bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5573: Highly multiplexed diagnostic test for the detection of extended EGFR del19 variants in patients with NSCLC
Authors: Mellert Hestia S. , Jackson Leisa , Alexander Kristin , Weaver Amanda , Maar Dianna , Shelton Dawne , Pestano Gary 
Published: August 2018

Abstract
The detection of nucleic acids in circulation has become an increasingly important part of the clinical workup and testing for cancer patients, particularly those with non-small cell lung cancer (NSCLC). The utilization of blood-based PCR platforms for detection of somatic variant mutations addresses several limitations of previously established molecular testing approaches such as an inability to access tissue, insufficient tissue quantity or quality, and slow turnaround time for results. However, the number of variants detected may be limited by use of some rapid PCR technologies. We have focused in this study on the analytic and clinical development of a highly multiplexed assay for the detection of EGFR del19 while maintaining a rapid turn-around time. The test system includes the prospective collection of whole blood into a cfDNA BCT and the reproducible detection of del19 variants out of plasma using ddPCR-based technology. Analytic specificity and sensitivity was examined using in vitro DNA designed to mimic the EGFR del19 variants in the assay. Analytic sensitivity was performed and demonstrates that the theoretical limit of detection of the test was below 0.02% minor variant frequency when using high concentrations of synthetic standards. Precision studies were conducted with both analytic and clinical samples at high, medium and low mutation frequencies, over three consecutive days, three runs in one day and with two operators. All test parameters were successfully met. Normal healthy donor (n = 11) and reference ddPCR positive and negative NSCLC donor (n = 80) samples were tested. EGFR del19 variants were not identified in the plasma from the normal healthy donors or the EGFR del19 reference negative NSCLC donors. All reference positive cases were accurately detected above our required threshold of 2 variant copies with detection ranging from 14 to 1584. For all donor specimens the wild-type copies were well above the predefined clinical QC threshold of 300, ranging from 380 to 760 copies. Of note, no negative reference samples contained more than two mutant copies. We conclude that the developed test is highly suited for the sensitive and reproducible detection of multiple EGFR del19 variants from blood specimens in the clinical laboratory.
Citation Format: Hestia S. Mellert, Leisa Jackson, Kristin Alexander, Amanda Weaver, Dianna Maar, Dawne Shelton, Gary Pestano. Highly multiplexed diagnostic test for the detection of extended EGFR del19 variants in patients with NSCLC [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 5573.
Abstract 5587: Sample quality control of cell-free DNA
Authors: Liu Melissa H. , Graf Eva 
Published: August 2018

Abstract
Sequencing of cell-free DNA (cfDNA) extracted from blood specimens or other body fluids is possible due to the establishment of low input library protocols for next-generation sequencing workflows. Accurate quantification of cfDNA samples is essential to determine suitable input amounts for cfDNA library preparation prior to sequencing. The main component of cfDNA samples is the mononucleosome with a size around 170 bp, sometimes with additional species representing nucleosome multimers. Further, cfDNA samples may contain larger DNA fragments dependent on the donor's health status, preanalytical sample treatment, or extraction method. High molecular weight material can negatively influence library preparation and subsequently result in lower sequencing depth. Therefore, reliable quantification of cfDNA requires a method that separates DNA fragments by size, such as electrophoresis. This poster shows the use of a new cfDNA assay for the 2100 Bioanalyzer system as an add-on for the High Sensitivity DNA assay. The assay enables automated cfDNA quantification with pre-defined regions. Moreover, the results include sample purity as a score to qualify cfDNA samples according to their contamination level with high molecular weight material. The features of the assay are described with examples of typical sample patterns.
Citation Format: Melissa H. Liu, Eva Graf. Sample quality control of cell-free DNA [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 5587.
Abstract 5588: Uneven distribution of CTCs in magnetic fields following binding with iron nanoparticles
Authors: Xue Chengsen , Swenson Christina D. , Closkey Thomas W. Mc 
Published: August 2018

