bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1210: Targeting the IDO1-Kynurenine-AhR pathway for cancer immunotherapy
Authors: Pinto Sheena , Steeneck Christoph , Albers Michael , Anderhub Simon , Birkel Manfred , Buselic-Wölfel Larisa , Eisenhardt Gisela , Kremoser Claus , Hoffmann Thomas , Deuschle Ulrich 
Published: August 2019

Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-controlled transcription factor that is primarily known to be a sensor of xenobiotics and tumor-promoting activities of halogenated hydrocarbons and polycyclic aromatic hydrocarbons. Several endogenous ligands such as metabolites produced by commensal microorganisms on skin and in gut and metabolites of L-Tryptophan - produced under control of the Tryptophan dioxygenases IDO1 and TDO2 such as L-Kynurenine and Kynurenic acid are known to modulate the transcriptional activity of AhR. The activity of AhR is predominant in many different immune and epithelial cells, thereby balancing immune responses towards various signals.
Activation of the IDO1-Kyn-AhR pathway and accumulation of nuclear AhR protein is frequently seen in different tumor types and possibly linked to the observed diminished anti-tumor immune response. AhR agonizing ligands produced by cancer cells and/or lymphocytes recruited to the TME reduce the anti-tumor immune response through increasing the numbers and function of regulatory T cells while reducing that of cytotoxic CD8+ T cells.
In order to reduce AhR-mediated immune-suppression in cancer patients, Phenex Pharmaceuticals initiated a program to identify small molecule AhR antagonists to block activated downstream signaling of AhR. To this end, we have identified novel AhR antagonists, which showed strong antagonistic activity against agonist-activated human AhR in a cell based CYP1A1 promoter-driven luciferase reporter assay in HepG2 cells. The compound series display good oral bioavailability and low clearance in mice. Our AhR antagonist molecules show single agent anti-tumor activity and increase the efficacy of Gemcitabine and anti-PD-L1 checkpoint inhibition in different syngeneic mouse tumor models. Overall, AhR antagonist treatment increased CD8+ T cell and M1 macrophage numbers, and decreased IL22 levels, which might be of functional relevance in the tumor context. Future research is directed to determine PK-PD markers suitable for clinical development and identification of human malignancies likely of responding to AhR antagonist treatment.
Citation Format: Sheena Pinto, Christoph Steeneck, Michael Albers, Simon Anderhub, Manfred Birkel, Larisa Buselic-Wölfel, Gisela Eisenhardt, Claus Kremoser, Thomas Hoffmann, Ulrich Deuschle. Targeting the IDO1-Kynurenine-AhR pathway for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1210.
Abstract 1213: RNA-based screens in primary human immune cells
Authors: Joubert Bronwyn , Ghirelli Cristina , Nett Isabelle , Prime John , Martin Glynn , Moore Jonathan , Cross Benedict , McCarthy Nicola J. 
Published: August 2019

