bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5455: Identifying somatic variants with defined confidence level in targeted sequencing of tumor DNA without a matched normal sample
Authors: Huang Yanmei , Young Amanda G. , Hughes Jason D. 
Published: September 2020

Abstract
Sequencing tumor DNA without a matched normal sample is currently routine practice for many clinical diagnostic services that use NGS to identify somatic mutations in a panel of cancer-relevant genes, due to cost constraints. Various computational algorithms have been developed to distinguish somatic mutations from germline variations in this “single sample” setting. However, the sensitivity and specificity of these methods have not been rigorously investigated, and factors affecting accuracy of the somatic classification have not been thoroughly mapped out. We seek to address these inadequacies and identify avenues towards better somatic variant identification in “single sample” setting. We use tumor/matched normal pairs to establish true somatic/germline status of variants and analyze how adjustments in the algorithms for variant calling and somatic/germline classification affect the ability to identify true somatic variants. We show that somatic variants can be identified with varying degrees of certainty under different circumstances and demonstrate that our algorithmic methods can effectively identify a substantial subset of calls that have a very high likelihood of being truly somatic. Tunable filtering methods and confidence scoring for somatic likelihood has utility in the development of complex biomarkers such as tumor mutational burden and ctDNA measurements.
Citation Format: Yanmei Huang, Amanda G. Young, Jason D. Hughes. Identifying somatic variants with defined confidence level in targeted sequencing of tumor DNA without a matched normal sample [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5455.
Abstract 5474: Identification of novel druggable fusions enabled through the use of an automated RNA fusion prioritization pipeline
Authors: Islam Sumaiya A. , Huether Robert , Kudalkar Emily 
Published: September 2020

Abstract
Gene fusions can serve as key drivers in the development of various cancers and represent important therapeutic targets and diagnostic biomarkers. Due to high detection of candidate fusions from RNA-sequencing data, there is a recognized need to build tools that will make reasonable and automated predictions to identify clinically or biologically relevant fusion events in a tumor sample. We developed a computational pipeline which scores and prioritizes all detected fusion transcripts within a sample to determine which fusions are likely driver events in the tumor. Specifically, the pipeline implements a categorization scheme that bins all scored fusion events into Low, Medium and High Confidence levels based on threshold read support levels and a DriverScore metric, which is derived from a binary classification algorithm using specific features, such as reading frame, breakpoint region, kinase domain and transcript isoform. We systematically analyzed 3200 fusion candidates from a previously published cohort of 500 paired tumor-normal samples sequenced with the Tempus xT assay. We found that 1.7% and 20.1% of fusion candidates were categorized in the High and Medium Confidence levels, respectively, while 78.2% of fusion events were deprioritized as Low Confidence calls. Of the 35 clinically-relevant fusions, 27 (77.1%) were captured in our prioritized set (High/Medium Confidence), including National Comprehensive Cancer Network actionable gene rearrangements involving RET, STAT6 and FUS, while the remaining 8 were assigned as Low Confidence due to an out of frame fusion transcript and insufficient read support. The frequency of prioritized fusions varied by cancer type, with prostate and breast cancer having the highest frequency of prioritized fusions. In addition to well-established canonical fusions, we also sought to characterize novel fusions, identifying a subset of 21 novel prioritized fusions which were also observed in The Cancer Genome Atlas tumor samples. Within this subset, 3% of fusion candidates contained a druggable domain such as a tyrosine kinase or Ras-binding domain, signifying the potential of categorization to enable novel fusion drug target discovery. Overall, our analysis highlights the utility of using an automated prioritization tool to detect known canonical fusion drivers and explore novel fusion drug targets and biomarkers.
Citation Format: Sumaiya A. Islam, Robert Huether, Emily Kudalkar. Identification of novel druggable fusions enabled through the use of an automated RNA fusion prioritization pipeline [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5474.
Abstract 5619: PBMC humanized NSG-(KbDb)null (IA)null mouse model to evaluate immune-oncology drug efficacy
Authors: Yao Li-Chin , Cheng Mingshan , Shultz Leonard D. , Keck James G. 
Published: September 2020