Abstract
Circulating tumor cell (CTC) detection and characterization have recently become an integral part of precision medicine. Several large, multicenter clinical studies confirmed that the prevalence of CTC is a useful predictor of treatment efficacy in metastatic breast cancer. The number of CTCs is strongly correlated with clinical progression. Oncology clinics widely use this biomarker to provide prognostic information. There are several platforms to isolate and measure CTCs. The only FDA-approved method is the CellSearch system developed by Veridex. The CellSearch System uses anti-EpCAM antibodies and polymer-coated iron nanoparticles in order to isolate CTC with the use of a magnetic field. The enriched CTC fraction is then placed in a MagNest chamber and the transparent slide is read by the automatic fluorescent CellTracks Analyzer. By using prelabeled breast cancer cells as quality control (QC) samples, we semiquantitated the distribution of CTC cells on slides in eleven QC samples. We found that CTC cells distribute unevenly on the slides. In order to count all CTCs, the whole area of the slide is divided into 175 small regions by the manufacturer. To better quantitate the CTC number, it is important to have all cells evenly spread over the slide. Our results showed that 41 out of 175 regions contained higher QC CTC counts. The heat map indicates that the magnetic field lines may have an effect on CTC localization. The CTC platforms are susceptible for underestimating actual CTC counts. Our findings indicate that cell concentration in certain regions caused by a magnetic field effect could be one of several contributing factors.
Citation Format: Chengsen Xue, Christina D. Swenson, Thomas W. Mc Closkey. Uneven distribution of CTCs in magnetic fields following binding with iron nanoparticles [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 5588.
Abstract 5589: Detection of epidermal growth factor receptor mutations from circulating tumor DNA versus archival tissue of lung cancer
Authors: Oh In-Jae , Seo Hyeong-Won , Cho Hyun-Ju , Park Ha-Young , Kho Bo-Gun , Chang Jin-Sun , Kim Tae-Ok , Shin Hong-Jun , Park Cheol Kyu , Lim Jung-Hwan , Kwon Yong-Soo , Kim Yu-Il , Lim Sung-Chul , Kim Young-Chul , Choi Yoo-Duk 
Published: August 2018

Abstract
Background: Epidermal growth factor receptor (EGFR) mutations are well known predictive marker of targeted therapy. We compared the sensitivity of EGFR mutation detection techniques between matched achival lung cancer tissue and peripheral blood sample.
Methods: We collected the paired samples from plasma and paraffin-embedded tumor tissue obtained before EGFR-tyrosine kinase inhibitor (EGFR-TKI). DNA extraction was performed using the QIAamp MinElute virus spin kit and EGFR mutation analysis was done by two detection methods. The current standard test is the PNAClampTM (Clamp) which is the PNA-based PCR clamping that selectively amplifies only the mutated target DNA sequence. The new technique is the PANAMutyperTM EGFR test (Mutyper), which use PNA clamping-assisted fluorescence melting curve analysis.
Results: A total of 295 (188 male and 107 female) patients were analyzed in this study. The histologic types were composed of 258 adenocarcinoma, 22 squamous cell carcinoma and 15 others. Most were clinical stage IV (137, 46.4%) and the EGFR mutation rate of tissue sample by standard Clamp test was 25.7%. Plasma sensitivity was significantly higher in Mutyper than Clamp (71.2% vs. 30.0%, p&lt;0.001) with tissue as reference. The overall concordance and degree of agreement between two samples were better in Mutyper (91.9%, k=0.762, p&lt;0.001) than Clamp (81.7%, k=0.344, p&lt;0.001). In tissue sample, the median progression-free survival (PFS) of EGFR sensitive group was significantly longer than negative group regardless of the two methods. In plasma sample, the median PFS was significantly longer only by Mutyper (9.9 vs. 2.2 months, p=0.001), not by Clamp (9.8 vs. 7.6 months, p=0.968).
Conclusions: Mutyper was useful liquid biopsy technique with better sensitivity than standard Clamp test.
Citation Format: In-Jae Oh, Hyeong-Won Seo, Hyun-Ju Cho, Ha-Young Park, Bo-Gun Kho, Jin-Sun Chang, Tae-Ok Kim, Hong-Jun Shin, Cheol Kyu Park, Jung-Hwan Lim, Yong-Soo Kwon, Yu-Il Kim, Sung-Chul Lim, Young-Chul Kim, Yoo-Duk Choi. Detection of epidermal growth factor receptor mutations from circulating tumor DNA versus archival tissue of lung 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 5589.
Abstract 5613: Generation of a therapeutic monoclonal antibody for acute myeloid leukemia by employing the U937 cell line as a surrogate antigen
Authors: Chen Bethany , Kandov Evelyn , Ghebrehiwet Berhane 
Published: August 2018