Abstract
Genetic screens have long been used as an approach to identify and validate new targets for drug discovery. The vast majority of these have been carried out in cell lines: mostly cancer cell lines. However, with improvements in tissue culture techniques, the increasing interest in using the immune system to tackle disease and the discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 mediated genome editing, screening primary cells that have not been subverted by transformation into immortal lines, is both appealing and feasible.
We have successfully carried out a CRISPR-Cas9 screen in primary T cells using a combined lentivirus and electroporation protocol. Freshly isolated primary T cells are stimulated with anti-CD3 and anti-CD28 antibodies and then transduced with a pooled sgRNA library. After antibiotic selection, T cells successfully transduced with sgRNAs are electroporated to introduce Cas9 mRNA.
We chose to validate this approach by carrying out a screen similar to that published by Birsoy et al., 2015, in which they ran a CRISPR-Cas9 screen in Jurkat T cells in the presence and absence of the electron transport chain inhibitor phenformin. In our screen, we exposed the CRISPR-Cas9 edited pool of primary T cells to a dose of phenformin that resulted in growth inhibition to a similar degree to that used by Birsoy and colleagues. Our data are in agreement with the published screen, showing that loss of the cytosolic aspartate aminotransferase GOT1 sensitises primary T cells to phenformin. We took multiple time points in our primary T cell screen and used T cells isolated from three different donors, allowing for the analysis of guide drop-out kinetics and reproducibility between donors.
We anticipate that these data will be useful in building more complex screens that assess T cell biology in the presence of additional cells, such as myeloid derived suppressor cells (MDSCs). With a view to this, we have also carried out an arrayed siRNA screen in MDSCs to look for genes that when knocked down reduce the capacity of MDSCs to inhibit T cell proliferation. The endpoint for this screen is based on co-culture of siRNA transfected MDSCs with proliferating primary T cells.
Using this complex data set, we have identified several potential targets, which when validated could provide new therapeutic targets through which the immunosuppressive nature of MDSCs in the tumour microenvironment can be mitigated.
Birsoy, K., et al. (2015) http://dx.doi.org/10.1016/j.cell.2015.07.016
Citation Format: Bronwyn Joubert, Cristina Ghirelli, Isabelle Nett, John Prime, Glynn Martin, Jonathan Moore, Benedict Cross, Nicola J. McCarthy. RNA-based screens in primary human immune cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1213.
Abstract 122: Stromal extracellular matrix is a microenvironmental cue promoting resistance to EGFR tyrosine kinase inhibitors in lung cancer cells
Authors: Zhang Ting , Guo Lixia , Wang Yuanyuan , Ren Tao , Yang Yanan 
Published: August 2019

Abstract
The acquisition of resistance to EGFR tyrosine kinase inhibitors (TKIs) remains a critical problem in lung cancer clinic, but the underlying mechanisms have remained incompletely understood. Although the TKI-induced or -selected genetic changes are known to drive resistance, resistance also occurs in tumor cells without genetic changes through poorly-characterized processes. Here, we show that the extracellular matrix (ECM) from various components of the tumor microenvironment, including neighboring tumor cells and fibroblasts, may be the driver of resistance in the absence of genetic changes. Unlike genetic changes, which may evolve during relatively long time of chronic EGFR TKI treatment to drive resistance, briefly culturing on de-cellularized ECM, or co-culturing with the ECM donor cells, immediately confers resistance to tumor cells that are otherwise sensitive to EGFR TKIs. We show evidence that collagen in the ECM may be its primary constituent driving resistance, at least partly through the collagen receptor Integrin-β1. Intriguingly, such effect of ECM and collagen is dose-dependent and reversible, suggesting a potential clinic-relevant application for targeting this effect. Collectively, our results reveal that the stromal ECM acts as a microenvironmental cue promoting EGFR TKI resistance in lung cancer cells, and targeting collagen and Integrin-β1 may be useful for treating resistance, especially the resistance without clearly-defined genetic changes, for which effective therapeutics are lacking.
Citation Format: Ting Zhang, Lixia Guo, Yuanyuan Wang, Tao Ren, Yanan Yang. Stromal extracellular matrix is a microenvironmental cue promoting resistance to EGFR tyrosine kinase inhibitors in lung cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 122.
Abstract 1220: High-resolution epitope mapping differentiates monoclonal antibodies in the crowded cancer immunotherapy space
Authors: Willis Sharon 
Published: August 2019

Abstract
Epitope mapping provides essential information for differentiating monoclonal antibodies (MAbs) that bind to proteins targeted by many competing drugs. In cancer immunotherapy, for instance, numerous approved or investigational MAbs target the immune checkpoint protein PD-1. Recent high-profile patent law cases have centered on epitope data, highlighting the importance of distinguishing MAb binding sites at amino-acid resolution. Additionally, epitope data can be used to distinguish the mechanisms by which MAbs exert their therapeutic effects, uncovering important differences between competing drugs. To achieve rapid and comprehensive conformational epitope mapping at the amino-acid level, we developed the Shotgun Mutagenesis Epitope Mapping platform. Every residue in a target protein is individually mutated by alanine scanning mutagenesis, expressed in human cells, and assayed by flow cytometry to determine the critical epitope residues. Data from our platform have been used to differentiate MAbs in terms of their binding residues and therapeutic mechanisms of action. We have used our platform to differentiate the unique binding residues and, in some cases, the mechanisms of action of novel MAbs on the crowded surfaces of cancer targets, such as HER-2, from those of benchmark MAbs.
Citation Format: Sharon Willis. High-resolution epitope mapping differentiates monoclonal antibodies in the crowded cancer immunotherapy space [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1220.
Abstract 1227: Immune modulatory effect of pramlintide for cutaneous squamous cell carcinoma treatment
Authors: Tordesillas Leticia , Hesterberg Rebecca , Ortiz-Rivera Ivannie , Sell Brittney R. , Chiang Omar Chavez , Nguyen Kimberly T. , Murphy Brian L. , Burnette Pearlie K. , Flores Elsa R. , Tsai Kenneth Y. 
Published: August 2019

