bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3493: Tumor treating fields (TTFields) significantly alters how tumor cells repair double stranded breaks using homeologous Alu sequences
Authors: Morales Maria E. , Kaul Tiffany K. , Deininger Prescott L. 
Published: August 2019

Abstract
Tumor Treating fields (TTfields) are an FDA-approved therapeutic modality that utilizes low intensity alternating electric fields. Although the therapy’s primary mechanism seems to cause aberrant mitosis in dividing cells and subsequently cellular death, TTfields have also been reported to alter DNA repair pathways. Recent reports showed that chromosomal double strand breaks (DSBs) repair is delayed after TTfields treatment of glioma cells. DSBs are often repaired by error-prone pathways that can be influenced by proximity of repetitive sequences, such as Alu elements. Alu elements are known to contribute to genetic instability though homeologous recombination due to their sequence similarity and high density in the genome. We find that different tumor cells resolve the Alu heteroduplexes formed during DNA repair in different ways. To understand the molecular mechanisms underlying the biological effects of TTfields exposure, we examined mechanistic aspects of DNA repair using our previously published Alu/Alu recombination system in HEK293 and HeLa cells. Of note, our assay probes the recombination properties that occur in the cells that survive TTfields treatment, thus providing potential insights into therapeutic resistance. Our Alu/Alu recombination system is able to efficiently measure both the rate of Alu/Alu recombination (Single Strand Annealing-SSA), as well as Alt-Non Homologous End Joining (Alt-NHEJ) deletions that cause a deletion in the vicinity of the two Alu elements in the system. Sequence verification confirmed that most of the genetic deletions that occurred post TTfields treatment were the result of Alu/Alu recombination events that predominantly arose from repair by SSA in HEK293 and HeLa. This increase in SSA repair could be the result of SSA-intermediates that escaped heteroduplex rejection. These observations suggest the possibility that treatment of TTfields significantly alters how tumor cells repair DSBs using homeologous Alu sequences.
Citation Format: Maria E. Morales, Tiffany K. Kaul, Prescott L. Deininger. Tumor treating fields (TTFields) significantly alters how tumor cells repair double stranded breaks using homeologous Alu sequences [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3493.
Abstract 3498: Highly specific macrocyclic ATR inhibitors for the targeted treatment of a broad spectrum of cancers showing lack of anemia or neutropenia in pre-clinical animal models
Authors: Pamarthy Sahithi , Li Dansu , Goliadze Ekaterine , Gill Tina , Jia Lanqi , George Erin , Butler Laura R. , Ragland Ryan L. , Afargan Michel , Simpkins Fiona A. , Brown Eric J. , Gilad Oren 
Published: August 2019

Abstract
Ataxia Telangiectasia and Rad3-related (ATR) and its downstream effector Checkpoint Kinase 1 (CHK1) are central to the protection of stalled replication forks.Specific targeting of the ATR is synthetically lethal with multiple cancer-associated changes including oncogenic stress and defects in the DDR pathway and represents an emerging strategy to treat a broad spectrum of cancers. Atrin Pharmaceuticals has rationally designed a novel series of conformationally constrained macrocyclic ATR inhibitors with higher potency and selectivity than other ATR inhibitors currently in clinical development. An in-depth characterization of the ATRN series identified ATRN-119 as our lead compound with an in vitro enzyme IC50 of 20 nM and inhibition of ATR substrate CHK1 Ser345 phosphorylation in cells at an IC50 of 5 nM. ATRN-119 inhibits ATR in cells at much lower concentrations and demonstrates higher selectivity (&gt;2000) for ATR over other closely-related PIK-kinases like ATM, DNA-PK and mTOR. Additionally, ATRN series have favorable ADME properties with increased water solubility and metabolic stability in human serum of up to 4 hours. Oral dosing of ATRN-119 showed significant antitumor effects in human pancreatic and colon cancer xenografts and in orthotopic ovarian Patient Derived Xenograft (PDX) tumors. Notably, hematological analysis of mice treated with daily oral dosing of ATRN-119 indicated no thrombocytopenia, anemia or neutropenia up to 4 weeks of treatment. Exploratory multiple high dosing toxicity studies in rats and dogs indicate significant exposure and good tolerability with lack of anemia or neutropenia. In a series of in-vitro cell viability assays, three dimensional organoid cultures and in-vivo combinationstudies, ATRN-119 showed significant synergism with various PARP inhibitors as well as restoration of PARPi sensitivity in PARPi resistant tumors. Our data suggests a new generation of highly potent and selective ATR inhibitors with favorable safety profile and a broad clinical therapeutic potential either as monotherapy, in combination with PARP inhibitors or as a synthetic lethal approach with key DDR mutations.
