bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB-B10: Transcriptional landscape in the human Knock-in isogenic line for p53 polymorphism codon 72
Authors: Lee Seo-Young , Chung Sun-Ku , Park Jung-Hyun , Oh Soo A , Won Kyoung-Jae 
Published: August 2018

Abstract
Background: Codon 72, the most representative polymorphism of p53, commonly encodes the two kinds of amino acids, proline (P) or arginine (R), which is interestingly located within proline-rich domain to regulate p53-dependent transactivation. Although the previous reports have compared the polymorphism-mediated p53 transactivation, the results have some limitations that have been mined artificially on abnormal cells or plasmid-based expression. Thus, overcoming the concerns, we here established the isogenic lines to identify codon 72 polymorphic-dependent p53 transactivation.
Experimental design: We established isogenic line based on human induced pluripotent stem cells (hiPSC) with either the proline or arginine at codon 72 of p53 (P and R-type p53), using BAC-mediated homologous recombination system. In addition, to set the baseline mRNA expression level of p53 target genes, p53-null hiPSC has been generated with simultaneous reprogramming-CRISPR system. We applied RNA-sequencing technology to profile transcription patterns between three cell lines, p53-P, p53-R, and p53-null hiPSCs, under genotoxic stress, Doxorubicin treatment.
Results: Molecular signature analysis shows the significant difference of transcriptional patterns in PI3K-Akt signaling pathway, focal adhesion, cell-cell adhesion and Wnt signaling pathway by KEGG pathway mapping between P- and R-type. We identified both PI3K-Akt signaling related genes and focal adhesion related genes increased in P-type p53 than R-type p53, but expression patterns are similar with p53-null cell in focal adhesion. On the other hand, cell-cell adhesion related gene patterns down regulated comparing with p53-null cell. Lastly, R-type p53 gene expression shows the most increased pattern than other two cell types.
Conclusions: The isogenic line-based p53 polymorphism study reveals the differences intrinsically in the p53 polymorphism dependent-cell survival signaling, PI3K-Akt signaling pathway.
Acknowledgements: This work was supported by Korea Institute of Oriental Medicine Grant K17131 and National Research Foundation of Korea Grants 2013M3A9B4076487.
Citation Format: Seo-Young Lee, Sun-Ku Chung, Jung-Hyun Park, Soo A Oh, Kyoung-Jae Won. Transcriptional landscape in the human Knock-in isogenic line for p53 polymorphism codon 72 [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-B10.
Abstract LB-B23: Prodrug activation by designer enzyme targeted to CD123-expressing tumors
Authors: Mannervik Bengt , Sjödin Birgitta I. 
Published: August 2018

Abstract
We propose the combination of tumor-targeting antibodies with a drug-activating enzyme and a prodrug, which could be expected to give synergy and enhanced therapeutic efficacy in the treatment of leukemia and other malignancies. We have engineered human glutathione transferase (GST) enzymes for increased catalytic activity with a prodrug with the aim of delivering the enzyme selectively to a tumor. Antibodies, or similar specific binding proteins, will bind to selected epitopes of the cancer cells where the accompanying enzyme will exert its drug-activating function. The approach is generic and could be implemented with alternative binding proteins and GSTs with different functionalities. Myeloid neoplasms represent 20% of leukemias in children and the majority of the pediatric patients have acute myeloid leukemia (AML). There is a need for improved therapies to eradicate tumor cells with particular focus on leukemic stem cells (LSC), which are responsible for recurrent disease. We are designing, by protein engineering and directed in-vitro evolution, glutathione transferase (GST) enzymes that trigger cytotoxicity via chemically activating chemotherapeutic prodrugs. By fusing the enzyme with an antibody with affinity for epitopes selectively expressed by tumor cells, the release of the toxic agent will be targeted to the neoplastic tissue and minimize collateral damage to normal cells. For proof-of-concept a glutathione transferase enzyme activating the prodrug azathioprine is targeted via an anti-CD123 antibody to acute myeloid leukemia (AML) cells ex vivo. The target receptor CD123 is also expressed on LSC, but not on normal hematopoietic stem cells. Following binding to tumor cells GST will catalyze the conversion of the subsequently administered azathioprine to the anti-metabolite 6-mercaptopurine, which will interfere with nucleotide metabolism and DNA synthesis. Alternative prodrugs activated by other GSTs are also available, indicating the versatility of our approach. An engineered GST with 175-fold enhanced activity with azathioprine has been fused with an scFv-anti-CD123 antibody and the designer enzyme produced by heterologous expression. The recombinant fusion protein is catalytically fully competent and maintains the binding activity of the parental scFv antibody.
