tbuckley/cabot-search huggingface dataset:
Abstract IA022: Uracil DNA glycosylase activity limits deoxyuridine contamination in genomic DNA and is essential for the type-1 interferon response in cells treated with ATR kinase inhibitors
Authors: Pinakin Pandya, Frank P. Vendetti, Joseph A. Ghoubaira, Sudipta Pathak, Joshua J. Deppas, Reyna E. Jones, Yunqi Zhang, Daniel Ivanov, Raquel Buj, Katherine M. Aird, Jan H. Beumer, Robert W. Sobol, Christopher J. Bakkenist
Journal: Cancer Research (2024)

Abstract Most chemotherapies target DNA replication, and their efficacy depends on the DNA damage response that integrates DNA repair with the cell cycle. Widely used standard-of-care antimetabolites inhibit thymidylate synthase and increase the incorporation of deoxyuridine (dU) into DNA by polymerases. Contamination of dU in DNA is limited by the DNA damage response kinase ATR that induces cell cycle checkpoints and reduces the rate of DNA replication. ATR inhibitors (ATRi) induce origin firing across active replicons and cause ribonuclease reductase degradation in otherwise unperturbed cells. This increases both the amount of DNA replication and the amount of free dUTP in cells. Thus, ATRi increase the incorporation of dU into DNA by polymerases. Since ATRi also inhibit cell cycle checkpoints, ATRi induce more dU contamination than antimetabolites. ATRi-induced dU contamination in DNA is associated with an innate immune response. We showed this with the simple observation that ATRi-induced dU contamination and IFN-α/β expression is reversed by low doses of thymidine. Here we show that ATRi-induced IFN-α/β response is dependent on uracil DNA glycosylase (UNG) which removes dU from DNA. Our data are consistent with a model in which UNG-dependent base excision repair (BER) removes dU from DNA, ultimately generating cytoplasmic dsDNA that induces IFN-α/β. We propose that ATRi-induced dU contamination contributes to dose-limiting leukocytopenia and inflammation in the clinic and CD8+ T cell dependent anti-tumor responses in mouse models of cancer treated with radiation therapy. Citation Format: Pinakin Pandya, Frank P. Vendetti, Joseph A. Ghoubaira, Sudipta Pathak, Joshua J. Deppas, Reyna E. Jones, Yunqi Zhang, Daniel Ivanov, Raquel Buj, Katherine M. Aird, Jan H. Beumer, Robert W. Sobol, Christopher J. Bakkenist. Uracil DNA glycosylase activity limits deoxyuridine contamination in genomic DNA and is essential for the type-1 interferon response in cells treated with ATR kinase inhibitors [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 IA022.
Abstract IA015: Using systems approaches to interrogate DNA double strand break signaling and repair for optimal tumor cell killing
Authors: Alex Kruswick, Bert van de Kooij, Tiffany R. Emmons, Ganapathy Sriram, Emma D. Martin, Anjali Arvind, Haico van Attikum, Michael B. Yaffe
Journal: Cancer Research (2024)

Abstract Repair of DNA double strand breaks (DSBs) occurs through multiple distinct repair pathways including canonical and microhomology-mediated/Pol Q-dependent end joining (c-NHEJ and alt-NHEJ), homologous recombination (HR), and single strand annealing (SSA). Exactly how a particular DSB dictates which pathway is selected for repair, and the extent to which different DSB repair pathways cross-talk with each other is incompletely understood, but appears to be influenced by the specific type of DNA ends, the extent of DNA resection, the cell state and stage of the cell cycle, and the chromatin context around the break. To simultaneously interrogate multiple DNA DSB repair pathways in a systems-based manner at the single cell level, we built upon the pioneering DSB repair reporter systems created by the Jasin, Stark, Scharenberg and Certo labs to create several new CRISPR-based DNA DSB reporter systems that readout the repair of a single genomic DNA DSB by error-free c-NHEJ, mutagenic c- and alt-NHEJ, HR or SSA using multi-color fluorescence-based imaging and flow cytometry approaches. Using these DSB reporter systems we show that competition between short-range and long-range end resection influences the choice between repair by HR versus SSA, demonstrate accepted and novel functions for a variety of DNA damage sensors and repair proteins in NHEJ and HR, and illustrate the feasibility of using this system to interrogate the effects of patient-specific mutations in DNA repair proteins on DNA DSB repair pathway choice. Finally, we show that DNA DSBs created by topoisomerase inhibitor treatment in live but DNA-damaged tumor cells are capable of activating anti-tumor immune responses by signaling through both canonical and non-canonical DNA break sensing and response pathways. Citation Format: Alex Kruswick, Bert van de Kooij, Tiffany R. Emmons, Ganapathy Sriram, Emma D. Martin, Anjali Arvind, Haico van Attikum, Michael B. Yaffe. Using systems approaches to interrogate DNA double strand break signaling and repair for optimal tumor cell killing [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 IA015.
Comparing Anticoagulation Strategies for Venous Thromboembolism Associated With Active Cancer
Authors: Tomohiro Fujisaki, Daisuke Sueta, Eiichiro Yamamoto, Conor Buckley, Guilherme Sacchi de Camargo Correia, Julia Aronson, Paulino Tallón de Lara, Koichiro Fujisue, Hiroki Usuku, Kenichi Matsushita, Roxana Mehran, George D. Dangas, Kenichi Tsujita
Journal: JACC CardioOncology (2024)

