Polymerase Epsilon Research Articles

Multitargeted inhibitory effect of Mitoxantrone 2HCl on cervical cancer cell cycle regulatory proteins: a multitargeted docking-based MM\GBSA and MD simulation study.

Cervical cancer remains a significant global health concern that starts in the cervix, the lower part of the uterus that connects to the vagina and is caused by the human papillomavirus (HPV), necessitating the development of effective multitargeted effective and resistance-proof therapies. In early-stage cervical cancer may not show any symptoms, however, as the cancer progresses, some people may experience- abnormal vaginal bleeding, watery or bloody vaginal discharge, pain in the pelvis or lower back, pain during sex, and frequent and painful urination. In this study, we screened the complete FDA-approved drug library using a multitargeted inhibitory approach against four cervical cancer proteins, namely mitotic arrest deficient -2, DNA polymerase epsilon B-subunit, benzimidazole-related -1, and threonine-protein kinase-1 which crucially plays its role for the in its development process. We employed the HTVS, SP and XP algorithms for efficient filtering and screening that helped to identify Mitoxantrone 2HCl against all of them with docking and MM\GBSA scores ranging from -11.63 to -7.802kcal/mol and -74.38 to -47.73kcal/mol, respectively. We also evaluated the interaction patterns of each complex and the pharmacokinetics properties that helped gain insight into interactions. Subsequently, we performed multiscale MD simulations for 100ns to understand the dynamic behaviour and stability of the Mitoxantrone 2HCl -protein complexes that revealed the formation of stable drug-protein complexes and provided insights into the molecular interactions that contribute to Mitoxantrone's inhibitory effects on these proteins and can be a better drug for cervical cancer. However, experimental studies of these findings could pave the way for therapies to combat cervical cancer effectively.

Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1

BackgroundGermline variants affecting the proofreading activity of polymerases epsilon and delta cause a hereditary cancer and adenomatous polyposis syndrome characterized by tumors with a high mutational burden and a specific mutational spectrum. In addition to the implementation of multiple pieces of evidence for the classification of gene variants, POLE and POLD1 variant classification is particularly challenging given that non-disruptive variants affecting the proofreading activity of the corresponding polymerase are the ones associated with cancer. In response to an evident need in the field, we have developed gene-specific variant classification recommendations, based on the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) criteria, for the assessment of non-disruptive variants located in the sequence coding for the exonuclease domain of the polymerases.MethodsA training set of 23 variants considered pathogenic or benign was used to define the usability and strength of the ACMG/AMP criteria. Population frequencies, computational predictions, co-segregation data, phenotypic and tumor data, and functional results, among other features, were considered.ResultsGene-specific variant classification recommendations for non-disruptive variants located in the exonuclease domain of POLE and POLD1 were defined. The resulting recommendations were applied to 128 exonuclease domain variants reported in the literature and/or public databases. A total of 17 variants were classified as pathogenic or likely pathogenic, and 17 as benign or likely benign.ConclusionsOur recommendations, with room for improvement in the coming years as more information become available on carrier families, tumor molecular characteristics and functional assays, are intended to serve the clinical and scientific communities and help improve diagnostic performance, avoiding variant misclassifications.

Prognostic value of lymphovascular space invasion according to the molecular subgroups in endometrial cancer

ObjectiveLymphovascular space invasion (LVSI) is a known prognostic factor for oncological outcome in endometrial cancer patients. However, little is known about the prognostic value of LVSI among the different molecular...

Multivariate analysis and genetic dissection of staygreen and stem reserve mobilisation under combined drought and heat stress in wheat (Triticum aestivum L.).

