bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 572: Genome-scale CRISPR/Cas9 screen identifies factors required for sensitivity to pyrimidine nucleoside analogs
Authors: SARR Awa , Bré Jennifer , Mullen Peter , Blagden Sarah , Um In Hwa , Harrison David J. , Reynolds Paul A. 
Published: August 2018

Abstract
NUC-1031 (NuCana plc), is a phosphoramidate transformation of gemcitabine, which bypasses cancer cell resistance mechanisms to gemcitabine. This compound showed promising results in clinical studies (phase I/II), demonstrating tumor reduction and durable disease control in patients who were refractory to or had relapsed on gemcitabine. Here, we adopted an unbiased approach to uncover genes and pathways involved in gemcitabine and NUC-1031 resistance. We performed a genome-wide knockdown screen using CRISPR/Cas9 technology in the pancreatic cancer cell line MiaPaCa2. Potential candidates from the screen were validated by gene inactivation using individual or combined single guide (sg)RNA targeting sequences. The effect of gene knockdown on NUC-1031 and gemcitabine resistance was assessed by monitoring cell survival after drug treatment using Celigo cytometry to assess cell number. EC50 values were determined using the resulting survival curves. This screen generated a list of 4 candidate genes potentially involved in NUC-1031 resistance. Two candidates were investigated further: DCK and DCTPP1, both involved in pyrimidine metabolism, especially in the maintenance of the dCMP/dCTP pool. DCK knockdown induced significant resistance to gemcitabine (EC50 350 times higher than in control cells) and a degree of resistance to NUC-1031 (EC50 7 times higher than in control cells). A less robust effect was observed when DCTPP1 was inactivated. DCTPP1 knockdown induced a small decrease in sensitivity to NUC-1031 (EC50 1.5 times higher than in control cells).
These results highlight the potential role of dCMP/dCTP pool regulation by DCK and DCTPP1 in sensitivity to pyrimidine nucleoside analogs and may provide a useful biomarker for patient selection.
Citation Format: Awa SARR, Jennifer Bré, Peter Mullen, Sarah Blagden, In Hwa Um, David J. Harrison, Paul A. Reynolds. Genome-scale CRISPR/Cas9 screen identifies factors required for sensitivity to pyrimidine nucleoside analogs [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 572.
Abstract 5737: Genomic drivers of cancer are enriched and mutually exclusive within non-T cell-inflamed tumors
Authors: Olson Brian , Bao Riyue , Fessler Jessica , Luke Jason , Gajewski Thomas F. , Patnaik Akash 
Published: August 2018

Abstract
While immunotherapy has seen dramatic successes in a variety of malignancies, the majority of patients fail to respond. In particular, less than 10% of patients with metastatic, castrate-resistant prostate cancer (mCRPC) respond to immunotherapy. Based on previous work demonstrating robust clinical activity of immunotherapies in patients with a T cell-inflamed tumor microenvironment, we investigated whether non-T cell-inflamed cancers show evidence for distinct genomic alterations that might mediate immune escape. RNA-seq gene expression data were analyzed from two prostate cancer cohorts, The Cancer Genome Atlas (TCGA) of primary tumors (n=437) and a Stand Up to Cancer (SU2C) mCRPC cohort (n=43). These datasets were interrogated for common molecular alterations and their association with non-T cell-inflamed and T cell-inflamed cancers, focusing on copy number deletions of PTEN, RB1/CDKN2A, and activating mutations in CTNNB1 (β-catenin). Similar approaches were used to analyze 30 solid tumor types from TCGA (n=9555). Our analysis identified that 94% of primary prostate cancers harbor a non-T cell-inflamed tumor microenvironment, with only 6% of patients having a T cell-inflamed gene signature. Similar results were found in mCRPC patients from the SU2C cohort. Higher frequencies of PTEN loss and CTNNB1 activation, as well as a significant enrichment of RB1/CDKN2A deletion, were found in non-T cell-inflamed primary and metastatic prostate tumors. Moreover, we observed a direct correlation between the expression of PTEN/RB1 and CD8A expression within the tumor microenvironment. Strikingly, analysis of 30 human cancers revealed that loss of PTEN and/or RB1/CDKN2A correlates with T-cell exclusion across multiple malignancies. When combined with β-catenin pathway activation, we found that these alterations are mutually exclusive, with only 1% of non-T cell-inflamed cancers sharing all three mechanisms, 24% sharing two out of the three, and 75% of the samples harboring only one mechanism. Taken together, these data reveal that deregulated PTEN/PI3K, Rb and Wnt-β-catenin signaling networks are enriched in a mutually exclusive manner within non-T cell-inflamed cancers, suggesting that such cancers evolutionarily co-opt nonredundant signaling pathways to achieve a common goal of immune evasion. Targeting these pathways pharmacologically may provide an opportunity to enhance responsiveness to immunotherapy across multiple malignancies.
Citation Format: Brian Olson, Riyue Bao, Jessica Fessler, Jason Luke, Thomas F. Gajewski, Akash Patnaik. Genomic drivers of cancer are enriched and mutually exclusive within non-T cell-inflamed tumors [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 5737.
Abstract 574: BRAF
V600E mutation and loss of CDX2 synergize in serrated colorectal tumorigenesis
Authors: Sakamoto Naoya , Feng Ying , Hattori Takuya , Shimoda Masayuki , Ishikawa Akira , Honma Ririno , Hinoi Takao , Egi Hiroyuki , Ohdan Hideki , Okada Yasunori , Fearon Eric , Yasui Wataru 
Published: August 2018