Citation Format: Bengt Mannervik, Birgitta I. Sjödin. Prodrug activation by designer enzyme targeted to CD123-expressing tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-B23.
Abstract LB-B31: FGFR inhibition in endometrial cancer induces caspase-independent cell death that can be augmented with ABT-737
Authors: Packer Leisl , Byron Sara , Stehbens Samantha , Bonazzi Vanessa , Loch David , Wortmann Andreas , Gartside Mike , Waterhouse Nigel , Gunter Jennifer , Pollock Pamela M. 
Published: August 2018

Abstract
Endometrial cancer (EC) is the most commonly diagnosed malignancy of the female reproductive tract. Unfortunately, 15-20% of women demonstrate persistent or recurrent tumors that are refractory to current chemotherapies with an associated poor prognosis. Our laboratory identified activating mutations in Fibroblast Growth Factor Receptor 2 (FGFR2) in 12% (stage I/II) to 17% (stage III/IV) endometrioid endometrial tumors and have since shown in a large (n=970) multi-institutional cohort they are associated with shorter progression free and cancer specific survival. Although FGFR inhibitors are in clinical trials in several cancer types, no detailed study of the mechanism of cell death has been published. We now show that treatment with BGJ398, AZD4547 and PD173074 leads to the induction of mitochondrial depolarization and changes in metabolic flux in two endometrial cancer cell lines (JHUEM2 and AN3CA) carrying activating mutations (C383R and N550K respectively). Despite this mitochondrial dysfunction, we have convincingly shown that the cell death following FGFR inhibition was caspase-independent, as evidenced by the lack of caspase-3, -7, and -9 activation, absence of PARP cleavage, and the inability of the broad-spectrum caspase inhibitor, Z-VAD-FMK, to prevent cell death. Knockdown of EndoG and AIF, common mediators of caspase-independent death, had no effect. Detailed quantification of LC3 positive puncta shows an increase in autophagy in JHUEM2 and AN3CA cells treated with all FGFR inhibitors. Knockdown of ATG3, ATG7 and ATG12 resulted in a slight increase in Annexin positive cell death indicating that the autophagy was cytoprotective in this context. We have now confirmed this novel caspase-independent cell death is mitochondrial dependent as it can be blocked by overexpression of Bcl-2 and/or Bcl-XL. Importantly we have shown that the combination of FGFR inhibitors with the BH3 mimetic ABT737 can markedly augment this caspase-independent cell death which may have implications for the design of more effective clinical trials.
Citation Format: Leisl Packer, Sara Byron, Samantha Stehbens, Vanessa Bonazzi, David Loch, Andreas Wortmann, Mike Gartside, Nigel Waterhouse, Jennifer Gunter, Pamela M. Pollock. FGFR inhibition in endometrial cancer induces caspase-independent cell death that can be augmented with ABT-737 [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-B31.
Abstract 1037: Comprehensive molecular profiles of gastric cancer patient derived xenograft (PDX) models and its implication in precision cancer medicine
Authors: Lee Jae Eun , Choi Yoon Young , Lim Ju Yeon , Shin Su-Jin , Lee Gunho , Kim Eun Young , Son Taeil , Kim Hyoung-Il , Hyung Woo Jin , Noh Sung Hoon , Kim Hyunki , Jung Minkyu , Kim Sangwoo , Paik Soonmyung , Cheong Jae-Ho 
Published: August 2018

Abstract
Background: Recent cancer research is focused on precision medicine with the advent of next generation sequencing (NGS) technology and patient tumor derived model systems. Here, we present molecular characteristics of gastric cancer patient derived xenograft (PDX) models and explore the potential of molecularly defined PDX model based drug development.