Introduction: Abiotic stresses significantly reduce crop yield by adversely affecting many physio-biochemical processes. Several physiological traits have been targeted and improved for yield enhancement in limiting environmental conditions. Amongst them, staygreen and stem reserve mobilisation are two important mutually exclusive traits contributing to grain filling under drought and heat stress in wheat. Henceforth, the present study was carried out to identify the QTLs governing these traits and to identify the superiors' lines through multi-trait genotype-ideotype distance index (MGIDI) Methods: A mapping population consisting of 166 recombinant inbred lines (RILs) developed from a cross between HD3086 and HI1500 was utilized in this study. The experiment was laid down in alpha lattice design in four environmental conditions viz. Control, drought, heat and combined stress (heat and drought). Genotyping of parents and RILs was carried out with 35K Axiom® array (Wheat breeder array). Results and Discussion: Medium to high heritability with a moderate to high correlation between traits was observed. Principal component analysis (PCA) was performed to derive latent variables in the original set of traits and the relationship of these traits with latent variables.From this study, 14 QTLs were identified, out of which 11, 2, and 1 for soil plant analysis development (SPAD) value, leaf senescence rate (LSR), and stem reserve mobilisation efficiency (SRE) respectively. Quantitative trait loci (QTLs) for SPAD value harbored various genes like Dirigent protein 6-like, Protein FATTY ACID EXPORT 3, glucan synthase-3 and Ubiquitin carboxyl-terminal hydrolase, whereas QTLs for LSR were found to contain various genes like aspartyl protease family protein, potassium transporter, inositol-tetrakisphosphate 1-kinase, and DNA polymerase epsilon subunit D-like. Furthermore, the chromosomal region for SRE was found to be associated with serine-threonine protein kinase. Serine-threonine protein kinases are involved in many signaling networks such as ABA mediated ROS signaling and acclimation to environmental stimuli. After the validation of QTLs in multilocation trials, these QTLs can be used for marker-assisted selection (MAS) in breeding programs.

Molecular subtypes of endometrial cancer: Implications for adjuvant treatment strategies.

When determining adjuvant treatment for endometrial cancer, the decision typically relies on factors such as cancer stage, histologic grade, subtype, and a few histopathologic markers. The Cancer Genome Atlas revealed molecular subtyping of endometrial cancer, which can provide more accurate prognostic information and guide personalized treatment plans. To summarize the expression and molecular basis of the main biomarkers of endometrial cancer. PubMed was searched from January 2000 to March 2023. Studies evaluating molecular subtypes of endometrial cancer and implications for adjuvant treatment strategies. Three authors independently performed a comprehensive literature search, collected and extracted data, and assessed the methodological quality of the included studies. We summarized the molecular subtyping of endometrial cancer, including mismatch repair deficient, high microsatellite instability, polymerase epsilon (POLE) exonuclease domain mutated, TP53 gene mutation, and non-specific molecular spectrum. We also summarized planned and ongoing clinical trials and common therapy methods in endometrial cancer. POLE mutated endometrial cancer consistently exhibits favorable patient outcomes, regardless of adjuvant therapy. Genomic similarities between p53 abnormality endometrial cancer and high-grade serous ovarian cancer suggested possible overlapping treatment strategies. High levels of immune checkpoint molecules, such as programmed cell death 1 and programmed cell death 1 ligand 1 can counterbalance mismatch repair deficient endometrial cancer immune phenotype. Hormonal treatment is an appealing option for high-risk non-specific molecular spectrum endometrial cancers, which are typically endometrioid and hormone receptor positive. Combining clinical and pathologic characteristics to guide treatment decisions for patients, including concurrent radiochemotherapy, chemotherapy, inhibitor therapy, endocrine therapy, and immunotherapy, might improve the management of endometrial cancer and provide more effective treatment options for patients. We have characterized the molecular subtypes of endometrial cancer and discuss their value in terms of a patient-tailored therapy in order to prevent significant under- or overtreatment.

Network Evolution Model-based prediction of tumor mutation burden from radiomic-clinical features in endometrial cancers

BackgroundEndometrial Cancer (EC) is one of the most prevalent malignancies that affect the female population globally. In the context of immunotherapy, Tumor Mutation Burden (TMB) in the DNA polymerase epsilon (POLE) subtype of this cancer holds promise as a viable therapeutic target.MethodsWe devised a method known as NEM-TIE to forecast the TMB status of patients with endometrial cancer. This approach utilized a combination of the Network Evolution Model, Transfer Information Entropy, Clique Percolation (CP) methodology, and Support Vector Machine (SVM) classification. To construct the Network Evolution Model, we employed an adjacency matrix that utilized transfer information entropy to assess the information gain between nodes of radiomic-clinical features. Subsequently, using the CP algorithm, we unearthed potentially pivotal modules in the Network Evolution Model. Finally, the SVM classifier extracted essential features from the module set.ResultsUpon analyzing the importance of modules, we discovered that the dependence count energy in tumor volumes-of-interest holds immense significance in distinguishing TMB statuses among patients with endometrial cancer. Using the 13 radiomic-clinical features extracted via NEM-TIE, we demonstrated that the area under the receiver operating characteristic curve (AUROC) in the test set is 0.98 (95% confidence interval: 0.95–1.00), surpassing the performance of existing techniques such as the mRMR and Laplacian methods.ConclusionsOur study proposed the NEM-TIE method as a means to identify the TMB status of patients with endometrial cancer. The integration of radiomic-clinical data utilizing the NEM-TIE method may offer a novel technology for supplementary diagnosis.