Citation Format: Sahithi Pamarthy, Dansu Li, Ekaterine Goliadze, Tina Gill, Lanqi Jia, Erin George, Laura R. Butler, Ryan L. Ragland, Michel Afargan, Fiona A. Simpkins, Eric J. Brown, Oren Gilad. Highly specific macrocyclic ATR inhibitors for the targeted treatment of a broad spectrum of cancers showing lack of anemia or neutropenia in pre-clinical animal models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3498.
Abstract 352: The effect of anti-TNF-alpha Ab in AOM/DSS-induced colitic cancer mouse model
Authors: Ohnuma Shinobu , Yang Wang Dang , Suzuki Hideyuki , Kanehara Keigo , Karasawa Hideaki , Kohyama Atsushi , Watanabe Kazuhiro , Miura Koh , Kamei Takashi , Naitoh Takeshi , Unno Michiaki 
Published: August 2019

Abstract
Aim: To reveal whether anti TNF-α antibody (Ab) induces colon carcinogenesis or not in colitic cancer models.
Methods: The effects of TNF-α and anti TNF-α Ab were analyzed with cell-proliferation, migration, and invasion assays in human colon cancer cell lines, in vitro. Then, the effects of anti TNF-α Ab, infliximab (10 mg/kg, i.p.) were investigated with drug-induced colitis-associated colon cancer model by azoxymethane (AOM: 10 mg/kg, i.p.)/dextran sodium sulfate (DSS: 2.5%, oral) in vivo.
Results: 50 ng/ml of TNF-α inhibited cell proliferation, migration, and invasion of HCT8 and COLO205, however, anti TNF-α Ab offset the TNF-α mediated-inhibition in vitro. Infliximab significantly attenuated the development of colon cancers in AOM/DSS treated mice. The microarray analyses revealed that mast cell related genes (mast cell protease1, mast cell protease 2, chymase 1, etc) were down-regulated in cancer tissues of the infliximab-treated AOM/DSS mice. The results of microarray were validated by real-time RT-PCR. Finally, the number of mast cells were also reduced in those mice.
Conclusions: Mast cell may have a pivotal role in the development of colitic cancer. Anti TNF-α Ab may prevent colitic cancer in the patients with inflammatory bowel diseases.
Citation Format: Shinobu Ohnuma, Wang Dang Yang, Hideyuki Suzuki, Keigo Kanehara, Hideaki Karasawa, Atsushi Kohyama, Kazuhiro Watanabe, Koh Miura, Takashi Kamei, Takeshi Naitoh, Michiaki Unno. The effect of anti-TNF-alpha Ab in AOM/DSS-induced colitic cancer mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 352.