Abstract
Cutaneous squamous cell carcinoma (cuSCC) accounts for 15-20% of skin cancers. Treatment of cuSCC with pramlintide, a synthetic analog of the hormone amylin, is currently under investigation in mouse models and human clinical trials. In cancer cells, pramlintide inhibits glycolysis, resulting in cell death and tumor regression. In order to investigate the potential use of pramlintide in combinatory therapies with checkpoint inhibitors, we aimed to study the immune modulatory effect of pramlintide in an immune competent mouse model of spontaneous ultraviolet radiation-induced cuSCC, as well as its effect on human T cells in vitro. To induce cuSCC, SKH-1 hairless mice were subjected to ultraviolet radiation until at least one tumor reached &gt;4mm of diameter. Mice were then treated with 45 µg/kg of pramlintide or vehicle control for 10 days, every other day. Skin-draining lymph nodes, spleen and tumors were harvested for immunophenotyping of the T cell and myeloid compartment by flow cytometry. While the proportion of CD103+ dendritic cells (DCs) and CD3+ T cells remained constant after pramlintide treatment, a significant decrease in the proportion of both monocytic and granulocytic myeloid-derived suppressor cells (m-MDSCs and g-MDSCs) was observed relative to vehicle-control treated mice. Interestingly, pramlintide abolished m-MDSC differentiation from bone marrow progenitors in vitro suggesting that pramlintide may regulate a pathway necessary for m-MDSC development. Purified human CD3+ T cells activated in the presence of pramlintide exhibited a time-dependent increase in intracellular and secreted IFN-γ. Therefore, pramlintide may have immune modulatory effects based on both a reduction in myeloid-dependent suppression and a direct stimulatory effect on T cells that would culminate in superior anti-tumor T cell responses that augment immunotherapeutic approaches for the treatment of cuSCC.
Citation Format: Leticia Tordesillas, Rebecca Hesterberg, Ivannie Ortiz-Rivera, Brittney R. Sell, Omar Chavez Chiang, Kimberly T. Nguyen, Brian L. Murphy, Pearlie K. Burnette, Elsa R. Flores, Kenneth Y. Tsai. Immune modulatory effect of pramlintide for cutaneous squamous cell carcinoma treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1227.
Abstract 123: Evaluating cellular cytotoxicity and potency of antibody-drug conjugates within 3-dimensional tumor models
Authors: Mandavilli Bhaskar S. , Langsdorf Chris , Chen Aimei , Hu Yi-Zhen , Wickett Marcy , Clark Scott T. 
Published: August 2019

Abstract
3-dimensional tumor spheroids provide biochemical conditions that closely resemble the tumor microenvironment in an intact organism. Noninvasive approaches such as fluorescence microscopy and high content analysis are highly advantageous as they allow for the study of these 3-dimensional systems. Here we investigate the penetration and potency of natural killer cells, cytotoxic T cells, and antibody-drug conjugates in three-dimensional models of breast and lung cancer. Unstimulated T cells produced minimal cytotoxicity, similar to untreated spheroids. Activated T cells penetrated and produced significant cytotoxicity throughout cancer spheroids. SKBR3 breast cancer cells form a compact, viable spheroid. Addition of NK cells leads to moderate cytotoxicity, while addition of NK cells and trastuzumab results in substantial cytotoxicity and degradation of spheroid structure. Trastuzumab labeled with iFL pHrodo Red becomes brightly fluorescent following specific endosomal internalization into breast cancer cells, but minimal toxicity is observed. Trastuzumab conjugated with both iFL pHrodo Red and MMAE internalizes into cells and results in cell killing. Fluorescence microscopy combined with novel cell and antibody labeling methods permits investigation of the penetration and potency of natural killer cells, cytotoxic T cells, and antibody-drug conjugates in three-dimensional solid tumor models.
Citation Format: Bhaskar S. Mandavilli, Chris Langsdorf, Aimei Chen, Yi-Zhen Hu, Marcy Wickett, Scott T. Clark. Evaluating cellular cytotoxicity and potency of antibody-drug conjugates within 3-dimensional tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 123.
Abstract 124: Evaluating heterogeneity of tumor microenvironment using single cell RNA sequencing
Authors: Cho Untack , Song Yong Sang , Park Woong-Yang , Lee Hae-Ock , Han Youngjin 
Published: August 2019

