bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 620: Defects of homologous recombination repair in breast cancer: Identification of a novel RAD51-associated protein complex.
Authors: Yuan Jingsong , Chen Junjie 
Published: August 2014

Abstract
Cells are continuously challenged by genotoxic agents from endogenous and exogenous sources. Severe DNA lesions, including DNA double-strand breaks (DSBs), have to be appropriately repaired for cell survival. Homologous recombination (HR) is particularly important for the repair of DSBs due to its ability to accurately restore genetic information. “Cancer is a disease of DNA repair”. The breast cancer susceptibility genes BRCA1 and BRCA2 encode DNA repair factors acting in the specific HR repair pathway. Germline mutations in many HR components, including BRCA1, BRCA2 and PALB2, are associated with cancers including breast cancer. Therefore, it is urgent to understand how HR repair is regulated in normal cells and how human cancers are defective in HR mediated repair.
The RAD51 recombinase plays a central role in HR. To further study HR process, we performed tandem affinity purification of RAD51. Here, we report the identification of a new RAD51-binding protein FIGNL1 (fidgetin-like 1). Our experiments showed that FIGNL1 specifically interacts with RAD51 via its conserved RAD51-binding domain. Cells depleted of FIGNL1 show defective HR repair and hypersensitivity to Camptothecin and ionizing radiation, common regimens for cancer treatment. However, FIGNL1 is recruited to sites of DNA damage in a manner that is independent of BRCA2, RAD51 and RAD51 paralogs. Conversely, FIGNL1 depletion does not affect the loading of RAD51 onto single-strand DNA. Our experiments also uncovered KIAA0146 as a binding partner of FIGNL1 and established that KIAA0146 acts together with FIGNL1 in HR repair. More interestingly, our further study revealed that FIGNL1 and KIAA0146 protein level is dramatically reduced in some breast cancer cell lines.
Altogether, our study reveals a sub-pathway of HR repair with newly identified components FIGNL1 and KIAA0146 and suggests their possible defects in breast cancer, therefore provides new potential directions for cancer diagnosis and therapy.
Citation Format: Jingsong Yuan, Junjie Chen. Defects of homologous recombination repair in breast cancer: Identification of a novel RAD51-associated protein complex. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 620. doi:10.1158/1538-7445.AM2013-620
Abstract 627: Fiber-induced DNA damage response in human lung epithelial cells.
Authors: Kettunen Eeva , Tuominen Päivi , Suhonen Satu , Catalán Julia , Anttila Sisko L. , Nymark Penny , Norppa Hannu 
Published: August 2014

Abstract
Asbestos, a group of naturally occurring mineral fibers, is a significant lung carcinogen. Exposure to asbestos fibers induces the formation of reactive oxygen species in cells and, subsequently, DNA double-strand breaks (DSBs), the most serious form of DNA damage related to transformation of cells. As a part of the DNA damage response, H2AX histone variant molecules are phosphorylated at ser139, producing γH2AX foci at the site of DSBs, and these serve as a docking site for DNA repair molecule complexes. Thereby, γH2AX foci are considered a sensitive marker for DSBs. DNA damage response has not thoroughly been investigated in particle carcinogenesis. Here, we studied fiber-induced DSB formation in two human lung epithelial cell lines, the cancer cell line A549 and the transformed cell line BEAS-2B to provide further knowledge on DNA damage associated with fiber exposure as a risk factor for lung cancer.A sub-lethal asbestos fiber concentration of 2 μg /cm2 was determined, by cell viability tests, as suitable for working with the A549 and BEAS-2B cells. Then, we studied the kinetics of fiber induced DSB formation in terms of H2AX phosphorylation. Foci of γH2AX can be detected using specific antibody in immunocytochemistry assays. A549 and BEAS-2B cells were exposed to asbestos fibers for 4, 24 and 48 h, and γH2AX foci were counted. Concurrent non-exposed control cultures were settled at each time point. At 4 h, the control group displayed remarkable endogenous DSB formation, possibly due to replication stress. In exposed cultures, the formation of γH2AX foci peaked at 24 h. We also explored whether it is possible, by using γH2AX antibody in a chromatin immunoprecipitation followed by next generation sequencing, to find out the distribution of DSBs at 24 h in the fiber-exposed A549 cells. The sequences involved in γH2AX foci were genome-widely distributed. To conclude, the kinetics of fiber-induced γH2AX foci formation in the A549 and BEAS-2B cells was partly interfered by endogenously formed DSBs. This study revealed sequences that may be implicated within γH2AX foci for further elucidation on their contribution to lung tumor progression in particle carcinogenesis.
Citation Format: Eeva Kettunen, Päivi Tuominen, Satu Suhonen, Julia Catalán, Sisko L. Anttila, Penny Nymark, Hannu Norppa. Fiber-induced DNA damage response in human lung epithelial cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 627. doi:10.1158/1538-7445.AM2013-627
Abstract 631: Role of thymidylate synthase in genomic instability and tumorigenesis.
Authors: Kulemina Lidia V. , Chen Min , Maeng Kyungah , Nawab Akbar , Zajac-Kaye Maria 
Published: August 2014

