bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1354: Developing 384-well and 1536-well cell growth inhibition assay workflow for screening drug-drug combination in tumor cell lines
Authors: Li Yvonne , Ma Mike , Chan Julie , Tian Yang , Pagratis Nikos , Stonich Derek , Chen Victor , Zhang Louis , Kenney Mark 
Published: July 2016

Abstract
Drug combination has been widely used in treating the most debilitating diseases such as cancer. The ideal drug-drug combination will broaden and/or deepen therapeutic efficacy while overcoming resistance and unwanted off-target effects. We have developed a 384-well combination compound plating method in 8×7 format (8 dilutions of Drug A and 7 dilutions of Drug B), and screened a number of compound pairs that showed synergistic effect in inhibiting tumor cell growth in either suspension or solid tumor lines. Compound vehicle DMSO was used as negative control and puromycin treatment as positive control for calculating% inhibition, and both HSA and Bliss independence synergy models were applied for calculating synergy scores. As 384-well 8×7 format contains one compound pair per plate, we aimed to increase the throughput by developing 384-well 5×5 format (5 dilutions of Drug A and 5 dilutions of Drug B) which contains 3 drug pairs per plate, and 1536-well 8×7 and 5×5 format which contains 4 and 12 drug pairs per plate, respectively. We compared EC50s and synergy scores generated from 384-well and 1536-well with both 8×7 and 5×5 formats, single agent EC50s within combination pairs were generally within 3 fold difference and synergy scores are largely consistent. Therefore, we have validated and enabled higher throughput drug-drug combination screen by using 384-well 5×5, 1536-well 8×7, or 5×5 format. The high-throughput method presented here can be readily adopted for combination studies in other disease areas.
Citation Format: Yvonne Li, Mike Ma, Julie Chan, Yang Tian, Nikos Pagratis, Derek Stonich, Victor Chen, Louis Zhang, Mark Kenney. Developing 384-well and 1536-well cell growth inhibition assay workflow for screening drug-drug combination in tumor cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1354.
Abstract 1356: Cell-based screening to identify repressors of wild type and mutated telomerase reverse transcriptase gene promoter activity
Authors: Bilsland Alan , Liu Yu , Burns Sharon , Jenkinson David , Roffey Jon , Keith W. Nicol 
Published: July 2016

Abstract
Cellular immortality is a near-universal phenotype of cancer cells with the central role played by the multicomponent telomerase complex firmly established. The reactivation of telomerase is found in approximately 85% of all cancers. Furthermore, frequent activating non-coding mutations in the hTERT promoter region have been identified in multiple tumour types. A considerable body of evidence supports the concept of targeting the signal transduction pathways that contribute to telomerase overexpression in cancer cells. We have exploited our knowledge in this area to develop cell-based luciferase reporter gene assays to measure hTERT and hTR gene promoter activity. To this end we undertook high throughput screening in the A2780 human ovarian cancer cell line against both hTR and hTERT promoters. Secondary specificity and cytotoxicity assays reduced the initial hits to a single chemical series of dual inhibitors which strongly suppress both hTR and hTERT promoter activity without primary cytotoxicity, as predicted of telomerase inhibitors. Through a process of Hit to Lead we have further developed the chemical series. Lead compounds are active across a panel of cell lines from distinct histological origins, reduce endogenous hTERT mRNA levels and decrease telomerase catalytic activity at nM concentrations. Furthermore, these compounds repress both wild type and mutant C228T and C250T hTERT promoter activity. In specificity assays no off-target activity has been identified in an expanded promoter screen against a panel of 15 off-target promoter reporters.
Citation Format: Alan Bilsland, Yu Liu, Sharon Burns, David Jenkinson, Jon Roffey, W. Nicol Keith. Cell-based screening to identify repressors of wild type and mutated telomerase reverse transcriptase gene promoter activity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1356.
Abstract 1359: Design, synthesis and evaluation of fluorinated antifolates for improved selectivity and potency against tumor cells
Authors: Gangjee Aleem , Ravindra Manasa P. , Wilson Mike R. , Povrik Adrianne W. , Hou Lisa P. , O’Connor Carrie , Hou Zhanjun , Matherly Larry H. 
Published: July 2016

