality of life and life expectancy. Besides genetic counseling, further research is required on formulating optimal management of XP, specifically the role and possibilities of gene therapy in XP.

Characterization of human XPD helicase activity with single-molecule magnetic tweezers

XPD helicase is a DNA-unwinding enzyme involved in DNA repair. As part of TFIIH, XPD opens a repair bubble in DNA for access by proteins in the nucleotide excision repair pathway. XPD uses the energy from ATP hydrolysis to translocate in the 5′ to 3′ direction on one strand of duplex DNA, displacing the opposite strand in the process. We used magnetic tweezers assays to measure the double-stranded DNA unwinding and single-stranded DNA translocation activities of human XPD in isolation. In our experimental setup, hXPD exhibited low unwinding processivity of ∼14 bp and slow unwinding rate of ∼0.3 bp/s. Measurements of the ssDNA translocation activity demonstrated that hXPD translocated on ssDNA at a similar rate as unwinding, revealing that slow rate was an intrinsic property of the hXPD translocation. Individual unwinding and translocation events were composed of pauses and runs with a distribution of lengths and rates. Analysis of these events unveiled similar mean run lengths and rates for unwinding and translocation, indicating that the unwinding behavior was a direct reflection of the translocation activity. The analysis also revealed that hXPD spent similar time stalling and unwinding/translocating. The detailed basal activity of hXPD reported here provides a baseline for future studies on how hXPD activity is regulated by other TFIIH components.