Abstract
Multiple types of humanized mouse models using immunodeficient NOD-scid IL2rgnull (NSG) mice have been developed by The Jackson Laboratory for preclinical studies of new cancer therapies. Humanized NSG mice engrafted with both human peripheral blood mononuclear cells (PBMC) and human cancers have been used for evaluating antibody-based therapeutics targeting T cells. Compared to CD34+ HSC-mediated humanization, NSG mice engrafted with PBMC are ready to use more quickly and are more cost-effective. The major limitation of PBMC engrafted NSG is the development of acute xenogeneic graft-versus-host disease (GVHD) due to human T cell activation through mouse MHC class I and class II molecules. The experimental window for drug efficacy evaluation is limited to three-four weeks post PBMC injection and strong xeno-GVHD may hinder drug-induced T cell activation. A new strain lacking murine MHC molecules, NSG-(KbDb)null (IA)null, was created to address this limitation. Here we engrafted non-irradiated adult NSG and MHC double knockout NSG-(KbDb)null (IA)null mice using the same human PBMC donors to compare their survival and engraftment level. We found that most of the MHC deficient mice can survive over 100 days and can support human T cell engraftment. We also evaluated drug efficacy response using checkpoint inhibitors anti-CTLA-4 (lpilimumab) and anti-PDL-1 (Avelumab) in human tumor xenograft models. Anti-CTLA-4 treatment resulted in reduced growth of mantle cell lymphoma Jeko-1. Anti-PDL-1 treatment reduced growth of a melanoma PDX. In consistent with their anti-tumor response, flow analysis showed increased T cell frequency in blood and tumor in the drug treated group when compared to the vehicle control. Additional cancer treatment evaluated in the PBMC engrafted NSG-(KbDb)null (IA)null mice will also be discussed.
Citation Format: Li-Chin Yao, Mingshan Cheng, Leonard D. Shultz, James G. Keck. PBMC humanized NSG-(KbDb)null (IA)null mouse model to evaluate immune-oncology drug efficacy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5619.
Abstract 5778: Hernia and Ewing sarcoma
Authors: He Di , Hansen Johnni , Federman Noah , Olsen Jorn , Ritz Beate , Heck Julia E. 
Published: September 2020

Abstract
Introduction: Ewing sarcoma (ES) is a rare cancer with an incidence that peaks in adolescence and young adulthood. The tumor occurs in bone and soft tissue and the etiology is unclear. Several studies have observed increased ES risk in children and young adults with hernia, including umbilical and inguinal hernia, suggesting a mechanism for a common causal pathway. A meta-analysis of 3 case-control studies reported a threefold increased risk of ES among hernia patients. The purpose of this study is to examine the association between hernia and ES in a population-based study.
Methods: We ascertained Ewing sarcoma cases (age &lt;20 years) from the Danish Cancer Registry (diagnoses 1977-2016; births 1977-2013), then randomly selected controls free of cancer at the date of corresponding cases diagnosis and matched (25:1) by sex and year of birth from the Central Population Register (N=4,160). Ewing sarcoma cases (N=122) were identified with the International Classification of Diseases for Oncology (ICD-O-1 and ICD-O-3 code 9260). Information on birth outcomes and gestational factors were taken from the Medical Birth Registry (1973+) and information on mother's and child's health was taken from the National Patient Register (1977+). We also searched this Register for diagnoses of hernia in the child based on procedure codes (a Nordic coding system from 1977-1995, and an extended version of ICD-10 thereafter). We used conditional logistic regression to determine associations for hernia and ES.
Results: 122 ES cases were identified, among whom 6 cases had a diagnosis of hernia (1 of them had hernia diagnosed within the first 3 years of life). Among controls, 203 (6.7%) had a diagnosis of hernia. Of all children diagnosed with hernia, 27 (12.9%) presented hernia during the first year of life and 74 (35.4%) presented during the first 3 years of life. In ES cases there was no increase in risk of hernia (OR= 0.53, 0.17-1.72). Adjustment for presence of other congenital malformations did not change the results for hernia (OR=0.65). Restriction to younger cases (diagnosed ≤15 years) showed similar results for hernia.
Conclusions: Previous studies have raised the possibility that inherited genes causing both developmental anomalies and cancer might be involved with the etiology of ES. However, based on registry and hospitalization data, we were not able to confirm previous associations with hernia. Either this study or earlier studies may have been influenced by small sample size. There is also a possibility that previous reports of positive associations are due to recall or publication biases.
Citation Format: Di He, Johnni Hansen, Noah Federman, Jorn Olsen, Beate Ritz, Julia E. Heck. Hernia and Ewing sarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5778.
Abstract 6248: Engineered probiotics for local delivery of checkpoint blockade nanobodies
Authors: Gurbatri Candice , Lia Ioana , Vincent Rosa , Coker Courtney , Castro Samuel , Treuting Piper , Hinchliffe Taylor , Arpaia Nicholas , Danino Tal 
Published: September 2020