Abstract
Thymidylate synthase (TS) is a well-established chemotherapy target frequently overexpressed in cancer. Multiple clinical studies demonstrated that high levels of TS correlate with the disease stage and resistance to fluoropyrimidine chemotherapy. Previous studies from our laboratory reassessed the paradigm of TS as a passive proliferation biomarker by providing evidence towards its tumor-promoting capabilities (Cancer Cell 2004; Oncogene 2007). We demonstrated that ectopic TS overexpression combined with loss of tumor suppressor genes significantly enhances the rate and severity of tumorigenesis; however the underlying mechanism of this process remained unclear. TS fuels DNA replication and repair through dTMP and folate biosynthesis. We hypothesized that TS overexpression could become a strong tumor-promoting force by inducing nucleotide imbalance that results in DNA misincorporation and damage. In this study, we analyze effects of TS overexpression in context of aberrant DNA repair and cell cycle misregulation by using Ink4/Arf−/- genetically engineered mouse model. We show that ectopic TS overexpression markedly enhances tumorigenesis in hTS/Ink4/Arf−/- mice compared to Ink4/Arf−/- control resulting in more aggressive tumors. HPLC analyses of mouse tumor-derived cell lines confirmed significant nucleotide imbalance and increase in dTMP, dTDP and dTTP levels in hTS/Ink4/Arf−/- mice compared to control. Analysis of chromosomal changes by spectral karyotyping demonstrated 4 to 5 fold increase in chromosomal aberrations and aneuploidy in hTS positive tumor cell lines. Chromosomal translocations were only found in hTS/Ink4/Arf−/- subtype, indicative of strand-break damage. We assessed extent of damage by Comet assay and yH2AX phosphorylation in mouse tumor cell lines and found increased DNA fragmentation and high yH2AX signal in hTS/Ink4/Arf−/- cells as opposed to Ink4/Arf−/- control. In summary, these studies demonstrate a novel capacity for TS to promote nucleotide imbalance, increase DNA susceptibility to damage and chromosomal aberrations, suggesting a new model where TS overexpression plays a role in the development of genomic instability and tumorigenesis.
Citation Format: Lidia V. Kulemina, Min Chen, Kyungah Maeng, Akbar Nawab, Maria Zajac-Kaye. Role of thymidylate synthase in genomic instability and tumorigenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 631. doi:10.1158/1538-7445.AM2013-631
Abstract 633: BAL1 and its partner E3 Ligase, BBAP, Link PARP activation, Ubiquitylation and double-strand DNA repair independent of ATM, MDC1 and RNF8.
Authors: Yan Qingsheng , Xu Rong , Zhu Liya , Cheng Xin , Wang Zhe , Manis John , Shipp Margaraet 
Published: August 2014