Current guidelines recommend several direct oral anticoagulant agents (DOACs) equally for managing cancer-associated venous thromboembolism (VTE). The aim of this study was to assess the efficacy and safety of DOACs in patients with active cancer. Literature searches were conducted in PubMed, Embase, and Cochrane Central in November 2022. Randomized controlled trials investigating anticoagulation strategies (vitamin K antagonists, parenteral anticoagulation [eg, low-molecular weight heparin], and DOACs) for VTE in patients with active cancer were identified for network meta-analysis. The outcomes included recurrent VTE, recurrent pulmonary embolism, recurrent deep venous thrombosis, major bleeding, clinically relevant nonmajor bleeding (CRNMB), and a composite outcome of major bleeding or CRNMB. Pooled HRs and 95% CIs were estimated using either the HR or relative risk provided from each study. Random-effects models were used for all the analyses. Seventeen randomized controlled trials involving 6,623 patients with active cancer were included. No significant differences were found among the DOACs for efficacy outcomes (recurrent VTE, pulmonary embolism, and deep venous thrombosis). In terms of major bleeding, apixaban was similarly safe compared with dabigatran and rivaroxaban but was associated with a decreased risk compared with edoxaban (HR: 0.38; 95% CI: 0.15-0.93). Regarding CRNMB, edoxaban was similarly safe compared with apixaban but was associated with a decreased risk compared with rivaroxaban (HR: 0.31; 95% CI: 0.10-0.91). Compared with parenteral anticoagulation, apixaban was associated with a reduced risk for recurrent VTE (HR: 0.60; 95% CI: 0.38-0.93) without increasing bleeding, edoxaban was associated with an increased risk for major bleeding or CRNMB (HR: 1.35; 95% CI: 1.02-1.79), and rivaroxaban was associated with an increased risk for CRNMB (HR: 3.76; 95% CI: 1.43-9.88). DOACs demonstrate comparable efficacy but exhibit different safety profiles. Apixaban may confer an antithrombotic benefit without an increased risk for bleeding, distinguishing it from other contemporary anticoagulation strategies in patients with active cancer and VTE.
Prevalence and predictors of cancer screening in transgender and gender nonbinary individuals
Authors: Michelle Lui, Walter Bockting, Kenrick Cato, Lauren C. Houghton
Journal: International Journal of Transgender Health (2024)

Current cancer screening guidelines for transgender individuals are guided primarily by expert opinion, and are extrapolated from guidelines for cisgender populations, despite the additional unique risks that transgender populations face in cancer risk and cancer care.
Abstract B022: C11ORF68 is essential for γH2AX formation after replication stress
Authors: Clarissa Chin Min Toh, Mai Phuong Hoang, Anand Jeyasekharan
Journal: Cancer Research (2024)

