bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4538: LiquidGxTMqPCR, an extremely sensitive qPCR-based liquid biopsy platform
Authors: Song Yang , Quintanilha Danielle , Chen Si , Huang Jun 
Published: August 2018

Abstract
In recent years, circulating cell-free tumor DNA has emerged as an excellent source of biomarkers for cancer detection, diagnosis and monitoring. One great challenge of detecting cell-free tumor DNA molecules is that they are usually found in a large background of wild-type DNA; therefore, assays with high sensitivity and low limit of detection are required. We have developed an extremely sensitive qPCR-based liquid biopsy platform, LiquidGxTM qPCR, to detect and track key driver mutations from patient blood. The platform takes advantage of our patent-pending technology BESTTM (Blocker-based Enrichment System of Tumor DNA) to specifically enrich mutant alleles from as low as 0.01% to more than 90%. With this platform, we currently have developed a CLIA-approved non-small cell lung cancer panel (EGFR T790M/L858R/C797S/Exon19Del, KRAS G12X/G13CD, BRAF V600E, ALK-EML4 fusion), and a colorectal cancer recurrence monitoring panel (KRAS G12X/G13CD, NRAS G12DV/Q61KR, PIK3CA E542K/E545K/H1047R, BRAF V600E). Our validation data show that the NSCLC panel has superior performance, with a LOD as low as 0.005%, analytical sensitivity more than 95% and analytical specificity of 100%. We have used this panel to test samples from nearly 200 NSCLC patients, and the results are highly concordant with those obtained by error-reducing NGS-based tests, despite some samples only detected via LiquidGxTM qPCR due to superior LOD. Other features of LiquidGxTM qPCR include (1) simultaneous enrichment of multiple mutants in the same reaction; (2) cost-effective and no special equipment required; and (3) fast turnaround time that takes as little as 0.5 days to get the results. In summary, we have developed a potent liquid biopsy platform for highly sensitive genomic biomarker test. With the technology, we have developed two cancer panels and this platform is also available as an assay development service.
Citation Format: Yang Song, Danielle Quintanilha, Si Chen, Jun Huang. LiquidGxTMqPCR, an extremely sensitive qPCR-based liquid biopsy platform [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 4538.
Abstract 4555: Potent Conditionally Active Biologic (CAB) PD-1 antibodies to reduce systemic toxicities associated with single agent and combination therapies
Authors: Chang Cathy , Frey Gerhard , Sharp Leslie L. , Liu Haizhen , Wang Jing , Xing Charles , Yalcin Safak , Ben Yong , Boyle William J. , Short Jay M. 
Published: August 2018

Abstract
PD-1 is an immune checkpoint inhibitor that limits T cell activity. The use of anti-PD-1 antagonist antibodies has demonstrated anti-tumor efficacy in mouse models and in a subset of human patients. However, blockade of PD-1 as a single agent and in combination with chemotherapy, targeted, and other immunomodulatory therapies has been limited clinically in part due to toxicities related to systemic immune-response related adverse events. In addition, there is increasing concern that systemic immune activation may lead to autoimmune-related adverse events in survivors.
The Conditionally Active Biologics (CAB) technology is a patented, proprietary platform that selects antibodies that reversibly bind to target antigen in the context of diseased tissues, but not normal tissues, by taking advantage of the unique cancer microenvironment that is produced largely as a result of glycolytic tumor metabolism including the Warburg effect. Using our CAB technology, we have identified anti-PD-1 Abs that reversibly bind human PD-1, and enhance T cell response to bacterial super-antigen under in vitro conditions that are present in the tumor microenvironment but not in normal tissues.
CAB-PD-1 Abs demonstrated anti-tumor efficacy, including tumor regression, against MC38 colorectal tumor in human PD-1 knock-in mouse model in which the mouse PD-1 gene has been replaced with human PD-1. The anti-tumor activity of CAB-PD-1 Abs was similar to a reference PD-1 Ab.
In conclusion, our data is consistent with our work on CAB-EGFR-ADC, CAB-AXL and CAB-ROR2-ADC antibodies, and suggests that anti-PD-1 Abs generated using the CAB technology provide potent, effective biologics with potential for increased therapeutic index. Specifically, the CAB-PD-1 is an excellent candidate for evaluation as a treatment for human cancers as a single agent or in combination with other anti-cancer therapies including immuno-oncology agents.
Citation Format: Cathy Chang, Gerhard Frey, Leslie L. Sharp, Haizhen Liu, Jing Wang, Charles Xing, Safak Yalcin, Yong Ben, William J. Boyle, Jay M. Short. Potent Conditionally Active Biologic (CAB) PD-1 antibodies to reduce systemic toxicities associated with single agent and combination therapies [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 4555.
Abstract 4557: Dual targeting of innate and adaptive checkpoints on tumor cells limits immune evasion
Authors: Fu Yang-Xin , Liu Xiaojuan 
Published: August 2018