Abstract
The prognosis of acute myeloid leukemia (AML) has improved for younger patients, but it still remains grim for patients over 65 years old with a likelihood of death within a year of diagnosis. Here, we evaluated the effects of novel anti-gC1qR monoclonal antibodies (mAbs) that were generated against intact U937 cells, which are used here as a model for AML. The U937 cell line is known to overexpress gC1qR, which in turn serves not only as a proliferative molecular signal but also provides a platform for the generation of angiogenic and metastatic factors. Cell viability results reveal that all of the mAbs significantly decrease (p&lt;0.05) the percentage of viable AML cells although the mixture of those mAbs was not significant when compared to the individual mAbs themselves. The anti-U937 antibodies, monoclonal and polyclonal, showed a significant difference (p&lt;0.05) against the anti-purified recombinant gC1qR antibodies. The anti-U937 mAb methodology of immunizing with the mammalian cell instead of the purified protein allowed the mAbs to better target the native endogenous protein present on human cells. Our study not only provided novel and potent mAbs against AML, but also implicated a potentially more efficient technique of creating therapeutic mAbs against cancer cells.
Citation Format: Bethany Chen, Evelyn Kandov, Berhane Ghebrehiwet. Generation of a therapeutic monoclonal antibody for acute myeloid leukemia by employing the U937 cell line as a surrogate antigen [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 5613.
Abstract 5637: Combination of oncolytic vaccinia virus and immune checkpoint blockade overcomes resistance to immunotherapy in renal cell carcinoma
Authors: Chon Hongjae , Kim Chan 
Published: August 2018

Abstract
Renal cell carcinoma (RCC) is a hypervascular tumor with variable immunogenic responses, and VEGF-targeted anti-angiogenic agent has become a standard treatment during the past decade. Recently, immune checkpoint inhibitor (ICI) has merged as another standard of care in RCC, but response is limited as a monotherapy. To determine the optimal combination strategy for immunotherapy in RCC, we employed JX594 (Pexa-Vec), an oncolytic vaccinia virus currently in phase 3 clinical trial, as a combination partner for ICI in RCC. Intratumoral injection of JX594 remodeled the tumor microenvironment of Renca tumor model through dynamic changes in immune system, leading to the conversion of an immunuosuppressive, non-inflamed tumor into an inflamed tumor. The JX594 virotherapy increased the intratumoral infiltration of CD8+ T cell by 16-fold, resulting in systemic and tumor-specific anti-cancer immune response against RCC. Moreover, the expression of immune checkpoint molecules such as PD-1 (4.0-fold), CTLA-4 (2.3-fold), and LAG-3 (3.1-fold) were increased. Depletion experiment showed that the therapeutic effect of JX594 is largely dependent on the cooperation of CD8+ and CD4+ T cells. In addition, GM-CSF has been shown to potentiate the immunotherapeutic efficacy of JX594. Combination of JX594 and ICI targeting PD-1 or CTLA-4 further increased the intratumoral infiltration of activated CD8+ T cells and effectively suppressed the growth of RCC. Furthermore, the optimal schedule was rationalized by
combination treatment of various administration methods. Finally, based on these combination results, triple combination of JX594, anti-PD-1, and anti-CTLA-4 maximized the anti-cancer immune responses and induced durable responses with improved overall survival. Collectively, we demonstrate that intratumoral injection of JX594 sensitizes non-inflamed RCC to ICI treatment through CD8+ T cell infiltration in tumor and induces anti-cancer immune responses that can overcome immunotherapy resistance.
Citation Format: Hongjae Chon, Chan Kim. Combination of oncolytic vaccinia virus and immune checkpoint blockade overcomes resistance to immunotherapy in renal cell carcinoma [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 5637.
Abstract 5648: Proteomics analysis of oral cancer cell-derived extracellular vesicles
Authors: Oliveira Ana K. , Busso-Lopes Ariane F. , Sá Jamile Oliveira , Rivera César , Leme Adriana F. Paes 
Published: August 2018