Abstract
Folates are important single carbon transferring cofactors required for the biosynthesis of purine and pyrimidine nitrogen bases and DNA. Antifolates inhibit synthesis of these nitrogenous bases and function as antineopastic agents. The use of currently marketed antifolates such as methotrexate (MTX and pemetrexed (PMX) is limited by dose-limiting toxicity due to non-selective transport by the ubiquitously expressed reduced folate carrier (RFC). We previously reported a series of 6-substituted pyrrolo[2,3-d]pyrimidine classical antifolates that are selectively transported by folate receptors (FR) and/or by the proton-coupled folate transporter (PCFT) over RFC and inhibit FR/PCFT expressing tumor cells (KB and IGROV1) at sub-nanomolar IC50 values. These antifolates are comparatively more potent and circumvent the important limitation of currently marketed clinical antifolates that lack selective uptake into tumors. As an extension of the SAR, we now report on the role of fluorine atom(s) in improving selectivity as well potency. Fluorine was incorporated into our 6-substituted pyrrolo[2,3-d]pyrimidine antifolates to improve pharmacodynamics by improving binding affinity to target proteins via a number of well documented electrostatic and hydrophobic interactions of fluorine. In addition, fluorines were strategically placed on the side chain of our targeted antifolates for improved potency and selectivity through induced conformational restriction due to a plausible intramolecular fluorine-hydrogen bonding interaction. The fluorinated analogs had IC50s in the subnanomolar range (IC50 = 0.33 to 0.29 nM) for KB tumor cells and nanomolar (IC50 = 2.77 to 3.47 nM) for IGROV-1 cells. In addition, these analogs showed 600- to 1000-fold selectivity for FRα expressing cells over RFC. Protection studies suggest that glycinamide ribonucleotide formyl transferase (GARFTase) is the intracellular targets. In vivo activity was established toward the SKOV3 tumor xenograft model. These preclinical studies suggest that these fluorinated analogs are candidates for possible clinical trial as antitumor agents.
Citation Format: Aleem Gangjee, Manasa P. Ravindra, Mike R. Wilson, Adrianne W. Povrik, Lisa P. Hou, Carrie O’Connor, Zhanjun Hou, Larry H. Matherly. Design, synthesis and evaluation of fluorinated antifolates for improved selectivity and potency against tumor cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1359.
Abstract 1365: Pseudo-cis and pseudo-trans amide conformations lead to potent targeted antifolates that are selectively transported by FR over RFC
Authors: Gangjee Aleem , Xiang Weiguo , Dehkne Aamod , Wilson Mike R. , Wallace-Povrik Adrianne , O’Connor Carrie , Hou Zhanjun , Matherly Larry H. 
Published: July 2016