Abstract
The BAL1 macro domain-containing protein and its partner E3 ligase, BBAP, are overexpressed in chemotherapy-resistant lymphomas. BBAP selectively ubiquitylates histone H4 and indirectly promotes early 53BP1 recruitment to DNA damage sites. However, neither BBAP nor BAL1 have been directly associated with a DNA damage response (DDR) and the function of BAL1 remains undefined.
DDR proteins assemble in a coordinated, sequential manner at sites of DNA breaks. The initial recruitment phase is rapid, transient and dependent upon PARylation at DNA damage sites. A second phase, which also begins within seconds but lasts for hours, includes the sequential phosphorylation of ATM, MDC1 and the RNF8-dependent ubiquitylation of multiple double-strand break (DSB) repair factors.
We have now defined a direct link between the rapid and short-lived PARP1 activation and PARylation at DNA damage sites, PAR-dependent recruitment of the BAL1 macro domain-containing protein and its partner BBAP E3 ligase, local BBAP-mediated ubiquitylation and subsequent recruitment of the checkpoint mediators, 53BP1 and BRCA1. The PARP1-dependent localization of BAL1/BBAP functionally limits both early and delayed DNA damage and enhances cellular viability independent of ATM, MDC1 and RNF8. These data establish BAL1 and BBAP as bona fide DDR pathway members and directly associate PARP1 activation, BRCA1 recruitment and DSB repair.
Citation Format: Qingsheng Yan, Rong Xu, Liya Zhu, Xin Cheng, Zhe Wang, John Manis, Margaraet Shipp. BAL1 and its partner E3 Ligase, BBAP, Link PARP activation, Ubiquitylation and double-strand DNA repair independent of ATM, MDC1 and RNF8. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 633. doi:10.1158/1538-7445.AM2013-633
Abstract 636: Role of PALB2 and the BRCA complex in G2/M checkpoint control.
Authors: Simhadri Srilatha R. , Cai Hong , Xia Bing 
Published: August 2014

Abstract
Breast cancer tumor suppressors BRCA1, BRCA2 and PALB2 form a complex that promotes faithful DNA repair by homologous recombination (HR). PALB2, the partner and localizer of BRCA2, mediates the physical and functional communication between BRCA1 and BRCA2. PALB2 binds to BRCA1 through its N-terminal coiled-coiled domain, and to the extreme N-terminal region of BRCA2 via its C-terminal WD40 repeats.
Recently, it was shown that BRCA2 and PALB2, like BRCA1, play key roles in the maintenance of the G2/M checkpoint. Here, we show that PALB2 also plays a role in the activation of the G2/M checkpoint. Cells in the mitotic phase were scored on the basis of Ser 10 phosphorylation in the histone, H3 before and one hour after ionizing radiation. PALB2-deficient Fanconi anemia (FA-N) cells exhibited a significant defect in G2/M checkpoint activation, which was corrected upon re-expression of wild-type PALB2. This function of the protein appears to be dependent on its binding to both BRCA1 and BRCA2, as PALB2 mutants abrogated for their BRCA1- or BRCA2-binding abilities were unable to correct the checkpoint activation failure.
Since TP53 is often mutated in BRCA- and PALB2-associated breast cancers and since FA-N cells express the SV40 T antigen which inactivates TP53, we studied whether TP53 is involved in PALB2-dependent checkpoint activation. However, depletion of PALB2 in isogenic TP53-wildtype and TP53-null HCT-116 colon cancer cells showed similar defects in checkpoint activation. Furthermore, mouse embryonic fibroblasts (MEFs) derived from a Palb2 knock-in strain, in which the endogenous PALB2-BRCA1 interaction is abrogated, also exhibited a defect in G2/M checkpoint activation. In conclusion, our results demonstrate that PALB2 plays an important role not only in the maintenance but also the activation of the G2/M checkpoint, and suggest that BRCA1, PALB2 and BRCA2 function together as a complex in the maintenance of genome integrity.
Citation Format: Srilatha R. Simhadri, Hong Cai, Bing Xia. Role of PALB2 and the BRCA complex in G2/M checkpoint control. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 636. doi:10.1158/1538-7445.AM2013-636
Abstract 649: A three-gene DNA methylation signature for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer.
Authors: Haldrup Christa , Mundbjerg Kamilla , Vestergaard Else Marie , Lamy Philippe , Wild Peter , Schulz Wolfgang A. , Arsov Christian , Borre Michael Borre , Høyer Søren , Ørntoft Torben F. , Sørensen Karina D. 
Published: August 2014