Abstract
Tumor microenvironment interacts with cancer cells, causing tumor progression. Tumor microenvironment consists of cellular and acelluar components. We investigated cellular components of tumor microenvironment and heterogeneity of ovarian cancer. We performed single cell RNA sequencing analysis of cellular components of malignant ascites from a patient with advanced ovarian cancer. Among the various cell types including cancer cells, B cells, macrophages and fibroblasts, macrophage was the most dominant in malignant ascites. To determine the heterogeneity of ovarian cancer, we obtained primary ovarian cancer tissue from ovarian cancer patient. We performed single cell RNA sequencing analysis of cellular components derived from ovarian cancer tissue. We determined intra-heterogeneity of ovarian cancer and cellular components of ovarian cancer tissue. Taken together, we determined cellular components of ovarian cancer tissue and ascites and intra-heterogeneity of ovarian cancer. This study can provide insight of tumor microvironment and help understanding of ovarian cancer heterogeneity.
Citation Format: Untack Cho, Yong Sang Song, Woong-Yang Park, Hae-Ock Lee, Youngjin Han. Evaluating heterogeneity of tumor microenvironment using single cell RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 124.
Abstract 1246: Comprehensive RNA interference induced by CRISPR/Cas13a gene editing system in human cancer cells
Authors: Wang Qixue , Wang Yunfei , Tan Yanli , Kang Chunsheng 
Published: August 2019

Abstract
RNA is the intermediate link of central dogma. However, RNA is rarely used as a therapeutic target for its flexible structure and instability. CRISPR/Cas13a is reported as a powerful tool for RNA knockdown. The potential amplification of CRISPR/Cas13a in cancer cells could be further studied. Here we overexpressed the Cas13a protein by lenti-virus vectors in glioma and other cancer cells, and found out that crRNA-EGFP could induce the “collateral effect” after knocking down the target gene. EGFRvIII is a unique EGFR mutant subtype in glioma. CRISPR/Cas13a system could induce cell death of EGFRvIII overexpression glioma cells. Single cell and RNA-seq analysis confirmed the comprehensive RNA interference by CRISPR/Cas13a treatment. Furthermore, CRISPR/Cas13a system could inhibit the formation of glioma intracranial tumor in mice. Our results exhibit the comprehensive RNA interference of CRISPR/Cas13a system in cancer cells, and demonstrated the powerful tumor elimination potential of this system.
Citation Format: Qixue Wang, Yunfei Wang, Yanli Tan, Chunsheng Kang. Comprehensive RNA interference induced by CRISPR/Cas13a gene editing system in human cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1246.
Abstract 125: Digital Spatial Molecular Profiling evidence from H&E stained FFPE that the tumor microenvironment confers gene expression phenotype specificity
Authors: Imler Elliot , Nagle Raymond , Seligmann Bruce 
Published: August 2019