Abstract
Checkpoint inhibitors have revolutionized cancer therapy but only work in a subset of patients and can lead to a multitude of toxicities, suggesting the need for more targeted delivery systems. Because of their preferential colonization of tumors, microbes are a natural platform for the local delivery of cancer therapeutics. Here, we engineer a probiotic bacteria system for the controlled production and intratumoral release of nanobodies targeting programmed cell death-ligand 1 (PD-L1) and cytotoxic T lymphocyte-associated protein-4 (CTLA-4) using a stabilized lysing release mechanism. We used computational modeling coupled with experimental validation of lysis circuit dynamics to determine the optimal genetic circuit parameters for maximal therapeutic efficacy. A single injection of this engineered system demonstrated an enhanced therapeutic response compared to analogous clinically relevant antibodies, resulting in tumor regression in syngeneic mouse models. Supporting the potentiation of a systemic immune response, we observed a relative increase in activated T cells, an abscopal effect, and corresponding increases in systemic T cell memory populations in mice treated with probiotically delivered checkpoint inhibitors. Last, we leveraged the modularity of our platform to achieve enhanced therapeutic efficacy in a poorly immunogenic syngeneic mouse model through effective combinations with a probiotically produced cytokine, granulocyte-macrophage colony-stimulating factor (GM-CSF). Together, these results demonstrate that our engineered probiotic system bridges synthetic biology and immunology to improve upon checkpoint blockade delivery.
Citation Format: Candice Gurbatri, Ioana Lia, Rosa Vincent, Courtney Coker, Samuel Castro, Piper Treuting, Taylor Hinchliffe, Nicholas Arpaia, Tal Danino. Engineered probiotics for local delivery of checkpoint blockade nanobodies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6248.
Abstract 6312: Use of differential sensing-based biosensors to quantify ERK kinase activity in complex biological samples
Authors: Zamora-Olivares Diana , Pridgen Jacey R. , Zeng Lingyu , Kaoud Tamer S. , Anslyn Eric V. , Dalby Kevin N. 
Published: September 2020