Unveiling the multitargeted repurposing potential of taxifolin (dihydroquercetin) in cervical cancer: an extensive MM\GBSA-based screening, and MD simulation study.

Cervical cancer is a significant cause of morbidity and mortality in women worldwide. Despite the availability of effective therapies, the development of drug resistance and adverse side effects remain significant challenges in cervical cancer treatment. Thus, repurposing existing drugs as multitargeted therapies for cervical cancer is an attractive approach. In this study, we extensively screened the complete prepared FDA-approved drugs and identified the repurposing potential of taxifolin, a flavonoid with known antioxidant and anti-inflammatory properties, as a multitargeted therapy for cervical cancer. We performed a computational analysis using molecular docking with various sampling algorithms, namely HTVS, SP, and XP algorithms, for robust sampling pose and filtered with MM/GBSA analysis to determine the binding affinity of taxifolin with potential targets involved in cervical cancer, such as Symmetric Mad2 Dimer, replication initiation factor MCM10-ID, TPX2, DNA polymerase epsilon B-subunit, human TBK1, and alpha-v beta-8. We then conducted MD simulations to investigate the stability and conformational changes of the complex formed between taxifolin and the mentioned proteins. Our results suggest that taxifolin has a high binding affinity ranging from -6.094 to -9.558kcal/mol, indicating its potential as a multitargeted therapy for cervical cancer. Furthermore, interaction fingerprints, pharmacokinetics and MD simulations revealed that the Taxifolin-target complexes remained stable over the simulation period, indicating that taxifolin may bind to the targets for an extended period. Our study suggests that taxifolin has the potential as a multitargeted therapy for cervical cancer, and further experimental studies are necessary to validate our findings.

Integrating POLE/POLD1 mutated for immunotherapy treatment planning of advanced stage non-small cell lung cancer.

In this study, we evaluated the potential of DNA polymerase epsilon (POLE) and DNA polymerase delta 1 (POLD1) as prognostic biomarkers for immune checkpoint inhibitor (ICI) treatment in patients with advanced stage non-small cell lung cancer (NSCLC). Disease stage, PD-L1 positivity, histological subtypes, POLE/POLD1 mutation status, tumor mutation burden (TMB), and response to ICIs in NSCLC cases were derived from AACR GENIE dataset (n = 24 120), TCGA-Pan Lung Cancer dataset (n = 1144), AACR GENIE BPC NSCLC v2.0-public (n = 2004), and Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets dataset (n = 350). The smoking history from TCGA and AACR GENIE datasets was grouped into current, former or never-smokers. POLE and POLD1 genetic alterations were identified in 5% and 2.6% of NSCLC patients, respectively. Current smokers had 9% and 4% of POLE/POLD1 mutations, respectively, versus 1.7% for both POLE and POLD1 mutations prevalence in never-smokers. POLE/POLD1 mutations were associated with elevated mutation counts than those with wild-type (median mutation counts 16 vs. 7, p < 0.0001), more advanced disease stages (stage I disease 15.19% vs. 29.42%), more prevalent squamous histology subtype (21.69% vs. 9.05%, p = 0.0427), and a higher percentage of PD-L1 positivity (66.67% vs. 43.87%, p < 0.001). Treatment with ICIs improved survival in patients with both POLE/POLD1 mutated and those with TMB > 18 (p < 0.001). Current smokers have a five-fold increased risk of having POLE mutations than never-smokers. POLE/POLD1 mutation status and TMB > 18 can be a composite biomarker for selecting NSCLC patients with survival benefits to ICI treatment.

CtDNA for clonal evolution surveillance and therapeutic efficacy prediction in unresectable locally advanced non-small cell lung cancer under radiotherapy.

