bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A017: Targeting Tlk2 impairs breast cancer growth and engages immune responses
Authors: Villamor-Payá Marina , Caballé Adrià , Smak Jordann , Benmebarek Mohamed-Reda , Attolini Camille Stephan-Otto , Stracker Travis H. 
Published: January 2024

Abstract
The Tousled like kinases 1 and 2 (TLK1 and TLK2) are evolutionarily conserved Ser/Thr kinases that are required for genome stability and normal development in numerous organisms. Both kinases contribute to histone deposition by targeting the histone chaperones ASF1A and ASF1B and are regulated by the DNA damage response (DDR). TLK1/2 expression is ubiquitous and often elevated in human cancers with suppressed immune gene expression. In some cancer types, elevated TLK levels correlate with decreased disease-free survival. In cultured cells, TLK depletion causes replication stress, DNA damage and altered chromatin maintenance. TLK1/2 depletion increases the efficacy of DNA damage checkpoint inhibitors and PARP inhibitors and induces the Alternative-lengthening of telomeres pathway and innate immune signaling. Collectively, this data suggests that TLK activity may be a druggable anti-cancer target. To test this, we generated a conditional Tlk2 allele in mice and introduced the Mouse Mammary Tumor Virus-Polyoma Middle Tumor-antigen (MMTV-PyMT) transgene to generate breast cancers. Deletion of Tlk2 in developing breast cancer resulted in impaired primary tumor growth and a complete inhibition of lung metastasis. Characterization of the tumor microenvironment revealed elevated immune infiltration that includes activated T cells with higher levels of PD-1, which could potentially sensitize these tumors to immune checkpoint blockade. To test this possibility, we established a syngeneic breast cancer model to allow us to combine Tlk2 depletion or deletion with DDR inhibitor and anti-PD-1 therapy in vivo. Preliminary data supports the strategy of targeting Tlk2 in cancer and we will share current data from tumor models and preliminary characterization of small molecule inhibitors.
Citation Format: Marina Villamor-Payá, Adrià Caballé, Jordann Smak, Mohamed-Reda Benmebarek, Camille Stephan-Otto Attolini, Travis H. Stracker. Targeting Tlk2 impairs breast cancer growth and engages immune responses [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 A017.
Abstract A024: Epigenetic control of topoisomerase 1 activity presents a cancer vulnerability
Authors: Lee Tae-Hee , Qiao Xuan C. , Wu Tongyu , Kuzin Vladislav , Zhou Xianzhen , Ramanarayanan Vijayalalitha , Baranello Laura , Oberdoerffer Philipp 
Published: January 2024

Abstract
Genome integrity is inherently at risk due to the torsional constraints imposed by DNA transactions. Topoisomerase 1 (TOP1) is essential for genomic stability by removing DNA supercoils generated during replication and transcription. Aberrant stabilization of TOP1:DNA cleavage complexes (TOP1ccs), however, result in DNA lesions that drive transcription-associated mutation burden and are a cytotoxic consequence of many clinically used chemotherapeutic agents. What protects genomic regions prone to elevated torsional stress from the cytotoxic potential of TOP1 enzymes remains unknown. Here, we identify macroH2A1.1, the only nucleosome component with an inherent ability to bind the TOP1cc repair-essential poly(ADP-ribose) (PAR) protein modification, as an essential means to establish a TOP1-permissive chromatin environment. MacroH2A1.1 is one of two alternatively spliced isoforms of the macro-histone variant macroH2A1, and comparative proteomics between the two isoforms uncovered a macroH2A1.1-specific and PARP activity-dependent interaction with the TOP1cc repair effector TDP1 as well as downstream base excision repair (BER) factors XRCC1 and LIG3. Consequently, macroH2A1.1 loss or inactivation of its PAR-binding domain resulted in impaired XRCC1 recruitment to damaged DNA and defective TOP1cc turnover, while the macroH2A1.2 splice isoform is unable to bind PAR or protect from TOP1ccs. Genome-wide mapping of macroH2A1.1, TOP1 and TOP1-DNA adducts identified macroH2A1.1 as a regulatory hub for TOP1 activity that ensures transcriptional integrity by preventing excessive TOP1cc accumulation at transcription start sites. Impaired macroH2A1.1 splicing, a frequent cancer feature, correlated with sensitivity to TOP1 poisons in a pharmaco-genomic screen in breast cancer cells, and macroH2A1.1 inactivation mirrored this effect. Finally, we find that aberrant macroH2A1 alternative splicing in cancer correlates with BER-related mutation signatures. We propose that macroH2A1 alternative splicing serves as an epigenetic modulator of TOP1-associated genome maintenance and a potential cancer vulnerability.
Citation Format: Tae-Hee Lee, Xuan C. Qiao, Tongyu Wu, Vladislav Kuzin, Xianzhen Zhou, Vijayalalitha Ramanarayanan, Laura Baranello, Philipp Oberdoerffer. Epigenetic control of topoisomerase 1 activity presents a cancer vulnerability [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 A024.
Abstract A028: Alcohol induces DNA damage and genomic instability in MCF-7 breast cancer cells and primary mammary tissues
Authors: Yang Xiaohe 
Published: January 2024