Abstract Introduction: Unresolved replication stress (RS) often leads to genomic instability – a feature of many diseases including cancer. RS can activate downstream DNA damage response (DDR) phenotypes such as phosphorylation of histone H2AX (γH2AX). Therefore, understanding the molecular foundation of DDR is crucial for identifying potential biomarkers or therapeutic targets. Our lab has identified an uncharacterized protein that is symmetrically dimethylated by PRMT5 under hydroxyurea (HU) induced RS. Therefore, we hypothesize that C11ORF68 is involved in the RS and DNA damage response. Materials and methods: RS and DNA damaging agents including HU and etoposide were used to induce RS or DNA damage in various cell lines. C11ORF68 was depleted using siRNA and dicer siRNA (dsiRNA) systems. Immunofluorescence and immunoblotting were used to evaluate DDR phenotypes. Results: One of the earliest phenomenon in DDR is phosphorylation of histone H2AX (γH2AX). Depletion of C11ORF68 under HU-induced RS reduced γH2AX foci formation as compared to cells treated with control siRNA or dsiRNA. Since HU affects cells entering S-phase, we evaluated if this is a cell cycle-related effect by using other DNA damaging agents that target cells in all phases of the cell cycle. Similarly, depletion of C11ORF68 under DNA damaging conditions showed reduced γH2AX foci formation. This may be due to a lack of upstream PIKK kinases activation as knockdown of C11ORF68 also attenuated phosphorylation of PIKKs important for H2AX phosphorylation after treatment with DNA damaging agents and RS-inducing agents. Conclusions: Our data suggests that C11ORF68 it appears to modulate early DDR even before H2AX phosphorylation and upstream PIKK activation. We are currently investigating if C11ORF68 is involved in initial events after DNA damage or RS such as PARylation events or MRN sensing of DNA breaks. Citation Format: Clarissa Chin Min Toh, Mai Phuong Hoang, Anand Jeyasekharan. C11ORF68 is essential for γH2AX formation after replication stress [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 B022.
Abstract A030: DNA repair gene polymorphism(s): Association with relapse of oral squamous cell carcinoma
Authors: Umaiya Abdali, Saima Saleem
Journal: Cancer Research (2024)

Abstract Differences in DNA repair capacity have been linked to the risk and prognosis of cancer. In specific types of cancer, certain variations known as Single Nucleotide Polymorphisms (SNPs) within DNA repair genes can influence the effectiveness of treatments. This phenomenon has been observed in patients with Oral Squamous Cell Carcinoma (OSCC), especially in those undergoing chemotherapy and radiation therapy. One such gene, Excision Repair Cross-Complementation 5 (ERCC5), contains a SNP (rs17655) G&amp;gt;C, leading to a missense variation and a change in amino acid from D to H. This variation has been noted in various cancer types. Hence, this study aimed to investigate the presence of this DNA repair gene polymorphism (rs17655) and its association with OSCC. To achieve this goal, blood samples were collected from OSCC patients exposed to chemotherapy and radiation therapy, as well as from OSCC patients not exposed to these treatments, following approval from the relevant institutional review committees. Informed consent was obtained from 100 patients, and an equal number of age and gender-matched controls. Genomic DNA was extracted using the salting-out method and analyzed for quality and quantity through agarose gel electrophoresis and nanodrop spectrophotometry. Primers were designed using online primer designing software. Genetic variations were identified using Tetra Primers-Amplifies Refractory Mutation System Polymerase Chain Reaction (t-ARMS PCR), and the amplified products were visualized via agarose gel electrophoresis. The genotypic frequency analysis of rs17655 revealed a higher prevalence of the homozygous mutant type (CC) in the blood samples of OSCC patients, both exposed and non-exposed to chemotherapy and radiation therapy. In contrast, the homozygous wild type (GG) was more prevalent among the control group. Statistical analysis, including a chi-square test (χ 2 = 36.76, p &amp;lt; 0.001) and odds ratio (10.27), demonstrated a significant association between the rs17655 polymorphism and oral squamous cell carcinoma, indicating an increased risk of OSCC due to this genetic variation. These genomic variants have the potential to serve as biomarkers for predicting clinical outcomes in OSCC patients undergoing chemotherapy and radiotherapy. Citation Format: Umaiya Abdali, Saima Saleem. DNA repair gene polymorphism(s): Association with relapse of oral squamous cell carcinoma [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 A030.
Endoscopic submucosal dissection for severe fibrosis using a combined water pressure and circumferential-inversion method
Authors: Hiroshi Takayama, Toshitatsu Takao, Douglas Motomura, Hitomi Hori, Yoshinori Morita, Takashi Toyonaga, Yuzo Kodama
Journal: Endoscopy (2024)