Abstract
CD47 on tumors inhibits phagocytosis, while PD-L1 limits T cell-mediated tumor killing. However, whether and how these two pathways coordinately evade immune responses are poorly understood. We reveal that both CD47 and PD-L1 on tumors coordinately evade innate and adaptive sensing. Targeted blockade of CD47 and PD-L1 on tumor cells with bispecific anti-PDL1-SIRPα showed better therapeutic efficacy than single blockades with reduced off-tumor targeting. Mechanistically, the dual-targeting approach significantly enhanced DNA sensing in dendritic cells (DC), DC cross-presentation and anti-tumor T cell response. Our data indicate that tumor cells evolve to utilize two-levels of checkpoints to evade anti-tumor immune responses, and tumor cell-specific dual-targeting of both innate and adaptive checkpoints represents a new strategy for increasing efficacy and reducing toxicity.
Citation Format: Yang-Xin Fu, Xiaojuan Liu. Dual targeting of innate and adaptive checkpoints on tumor cells limits immune evasion [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 4557.
Abstract 4562: Tumor B7-H3 (CD276) expression and survival of patients with pancreatic cancer
Authors: Inamura Kentaro , Yokouchi Yusuke , Kobayashi Maki , Inoue Yosuke , Saiura Akio , Takazawa Yutaka , Ishikawa Yuichi 
Published: August 2018

Abstract
Background: B7-H3 (CD276) belongs to a family of immune modulators that includes PD-L1 (B7-H1 or CD274), and has been associated with tumor immunosuppression. Although several studies have reported the association of B7-H3 expression with prognosis in pancreatic cancer, the results are conflicting and inconclusive. We therefore examined the association of tumor B7-H3 expression with prognosis of pancreatic cancer.
Methods: Using tissue microarrays of 150 consecutive cases of pancreatic cancer, we evaluated tumor B7-H3 expression by immunohistochemistry. We examined the prognostic association of B7-H3 expression, using the log-rank test. We also used Cox proportional hazards regression models to compute the mortality hazard ratio (HR), adjusted for covariates including pathological-stage, tumor differentiation, preoperative levels of CEA and CA19-9, and adjuvant chemotherapy.
Results: Tumor B7-H3 positivity (10% of tumor cells) was observed in 99 (66%) of 150 cases of pancreatic cancer. In a log-rank test, B7-H3 positivity was associated with higher pancreatic cancer-specific mortality (P = 0.0005). In a multivariable analysis, B7-H3 positivity was independently associated with higher pancreatic cancer-specific mortality (multivariable HR = 1.82; 95% confidence interval [CI] = 1.25-2.71; P = 0.0016). When we divided immunoreactivity of B7-H3 into four scores; i.e., score 0, negative; score 1, weak; score 2, moderate; score 3, strong, the immunoreactivity scores of B7-H3 were 51 (34%), 67 (45%), 20 (13%), 12 (8%) for score 0, 1, 2, 3, respectively. In a log-rank test, higher score of B7-H3 immunoreactivity was associated with higher pancreatic cancer-specific mortality (P = 0.0014). In a multivariable analysis, higher B7-H3 immunoreactivity was independently associated with higher pancreatic cancer-specific mortality (comparing score 3 versus score 0: multivariable HR = 2.78; 95% CI = 1.38-5.25; P for trend = 0.0011).
Conclusion: Tumor B7-H3 positivity and higher B7-H3 immunoreactivity are both independently associated with higher mortality of pancreatic cancer.
Citation Format: Kentaro Inamura, Yusuke Yokouchi, Maki Kobayashi, Yosuke Inoue, Akio Saiura, Yutaka Takazawa, Yuichi Ishikawa. Tumor B7-H3 (CD276) expression and survival of patients with pancreatic 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 4562.
Abstract 4567: Immunomodulatory action of SGI-110 and combination with γδ T cell immunotherapy in ovarian cancer
Authors: Natoli Marina , Karadimitris Anastasios , Ghaem-Maghami Sadaf 
Published: August 2018