Abstract
Alcohol consumption has been associated with increased breast cancer risk. Previous studies indicated that alcohol-induced DNA damage plays a central role in carcinogenesis. However, the underlying molecular mechanisms remain unclear. This study aimed to examine the effect of alcohol exposure on key DNA damage/repair pathways in both in vitro and in vivo settings. When MCF-7 breast cancer cells were exposed to 0.1 ~ 0.8% alcohol, the treatment induced concentration-dependent DNA damage, as indicated by the increased 8-OHdG (8-hydroxy 2 deoxyguanosine) production and p-H2AX foci formation. Signal transduction analysis showed that alcohol induced DNA damage signals, including p53, p21, E2F-1 and CHK1, and the markers in DNA repair pathways, including XLF, Rad50 and DNA-PK. p53 knockdown in MCF-7 cells resulted in enhanced DNA damage and DNA repair responses, which underscores the role of p53 in alcohol-induced cellular regulation. We also demonstrated that alcohol induces sister chromatid exchanges (SCEs) in MCF-7 cells, and ALDH2 knockout enhanced alcohol induced SCEs, which suggests that alcohol-induced acetaldehyde (AA) is a key mediator in this process. Moreover, we examined the DNA damage markers in mammary tissues of FVB/N mice exposed to alcohol and showed that alcohol exposure in vivo induced similar patterns of DNA damage and repair responses. Taken together, our data highlights the contribution of alcohol-induced DNA damage in cellular injury and the consequent tumorigenesis, which provide fundamental support for further studies on alcohol-induced DNA damage and carcinogenesis.
Citation Format: Xiaohe Yang. Alcohol induces DNA damage and genomic instability in MCF-7 breast cancer cells and primary mammary tissues [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 A028.
Abstract A032: Identifying the binding partners of a long noncoding RNA involved in the DNA damage response
Authors: Correa Michele Ramos , Castillo Jonathan , Marconett Crystal N. 
Published: January 2024