Use of the water pressure method during endoscopic submucosal dissection (ESD) has been reported to shorten procedure times for colorectal lesions with fibrosis [1] [2]; however, ESD for cases with severe fibrosis remains extremely challenging [3]. We recently reported a novel traction method called the circumferential-inversion method (CIM), which involves inverting the lesion circumferentially [4]. In this report, we describe the effectiveness of ESD using a novel approach that combines the water pressure method and CIM (WP-CIM) for lesions with severe fibrosis ([Video 1]).
Abstract B004: Polymerase theta (Pol θ) is essential to repair a subset of DNA breaks in HR proficient cells
Authors: Chelsea M. Smith, Dennis Simpson, Wanjuan Feng, Gaorav Gupta
Journal: Cancer Research (2024)

Abstract DNA polymerase theta (Pol θ), functions in theta-mediated end joining (TMEJ), an error-prone DNA double strand break repair pathway. Pol θ is synthetic lethal with homologous recombination (HR) factors, and this finding has led to the development of Pol θ inhibitors and clinical trials to determine their effectiveness in HR-deficient tumors. Despite this, the biological functions of Pol q that promote genome integrity in normal cells are poorly understood. Here, we elucidate an essential role for Pol θ during mammalian interstrand crosslink (ICL) repair. We show that Pol θ is recruited downstream of ICL nucleolytic incision, BRCA2-dependent Rad51 loading, and FBXO5-mediated Rad51 ubiquitylation at sites of unsuccessful HR. Genomic scar analyses reveal that TMEJ is specifically required for repair of clustered ICLs, which are not amenable to HR-mediated repair. Thus, Pol q may be the predominant repair pathway for clustered lesions that generate two-ended double strand breaks during DNA replication. These findings suggest that Pol θ has essential roles in DNA repair in HR proficient cells, suggesting that Pol θ inhibitors may also be beneficial in the treatment of HR proficient tumors. Citation Format: Chelsea M. Smith, Dennis Simpson, Wanjuan Feng, Gaorav Gupta. Polymerase theta (Pol θ) is essential to repair a subset of DNA breaks in HR proficient cells [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 B004.
Ophthalmic and Systemic Factors of Acute Nonarteritic Anterior Ischemic Optic Neuropathy in the Quark207 Treatment Trial
Authors: Mark J. Kupersmith, Clare L. Fraser, Rachelle Morgenstern, Neil R. Miller, Leonard A. Levin, Nathalie Jette, Fraser Clare, Chen Celia, Shuey Neil, Colley Stephen, Ningli Wang, Hongliang Dou, Yong Zhong, Luosheng Tang, Quanhong Han, Sandner Dirk, Gamulescu Maria-Andreea, Eter Nicole, Wilhelm Helmut, Lorenz Katrin, Krishna G. Santhosh, Kekunnaya Ramesh, Ambika S, Sharma Kumudini, Vivekanand Uttamrao Warkad, Saxena Rohit, Kumar S. Mahesh, Das Dipankar, Hegade Atul, Mazumdar Shahana, Daighavane Sachin, Sachdeva Virender, Kalish Hadas, Klein Ainat, Huna-Baron Ruth, Leiba Hana, Goldenberg-Cohen Nitza, Shneck Marina, Kruger Joshua, Ciardella Antonio Pasquale, Virgili Gianni, Carta Arturo, Bianchi Marzoli Stefania, Sharon Tow, Chin Chee Fang, MacIntosh Peter, Bennett Jeffrey, Lam Byron, Katz Bradley, Williams Zoe, Lee Michael, Tamhankar Madhura, Banik Rudrani, Rauser Michael, Levy Marc, Liao Yaping Joyce, Luu James, Tibbetts Michael, Scales David, Lesser Robert, Patel Anil, Givre Syndee, Van Stavern Gregory, Hamilton Steven, Rismondo Vivian, Francis Courtney, Cestari Dean, Dinkin Marc, Pula John, Sudhakar Padmaja, Newman Steven, Tang Rosa, Chacko Joseph, Kedar Sachin, Quiros Peter, Frohman Larry, Volpe Nicholas, Sibony Patrick, Chen John, Mejico Luis, Kosmorsky Gregory, Alfaro Daniel Virgil, Katz David, Lee Andrew, DeLott Lindsey, Patel Vivek, Bose Swaraj, Peeler Crandall, Tariq Bhatti
Journal: Ophthalmology (2024)
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products
Authors: Tao Yu, Yingfeng Luo, Xinyu Tan, Dahe Zhao, Xiaochun Bi, Chenji Li, Yanning Zheng, Hua Xiang, Songnian Hu
Journal: Genomics Proteomics & Bioinformatics (2023)