Abstract
While many CRCs arise from adenomatous polyps through what we call “adenoma-carcinoma sequence,” it has been estimated that up to 20% of CRCs likely evolve from an alternative pathway, so-called ‘‘serrated pathway.' However, only 8-10% of CRCs display definitive serrated morphology at diagnosis. We previously examined expression of differentiation and molecular markers that are most likely to be involved in serrated tumor development by using 36 serrated CRCs and found CDX2 loss or BRAF mutations often together. We then generated a mouse model that can be induced concurrent biallelic inactivation of Cdx2 (Cdx2-/-) and expression of mutant BRAFV600E in adult mouse colon epithelium, and the Cdx2-/-/BrafV600E tumors showed a quite similar phenotype to that of CDX2-negative serrated CRCs. Through the validation of global gene expression profile including the mouse models and human CRCs, we focused on ADAM28 as a candidate because ADAM28 was significantly upregulated in Cdx2-/-/BrafV600E tumor and CRCs with low CDX2 expression and BRAFV600E mutation. We examined ADAM28 expression using 12 CRC cases with BRAFV600E mutation (8 of 12 displayed serrated feature) and 12 CRC cases with KRAS codon 12/13 mutation and found that ADAM28 was specifically upregulated in BRAF mutant CRC cases. Among 10 CRC cell lines (DLD-1, Lovo, SW48, SW480, SW837, SW1116, Caco2, RKO, HT-29, HCT-116), only HT-29, which has many phenotypic and genetic similarities to serrated CRC, showed a robust expression of membranous type ADAM28, and 9 of 10 CRC cells, except for RKO, showed weak to modest expression of active-form ADAM28. Further in-depth studies are ongoing to clarify the solid evidences, especially the utility of ADAM28 as a diagnostic marker for serrated CRCs and the direct effect of ADAM28 onto cell growth of CRC cells using ADAM28-specific antibody. We present a novel transgenic model of human serrated CRC to highlight the suitability of centering on CDX2 loss and BRAFV600E in the pathogenesis. This model has a great potential to figure out the mechanisms underlying in serrated tumor progression and identify the candidates of new biomarkers and therapeutic targets of CRCs with serrated morphology.
Citation Format: Naoya Sakamoto, Ying Feng, Takuya Hattori, Masayuki Shimoda, Akira Ishikawa, Ririno Honma, Takao Hinoi, Hiroyuki Egi, Hideki Ohdan, Yasunori Okada, Eric Fearon, Wataru Yasui. BRAFV600E mutation and loss of CDX2 synergize in serrated colorectal tumorigenesis [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 574.
Abstract 5755: Cancer immunity contributes to genome stability by suppressing L1 retrotransposition in gastrointestinal cancers
Authors: Jung Hyunchul , Choi Jung Kyoon , Lee Eunjung Alice 
Published: August 2018

Abstract
Long interspersed nuclear element-1 (L1) retrotransposons are normally suppressed in somatic tissues, mainly by DNA methylation and antiviral defense. However, L1s can be de-suppressed in cancers to act as insertional mutagens and cause genomic instability by creating DNA double-strand breaks and chromosomal rearrangements. Whereas the frequency of somatic L1 insertions varies greatly among individual tumors, much remains to be learned about underlying genetic, cellular, or environmental factors. Here, our pan-gastrointestinal cancer genome analyses for stomach, colorectal, and esophageal tumors identified multiple correlates of L1 activity. Clinical indicators of tumor progression, such as tumor grade and patient age, showed positive association. Potential L1 expression suppressors such as TP53 and DNMT1, a DNA methyltransferase, were inactivated in tumors with frequent L1 insertions. Importantly, tumors with high immune activity, for example, due to viral infection or high tumor-antigen load, tended to carry a low number of L1 insertions in their genomes with high expression levels of L1 suppressors such as APOBEC3s and SAMHD1. Our analysis of the transcriptional effects of intragenic retrotransposon insertions demonstrated an increased risk of gene disruption in retrotransposition-prone cancers. In particular, we found a splicing-disrupting L1 insertion in an exon of MOV10, a key L1 suppressor, which caused exon skipping with evidence of nonsense-mediated decay in a tumor with a high L1 insertion load. Our results indicate that cancer immunity may contribute to genome stability by suppressing L1 retrotransposition, particularly in gastrointestinal cancers.
Citation Format: Hyunchul Jung, Jung Kyoon Choi, Eunjung Alice Lee. Cancer immunity contributes to genome stability by suppressing L1 retrotransposition in gastrointestinal cancers [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 5755.
Abstract 5763: Large-scale use of knockout validation to confirm antibody specificity to key oncology targets
Authors: Heaton Sam , Sassi Monica , Solache Alejandra , Hamilton Bruce , Dave Sambhav 
Published: August 2018