Abstract
Lung adenocarcinoma (LUAD) is the most common histological subtype of the deadliest cancer in the United States. This cancer can arise from a high rate of mutations exaggerated by dysregulation in DNA damage and repair signaling that cause genomic instability. LUAD has largely been studied in the context of protein-coding genes, however, recent studies have implicated long noncoding RNAs (lncRNAs) as critical regulators of gene expression in the DNA damage response, controlling the repair mechanism response's magnitude, duration, and resolution. My lab has identified the lncRNA LINC00261 as a tumor suppressor in LUAD that regulates the activation of the DNA damage repair system; however, its exact mechanisms of action remain unknown. We found that the reintroduction of LINC00261 in LUAD is associated with G2/M cell cycle arrest and phosphorylation-mediated activation of key DNA damage response pathway components. We hypothesize that LINC00261 protects DNA fidelity through direct interaction with repair components and aim to obtain insights into the essential functions that LINC00261 plays in the DNA damage response. We observe that LINC00261 is differentially highly expressed upon increased DNA damage with UV-light and ionizing radiation alongside enhanced expression of DDR components like p53. We have conducted initial RNA-FISH and ChIRP-MS studies to characterize the molecular mechanisms of this lncRNA. We demonstrate that subcellular localization of LINC00261 is found to be distributed in both the cytoplasm and nucleus, inferring an ability to function in cis and in trans to interact with partners locally and genome wide. Initial ChIRP mass spectrometry pilot data shows significant enrichment for DNA replication and p53 pathway activity. These findings contribute valuable information to understanding the role of LINC00261 in the DNA damage response and have implications for how lncRNA-mediated dysregulation of DNA repair leads to genomic instability and oncogenic activation.
Citation Format: Michele Ramos Correa, Jonathan Castillo, Crystal N. Marconett. Identifying the binding partners of a long noncoding RNA involved in the DNA damage response [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 A032.
Abstract B004: Polymerase theta (Pol θ) is essential to repair a subset of DNA breaks in HR proficient cells
Authors: Smith Chelsea M. , Simpson Dennis , Feng Wanjuan , Gupta Gaorav 
Published: January 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.
Abstract B016: Developing diagnostic tools via mutational spectra analysis and multiomic plasma profiling from liquid biopsies to identify potential signatures in cancer in Trinidad and Tobago
Authors: Ramlachan Nicole , West Samuel M. 
Published: January 2024

Abstract
Cancer, especially lung cancer is a leading cause of nosocomial deaths worldwide. Non-small cell lung cancer (NSCLC) has a five-year survival rate of only 24%. Early diagnoses markedly improves survival with personalized cancer therapies using non-invasive techniques for asymptomatic detection of mutational spectrum-related by genotyping NSCLC patients, even prior to symptoms. Analysis of conformational change in proteins due to mutations in oncogenes allow for mutation-specific treatment with specialized cancer drugs. In addition, tumor mutational burden (TMB) is a promising predictive biomarker for cancer immunotherapy as high TMB patients respond better to immune checkpoint inhibitors cancer drugs. Treatment planning for non-small cell lung cancer generally requires testing for EGFR, ALK, ROS1, BRAF, MET, RET and KRAS gene alterations or whole genome analysis to assess TMB. The Caribbean region remains disadvantaged by the lack of available genetic testing mainly due to accessibility. We propose the genotyping of 30 stage III-IV NSCLC patients via next-generation sequencing (NGS) to improve personalized therapies. Through the analysis of tumor-specific alterations amongst a complete mutation spectrum analysis, including single nucleotide variants (SNVs), insertions, deletions, copy number variations (CNVs), and methylation alterations, we would generate data to be used as an accurate form of cancer genotyping for diagnostic purposes. We intend to include these genes as biomarkers in a mutational spectrum analysis, to be collated into a predictive DNA assay to be used for the first time as a diagnostic/prognostic tool in a medically underserved community. We intend to also identify TMB-high patients without cost-prohibitive whole genome sequencing by focusing on DNA damage repair (DDR) genes. There is an increasing utilization of agnostic testing which involves the analysis of all potentially actionable genes across all tumor and cancer types. The invention of genomic-tailored specialized cancer treatments has resulted in a spectacular improvement in disease outcomes for a significant portion of cancer patients, which we hope to offer to improve clinical outcomes and prognosis in the racially diverse population of Trinidad and Tobago.
Citation Format: Nicole Ramlachan, Samuel M. West. Developing diagnostic tools via mutational spectra analysis and multiomic plasma profiling from liquid biopsies to identify potential signatures in cancer in Trinidad and Tobago [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 B016.
Abstract B019: BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response
Authors: Jiang Haoyang , Zhang Tianpeng , Kaur Hardeep , Shi Tao , Krishnan Aravind , Kwon Youngho , Sung Patrick , Greenberg Roger 
Published: January 2024