Abstract 3522: Enzymatic DNA repair enables high quality library preparation and accurate sequencing from highly damaged DNA inputs
Authors: Heider Margaret R. , Chen Lixin , Song Chen , Sun Luo , Liu Pingfang , Ettwiller Laurence , Higgins Lauren , Dimalanta Eileen , Davis Theodore , Evans Thomas 
Published: August 2019

Abstract
High-throughput sequencing is key for clinical diagnostic applications such as disease mutation profiling and identifying pathogens with high taxonomic specificity. Preparation of high quality next-generation sequencing (NGS) libraries is critical for obtaining accurate patient data, but clinical scientists are often limited by input DNA quality. In cancer genomics, formalin-fixed, paraffin-embedded (FFPE) tissue from patient biopsy is a common source of DNA, but the extracted DNA is often poor in both yield and quality due to fixation- and storage-induced damage. Additionally, these damage-induced sequencing artifacts raise the background level of mutations, making it difficult to discern true, low frequency, disease-related variants from noise. Even relatively high-quality DNA inputs contain nicks and gaps limiting library yields and read lengths for long read sequencing platforms including Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio).
We developed a second-generation DNA repair enzyme mix (V2) that efficiently repairs the most prevalent damage types found in FFPE DNA and further improves the quality and yield of NGS libraries through efficient nick and gap repair. Illumina library yield and quality were improved when DNA samples were treated with FFPE DNA Repair V2 before library preparation. Target enrichment and whole exome enrichment experiments showed that the V2 repair mix did not alter the overall frequency of variants identified, thus it did not introduce bias, but significantly improved the sequencing accuracy by reducing the number of false variant calls due to damage-induced sequence artifacts. True mutation frequencies were validated using droplet digital PCR (ddPCR). Repaired ONT libraries using DNA inputs of varying quality also showed improved library quality as well as greater read lengths. Therefore, enzymatic DNA repair prior to NGS library preparation is a critical first step for improving the quality and accuracy of short- and long-read sequencing libraries.
Citation Format: Margaret R. Heider, Lixin Chen, Chen Song, Luo Sun, Pingfang Liu, Laurence Ettwiller, Lauren Higgins, Eileen Dimalanta, Theodore Davis, Thomas Evans. Enzymatic DNA repair enables high quality library preparation and accurate sequencing from highly damaged DNA inputs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3522.
Abstract 3527: Combined high-throughput DNA genotyping and protein quantification in single cancer cells
Authors: Demaree Benjamin , Delley Cyrille , Ruff David , Treusch Sebastian , Eastburn Dennis , Jones Keith , Abate Adam 
Published: August 2019

Abstract
Clonal genetic diversity is a hallmark of tumor biology. In many cancers, clonal evolution has been implicated as a driver of tumor initiation, progression, and relapse, and can be a prognostic indicator of disease outcome. Cancer cells are also phenotypically heterogeneous, constituting features which can enable intravasation and metastasis, or which can impart immunoevasive capabilities. Clinically, a combination of single-cell genotype and phenotype data from cancer biopsies could provide valuable insights into oncological disease states, such as metastatic risk or drug response. Here we present a multiomic technology for the simultaneous, high-throughput capture of DNA genotype and protein information from single cells, demonstrated through the analysis of acute myeloid leukemia (AML) derived cell lines. The experimental workflow leverages the high-throughput single-cell microfluidic droplet technology on the Mission Bio Tapestri platform, a system optimized to conduct multiplex targeted genomic DNA amplification from &gt;50 AML-associated loci. In our modified workflow, cells are stained with a pool of monoclonal antibodies conjugated with barcoded oligonucleotides, enabling a sequencing-based readout of single-cell protein signatures. The sequencing data is analyzed with a bioinformatic pipeline that separates antibody signal from targeted genotyping data on a cell-by-cell basis. We find that on a mixed population of myelogenous leukemia cells and B-cells, single-cell genotype information effectively distinguishes between cell lines, while the protein data independently recapitulates the biological signal from conventional flow cytometric methods. In conclusion, this technology opens up a new era for discovery using multiomic analysis of the complex relationships between genotype and phenotype in cancer, paving the way for future studies analyzing primary tissue samples.