Abstract
Identifying the molecular phenotype of cells within the context of their tumor tissue microenvironment may be critical to understanding cancer and improving patient treatments and outcomes. TempO-Seq® (DOI:10.1371/journal.pone.0178302, doi.org/10.1093/toxsci/kfx153) can be used to profile gene expression from lysates of scraped FFPE tissue down to 2 mm2 areas of 5 μm thick sections. We report use of an in situ TempO-Seq transcriptomic assay carried out on slide-mounted FFPE by an automated stainer (Leica BOND), followed by H&E staining and imaging to perform standard histology. Regions of interest (ROIs) down to 20 μm in diameter are selected at the same time. Probes from these ROIs are automatically eluted, obtaining a detailed gene expression profile. This process is called Digital Spatial Molecular Profiling (DSMP). DSMP was used to profile gene expression from histologically discrete areas within tumor sections. A pan cancer assay of 5,207 genes was used, containing biomarkers for cancer, immune responses and interactions, as well as the S1500v2 whole transcriptome surrogate assay (doi.org/10.1371/journal.pone.0191105), permitting all known molecular pathways to be mapped. Data analysis was carried out using the automated TempO-SeqR™ software package. Replicate areas of cancer, high grade PIN (prostatic intraepithelial neoplasia), normal epithelium, and stroma within prostate cancer FFPE sections were profiled and compared to the profiling of a 2 mm2 scraped area of tissue defined as 100% cancer. What was notable from the DSMP data was that key cancer and immune cell biomarkers were not detected at all in normal, key normal biomarkers were not detected at all in cancer, PIN expressed a collection of normal, cancer and immune biomarkers, and stromal biomarkers were not detected in normal, PIN or cancer glands, while housekeepers were detected in all tissue types. In contrast, housekeeper genes and key biomarkers of cancer, normal, stroma, and immune cells, were all expressed in the 100% pure area of cancer, lacking the biomarker specificity afforded by histologically focused DSMP profiling. The DSMP specificity obtained from the FFPE tissue was striking, leading us to hypothesize that factors within the tumor microenvironment (whether it is adjacent cells, the structural effects of tissue, or sequestration/gradients of extracellular modulators within the tissue) exert molecular specificity on cells within the tissue not present in cultured or dissociated cells devoid of context.
Citation Format: Elliot Imler, Raymond Nagle, Bruce Seligmann. Digital Spatial Molecular Profiling evidence from H&E stained FFPE that the tumor microenvironment confers gene expression phenotype specificity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 125.
Abstract 1265: Validation of the interaction between a candidate compound and the intended drug target by a phenotypic rescue approach
Authors: Geerts Lieke , Grandmoursel Laure , Aarbiou Jamil , DeGroot Jeroen , Schüler Julia , Waddell Ian , Zuurmond Anne-Marie 
Published: August 2019

Abstract
New targets for cancer treatment frequently emerge in literature, but the thorough target validation required to consider these targets for a drug discovery program is often lacking. In pharmacological or genetic perturbation studies using complex biological assays, undesired off-target effects cannot be easily distinguished from the intended mode of action at the desired target. This is especially evident in cancer drug development where it is important to discriminate on-target effects on cell viability from off-target effects resulting in non-specific loss of cellular fitness. Neglecting the possibility of being deceived by off-target effects can have tremendous scientific and financial impact on a drug discovery program. Ideally confidence in a preclinical drug target and a modulating compound is boosted in an early stage by more extensive analysis and validation of the actual drug-target relationship. Rescue of a disease-relevant phenotype by genetic restoration of a target mutation is a gold standard approach in drug discovery by which target validation can be achieved. We aim to follow this approach targeting the BRAF V600E mutation in a number of well described melanoma lines as well as the MAP2K1 Q56P mutation in non-small cell lung cancer cell line H1437. Target validation for both BRAF and MAP2K1 will be addressed by assessing viability, phenotypic changes and sensitivity to compound modulation upon CRISPR/Cas9 repair of the target mutation or by exogenous re-expression of the wildtype variant. Compounds tested will be Vemurafenib for BRAF and Trametinib for MAP2K1. Further investigation into target validity will be done using a physiologically relevant 3D spheroid based co-culture system. Mimicking the tumor microenvironment increases the knowledge about “drug-ability” of a target and sustainability of the target modulation at an early time point in the development process. Such early in-depth validation of the relationship between a compound and the drug target is vital to mitigate the risk of failure at later steps of drug development.
Citation Format: Lieke Geerts, Laure Grandmoursel, Jamil Aarbiou, Jeroen DeGroot, Julia Schüler, Ian Waddell, Anne-Marie Zuurmond. Validation of the interaction between a candidate compound and the intended drug target by a phenotypic rescue approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1265.