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.
Multi-omics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity
Authors: Simone J.C.F.M. Moorlag, Lukas Folkman, Rob ter Horst, Thomas Krausgruber, Daniele Barreca, Linda C. Schuster, Victoria Fife, Vasiliki Matzaraki, Wenchao Li, Stephan Reichl, Vera P. Mourits, Valerie A.C.M. Koeken, L. Charlotte J. de Bree, Helga Dijkstra, Heidi Lemmers, Bram van Cranenbroek, Esther van Rijssen, Hans J.P.M. Koenen, Irma Joosten, Cheng-Jian Xu, Yang Li, Leo A.B. Joosten, Reinout van Crevel, Mihai G. Netea, Christoph Bock
Journal: Immunity (2024)

Immune responses are tightly regulated yet highly variable between individuals. To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live-attenuated vaccine induces not only an adaptive immune response against tuberculosis but also triggers innate immune activation and memory that are indicative of trained immunity. We established personal immune profiles and chromatin accessibility maps over a 90-day time course of BCG vaccination in 323 individuals. Our analysis uncovered genetic and epigenetic predictors of baseline immunity and immune response. BCG vaccination enhanced the innate immune response specifically in individuals with a dormant immune state at baseline, rather than providing a general boost of innate immunity. This study advances our understanding of BCG's heterologous immune-stimulatory effects and trained immunity in humans. Furthermore, it highlights the value of epigenetic cell states for connecting immune function with genotype and the environment.
Abstract B034: Polymorphisms in XRCC1 Arg399Gln and XRCC3 Thr241Met DNA repair genes elevate cervical cancer risk among Bangladeshi female population
Authors: Md. Mustafizur Rahman, Laboni Das, Sadia Rahman, Amir Hossain, Razia Sultana
Journal: Cancer Research (2024)

Abstract Introduction and Objective: Cervical cancer is the second most common cancer in women worldwide and is both a preventable and a curable disease especially if identified at an early stage. Sequence variations in DNA repair genes can cause aberration in cellular functions leading to cancer. Genetic polymorphisms in XRCC1 (Arg399Gln) and XRCC3 (Thr241Met) genes result in individual variation in their DNA repair capacity. The aim of this study was to identify the association between XRCC1 Arg399Gln and XRCC3 Thr241Met single nucleotide polymorphisms (SNPs) and susceptibility to cervical cancer in Bangladeshi populations. Methods: The case-control study comprised 124 cervical cancer patients and 148 healthy controls. Genomic DNAs were isolated from peripheral blood and genotyped for candidate SNPs using polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) method. Results: For XRCC1, heterozygous Arg/Gln and combined heterozygous plus variant homozygous Gln/Gln genotypes showed 1.78-fold (95% CI 1.0037 to 2.8771, p=0.0484) and 1.8627-fold (95% CI 1.1470 to 3.0250, p = 0.0119) increased risk of cervical cancer, respectively, when compared with normal homozygous Arg/Arg genotype. The variant Gln allele was positively associated with cervical cancer by 1.68-fold increase (95% CI 1.1732 to 2.3980, p = 0.0046). Similarly, for XRCC3, Thr/Met heterozygous and combined Thr/Met + Met/Met genotypes were found to be associated with 1.6993-fold (95% CI 1.0398 to 3.0166, p=0.0354) and 1.8312-fold (95% CI 1.0890 to 3.0791, p = 0.0225) higher risk, respectively, when compared with normal homozygous Thr/Thr genotypes. The variant Met allele showed significant association with 1.71-fold increased risk. Conclusion: XRCC1 (Arg399Gln) and XRCC3 (Thr241Met) polymorphisms may be associated with increased cervical cancer risk in Bangladeshi females. Citation Format: Md. Mustafizur Rahman, Laboni Das, Sadia Rahman, Amir Hossain, Razia Sultana. Polymorphisms in XRCC1 Arg399Gln and XRCC3 Thr241Met DNA repair genes elevate cervical cancer risk among Bangladeshi female population [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 B034.