Citation Format: Benjamin Demaree, Cyrille Delley, David Ruff, Sebastian Treusch, Dennis Eastburn, Keith Jones, Adam Abate. Combined high-throughput DNA genotyping and protein quantification in single cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3527.
Abstract 3528: Novel enzymatic DNA fragmentation integrated into library construction
Authors: Panchapakesa Vaishnavi , Apone Lynne , Duggan Karen , Langhorst Bradley , Song Chen , Liu Pingfang , Shtatland Timur , Rozzi Christine , Sumner Christine , Stewart Fiona , Dimalanta Eileen , Davis Theodore 
Published: August 2019

Abstract
Next Generation Sequencing (NGS) is rapidly becoming a powerful tool, by providing a high resolution and global view of the cancer genome mainly through whole genome, whole exome and transcriptome sequencing. This knowledge is important to support drug development targeted towards precision medicine. Obtaining high quality sequencing data begins with optimal sample preparation. DNA fragmentation is one of the critical first steps in the construction of high quality libraries for NGS, but current fragmentation methods create a bottleneck on library preparation throughput. We have developed an efficient, one tube fragmentation system that integrates enzyme-based DNA fragmentation with end-repair and dA-tailing in a single step, followed by adaptor ligation in the same tube. This streamlined method is compatible with a wide range of DNA samples and input amounts, resulting in reproducible and reliable fragment sizes.
Genomic DNA (100pg to 500ng) with various GC content, was used in the construction of libraries, that were sequenced on an Illumina platform. For low input samples, PCR amplification was performed prior to sequencing. Libraries constructed using intact genomic DNA and this novel library preparation method produced substantially higher yields than standard methods and mechanically-fragmented DNA. Enzyme-based shearing increases library yield by reducing DNA damage and sample loss. High library yields also enable PCR-free workflows from as little as 50ng starting material. This method can be used for DNA extraction and library preparation from whole blood and dried blood samples.Sequencing quality of libraries generated with inputs ranging from 100pg to 500ng DNA show similar coverage uniformity and fragment size distribution, with minimal GC bias.
We have developed an enzymatic DNA fragmentation kit that enables the construction of high quality libraries from a range of sample types and inputs with minimal sequence bias, high yields and low duplication rates. This method eliminates the need for expensive equipment to fragment DNA as well as numerous cleanup and liquid transfer steps thereby reducing the time, cost and errors associated with library construction. These advances in NGS technologies, supported by powerful bioinformatics tools, promises to revolutionize cancer research, diagnosis and therapy.
Citation Format: Vaishnavi Panchapakesa, Lynne Apone, Karen Duggan, Bradley Langhorst, Chen Song, Pingfang Liu, Timur Shtatland, Christine Rozzi, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis. Novel enzymatic DNA fragmentation integrated into library construction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3528.
Abstract 3535: Identification of multiple hepatocellular carcinoma using genomic approach
Authors: Midorikawa Yutaka , Yamamoto Shogo , Tatsuno Kenji , Ueda Hiroki , Takayama Tadatoshi , Aburatani Hiroyuki 
Published: August 2019

Abstract
Multiple hepatocellular carcinoma (HCC) is categorized into two types; multicentric hepatocarcinogenesis (MC) and intrahepatic metastasis (IM). Although clinical discrimination of the types of multiple HCC has been proposed, it is quite difficult to determine it correctly even after histological diagnosis. In order to diagnose multiple HCC as MC or IM, we compared pairs of multiple HCC samples from 60 patients with multiple HCC and 2 patients with pairs of primary HCC and extrahepatic metastasis such as adrenal grand and lung metastasis with regard to molecular aberrations. Exome or capture sequences showed that more than 70% of somatic mutations were common in the pairs of IM, which were consistent with the result of a pair of primary HCC and extrahepatic metastasis, while no common somatic mutations was detected in genomic MC pairs. Notably, more than 60% of patients who were clinically diagnosed metachronous MC were genetically IM due to the concordance of mutation and shows significantly frequent tumor thrombus, suggesting that genomic IM pairs developed from the common ancestor. Epigenetically, methylation profiles were similar in a pair of IM, while those of MC were different each other. Consequently the accuracy of clinical diagnosis of multiple HCC was only 53.3%. In addition, cell-free DNA was analyzed using exome sequence in five patients with recurrent HCC, and found that somatic mutations of cell free DNA were similar to the primary HCC only in genomic IM but not in genomic MC cases. Intriguingly, overall survivals of patients with clinical IM was significantly shorter than those with clinical MC, while overall survivals of patients with genomic IM and genomic MC were almost similar. Taken together, comparison of mutations in a pair of HCCs makes it possible to classify multiple HCC into MC and IM, which is difficult to be correctly determined in clinical practice. In addition our data showed that it is not clinically important to determine the types of multiple HCC. Furthermore liquid biopsy for mutation analysis is available to make treatment plans for multiple HCC patients.