Abstract
Ovarian cancer (OC) is regarded as being an immunogenic cancer and strategies to enhance immune function in patients are thought to confer benefit and improve prognosis. Immunotherapy has been shown to be most promising when combined with other therapeutic approaches. Recent evidence in the field and preliminary data from our group suggest that treatment with epigenetic drugs, such as DNA methyltransferase inhibitors (DNMTi), can lead to improved immune activation in several cancers including ovarian.
The purpose of this study is to test the hypothesis that treatment with next generation hypomethylating agent SGI-110 can induce the re-expression of immunomodulatory genes and endogenous retroviruses (ERVs), which shifts OC cells towards a more immunogenic expression profile.
OC cell lines SKOV3, Kuramochi and OVSAHO were treated with low dose SGI-110 and assessed for increased immunogenicity. Expression of immune biomarkers and ERVs was assessed at different time points at mRNA levels by qPCR and protein levels by Flow Cytometry. Treated cell lines were functionally tested for increased immunogenicity by co-culture with γδ T cells, which were isolated from healthy donors and expanded by zoledronic acid selection. MTT assays were performed to assess cell viability and T cell killing following co-culture. IFNγ and Granzyme B release from T cells and chemokine release from tumor cells were assessed by ELISA.
Our results show up-regulation of key immunogenicity biomarkers and ERVs in our panel of OC cell lines, following treatment with SGI-110. Co-culturing SGI-110-treated cell lines with γδ T cells resulted in increased tumor cell killing and T cell activity.
We are now analysing RNA-sequencing data of SGI-110-treated OC cell lines in an effort to dissect the immunomodulatory mechanism of action of this novel hypomethylating agent. Moreover, we plan to test the in vivo feasibility of a SGI-110/γδ T cell combination therapy, which if successful might be further optimised for a clinical trial.
Citation Format: Marina Natoli, Anastasios Karadimitris, Sadaf Ghaem-Maghami. Immunomodulatory action of SGI-110 and combination with γδ T cell immunotherapy in ovarian 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 4567.
Abstract 4575: Efficient and accurate NGS approach for liquid biopsy detection and monitoring
Authors: Tang Ke , Kasbek Christopher , Song Yang , Song Qingxuan , Chen Si , Almalki Nouran , Zhang Xu , Huang Jun T. 
Published: August 2018

Abstract
Liquid biopsy detection using ctDNA has great potential in cancer diagnosis, monitoring, and predicting survival. However, detection sensitivity and specificity remains a major challenge at the current stage. Here we utilized targeted next-generation sequencing (NGS) approach to develop a noninvasive test to identify SNVs, indels, and fusions present at low frequencies in lung cancer patients. Target regions of interest were sequenced using tagging of individual molecules, followed by amplicon library generation and massive parallel sequencing using Illumina platform. The variants were called and annotated using our in-house AGIS (Actionable Genomic Interpretation System) bioinformatics pipeline. This CLIA-approved NGS panel (LiquidGx™ Lung) detects 112 variants in 10 genes (AKT1, ALK, BRAF, EGFR, ERBB2, KRAS, MET, PIK3CA, RET, and ROS1) with detection limit of 0.1%. Mutations are detected with 94% sensitivity and 99.8% specificity in a short turnaround time of 4-6 days. To assess the performance in a clinical setting, accurate sequencing was performed on 210 lung cancer patients; the frequency of mutations identified of each gene closely mirrored the published lung cancer tissue biopsy data. In summary, we have developed a potent liquid biopsy platform for highly sensitive genomic biomarker test. Our technology is also available as an assay development service and can be easily adaptable to the diagnosis and monitoring of other cancer types.
Citation Format: Ke Tang, Christopher Kasbek, Yang Song, Qingxuan Song, Si Chen, Nouran Almalki, Xu Zhang, Jun T. Huang. Efficient and accurate NGS approach for liquid biopsy detection and monitoring [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 4575.
Abstract 4580: Changes in the efficacy of anti-EGFR antibody drugs by exosomes derived from colorectal cancer patients
Authors: Morimura Rii , Tsukamoto Kei , Irie Shinji , Kitano Shiro , Shinozaki Eiji , Yamaguchi Kensei 
Published: August 2018