Abstract
Drugs usually bind to different targets in different conformations. As antitumor agents, antifolates first need to be selectively transported by tumor cells via the reduced folate carrier (RFC), the proton-coupled folate transporter (PCFT) or folate receptors (FRs). The second step is the binding of antifolates with the intracellular targets. We are systematically developing novel folate analogs with selective membrane transport for FRs and PCFT over the ubiquitously expressed RFC. These 6-substituted pyrrolo[2,3-d]pyrimidine antifolates are principally inhibitors of de novo purine biosynthesis at the steps catalyzed by glycinamide ribonucleotide formyl transferase (GARFTase) and 5-aminoimidazole-4-carboxamide (AICA) ribonucleotide formyltransferase (AICARFTase). We previously demonstrated that classical antifolates bind to FRα and GARFTase in different conformations. An amide in the bridge region of classical antifolates has two interchangeable lowest energy conformers, pseudo-cis and pseudo-trans. We reported that a novel antifolate (AGF238) with an amide in the bridge region binds to FRα in a pseudo-trans conformation and binds to GARFTase in a pseudo-cis conformation. As part of our continued efforts to pursue targeted antifolates as antitumor agents, we designed an expand series of amide-bridged classical antifolates with different energy barriers between the pseudo-cis and pseudo-trans conformers. Among these, AGF266 was exclusively transported by Chinese hamster ovary (CHO) cells engineered to express human FRα (IC50 = 0.42 nM) or FRβ (IC50 = 0.88 nM) over CHO expressing human RFC (IC50 &gt; 1000 nM). AGF266 was also found to exhibit highly potent antitumor activity (IC50 = 0.79 nM in KB human tumor cells). AGF266 inhibited GARFTase as its principal cellular target, based on patterns of protection from growth inhibition by adenosine and AICA. Our in vitro findings of antitumor activity associated with FR selectivity suggest that further preclinical evaluation of AGF266 as a potential antitumor agent is warranted.
Citation Format: Aleem Gangjee, Weiguo Xiang, Aamod Dehkne, Mike R. Wilson, Adrianne Wallace-Povrik, Carrie O’Connor, Zhanjun Hou, Larry H. Matherly. Pseudo-cis and pseudo-trans amide conformations lead to potent targeted antifolates that are selectively transported by FR over RFC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1365.
Abstract 1375: An ultra-sensitive cell free DNA liquid biopsy assay for cancer treatment monitoring
Authors: Zhao Grace , Weng Li , Tang Paul , Sun Johnny , Huang Yi , Guo Lingchen , Wang Hongyan , Kang Xiaozheng , Shen Wei , Ying Kang , Lin Shengrong 
Published: July 2016

Abstract
In order to take advantage of the narrow time window for optimal treatment efficacy, highly sensitive disease monitoring is critical in the successful management of cancer. Currently, treatment efficacy is assessed by using a combination of protein cancer biomarkers and imaging. However, both methods present limitations with regard to specificity or sensitivity due to their dependency on tumor size. Recently, a number of studies have suggested that monitoring cell free DNA (cfDNA) may provide a more specific alternative for tracking cancer treatment with greatly improved sensitivity. Here we introduce a novel next-generation sequencing based mutation detection system aimed at improving the sensitivity, reliability, and clinical utility of cancer treatment monitoring. Our system, comprised of Nebula, a whole genome amplification technology that is capable of amplifying nanogram quantities of cfDNA &gt;1000-fold, and Firefly, a proprietary technology combining molecular biology and computational algorithm for error-suppression, has reduced the rate of random sequencing errors to 10-6. As a result, we are able to detect 1.5 variant copies from 10ng of input cfDNA with a detection rate of 46%. We have validated the Nebula-Firefly assay on a patient cohort with either colorectal (CRC) or lung cancer. Here we report the successful detection of drug resistant mutations and various genomic alterations associated with minimal residual detection (MRD) in sample cfDNA. These initial findings have led to the exploration of Nebula-Firefly as the technological backbone for a noninvasive, scalable approach for the early detection, treatment, and monitoring of cancer.
Citation Format: Grace Zhao, Li Weng, Paul Tang, Johnny Sun, Yi Huang, Lingchen Guo, Hongyan Wang, Xiaozheng Kang, Wei Shen, Kang Ying, Shengrong Lin. An ultra-sensitive cell free DNA liquid biopsy assay for cancer treatment monitoring. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1375.
Abstract 1378: Generating quality control reference standards to evaluate ultrasensitive variant detection
Authors: Debeljak Marija , Haley Lisa , Anderson Derek A. , Adams Emily M. , Suenaga Masaya , Beierl Katie , Lin Ming-Tseh , Goggins Michael , Gocke Christopher D. , Eshleman James R. 
Published: July 2016