Citation Format: Yutaka Midorikawa, Shogo Yamamoto, Kenji Tatsuno, Hiroki Ueda, Tadatoshi Takayama, Hiroyuki Aburatani. Identification of multiple hepatocellular carcinoma using genomic approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3535.
Abstract 3537: Targeted deep sequencing of driver mutations in airway epithelial cells from smokers
Authors: Craig Daniel J. , Blomquist Thomas M. , Crawford Erin L. , Willey James C. 
Published: August 2019

Abstract
Background: Inter-individual variation in risk for lung cancer is based on variation in both exposure to environmental factors and genetic predisposition. As such, it is reasonable to hypothesize that prevalence of mutations in the airway epithelium will vary based on the combined effects of these lung cancer risk factors. Genes most commonly mutated in non-small cell lung cancer were recently reported from The Cancer Genome Atlas (TCGA) project. The purpose of this study was to use targeted deep sequencing to assess the prevalence of these mutations in bronchial epithelial cells (BEC) of individuals at high demographic risk for lung cancer.
Methods: We enrolled 19 individuals with varying demographic risk for lung cancer, who were undergoing standard-of-care bronchoscopy into an IRB-approved research study in which we collected 1-5 million BEC via bronchoscopic brush biopsy and extracted genomic DNA. 10 subjects were smokers with lung cancer, 6 subjects were smokers without lung cancer, and 3 subjects were non-smokers without lung cancer. For targeted deep sequencing, we prepared synthetic spike-in competitive internal standards for each of 12 gene loci commonly mutated in lung cancer based on TCGA results and combined them into an IS mixture (ISM). DNA aliquots from each patient were quantified and mixed with equivalent genome equivalents of ISM prior to library preparation to control for technical artifacts associated with library preparation and NGS platform-specific error. The DNA input varied depending on sample quantity; there were 5 samples with 50,000 genome copies loaded, 12 samples with 100,000 genome copies loaded, and 2 samples with 1 million genome copies loaded. This approach enabled reliable measurement of 95% confidence limits of variant allele frequency (VAF), controlled for technical sequencing error, and allowed confident call of variants at a VAF of 0.1% and lower. Libraries for specimens from each of the 19 subjects were first sequenced using the Illumina MiSeq platform to ensure equal coverage across targets and samples. Deeper sequencing was then obtained using the Illumina NextSeq platform.
Results: Preliminary results showed that smokers harbored mutations up to 1.6% in gene loci associated with non-small cell lung cancer according to TCGA, while none were identified in non-smoking controls.
Conclusion: Initial results suggest that airway epithelial cells in smokers acquire somatic mutations that gradually lead to malignant conversion. Deep sequencing replicate experiments are underway to expand these results.
Citation Format: Daniel J. Craig, Thomas M. Blomquist, Erin L. Crawford, James C. Willey. Targeted deep sequencing of driver mutations in airway epithelial cells from smokers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3537.