e20555 Background: Therapeutic efficacy differs across unresectable locally advanced non-small cell lung cancer (LA-NSCLC) patients receiving definitive radiotherapy/chemoradiotherapy (RT/CRT), but the underlying resistance mechanism, clonal evolution and molecular prognostic factors remain poorly understood. Methods: Unresectable LA-NSCLC patients treated with definitive RT/CRT were consecutively enrolled between May 2018 and November 2020. Next-generation sequencing covering 474 cancer-relevant genes was performed on plasma ctDNA collected at pre-treatment (TP0), 4-week post-RT (TP1), 1-month post-RT (TP2), 3-month post-RT (TP3), and progression (TP4). Main study endpoints included disease progression, progression-free survival (PFS), death from any cause, overall survival (OS), distant metastasis and distant metastasis free survival. Fisher’s exact test and two-sample t-tests were performed to compare the frequencies and means of independent groups, respectively. The median follow-up time was estimated using the reverse Kaplan-Meier method. Hazard ratios (HR) with 95% confidence intervals (CI) were estimated by Cox proportional hazards models. Results: A total of 46 patients were included (median age: 63 [range: 40–80], males: 87%, clinical stage IIIB: 52%, squamous cell carcinoma: 54%, TP0 ctDNA shedding: 63%, consolidation immunotherapy: 33%). Twenty-nine (63%) patients developed disease progression by the end of follow-up (median follow-up: 23.7 months), with median PFS and OS being 15.5 and 25.4 months, respectively. The polymerase epsilon ( POLE) mutational signature at TP0 indicated inferior PFS (HR: 5.32, 95% CI: 1.83–15.45) and worse OS (HR: 20.68, 95% CI: 3.94–108.62). Notably, newly-discovered/lost mutations were rarely observed at TP4 when compared to TP0. Patients with a high ratio of mean over max variant allele frequency (m/mVAF) in TP0 samples, indicative of a clonal predominant tumor with a low subclone fraction ( P&lt; 0.01), had relatively poor OS, compared to patients with low m/mVAF (HR: 2.92, 95% CI: 0.82–10.46) or undetectable ctDNA (HR: 3.39, 95% CI: 0.98–11.75). The prognostic value was validated in an independent publicly available dataset of 431 LA-NSCLC patients receiving definitive RT/CRT, showing patients with high m/mVAF demonstrated worse OS than those with low m/mVAF (HR: 1.43, 95% CI: 1.08–1.89). Additionally, increased m/mVAF between TP0 and TP1 indicated an elevated risk for disease progression ( vs. non-increase, HR: 3.49, 95% CI: 1.20–10.16), especially for distant metastasis ( vs. non-increase, HR: 2.85, 95% CI: 0.84–9.69). Conclusions: Our findings demonstrated the clinical value of plasma ctDNA and its derived molecular features in delineating clonal evolution, monitoring therapeutic resistance, and predicting prognosis of LA-NSCLC under definitive RT.

Molecular classification of endometrial carcinoma: Analysis of a multicentre Portuguese cohort.

e17615 Background: Management of endometrial carcinoma (EC) relies on prognostic risk group classification to help to determine the individual risk of recurrence and the need for adjuvant treatment after surgery. A molecular classification with four distinct prognostic EC subtypes based on genomic abnormalities - DNA polymerase epsilon ( POLE) mutated ( POLEmut), mismatch repair deficient (MMRd), p53 abnormal (p53abn) and no specific molecular profile (NSMP) - has emerged, that raises the possibility of a more precise tailoring of adjuvant therapy. This study aimed to describe the clinicopathological and molecular characteristics of an EC Portuguese cohort, assess its potential impact in patient management and evaluate its prognostic value. Methods: Multicentre, retrospective cohort study of 230 patients with EC diagnosed between 2019 and 2022. Sample processing, clinicopathological, treatment and follow-up data was collected. Molecular classification was obtained by p53 and mismatch repair proteins immunohistochemistry, and POLE next-generation sequencing. Results: Overall, 230 patients from two institutions were included. Median age at diagnosis was 68 years. The most frequent histology was endometrioid (n=163; 70.9%) and most were low-grade (n=129, 56.1%).At diagnosis, disease was confined to the uterus in the majority of patients (FIGO stage I/II, n=153, 66.5%). Most had surgery upfront (n=196, 85.2%) and, of those, 120 (52.2%) received adjuvant treatment. 26 (11.3%) had metastatic disease. Median follow-up time was 15.4 months. Regarding molecular subgroups, the majority were classified as NSMP (n=87, 37.8%), followed by p53abn (n=73, 31.7%), MMRd (n=56, 24.3%), and POLEmut (n=14, 6.1%); 11 (4.8%) were multiple-classifier. Integration of these results led to a change in adjuvant treatment in 3 patients. Median disease-specific survival (DSS) was 108 months. Factors that significantly influenced survival included age (p=0.030), histological type (p&lt;0.001), grade (p&lt;0.001) and FIGO stage (p=0.006). Overall, 35 (15.2%) patients developed recurrences. Median recurrence-free survival (RFS) was 46.7 months. Kaplan-Meier survival analysis showed that molecular alterations were significantly associated both with DSS and RFS (p=0.0092 and p=0.0139, respectively). Tumours with p53abn had the worst prognosis, and patients with POLEmut tumours experienced an excellent prognosis. Comparative measures (BIC, C-index, log-likelihood) showed that considering the molecular classification in establishing risk groups for adjuvant treatment had prognostic significance. Conclusions: The molecular classification has prognostic value and should be considered in adjuvant treatment decisions. It allows for a more personalised approach, helps to reduce under and overtreatment, and therefore reduce patient morbidity associated with treatment toxicities, and healthcare related costs.