Abstract
Introduction: Ultrasensitive point mutation detection can facilitate minimal residual disease detection, early detection of cancer, and therapeutic monitoring of cancer patients. However, nearly identical mutant and wildtype molecules exhibit crosstalk with most technologies, thus producing high background levels. To evaluate technologies against each other for accurate ultrasensitive point mutation detection it is crucial to supply laboratories with reference samples of various dilutions.
Methods: We tested a series of sample mixes with digital-droplet PCR and next generation sequencing. Using linearity and accuracy as the gold standard, we empirically introduced two corrections to generate improved quality control reagents. Baseline variant allele frequency (VAF) in the parental cell line was used to correct for copy number variation of variant, while haplotype counting was used to correct technical errors (cell counting and pipetting).
Results: Correlation between the level of dilution and the measured VAF was relatively good (R2 = 0.80) when measured using ddPCR. However, correcting for the parental VAFs substantially improved the correlation (R2 = 0.97). In contrast, correlation of the cell count dilution and the measured VAF, as determined by next generation sequencing (AmpliSeq), was initially relatively poor (R2 = 0.63). However, substantial improvement in correlation was achieved by correcting for the parental VAFs (R2 = 0.94). In addition, correcting by haplotype counting alone only slightly improved accuracy in both technologies (ddPCR, from R2 = 0.80 to R2 = 0.81; AmpliSeq, from R2 = 0.63 to R2 = 0.64). Furthermore, correcting for both factors resulted in the best correlation for ddPCR-generated data (R2 = 0.99); however, introducing both corrections for AmpliSeq data did not prove more beneficial than correcting for parental VAFs alone (both corrections, R2 = 0.94 compared to parental VAF correction only, R2 = 0.94).
Conclusions: Validation of ultrasensitive variant detection requires standardized reference samples. These will also permit assessing various ultrasensitive detection technologies against one another.
Citation Format: Marija Debeljak, Lisa Haley, Derek A. Anderson, Emily M. Adams, Masaya Suenaga, Katie Beierl, Ming-Tseh Lin, Michael Goggins, Christopher D. Gocke, James R. Eshleman. Generating quality control reference standards to evaluate ultrasensitive variant detection. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1378.
Abstract 1398: RNA DIRECT: A novel strategy for targeted RNA enrichment of transcripts associated with solid tumors
Authors: Patel Kruti M. , Bowman Sarah K. , Davis Theodore B. , Russello Salvatore , Kraushaar Daniel C. , Emerman Amy B. , Henig Noa , Hendrickson Cynthia L. 
Published: July 2016

Abstract
RNA sequencing (RNA-seq) has become a powerful platform for profiling transcriptomes that enables gene expression analysis and identification of nucleotide or structural variations. RNA-seq, however, can be cost prohibitive due to the size and complexity of most transcriptomes, which require deep sequencing coverage to achieve the necessary sensitivity for a reliable analysis. By combining targeted enrichment strategies with next-generation sequencing (NGS), a subset of transcript regions or sequences can be enriched for and analyzed with the resolution required for both research and clinical applications.
The RNA DIRECT targeted enrichment method utilizes probe-based hybridization to capture only relevant cDNA sequences. Targeted sequences are then ligated to NGS platform specific adaptors and amplified by PCR. The RNA DIRECT strategy provides a robust and cost effective method for the enrichment of transcript sequences for the purpose of identification and detection of known or novel variants and gene fusions. To demonstrate the high specificity, sensitivity and uniformity of this method, we have applied it to the capture of targets commonly associated with solid tumors.
Citation Format: Kruti M. Patel, Sarah K. Bowman, Theodore B. Davis, Salvatore Russello, Daniel C. Kraushaar, Amy B. Emerman, Noa Henig, Cynthia L. Hendrickson. RNA DIRECT: A novel strategy for targeted RNA enrichment of transcripts associated with solid tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1398.
Abstract 1404: Pemetrexed decreases circulating S100A9-myeloid derived suppressor cells in patients with non-small cell lung cancer
Authors: Feng Po-Hao , Lee Kang-Yun 
Published: July 2016