Abstract
Alternative Lengthening of Telomeres (ALT) is a homology-directed repair (HDR) mediated telomere maintenance mechanism that is prevalent in cancers of mesenchymal origin. ALT cells exhibit more endogenous replication stress and DNA damage at the telomere compared to ALT-negative cells. The Bloom Syndrome helicase (BLM) is critical for ALT and promotes replication stress and DNA damage specifically at telomeres in ALT cells. Here, we determine that BLM helicase acts on lagging strand telomere intermediates that occur specifically in ALT-positive cells to assemble a replication stress-associated DNA damage response. Loss of ATRX was permissive for BLM localization to ALT telomeres in S and G2 commensurate with the appearance of telomere C-strand specific single-stranded DNA. Moreover, DNA2 nuclease deficiency increased 5’-flap formation in a BLM-dependent manner, and BLM promoted ALT in response to telomere C-strand, but not G-strand, nicks. These findings define the seminal events in the ALT DNA damage response, linking aberrant lagging strand DNA replication with a BLM-directed HDR mechanism that sustains telomere length in a subset of human cancers (Jiang et al. submitted). These findings will be discussed and how BLM activity is a key determinant of the specific vulnerability of ALT cells to FANCM inhibition, which is currently being developed to target ALT-dependent cancers.
Citation Format: Haoyang Jiang, Tianpeng Zhang, Hardeep Kaur, Tao Shi, Aravind Krishnan, Youngho Kwon, Patrick Sung, Roger Greenberg. BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response [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 B019.
Abstract B021: Assessing replication stress as an actionable therapeutic opportunity in chordoma
Authors: Punturi Nindo , Leung Wendy , Levy Joan , Zou Lee , Cote Gregory M. , Freed Dan M. 
Published: January 2024

Abstract
Chordoma is a rare bone cancer with a high rate of disease recurrence and no approved systemic therapies. Tumor profiling and functional genomics studies suggest a significant number of chordomas are characterized by molecular alterations associated with increased replication stress, and a dependence on replication stress response pathways. We confirm here in preclinical models that chordomas exhibit a replication stress phenotype, which creates an actionable therapeutic vulnerability exploitable by induction of replication stress and/or inhibition of the ATR-dependent replication stress response. A panel of chordoma cell lines was treated with gemcitabine or the ATR inhibitor (ATRi) elimusertib (BAY 1895344). In a subset of cell lines, gemcitabine or elimusertib demonstrated low-nanomolar EC50 values. Upon treatment with the ATRi ceralasertib (AZD6738), DNA fiber assays revealed a mild decrease in replication fork speed and a significant increase in fork asymmetry in cells sensitive to ATR inhibition, suggesting possible fork stalling or collapse. Alkaline and neutral comet assays were performed to determine the presence of genome-wide ssDNA and/or dsDNA breaks, respectively, with orthogonal evaluation of H2A.X activation during S-phase to assess DNA strand integrity after ATR and DNA synthesis inhibition. In a panel of chordoma PDX models, striking differential sensitivity to ATR inhibition was observed. In sensitive models, elimusertib (50 mg/kg, po, bidx3) promoted 85-90% tumor growth inhibition, in contrast to resistant models, where elimusertib treatment had no effect on tumor growth. PDX models sensitive to ATR inhibition were also highly sensitive to gemcitabine, further suggesting gemcitabine induces an ATR-dependent replication stress response in chordoma models. Indeed, combining gemcitabine with ATRi revealed exceptional synergy in chordoma cell lines. Collectively, our data indicate that a subset of chordomas are characterized by intrinsic replication stress that can be therapeutically exploited through the synergistic activity of gemcitabine and ATRi.
Citation Format: Nindo Punturi, Wendy Leung, Joan Levy, Lee Zou, Gregory M. Cote, Dan M. Freed. Assessing replication stress as an actionable therapeutic opportunity in chordoma [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 B021.
Abstract B022: C11ORF68 is essential for γH2AX formation after replication stress
Authors: Toh Clarissa Chin Min , Hoang Mai Phuong , Jeyasekharan Anand 
Published: January 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.