P-164 Efficacy and safety of dostarlimab in UK-specific patients with mismatch repair deficient (dMMR)/microsatellite instability-high (MSI-H) or DNA polymerase epsilon, catalytic subunit (POLƐ)-mutated solid tumours in the GARNET study

P-164 Efficacy and safety of dostarlimab in UK-specific patients with mismatch repair deficient (dMMR)/microsatellite instability-high (MSI-H) or DNA polymerase epsilon, catalytic subunit (POLƐ)-mutated solid tumours in the GARNET study

Prognostic significance of L1CAM expression in addition to ProMisE in endometrial cancer

ObjectiveTo investigate the prognostic significance of L1 cell-adhesion molecule (L1CAM), β-catenin, and programmed death-ligand 1 (PD-L1) in endometrial cancer (EC) patients, with a focus on p53 wild-type subgroup, for additional risk stratification. MethodsThis retrospective cohort study included EC patients classified according to Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE) who underwent primary surgical treatment at the single center between January 2014 and December 2018. Immunohistochemical staining was performed for four mismatch repair (MMR) proteins, p53, L1CAM, β-catenin, and PD-L1. DNA polymerase epsilon (POLE) mutation was detected by hot spot sequencing via droplet digital polymerase chain reaction. Survival outcome of each subgroup of L1CAM, β-catenin, and PD-L1 was measured according to their expression. ResultsA total of 162 EC patients were included. Endometrioid histologic type and early-stage disease were 140 (86.4%) and 109 (67.3%), respectively. ProMisE classification assigned 48 (29.6%), 16 (9.9%), 72 (44.4%), and 26 (16.0%) patients to MMR-deficient, POLE-mutated, p53 wild-type, and p53 abnormal subgroups, respectively. L1CAM was identified as an independent poor prognostic factor for progression-free survival (PFS; adjusted hazard ratio [aHR], 3.207; 95% confidence interval (CI), 1.432–7.187; P = 0.005), whereas β-catenin and PD-L1 positivity were not associated with recurrence (P = 0.462 and P = 0.152, respectively). In p53 wild-type subgroup, L1CAM positivity was associated with worse PFS (aHR, 4.906; 95% CI, 1.685–14.287; P = 0.004). ConclusionL1CAM positivity was associated with poor prognosis in EC and further stratified the risk of recurrence in p53 wild-type subgroup, whereas β-catenin and PD-L1 were not informative for risk stratification.

“Surface epithelial slackening” pattern in endometrioid carcinoma: A morphological feature for differentiating the POLE mutation-subtype from the no specific molecular profile subtype

Endometrial cancers are classified into mismatch repair (MMR) deficient- (MMRd), p53 mutation- (p53mut), DNA polymerase epsilon (POLE) mutation (POLEmut), and no specific molecular profile (NSMP) subtypes according to The Cancer Genome Atlas (TCGA). The distinction between POLEmut and NSMP subtypes is made on the basis of molecular analysis because the specific histological and immunohistochemical features of these two subtypes are still unknown. In this study, we analyzed histological features by scoring the presence of a mucinous pool, giant cells, clear cells, keratinization, neutrophilic abscess, and surface proliferating pattern in 82 cases of endometrial cancers in which an integrative diagnosis was confirmed by immunohistochemistry and genomic profiles showing POLE mutations, tumor mutation burden, and microsatellite instability. In contrast to the hierarchical branching of micropapillary proliferation observed in serous carcinoma, POLEmut-subtype endometrioid carcinomas often showed a surface epithelial slackening (SES) pattern in the tumor cells facing the uterine surface. The POLEmut subtype exhibited higher scores for clear cells and SES patterns than the other three subtypes. The scores for giant cells, clear cells, and the SES pattern were significantly higher in the POLEmut subtype than in the NSMP subtype, suggesting that these morphometric parameters are useful for differentiating POLEmut- and NSMP-subtype endometrioid carcinomas, although genomic profiling is still necessary for a definite molecular diagnosis.