Abstract
Background: We previously reported that S100A9-myeloid derived suppressor cells (MDSCs) are negatively associated with chemotherapy effect in non-small cell lung cancer (NSCLC) patients. Pemetrexed-cisplatin chemotherapy is a standard treatment for advanced lung adenocarcinoma. The effect of chemotherapy on MDSCs is still not clear.
Methods: We prospectively enrolled nineteen stage 4 lung adenocarcinoma patients without known driving mutation before chemotherapy. Fourteen patients received pemetrexed-cisplatin and five with docetaxel-cisplatin as first line chemotherapy. Peripheral blood MDSCs percentage was evaluate by flow cytometry before first cycle and second cycle of chemotherapy.
In vitro migration assay with transwell MDSC/A549 cell co-culture system was used to test the effect of chemotherapy on chemotactic ability of A549 cell. Chemotherapy pretreated-A549 cells were cultured in the bottom chamber, and MDSCs, isolated from PBMC with CD14+ magnetic bead, were cultured in the upper chamber.
Results: MDSCs percentage decreased after patients received first cycle pemetrexed-cisplatin treatment (mean ±SD MDSC% in PBMC: 25.9±13.9% vs 16.3±11.3%, p&lt;0.05, n = 5). In the subgroup patients that had partial response to pemetrexed and cisplatin, the MDSCs percentage decreased most significantly. (25.0±9.1 to 7.1±5.2, p&lt;0.05, n = 5) In vitro study confirmed that pemetrexed reduced numbers of CD14+ MDSC (pemetrexed vs control: 15.0±6.6 vs 107.8± 56.8, p0.05) or cisplatin (96.7±98.2 vs 107.8 ±56.8, p&gt;0.05)
Conclusion: Pemetrexed-cisplatin, but not docetaxel-cisplatin, decreased S100A9-MDSC in patients with lung adenocarcinoma, an effect might be due to a reduction in chemotactic ability of tumors by pemetrexed. In addition to cytotoxic effect, clinical benefit of pemetrexed might be also due to the effect on microenvironment.
Citation Format: Po-Hao Feng, Kang-Yun Lee. Pemetrexed decreases circulating S100A9-myeloid derived suppressor cells in patients with non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1404.
Abstract 1406: Analysis of immune responses as a consequence of androgen deprivation therapy in patients with biochemical progression of prostate cancer
Authors: Jochems Caroline , Madan Ravi A. , Fernando Romaine I. , Gulley James L. , Tsang Kwong Y. , Schlom Jeffrey 
Published: July 2016

Abstract
We evaluated the immune responses in 28 patients enrolled in a phase II trial at the National Cancer Institute (NCI). The aim was to investigate the effects of 3 months of androgen deprivation therapy (ADT) with goserelin on the immune responses in patients with biochemical progression of prostate cancer following local definitive therapy. PBMC and sera were collected before treatment and after 3 months. We performed flow cytometry to evaluate the frequencies of subsets of CD4+ and CD8+ T-cells, regulatory T-cells (CD4+ CD25hi CD127− FoxP3+), MDSCs and CD4 and CD8 recent thymic emigrants. CD4 T-cell proliferation and NK-cell lytic activity were evaluated. Serum samples were analyzed for cytokines, sCD27 and sCD40L.
The baseline characteristics were: median age 64 years, testosterone 361 ng/dl, PSA 2.2 ng/ml, PSA-doubling time 7.0 months, and Gleason score 7. After 3 months of ADT we found no significant changes in NK-cell function or frequencies of NK subsets. CD4+ T-cell proliferation decreased slightly. The number of CD4+ effector memory T-cells decreased, but other CD4 subsets were unchanged. The frequencies of CD4 and CD8 recent thymic emigrants did not change. Regulatory T-cells (including the CTLA4+ subset), and the effector:Treg ratio did not change. In contrast, the frequency of granulocytic MDSC decreased (P&lt;0.01). There was an increase in the sCD27:sCD40L ratio (P = 0.012), due to decreased sCD40L. There was a decrease in the serum levels of IL-1β, IL-2, IL-6, IL-8, IL-10, IL-12p70, GM-CSF and IFNγ. There were no changes in the serum levels of TNFα or CXCL2 after therapy.
In conclusion, three months of ADT with goserelin did not alter the immune response in a way that would decrease the likelihood of successful immunotherapy after this treatment. The decreased MDSC and the increased sCD27:sCD40L ratio could indicate a more favorable immune environment.
Citation Format: Caroline Jochems, Ravi A. Madan, Romaine I. Fernando, James L. Gulley, Kwong Y. Tsang, Jeffrey Schlom. Analysis of immune responses as a consequence of androgen deprivation therapy in patients with biochemical progression of prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1406.