Abstract
The expeditious quantification of signalling in complex biological system by novel technologies will aid in the development of biological models, help to identify targets for treatment, and assess treatment plans. The biochemical process of protein phosphorylation, which underlies almost all aspects of cell signaling, is typically evaluated by immunoblotting procedures like western blot. More recently, proteomics procedures, which provide qualitative estimates of the concentration of proteins and their modifications in cells have also been used. However, enzyme activity can be difficult to correlate to protein modifications.vRecently we reported a differential sensing-based approach to differentiate nine MAPKs from each other. From this we developed a cabilbration regression model to measure ERK activation and inhibition while both JNK and p38 MAPKs were present. Our previous studies were carried out using purified MAPKs, which do not necessarily reflect endogenous activity. Here, we report a similar approach to rapidly quantify unknown levels of endogenous ERK activity in biological samples. To do so, a library of cross-reactive SOX-peptide-based biosensors along with chemometric analysis, was used to quantify nanograms of active ERK in micrograms of unfractionated cell lysates and tumor extracts. This approach can be used to measure multiple samples quickly, allowing for faster analysis of the response of actual ERK activity in treatments in cell lines or animal models than other methods. This approach might also provide an alternative to assessing ERK activity in human tumor biopsies, which would be valuable for evaluating treatments and inhibitor resistance.
Citation Format: Diana Zamora-Olivares, Jacey R. Pridgen, Lingyu Zeng, Tamer S. Kaoud, Eric V. Anslyn, Kevin N. Dalby. Use of differential sensing-based biosensors to quantify ERK kinase activity in complex biological samples [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6312.
Abstract 6415: RAF dimer inhibitor lifirafenib enhances the antitumor activity of MEK inhibitor mirdametinib in RAS mutant tumors
Authors: Yuan Xi , Zhang Xinwen , Du Rong , Cheung Shing-Hu , Wei Min , Zhou Changyou , Wang Lai , Shearer Todd , Edris Badreddin , Smith Mary , Yao Zhan , Thant Claire N. , Rosen Neal , Luo Lusong 
Published: September 2020

Abstract
K-RAS mutation represents one of the most frequent genetic alterations in cancers. Monotherapy approaches targeting RAS downstream effectors such as MEK and ERK have had limited clinical success in patients with K-RAS-mutated cancers. The reduced sensitivity of K-RAS-mutated cells to certain MEK inhibitors is associated with feedback phosphorylation of MEK and reactivation of mitogen-activated protein kinase (MAPK) signaling. Herein, we report that RAF dimer inhibitor lifirafenib (BGB-283) shows strong synergistic effect with MEK inhibitor mirdametinib (PD-0325901) in suppressing proliferation of K-RAS-mutated cancer cell lines. This synergistic effect was not observed using vemurafenib, a first-generation B-RAFV600E selective inhibitor. Mechanistic analysis revealed that RAF dimer inhibition could suppress RAF-dependent MEK reactivation and led to sustained inhibition of MAPK signaling in K-RAS-mutated cells. Furthermore, combination synergy was observed in K-RAS mutant xenograft models. Pharmacodynamic analysis supported the role of synergistic phospho-ERK blockade in enhancing the antitumor activity in the K-RAS mutant models. These findings support the rationale to combine a RAF dimer inhibitor and a MEK inhibitor to treat K-RAS-mutated cancers and led to the ongoing a Phase Ib/II clinical trial of lifirafenib and mirdametinib in patients with K-RAS mutations or other MAPK pathway aberrations (Clinical Trial ID: NCT03905148).
Citation Format: Xi Yuan, Xinwen Zhang, Rong Du, Shing-Hu Cheung, Min Wei, Changyou Zhou, Lai Wang, Todd Shearer, Badreddin Edris, Mary Smith, Zhan Yao, Claire N. Thant, Neal Rosen, Lusong Luo. RAF dimer inhibitor lifirafenib enhances the antitumor activity of MEK inhibitor mirdametinib in RAS mutant tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6415.
Abstract 6527: Targeting glycosylated PD-1 induces potent anti-tumor immunity
Authors: Wang Yuhan , Sun Linlin , Yang Riyao , Liu Jielin , Qiu Yufan , Hsu Jennifer L. , Cha Jong-ho , Chan Li-Chuan , Hsu Jung-Mao , Lee Heng-Huan , Lai Yun-Ju , Khoo Kay-Hooi , Chung Ezra M , Li Chia-Wei , Kim Yong-Soo , Park Andrew H , Yang Yi , Yoo Stephen S. , Hung Mien-Chie 
Published: September 2020