Abstract
Purpose: Diagnostic and prognostic tools for prostate cancer (PC) are suboptimal causing overtreatment of indolent PC and risk of delayed treatment of aggressive PC. Here, we identify six novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential.
Methods: Microarray-based screening and bisulfite sequencing of 20 non-malignant and 29 PC tissue specimens were used to identify new candidate DNA hypermethylation markers for PC. Diagnostic and prognostic potential was evaluated in 35 formalin-fixed paraffin-embedded (FFPE) nonmalignant prostate tissue samples, 293 FFPE malignant radical prostatectomy (RP) samples (cohort 1), and 148 fresh-frozen malignant RP samples (cohort 2) collected in Denmark, Switzerland, Germany, and Finland. Sensitivity and specificity for PC was evaluated by receiver operating characteristic analyses. Correlations between DNA methylation levels and biochemical recurrence were assessed by log rank tests as well as uni- and multivariate cox regression analyses. A methylation-based prognostic model was developed in cohort 1 and validated in cohort 2. Results: Hypermethylation of AOX1, C1orf114, GAS6, HAPLN3, KLF8, and MOB3B was highly cancer-specific (AUCs 0.89-0.98). Furthermore, a three-gene methylation signature (AOX1/C1orf114/HAPLN3) was developed in cohort 1 and validated in cohort 2. High AOX1/C1orf114/HAPLN3 methylation was significantly associated with biochemical recurrence in multivariate analysis (P&lt;0.05) with hazard ratios of 1.79 (1.20-2.68) and 1.98 (1.02-3.83), respectively, independently of routine clinicopathological variables in both cohorts. Conclusion: We identified six novel candidate DNA methylation markers for PC and developed a three-gene methylation signature, which was an independent predictor of time to biochemical recurrence after RP in two PC patient cohorts.
Citation Format: Christa Haldrup, Kamilla Mundbjerg, Else Marie Vestergaard, Philippe Lamy, Peter Wild, Wolfgang A. Schulz, Christian Arsov, Michael Borre Borre, Søren Høyer, Torben F. Ørntoft, Karina D. Sørensen. A three-gene DNA methylation signature for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 649. doi:10.1158/1538-7445.AM2013-649
Abstract 652: GPX3 promoter hypermethylation predicts platinum sensitivity in colorectal cancer cells.
Authors: Pelosof Lorraine , Yerram Sashidhar , Azad Nilofer , Herman James 
Published: August 2014

Abstract
An estimated 52,000 people will die from colorectal cancer (CRC) in 2012 in the U.S. Unfortunately, these tumors do not respond uniformly to the available chemotherapeutic agents and molecular heterogeneity in these tumors is an important factor in determining their sensitivity to the different agents. Epigenetic regulation of gene expression is a critical determinant of normal and tumor cellular phenotypes. By combining tumors’ epigenetic alterations with existing knowledge of drugs’ mechanisms, specific DNA methylation alterations can serve as predictive biomarkers for the efficacy of particular chemotherapeutic agents which can then direct patients’ treatments for improved outcomes. The glutathione peroxidase family of enzymes is a critical cellular antioxidant system and increased glutathione peroxidase activity has been linked to platinum resistance in tumors such as prostate and ovarian cancer. Using methylation-specific PCR (MSP), we demonstrate that the glutathione peroxidase 3 (GPX3) promoter is hypermethylated in six of nine colorectal cancer cell lines and those lines with methylated GPX3 have significantly decreased GPX3 mRNA expression by real-time polymerase chain reaction (RT-PCR). Importantly, the cisplatin IC50 for the CRC cell lines with methylated GPX3 and thus lower GPX3 expression ranges between 2.5 and 6 micromolar compared to 15-50 micromolar in the cell lines with unmethylated GPX3. Initial studies demonstrate similar findings with oxaliplatin. We also examined primary colorectal cancer xenografts and find that 11 of 42 (26%) have GPX3 promoter hypermethylation, with reduction in GPX3 expression also demonstrated for methylated tumors. Analysis is underway to assess the impact that methylated GPX3 has on these primary tumor samples’ sensitivity to platinum agents. To further define the importance of GPX3 promoter hypermethylation in platinum sensitivity, experiments using azacitidine to demethylate GPX3 in cells with methylated GPX3 will be used to determine if increased platinum sensitivity can be restored. Our studies suggest that epigenetically silenced GPX3 may serve as a valuable predictive biomarker for platinum agent sensitivity.
Citation Format: Lorraine Pelosof, Sashidhar Yerram, Nilofer Azad, James Herman. GPX3 promoter hypermethylation predicts platinum sensitivity in colorectal cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 652. doi:10.1158/1538-7445.AM2013-652
Abstract 654: Do epimutations affect MLH1 alone or a broad spectrum of genes to increase the severity of the associated cancer phenotype.
Authors: Silva Amanda G. , Duesing Konsta , Ward Robyn , Hitchins Megan 
Published: August 2014