Contributions of replicative and translesion DNA polymerases to mutagenic bypass of canonical and atypical UV photoproducts

UV exposure induces a mutation signature of C > T substitutions at dipyrimidines in skin cancers. We recently identified additional UV-induced AC > TT and A > T substitutions that could respectively cause BRAF V600K and V600E oncogenic mutations. The mutagenic bypass mechanism past these atypical lesions, however, is unknown. Here, we whole genome sequenced UV-irradiated yeast and used reversion reporters to delineate the roles of replicative and translesion DNA polymerases in mutagenic bypass of UV-lesions. Our data indicates that yeast DNA polymerase eta (pol η) has varied impact on UV-induced mutations: protecting against C > T substitutions, promoting T > C and AC > TT substitutions, and not impacting A > T substitutions. Surprisingly, deletion rad30Δ increased novel UV-induced C > A substitutions at CA dinucleotides. In contrast, DNA polymerases zeta (pol ζ) and epsilon (pol ε) participated in AC > TT and A > T mutations. These results uncover lesion-specific accurate and mutagenic bypass of UV lesions, which likely contribute to key driver mutations in melanoma.

DNA repair-related genes are the key for stony coral ancestors to survive under elevated levels of UVR

DNA damage response (DDR) is a complicated network to defend against physical or chemical changes in DNA in all animals. Elevated levels of ultraviolet radiation (UVR) caused DNA damage, which was a reason for the mass extinction that occurred at the Devonian/Carboniferous (D/C) boundary approximately 359 million years ago (Ma). However, the molecular adaptation of the stony coral ancestors that strangely survived the D/C boundary mass extinction is not well understood. In the present study, the molecular clock analysis using fourfold degenerate sites of 1,463 homologous genes of different stony coral species (a representative group of marine organisms with calcareous skeletons) suggested that their common ancestors originated 384.24 Ma, i.e., slightly earlier than the D/C transition. We identified 21 rapidly evolving genes (REGs) and 49 positive selection genes (PSGs) that were significantly enriched in diverse pathways, including the mitotic cell cycle process, intracellular protein transport, and DNA synthesis involved in DNA repair. Interestingly, four REGs and 21 PSGs were significantly enriched in DDR pathways, including the mitotic cell cycle process, DNA synthesis involved in DNA repair, and cellular response to DNA damage stimulus pathways. We hypothesize that enriched DDR genes are likely involved in the enhanced ability of ancient stony corals to detect and repair DNA damage. For example, the DNA polymerase epsilon catalytic subunit (POLE) gene, which encodes the DNA polymerase epsilon catalytic subunit A, mediates interaction with the other three catalytic subunits through its nonenzymatic carboxy-terminal domain. POLE may potentially enhance the binding ability to other subunits to strengthen its function because eight positive selection sites were distributed in the C-terminal of POLE and on the surface of the simulated 3D protein model. Therefore, our results demonstrated for the first time that the precise transfer of DNA information may help stony coral ancestors survive in elevated levels of ultraviolet radiation, suggesting that DDR levels may be critical to the environmental adaptation of calcareous skeletal organisms during climate change.

Clinical Characteristics and Detection of Polymerase Epsilon Mutant Endometrial Carcinoma

Polymerase Epsilon (POLE)-mutant endometrial cancer accounts for 7%-12% of endometrial cancer molecular types, and most of these patients are early-stage endometrioid carcinoma. Although POLE-mutant endometrial cancer has some unfavorable pathological features such as being poorly differentiated, the overall prognosis is good, and postoperative adjuvant treatment may be considered for de-escalation. POLE-mutant endometrial cancer is relatively less sensitive to postoperative adjuvant chemotherapy or radiotherapy, but because of its ultra-high tumor mutation load, recurrent or advanced patients are expected to benefit from programmed cell death receptor 1 (PCDR1) blockade therapy. This review will discuss the clinical features of POLE-mutated endometrial carcinoma and the progress made in the detection of POLE gene mutations.

POLE2 knockdown suppresses lymphoma progression via downregulating Wnt/β-catenin signaling pathway.