Abstract
Immunotherapy targeting programmed cell death protein 1 (PD-1) and programmed cell death 1 ligand 1 (PD-L1) immune checkpoints represents a major breakthrough in cancer treatment. PD-1 is an inhibitory receptor expressed on the surface of activated T cells that dampens T-cell receptor (TCR)/CD28 signaling by engaging with its ligand PD-L1 expressed on cancer cells. Despite the clinical success of PD-1 blockade using monoclonal antibodies, most patients do not show promising results, and the underlying regulatory mechanisms of PD-1 remain incompletely defined. Here, we showed that PD-1 is extensively N-glycosylated in T cells, and the intensities of its specific glycoforms are altered upon TCR activation. Glycosylation is critical for maintaining PD-1 protein stability and cell surface localization. Importantly, the glycosylation of PD-1, especially at the N58 site, is essential for mediating the interaction with PD-L1. A monoclonal antibody that specifically targets glycosylated PD-1, STM418, exhibits higher binding affinity to PD-1 than FDA-approved PD-1 antibodies, potently inhibits PD-L1/PD-1 binding, and enhances anti-tumor immunity. Our findings provide novel insights into the functional significance of PD-1 glycosylation and offer a rationale for targeting glycosylated PD-1 as a potential strategy for immunotherapy.
Citation Format: Yuhan Wang, Linlin Sun, Riyao Yang, Jielin Liu, Yufan Qiu, Jennifer L. Hsu, Jong-ho Cha, Li-Chuan Chan, Jung-Mao Hsu, Heng-Huan Lee, Yun-Ju Lai, Kay-Hooi Khoo, Ezra M Chung, Chia-Wei Li, Yong-Soo Kim, Andrew H Park, Yi Yang, Stephen S. Yoo, Mien-Chie Hung. Targeting glycosylated PD-1 induces potent anti-tumor immunity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6527.
Abstract 6528: Anti-PD-1 induces the endocytosis of the co-receptor from the surface of T-cells: Nivolumab is more effective than Pembrolizumab
Authors: Saad Elham Ben , Oroya Andres , Rudd Christopher E. 
Published: September 2020

Abstract
Immune checkpoint blockade (ICB) has revolutionized the treatment of cancer. Present models show that anti-PD-1 operates simply by blocking co-receptor binding to its ligand PD-L1. Surprisingly, no previous studies have assessed whether ICB also induces the internalization or endocytosis of PD-1 from the cell surface. Many, but not all receptors, undergo endocytosis upon antibody or ligand binding. In this study, PD-1 internalization was assessed on activated human T cells by flow cytometry and fluorescence microscopy. Immunoprecipitation and western blotting were performed to assess the destiny of PD-1 after internalization. Our results report that anti-PD-1 induces the rapid internalization of PD-1 from the surface of T-cells in a manner comparable to CD28. A substantial minority of receptors were also resistant to antibody-induced endocytosis. Further, Nivolumab was considerably more effective than Pembrolizumab in inducing the endocytosis of PD-1 in primary human T-cells. This difference was the result of several factors where Nivolumab bound to a greater number of PD-1 molecules on the surface of T-cells than Pembrolizumab, indicating that the co-receptor might exist with different conformations on activated cells. Moreover, Nivolumab induced more rapid endocytosis (5.5 versus 3.6% per minute) and a greater percentage of PD-1 molecules than Pembrolizumab (70% versus 50%). The relative effect of anti-PD-1 molecules on internalization was seen equally on activated CD4 helper and CD8+ effector/memory T-cells. The internalization and the degradation of PD-1 were partially blocked by the inhibition of clathrin-mediated endocytosis and proteasome activity. Our studies show for the first time that ICB involves a second level of modulation involving the internalization of PD-1 from the surface of T-cells, an event which will contribute to the efficacy of ICB.
Citation Format: Elham Ben Saad, Andres Oroya, Christopher E. Rudd. Anti-PD-1 induces the endocytosis of the co-receptor from the surface of T-cells: Nivolumab is more effective than Pembrolizumab [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6528.