Materials and Methods: We generated PDX models from patient tumors with advanced gastric cancer. The genomic alterations of tumors were profiled by whole exome sequencing (WES), RNA sequencing (RNAseq), targeted sequencing, in-situ hybridization (ISH) and immunohistochemistry (IHC). Further, we developed overcoming strategy of chemotherapy resistance mechanism by combination of signaling pathway inhibitor and standard chemotherapy regimen in “N-of-1” PDX trial.
Results: Thirty-five PDX models were successfully established and categorized into four subgroups of The Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG) classifications: EBV (2.9%), MSI (20.6%), GS (23.5%) and CIN (52.9%) subtypes by TCGA while MSI type (11.4%), MSS/EMT type (17.1%), MSS/TP53+ (31.4%) and MSS/TP53- type (40.0%) by ACRG. In the protein levels by IHC, there were 21 cases (60.0%) of any RTK proteins overexpression; nine of HER2 (25.7%), 14 of EGFR (40.0%), and 16 of c-MET (45.7%). Five tumors (14.3%) were related to PTEN loss and 22 tumors (62.9%) showed p53 overexpression or null. Targeted sequencing identified that ERBB2 (25.7%), KRAS (11.4%), and CCND1 (11.4%) were found frequently amplified gene while PIK3CA (11.4%) and CTNNB1 (8.6%) were found most mutated genes. N-of-1 PDX trial demonstrated that the response to FOLFOX in PDX tumor was concordant with that of corresponding patient. In FOLFOX resistant tumors, multiple signaling pathways were up-regulated and inhibition of these signaling pathways was regressed tumor growth.
Conclusions: The utilization of molecularly catalogued gastric cancer PDX models will guide precision medicine for cancer therapy and be a useful tool for drug development and repurposing.
Citation Format: Jae Eun Lee, Yoon Young Choi, Ju Yeon Lim, Su-Jin Shin, Gunho Lee, Eun Young Kim, Taeil Son, Hyoung-Il Kim, Woo Jin Hyung, Sung Hoon Noh, Hyunki Kim, Minkyu Jung, Sangwoo Kim, Soonmyung Paik, Jae-Ho Cheong. Comprehensive molecular profiles of gastric cancer patient derived xenograft (PDX) models and its implication in precision cancer medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1037.
Abstract 1107: Cell-surface vimentin-positive macrophages like CTCs as novel biomarkers of metastatic gastrointestinal stromal tumors
Authors: Li Heming , Meng Qing H. , Noh Hyangsoon , Somaiah Neeta , Torres Keila E. , Xia Xueqing , Batth Izhar Singh , Joseph Cissimol P. , Mulder Zachary A. , Wang Ruoyu , Li Shulin 
Published: August 2018

Abstract
Background: Gastrointestinal stromal tumors (GISTs) are the most common gastrointestinal tract sarcomas and are heavily infiltrated with tumor-associated macrophages (TAMs). Biomarkers specifically capturing circulating tumor cells (CTCs) that can be used to noninvasively determine the disease status in GIST patients have been lacking.
Patients and Methods: To fill this gap, we captured both regular CTCs and TAMs from GIST patients' blood and tumor samples using our proprietary cell-surface vimentin (CSV) antibody 84-1 and the TAM markers CD14 and CD68 based on our previous established CTC detection method from 104 localized or metastatic sarcoma patients and 10 healthy donors. Also, freshly procured metastatic GIST tissues were obtained from four patients.
Results: We defined a rare population of CSV+ macrophage-like CTCs (ML-CTCs) in metastatic GIST patients' blood samples with expression of CD14 and CD68 but not CD45. Also, we demonstrated CSV+ ML-CTCs to be tumor microenvironment-derived. Metastatic GIST patients had markedly higher numbers of CSV+ ML-CTCs than localized GIST patients and healthy blood donors. However, regular CTC counts could not predict metastasis of GISTs but could for other types of sarcoma. Notably, CSV+ ML-CTCs were represented as M1-like macrophages in their phenotype and function.