Abstract
Background: One of the biggest hurdles in cancer treatment is drug resistance. Exosomes are small membrane vesicles of endocytic origin, which contain mRNAs, DNA fragments, and proteins, and are released by many different cell types, including cancer cells. Several studies have shown exosome-mediated drug resistance mechanisms: drug export via the exosome pathway, neutralization of antibody-based drugs and exosome-mediated transfer of miRNAs. Here, we demonstrated the effect of exosomes derived from colorectal cancer (CRC) patients on the efficacy of anti-EGFR agent by in vitro cell-based assay.
Method: Exosomes were purified by ultracentrifugation from culture media of HCT116 cell line and the sera of CRC patients with stage IV pre- and post-treatment with cetuximab (Cmab). As a control, sera from healthy volunteers were used. The number of exosomes and amount of protein were determined by NanoSight and Qubit fluorometer, respectively. The isolated exosomes and 0.01 mg/mL and 0.1 mg/mL of Cmab were added to HT29 and NCI-H508, which stained with PKH dye previously. NCI-H508 is a Cmab super sensitive cell line. After culturing for 3 days, the cells were collected, stained with trypan blue, and the number of the remaining viable cancer cells was calculated with a cell counter. Cmab in the exosome fraction was quantified by ELISA.
Result: HT29 became drug ineffective depending on the number of exosomes produced by Cmab-insensitive HCT-116 harboring KRAS G13D mutation. In addition, exosomes in 9 of 18 cases of colorectal cancer patients changed NCI-H508 into a drug-ineffective state and also correlated with clinical information. In contrast, NCI-H508 was not converted into a drug-ineffective state by exosomes of healthy volunteers and Cmab responder patients. However, on the other hand, quantitative results by ELISA showed that Cmab in sera of some patients remained in the exosome fraction and inhibited the growth of NCI-H508. As a remarkable point, exosomes derived from healthy volunteers significantly promoted the efficacy of Cmab.
Conclusion: In this feasibility study, Cmab resistance in CRC patients may be reproducible by cell-based assay using exosomes. We believe that understanding this mechanism of action will contribute to drug discovery and personalized medicine in the future. Now, we are searching for biomarkers in these exosomes that change the efficacy of Cmab.
Citation Format: Rii Morimura, Kei Tsukamoto, Shinji Irie, Shiro Kitano, Eiji Shinozaki, Kensei Yamaguchi. Changes in the efficacy of anti-EGFR antibody drugs by exosomes derived from colorectal cancer patients [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 4580.
Abstract 4590: Larger family sizes improve stochastic error correction during untargeted searches of very-low frequency variant alleles in circulating cell-free DNA (ccfDNA)
Authors: Bhetariya Preetida J. , Nix David , Hellwig Sabine , Marth Gabor , Bronner Mary , Underhill Hunter 
Published: August 2018