Lymphoma is the most common malignant tumor arising from immune system. Recently, DNA polymerase epsilon subunit 2 (POLE2) was identified to be a tumor promotor in a variety of malignant tumors. However, the biological role of POLE2 in lymphoma is still largely unclear. In our present study, the expression patterns of POLE2 in lymphoma tissues were identified by immunohistochemistry (IHC) staining of human tissue microarray. Cell viability was determined by CCK-8 assay. Cell apoptosis and cycle distribution were evaluated by Annexin V and PI staining, respectively. Cell migration was analyzed by transwell assay. Tumor growth in vivo was observed by a xenograft model of mice. The potential signaling was explored by human phospho-kinase array and immunoblotting. POLE2 was significantly upregulated in human lymphoma tissues and cells. POLE2 knockdown attenuated the proliferation, migration capabilities of lymphoma cells, as well as induced cell apoptosis and cycle arrest. Moreover, POLE2 depletion impaired the tumor growth in mice. Furthermore, POLE2 knockdown apparently inhibited the activation of β-Catenin and downregulated the expression of Wnt/β-Catenin signaling-related proteins. POLE2 knockdown suppressed the proliferation and migration of lymphoma cells by inhibiting Wnt/β-Catenin signaling pathway. POLE2 may serve as a novel therapeutic target for lymphoma.

CTF18-RFC contributes to cellular tolerance against chain-terminating nucleoside analogs (CTNAs) in cooperation with proofreading exonuclease activity of DNA polymerase ε

Chemotherapeutic nucleoside analogs, such as cytarabine (Ara-C), are incorporated into genomic DNA during replication. Incorporated Ara-CMP (Ara-cytidine monophosphate) serves as a chain terminator and inhibits DNA synthesis by replicative polymerase epsilon (Polε). The proofreading exonuclease activity of Polε removes the misincorporated Ara-CMP, thereby contributing to the cellular tolerance to Ara-C. Purified Polε performs proofreading, and it is generally believed that proofreading in vivo does not need additional factors. In this study, we demonstrated that the proofreading by Polε in vivo requires CTF18, a component of the leading-strand replisome. We found that loss of CTF18 in chicken DT40 cells and human TK6 cells results in hypersensitivity to Ara-C, indicating the conserved function of CTF18 in the cellular tolerance of Ara-C. Strikingly, we found that proofreading-deficient POLE1D269A/-, CTF18-/-, and POLE1D269A/-/CTF18-/- cells showed indistinguishable phenotypes, including the extent of hypersensitivity to Ara-C and decreased replication rate with Ara-C. This observed epistatic relationship between POLE1D269A/- and CTF18-/- suggests that they are interdependent in removing mis-incorporated Ara-CMP from the 3' end of primers. Mechanistically, we found that CTF18-/- cells have reduced levels of chromatin-bound Polε upon Ara-C treatment, suggesting that CTF18 contributes to the tethering of Polε on fork at the stalled end and thereby facilitating the removal of inserted Ara-C. Collectively, these data reveal the previously unappreciated role of CTF18 in Polε-exonuclease-mediated maintenance of the replication fork upon Ara-C incorporation.

Abstract 6072: Chromosomal aneuploidy, whole-genome doubling and mutational signatures in NCI PDMR models