Abstract
More than 300,000 new cases of head and neck cancer occur each year around the world, and although it is not one of the most common tumors in the world, has an elevated morbidity rate (37.8%) after five years of diagnosis. The development and progression of the Oral Squamous Cell Carcinoma (OSCC) involve complex cellular mechanisms which contribute to a tumor progression. Recently extracellular vesicles (EVs) have taken a significant physiological and pathological role in cell-cell communication through interactions mediated by receptors or by transfer of bioactive molecules such as receptors, proteins, lipids, mRNA, microRNA, and DNA, by changing the phenotype of the recipient cell. The tumor cells can transfer information to different cell types using EVs as a vehicle, modifying the characteristics of the tumor microenvironment, and contributing to cancer sustaining. The detection of alterations in the EVs proteome may, therefore, contribute to the understanding the cellular mechanisms modulated in OSCC and help to improve the clinical prognosis and potential therapeutic targets in oral cancer. Thus, this study analyzed the cargo proteins of different EVs from less and high aggressive oral cancer cells to understand their possible role in microenvironment modulation and oral cancer progression. Our results indicate that EVs of aggressive cells have exclusive proteins that may contribute to lymph node metastasis, which is the worse prognostic factor in OSCC and can be considered potential targets in OSCC.FAPESP: 2016/19337-3
Citation Format: Ana K. Oliveira, Ariane F. Busso-Lopes, Jamile Oliveira Sá, César Rivera, Adriana F. Paes Leme. Proteomics analysis of oral cancer cell-derived extracellular vesicles [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 5648.
Abstract 5685: Nanocage-therapeutics prevailing phagocytosis and immunogenic cell death awakens immunity against cancer
Authors: Nam Gihoon , Kim Gi Beom , Kim In-San 
Published: August 2018

Abstract
A growing appreciation of the relationship between the immune system and tumorigenesis has led to the development of strategies aimed at ‘re-editing' the immune system to kill tumors. Here, we report a novel tactic for overcoming the activation-energy threshold of the immunosuppressive tumor microenvironment and mediating the delivery and presentation of tumor neoantigens to the host's immune system. This nature-derived nanocage not only efficiently presents ligands that enhance cancer cell phagocytosis, it also delivers drugs that induce immunogenic cancer cell death. The designed nanocage-therapeutics induces the release of neoantigens and danger signals in dying tumor cells, and leads to enhancement of tumor cell phagocytosis and cross-priming of tumor specific T cells by neoantigen peptide-loaded antigen-presenting cells. We observed potent inhibition of tumor growth and complete eradication of tumor through systemic tumor-specific T-cell responses in tumor draining lymph node and spleen and further, infiltration of CD8+ T cells into the tumor site. Remarkably, after removal of the primary tumor, all mice treated with this nanocage-therapeutics are protected against subsequent challenge with the same tumor cells, suggesting development of lasting, tumor-specific responses. This designed nanocage-therapeutics ‘awakens' the host's immune system and provokes a durable systemic immune response against cancer.
Citation Format: Gihoon Nam, Gi Beom Kim, In-San Kim. Nanocage-therapeutics prevailing phagocytosis and immunogenic cell death awakens immunity against 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 5685.
Abstract 5712: Identification of a highly suppressive Treg subset associated with immunotherapy response
Authors: Troiani Teresa , Romano Simona , D'Arrigo Paolo , Rea Anna , Tufano Martina , Giunta Emilio F. , Matarrese Giuseppe , Procaccini Claudio , Novizio Nunzia , Vigorito Vincenza , Faicchia Deriggio , Argenziano Giuseppe , Ciardiello Fortunato , Romano Maria F. 
Published: August 2018