Abstract
Detection of ccfDNA derived from non-metastatic solid tumors requires discrimination of very-low frequency true variants from NGS library preparation and sequencing noise that commonly occurs at a similar frequency (&lt;1%). Correction of NGS-related errors is particularly important during searches of unknown tumor-associated variants with multi-gene panels. Unique molecular identifiers (UMIs) have been used during in silico error correction by molecular barcoding and performing a consensus base calling at each position from DNA labelled with the same UMI (i.e., PCR duplicates). In this study, we sought to determine the utility of UMIs for error correction of stochastic noise in ccfDNA. ccfDNA was isolated from the plasma of 11 healthy participants. An eight base-pair random barcode (UMI) was ligated prior to library amplification. Libraries were enriched using a custom capture probe set (128 genes; 128 kb) and then sequenced (HiSeq 2500). Reads were aligned, grouped based on UMI similarity, and a consensus read sequence was determined. The number of PCR duplicates that yielded a single consensus sequence was defined as family size (FS). For non-reference alleles detected at a variant allele frequency (VAF) ≥ 0.1% and ≤ 1.0%, there was a significant reduction in observed counts with increasingly larger FSs (Table 1). This effect was observed for both unique and common non-reference allele counts (Table 1). Of note, counts of unique non-reference alleles (stochastic noise) were consistently greater than the common non-reference alleles regardless of family size (Table 1). The use of larger family sizes reduced the stochastic noise that may confound detection of very-low frequency variants present in ccfDNA during searches for unknown tumor-associated variants. Strategies that generate larger family sizes or suppress early PCR errors may further improve NGS specificity to broaden liquid biopsy clinical applications.
Table 1. Mean (SD) Non-Reference Allele Counts with a VAF between 0.1% and 1.0% in Cell-Free DNAFS &gt;= 1FS &gt;= 5FS &gt;= 10FS &gt;= 15FS &gt;= 20ANOVA Results F(4,50)P-valueAll Variants5536 (1230)3988 (881)2621 (805)1028 (552)1028 (552)49.8&lt;0.001Unique Variants3597 (1107)2635 (766)1112 (526)709 (434)709 (434)27.6&lt;0.001Common Variants1939 (161)1353 (188)521 (141)318 (121)318 (121)186.1&lt;0.001
Citation Format: Preetida J. Bhetariya, David Nix, Sabine Hellwig, Gabor Marth, Mary Bronner, Hunter Underhill. Larger family sizes improve stochastic error correction during untargeted searches of very-low frequency variant alleles in circulating cell-free DNA (ccfDNA) [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 4590.
Abstract 4591: Integration of genomic analysis and assessment of pre-analytic variables in the HD-SCA workflow: A technical validation study
Authors: Shishido Stephanie Nicole , Rodriguez_Lee Mariam , Kolatkar Anand , Xu Liya , Restrepo-Vassalli Sara , Welter Lisa , Carlsson Anders , Greenspan Emily , Hwang Shelley , Waitman Kathryn , Nieva Jorge , Bethel Kelley , Hicks James , Kuhn Peter 
Published: August 2018

Abstract
The liquid biopsy allows assessment of multiple biological analytes over time to provide dynamic temporal information with the potential for improving clinical management and guiding treatment decisions. While the promise of liquid biopsies for prediction and response monitoring are intensely investigated, the pre-analytic variables are of primary concern for its implementation in diagnostic clinical medicine, including such categories as collection method, shipping conditions, and sample storage. Here we utilize an integrated high-definition single cell analysis (HD-SCA) workflow for genomic analysis of rare cells and cfDNA from the liquid biopsy to characterize the effects of pre-analytical variation and reproducibility of data analysis from the same cohort of patients. The results presented here confirm consistent rare cell enumeration and morphometric characterization between 24h and 48h time to assay (TTA), with a high efficiency and capacity for both copy number variation (CNV) and single nucleotide variation (SNV) analysis at the single cell level. Additionally, the freezing process neither diminishes or increases the DNA quantity, nor does it affect the DNA quality for CNV or SNV analysis. The integration of genomic information is imperative to reveal essential disease-implicated mutational profiles, but effective molecular diagnostic tests require reproducible coverage over a broad dynamic range. The performance of the HD-SCA platform quantified here may be utilized as a guide for implementation into patient care and/or research biorepository processes.
Citation Format: Stephanie Nicole Shishido, Mariam Rodriguez_Lee, Anand Kolatkar, Liya Xu, Sara Restrepo-Vassalli, Lisa Welter, Anders Carlsson, Emily Greenspan, Shelley Hwang, Kathryn Waitman, Jorge Nieva, Kelley Bethel, James Hicks, Peter Kuhn. Integration of genomic analysis and assessment of pre-analytic variables in the HD-SCA workflow: A technical validation study [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 4591.