Abstract Introduction: Structural variants (SVs) are a unique class of mutations which have certain therapeutic implications for the tumor. Certain SVs, such as chromosomal aneuploidy, whole-genome doubling (WGD), have specific therapeutic implications. The underlying cellular processes present in the tumor are reflected in mutational signatures. Here, we describe the landscape of chromosomal aneuploidy, WGD and mutational signatures in the National Cancer Institute’s Patient-Derived Models Repository (NCI PDMR) to facilitate the investigation of their roles in therapeutic responses of the preclinical models. Method: Chromosome arm-level aneuploidy was called by scoring at the individual arm level if &amp;gt;90% of the arm copy number (CN) was gained/lost based on whole-exome sequencing (WES) data. Aneuploidy score was defined as number of arms with aneuploidy. WGD was determined by derived allelic specific CN, purity and ploidy from tumor/normal matched samples and permutation test. Mutational signatures (COSMIC v3) including single base substitutions (SBS), doublet base substitutions (DBS), small insertions and deletions (ID) and CN signatures were derived using SigProfiler for specimens with somatic mutations and CNs. Results: A large fraction (85%) of patient-derived xenograft (PDX) models (N=755) have at least one arm -level aneuploidy. Certain chromosomes and arms (7, 8, 17p and 18) are more frequently aneuploid, which might be biased due to the overrepresentation of gastrointestinal cancer in the cohort. Histology specific differences were observed in the frequency of arm level aneuploidies. For example, synovial sarcoma (SYNS) and endometrioid carcinoma (UEC) have much lower level of aneuploidy than non-small cell lung cancer (NSCLC) or clear cell renal carcinoma (ccRCC) models. 61% of PDX models (N=277) have WGD, in which certain histologies have more WGD [NSCLC: 81%, head and neck squamous cell carcinomas (HNSCC): 71%] than others. Samples having WGD have a higher degree of aneuploidy and chromosomal instability. WGD and aneuploidy remain stable along the passages in 78% PDX models. Intra-model heterogeneity of WGD was observed due to lineage difference. Mutational signatures (SBS6,15,20) indicating concurrent DNA polymerase epsilon (POLE) mutation and defective DNA mismatch repair were highly enriched in microsatellite instability-high models (p&amp;lt;0.01, Fisher’s exact test). Among 30 PDX models where the patients had known platinum-based chemotherapy history, 40% of them had an identifiable platinum chemotherapy treatment signature (SBS31 or DBS5). Chromothripsis associated amplification signature (CN8) was enriched in models with WGD (p&amp;lt;0.05). Conclusion: We have characterized chromosomal aneuploidy, WGD and mutational signatures in NCI PDMR models. The models with SVs can be utilized in preclinical drug studies to understand their role in therapeutic response in patients. Citation Format: Li Chen, Biswajit Das, Ting-Chia Chang, Yvonne A. Evrard, Chris A. Karlovich, Alyssa Chapman, Brandie Fullmer, Ashley Hayes, Ruth Thornton, Nikitha Nair, Shahanawaz Jiwani, Lindsay Dutko, Kelly Benauer, Gloryvee Rivera, Corinne Camalier, John Carter, Suzanne Borgel, Tiffanie Miner, Chelsea McGlynn, Justine Mills, Shannon Uzelac, Tia Shearer, Lauren Hicks, Michelle Norris, Carley Border, Sergio Alcoser, Thomas Walsh, Michael Mullendore, Michelle Eugeni, Dianne Newton, Melinda G. Hollingshead, P. Mickey Williams, James H. Doroshow. Chromosomal aneuploidy, whole-genome doubling and mutational signatures in NCI PDMR models. [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 6072.

Abstract 3505: Cancer disparities in race exposed through geospatial analysis of mutational signatures and environmental exposure

Abstract Background: Cancer has been disproportionally affecting minorities in the US due to socioeconomic, environmental, and genetic disparities. Cancer disparities are usually measured in incidence, mortality, survival, etc. Genomic-based cancer disparity analyses have been less common. In the past decade, mutational signatures were proposed as characteristic footprints of endogenous or exogenous carcinogens, which remarkably propelled the progress of genomic cancer research. The disparities caused by uneven exposure to environmental pollutants may be recorded in mutational signatures. Method: The Cancer Genome Altas is one of the richest genomic cancer datasets, empowering hundreds of secondary and tertiary cancer studies. One aspect of TCGA data that is seldomly utilized is geospatial information. Based on the contribution hospital location, we estimated the patients’ approximate location. Furthermore, utilizing data on 450 pollutants released by the Environmental Protection Agency from 2007-2017, we were able to establish associations between mutational signatures and certain pollutants. To remove the noise introduced by approximating the location and average pollution level, stringent statistical procedures were applied. Results: First, we showed that mutation frequencies varied substantially between different races. For example, TP53 was mutated in 46% of Black breast cancer patients, compared to 31% in Whites. Such differences in single genes translated to the level of mutational signatures. Liver cancer has aflatoxin as an affirmed carcinogen, and we compared the quantities of aflatoxin signature across races. It was found that aflatoxin contributed significantly higher (FDR = 0.002) to mutations in Asian than in Caucasians. In-depth analyses revealed that aflatoxin had a strong effect on hepatitis C virus infection in addition to the previously reported effect on hepatitis B virus infection. Similarly, as a known critical player in head and neck tumors, APOBEC signature was found at a significantly higher level (FDR = 0.01) in patients with positive infection of human papillomavirus. Furthermore, analyses from the geospatial perspective revealed several potential associations between pollutants and mutational signatures. For example, the pollutant carbofuran is positively associated with mutational signature SBS10a with the etiology of Polymerase epsilon exonuclease domain mutations (FDR = 0.02). Summary: We conducted a thorough mutational signature-based cancer disparity analysis. Our results reinforced previously known facts and expectations of oncogene mutations. The novel results demonstrated representative links between various forms of cancer disparity and genomic mutation footprints. Most importantly, such disparities can be interrogated at the mutational signature level and correlated to environmental pollutants. Citation Format: Yan Guo, Judy Bai, Katherine Ma, Shangyang Xia, Shuguang Leng, Hui Yu, Xi Gong. Cancer disparities in race exposed through geospatial analysis of mutational signatures and environmental exposure [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 3505.