Conclusions: CSV+ ML-CTCs are novel biomarkers for prediction of metastatic risk and therapeutic response in GIST patients. Routinely monitoring these cells will be an important approach to liquid biopsy analysis of GISTs.
Citation Format: Heming Li, Qing H. Meng, Hyangsoon Noh, Neeta Somaiah, Keila E. Torres, Xueqing Xia, Izhar Singh Batth, Cissimol P. Joseph, Zachary A. Mulder, Ruoyu Wang, Shulin Li. Cell-surface vimentin-positive macrophages like CTCs as novel biomarkers of metastatic gastrointestinal stromal tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1107.
Abstract 1218: An eQTL and mQTL study of 147 genetic variants associated with prostate cancer susceptibility
Authors: Wang Xiaoyu , Cheng Anqi ,   the PRACTICAL Consortium, Stanford Janet L. , Dai James Y. 
Published: August 2018

Abstract
Genome-wide association studies by the PRACTICAL consortium have identified and validated 147 single nucleotide polymorphisms (SNPs) associated with prostate cancer (PCa) risk (Schumacher et al., Nat Genet 2017). However, most of these genetic variants are in noncoding regions, which poses a challenge for understanding the molecular mechanisms underlying these risk loci. Herein we study both expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) among these PCa risk loci to identify molecular alterations associated with these genetic variants. Data were available for a Fred Hutchinson (FH)-based cohort of patients diagnosed with localized stage PCa, including SNP genotypes (Infinium iCOGS and OncoArray-500K BeadChips) from the PRACTICAL consortium and genome-wide DNA methylation (Infinium Human Methylation450 BeadChip) and gene expression (HumanHT-12 v4 BeadChip) profiling of primary tumor tissues obtained at radical prostatectomy. Missing genotypes were imputed using the October 2014 (Phase 3) release of the 1KGP data as the reference panel. These data were used to identify eQTL (N=355) and mQTL (N=377) in cis-acting associations where the transcripts or CpG sites are located within 2Mb (±1Mb) of the genetic variants. The Matrix eQTL software was used to conduct eQTL and mQTL analyses. In total, 4,300 SNP-transcript pairs and 104,600 SNP-CpG pairs were tested for eQTL and mQTL, respectively, among which we identified 64 eQTL-transcript pairs (37 PCa risk loci and transcripts in 54 genes) and 1,405 mQTL-CpG pairs (116 PCa risk loci and CpGs in 321 genes), after correction for multiple testing (FDR&lt;0.05). The remaining 29 (20%) PCa risk loci were neither eQTLs nor mQTLs. Interestingly, 35 (95%) eQTLs were also mQTLs, while the majority of mQTLs were not eQTLs (Fisher's exact test of independence, p=0.005), suggesting that DNA methylation may have alternative biologic regulatory functions other than directly affecting gene expression. Several of these genes associated with eQTLs such as INCENP, NUDT11, RGS17, ASCL2, C10orf32, MSMB, BHLHA15, and IRX4 were previously found in PCa. Furthermore, we discovered a number of novel genes such as HLA-DRB3 and HLA-DRB4 associated with eQTLs in our data. Further validation using the TCGA-PRAD data is under way. In summary, we identified eQTLs and mQTLs among newly established genetic risk loci for PCa. These results provide new insight into both the genetic and epigenetic mechanisms through which these SNPs may alter susceptibility to PCa.
Citation Format: Xiaoyu Wang, Anqi Cheng, the PRACTICAL Consortium, Janet L. Stanford, James Y. Dai. An eQTL and mQTL study of 147 genetic variants associated with prostate cancer susceptibility [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1218.