Abstract
Melanoma often exploits Treg to avoid immune attack. Treg is a heterogeneous population with respect to immunosuppressive capability. Lymphocytes are particularly rich in FKBP51 (encoded by FKBP5 gene), known as the receptor for FK506. Melanoma aberrantly expresses this protein, which sustains resistance and invasion. Melanoma/immune cell interaction, through PD-L1/PD1, bidirectionally generates FKBP5 splicing inducing a lower molecular weight form termed FKBP51s. In 64 advanced melanoma patient PBMCs, we found that FKBP51s marked a Treg subset that correlated to anti-CTLA4 response. More precisely, a Treg FKBP51s+ count &lt;1% was associated with unresponsiveness (normal donor-range 0.1-0.7%). Aim of the present study was to assess the role of Treg FKBP51s+ as potential biomarker of response in a different cohort of patients treated with anti-PD1. In addition, the suppressive potential of Treg FKBP51s+ in comparison with that of Treg FKBP51s- is investigated. To date, we have outcomes of 11 patients. For each patient, we have collected up to 10 blood samples, at T0 and before each treatment, to monitor Tregs. In 5 responder patients, Treg FKBP51s+ was &gt;1.2 and &lt;4.8; in 5 non responder patients, the count was &gt;0.04 and &lt;0.8 After a transient increase following the first administration, the count decreased to 0.3+0.2% in responder patients. Interestingly, a patient with count =0.7% developed autoimmune side effects that led to therapy discontinuation. Resolution of side effects was accompanied by a value increase to 9.9%; anti-PD1 re-administration was then successful. In vitro iTreg generation showed that FKBP51s was upregulated in Treg CD25high, Ki67high and p70S6khigh, corresponding to a highly metabolically active profile with strong suppressive capability. In conclusion, melanoma patients that benefit from immune checkpoint targeted therapy are recognizable by an expansion of a Treg subset which is marked by FKBP51s, a splicing protein isoform generated by triggering of surface antigens (PD-L1, PD1), abundantly expressed on highly suppressive Tregs.
Citation Format: Teresa Troiani, Simona Romano, Paolo D'Arrigo, Anna Rea, Martina Tufano, Emilio F. Giunta, Giuseppe Matarrese, Claudio Procaccini, Nunzia Novizio, Vincenza Vigorito, Deriggio Faicchia, Giuseppe Argenziano, Fortunato Ciardiello, Maria F. Romano. Identification of a highly suppressive Treg subset associated with immunotherapy response [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 5712.
Abstract 5719: RNA-based tumor neoantigens from intron retention
Authors: Margolis Claire A. , Smart Alicia C. , Adeegbe Dennis , Miao Diana , He Meng Xiao , Pimentel Harold , Fugmann Tim , Wong Kwok-Kin , Allen Eliezer M. Van 
Published: August 2018

Abstract
Background: Tumor neoantigens contribute to cancer immunity and may influence selective immune checkpoint inhibitor response. Translation of nonsynonymous somatic mutations in tumor cells generates mutant peptides that can be recognized as foreign by the host immune system. Alterations in tumor RNA, rather than DNA, may also contribute to the tumor neoantigen landscape. Intron retention, a widespread feature of cancer transcriptomes, represents a novel source of tumor neoantigens.
Methods: We developed an in silico pipeline leveraging existing tools and novel methods to computationally identify retained-intron neoantigens (RI-neoantigens) from transcriptome sequencing data. We applied our computational pipeline to three cohorts of melanoma patients (n = 89) treated with immune checkpoint blockade.
Results: This approach identified a mean RI-neoantigen burden of 3,643 across cohorts, which augments the mean DNA-derived somatic neoantigen burden by roughly 4.5-fold. 3,253 RI-neoantigens were exclusively present in two or more patients who responded to immunotherapy. A subset of responder-exclusive RI-neoantigens were validated by peptide restimulation assay. A candidate RI-neoantigen from a cancer cell line was identified in complex with MHC I by mass spectrometry, supporting the hypothesis that aberrant splicing results in intron retention, which generates abnormal transcripts that are translated into immunogenic peptides and presented to the immune system.
Conclusions: Our results demonstrate the contribution of transcriptional dysregulation to the overall burden of tumor neoantigens. Further study of RI-neoantigens may expand our understanding of tumor immunity and identify immunogenic peptide sequences for personalized cancer vaccines.
Citation Format: Claire A. Margolis, Alicia C. Smart, Dennis Adeegbe, Diana Miao, Meng Xiao He, Harold Pimentel, Tim Fugmann, Kwok-Kin Wong, Eliezer M. Van Allen. RNA-based tumor neoantigens from intron retention [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 5719.