Abstract
Germline mutations of the DNA mismatch repair genes, MLH1 and MSH2, are the major cause of Lynch syndrome, characterised by a predisposition to the development of microsatellite unstable colorectal, endometrial and additional cancers below 50 years of age. However, approximately one third of cases with a clinical suspicion have no identifiable mismatch repair sequence mutation. In recent years, constitutive epigenetic dysregulation of MLH1, so-called “constitutional epimutation," has been identified in a small proportion of these mutation-negative cases. The mechanism of onset and stochastic intergenerational transmission of this defect remains unknown, but may involve the co-inheritance of a trans-acting factor that causes aberrant epigenetic programming of MLH1, and possibly additional loci, in the germline or early embryo. The aim of this work is to determine if constitutional MLH1 epimutations occur in a focal manner, or in the context of a more generalised epigenomic mechanism that may exacerbate the cancer phenotype. Using the Illumina HumanMethylation450k BeadChip we studied 6 confirmed carriers of an MLH1 epimutation and 6 healthy controls matched for age and gender to determine if MLH1 epimutations are accompanied by additional epigenetic defects. Preliminary results have shown that other genes are indeed concomitantly and aberrantly methylated or hypomethylated alongside MLH1 and the methylation status of these genes is currently under validation. The finding of concomitant methylation or hypomethylation of additional loci would provide strong evidence for a defective trans-acting factor as the underlying cause of epimutations and may also contribute to the phenotypic expression of this aetiological mechanism.
Citation Format: Amanda G. Silva, Konsta Duesing, Robyn Ward, Megan Hitchins. Do epimutations affect MLH1 alone or a broad spectrum of genes to increase the severity of the associated cancer phenotype. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 654. doi:10.1158/1538-7445.AM2013-654
Abstract 676: Substrate specificity and inhibitors of histone lysine HMTase NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1.
Authors: Di Luccio Eric , Morishita Masayo 
Published: August 2014

Abstract
The nuclear receptor binding SET domain proteins (NSDs) is a family of three histone-lysine N-methyltransferases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1. The NSDs are oncogenes. The amplification of NSD1 has been reported in multiple myeloma, lung cancer, neuroblastomas and glioblastomas. The amplification of either NSD1 or NSD2 triggers the cellular transformation to cancer formation. NSD2 is associated with tumor aggressiveness or prognosis in most types of cancers including prostate cancer and multiple myeloma and is overexpressed in at least 15 different cancers. Increased NSD2 activity was reported in tumor proliferation in glioblastoma multiforms and myeloma, resulting in aberrantly high global levels of H3K36me2. NSD3 is involved in lung cancer and found amplified in breast cancer cell lines and primary breast carcinomas. The abnormal NSD1-NUP98 and NSD3-NUP98 fusions increase H3K36 methylation, leading to acute myeloid leukemia. Although the NSD proteins are instrumental in the development of numerous cancers, their mechanisms of action in this context remain unclear. However, it appears that consequently increased H3K36 methylation by deregulated NSDs concomitant with decreased H3K27 methylation is perhaps one of the underlying mechanisms that alter gene expression profiles. In this study, we defined the molecular determinants of the recognition of histone marks by the NSDs to provide medicinal chemistry insights into the design of selective and specific NSDs inhibitors. Our data highlights the catalytic versatility of NSD1, NSD2, and NSD3 in regulating the epigenome. Our results propose the first molecular models of the binding of 6-mer peptides H3K4 a.a.1-7; H3K9 a.a.5-11; H3K27 a.a.23-29; H3K36 a.a.32-38; H3K79 a.a.75-81; H4K20 a.a.16-22 with the catalytic domain of the NSDs. Exploiting this data, we derived a virtual ligand screening strategy to identify inhibitors targeting NSD1, NSD2 and NSD3. In vitro, using recombinant NSDs-SET purified enzyme, we performed H3K36me1 inhibitory assays with the top candidates. Here for the first time, we report the discovery of a small subset of NSD inhibitors (namely LEM-xx) that do not violate the empirical Lipinski's rule of five, have a wcLogP &lt; 3 and a total polar surface area &lt;90 A**2.
Citation Format: Eric Di Luccio, Masayo Morishita. Substrate specificity and inhibitors of histone lysine HMTase NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 676. doi:10.1158/1538-7445.AM2013-676
Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.