Abstract 122: Hypoxia-enhanced proliferation and effector function of NK cells
Authors: Moon Yunwon , Lim Seon Ah , Lee Kyung-Mi , Park Hyunsung 
Published: August 2018

Abstract
Hypoxia promotes tumor cell survival while providing immune cell shaping and resistance. Although NK cells function within hypoxic lymphatics and inflamed tissues, they were shown to mount impaired anti-tumor effector functions in ex-vivo hypoxic environment. This raises a question that additional cues exist in vivo to allow full NK cell activation. By varying the percentage and time of pO2 exposure ex-vivo, we were able to fine-tune a condition that reverses hypoxia-induced NK cell suppression to become highly proliferative and enhanced cytolytic phenotypes. We found that exposing NK cells to moderate hypoxia in the presence of IL-2 and feeder cells allowed HIF-1α stabilization and its target gene expression, metabolic changes toward glycolysis, specific upregulation of NKp44 receptor, and increased STAT3 phosphorylation with concomitant reduction of apoptosis and p16 senescence pathways. Therefore, the hypoxic exposure allows HIF-1α-mediated adaptation of mature NK cells toward highly proliferative and cytolytic NK phenotypes, which may occur in vivo at the time of tumor growth and inflammation. [This work was supported by the National Research Foundation of Korea (NRF), grants NRF-2013M3A9D3046248]
Citation Format: Yunwon Moon, Seon Ah Lim, Kyung-Mi Lee, Hyunsung Park. Hypoxia-enhanced proliferation and effector function of NK cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 122.
Abstract 1289: Crosstalk between methylation and alternative splicing in cancer
Authors: Kim Dongwook , Han Seonggyun , Lee Younghee 
Published: August 2018

Abstract
Background: DNA methylation in promoter regions leads to transcriptional silencing, such as of tumor suppressor genes in cancer. However, the functions of DNA methylation in the gene body (intragenic, i.e., exons and introns) have not yet been completely elucidated. Recently, hyper-methylation has been implicated in enhancing exon recognition by recruiting methyl-CpG-binding protein (MECP2) to hyper-methylated sites. In this study, we examined intragenic methylation in splicing regulatory elements (SREs: exonic splicing enhancer (ESE), exon splicing silencer (ESS), intronic splicing enhancer (ISE)) as a mechanism to understand how epigenetic factors contribute to alternative splicing events in cancer.
Hypothesis: Methylation patterns of SREs are involved in directing alternative splicing events in cancer.
Methods: We developed a splicing decision model to identify actionable methylation loci potentially affecting splicing events (i.e., exon skipping) among CpG sites in putative intragenic SRE regions. We used DNA methylation and RNA-Seq data for breast and lung cancer samples and normal cases from The Cancer Genome Atlas (TCGA). We additionally used hyper- and hypo-methylation data published in Selamat et al. (2013) as an independent lung cancer dataset. To identify regions hyper- and hypo-methylated in cancer, we performed an unpaired t-test for normally distributed data and a Mann-Whitney-Wilcox test for non-normally distributed data for differential methylation status (beta value) between cancer and normal cases. Multiple testing was accounted for by controlling the false discovery rate (p&lt; 0.05 with FDR&lt; 0.1).
Results: We investigated whether specific patterns of methylation were enriched in SRE regions affecting exon skipping. We found that for breast cancer samples, differential methylation status was enriched in SRE regions but not in non-SRE regions. Particularly, hypo-methylation in cancer showed a greater enrichment in ESE regions with putative exon skipping events. Similar results were observed in the both the TCGA lung cancer cases and an independent lung cancer dataset. We calculated GC contents and the methylation frequencies at each position of the hexameric sequence of SREs and further investigated whether certain SREs are prevalent to be with methylation or not. These data suggest that hypo-methylation in SRE regions may cause failure to recruit MECP2, therefore leading to exon skipping.
Conclusion: Our study suggests that intragenic methylation status is important for splicing regulation and may improve our understanding of how intragenic epigenetic markers play a role in gene regulation by affecting alternative splicing.
Citation Format: Dongwook Kim, Seonggyun Han, Younghee Lee. Crosstalk between methylation and alternative splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1289.