Abstract
Antibodies are the most common tools in basic science and clinical research. Over the past several years there has been an ongoing discussion around antibody validation in light of poor experimental reproducibility between laboratories. This is in part due to the cross-reactivity between antibodies and off-target proteins and the variability between different antibody batches. As a result, experimental irreproducibility leads to wasted resources and compromises the advancement of science. In response to this, Abcam has introduced knockout (KO) validation to help produce target-specific antibodies. This initiative uses KO cells lines made possible through a partnership with Horizon Discovery. Target genes are mutated via CRISPR-Cas9 within a haploid cell line. This results in a frameshift and a complete loss of gene expression. These KO cell lines provide a true negative control for antibody validation as a lack of signal confirms that the antibody binds to its intended target. As a result, both antibody specificity and reproducibility on a large scale can be addressed. We have KO-validated over a thousand antibodies, including several that are relevant to immuno-oncology research. Examples of such targets are the ERK1/2 pathway, which regulates cell survival, proliferation and cell death. Inhibition of this pathway is an attractive target for the treatment of malignant tumors with increased ERK1/2 activity. Similarly, Ki67 expression is strongly associated with tumor cell proliferation and can be used as a marker for tumor aggressiveness. Finally, overexpression of vimentin in tumors correlates with increased growth and invasion, leading to poor prognosis. It is imperative that reproducible data can be produced on these targets to further our understanding of tumor biology and patient prognosis. Here we present the data for antibodies to these key targets that have been validated in both flow cytometry and immunocytochemistry. The antibodies have been tested in KO and wild-type cells to confirm their specificity. The antibodies shown gave signal in wild-type cells but showed complete loss of signal when tested in knockout cell lines. By providing researchers with reliable and specific antibodies that work first time we hope to minimize wasted resources and improve reproducibility.
Citation Format: Sam Heaton, Monica Sassi, Alejandra Solache, Bruce Hamilton, Sambhav Dave. Large-scale use of knockout validation to confirm antibody specificity to key oncology targets [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 5763.
Abstract 5766: Multifunctional biologics for targeted T-cell therapy based on in vivo matured fully human VH domains
Authors: Mcguinness Brian , Legg James , Bland-Ward Phil , Pack Peter 
Published: August 2018

Abstract
Crescendo Biologics has created a proprietary transgenic mouse devoid of any antibody light chains from which it generates highly diverse fully human VH domain (‘Humabody') building blocks. In vivo maturation optimizes Humabody potency and develops superior biophysical properties. Their small size (13kDa) and high stability permits Humabody assembly into an almost limitless array of multifunctional formats optimally configured for therapeutic efficacy. These small versatile single VH domain building blocks permit the rapid exploration of a vast range of 3D format space to identify optimal therapeutic solutions. This fully modular plug & play approach lacks the constraints of traditional mAbs and enables a radical rethink of how a multifunctional molecule can be designed and assembled to deliver enhanced therapeutic benefit. Such molecules are capable of target engagement that is unachievable using regular mAbs. Using Humabody VH addressing key targets in the immune-oncology space, Crescendo has exemplified the potential for optimally configured molecules to deliver enhanced efficacy both in vitro and in vivo. Examples include: CB307, a unique T-cell engaging format with a novel mode of action. CB201, a biparatopic antagonist which ‘handcuffs' PD1: one domain binding and blocking PD1 from engaging with its ligands, the other binding a nonblocking epitope. With a binding affinity of 175pM and a unique ability to localise rapidly to PD-1 positive T-cells, CB201 demonstrates significantly enhanced in vivo efficacy over IgG-based PD-1 antagonists in a PDX tumour model in NSG mice. CB108, a half-life extended paratopic Humabody binding PSMA has demonstrated superior tumour targeting with enhanced internalisation and highly efficient accumulation in target-positive tumours with up to 18 percent ID per g recorded in a 24hr imaging study. These data support the progression of highly differentiated therapeutics into the clinic.
Citation Format: Brian Mcguinness, James Legg, Phil Bland-Ward, Peter Pack. Multifunctional biologics for targeted T-cell therapy based on in vivo matured fully human VH domains [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 5766.
Abstract 5772: Engineered lectins to treat cancer
Authors: Murarasu Thomas , Johannes Ludger 
Published: August 2018

Abstract
Targeted delivery of cytotoxic compounds to tumors has become one of the most dynamic areas of research and development in the cancer therapy field. In this context, glycosphingolipids (GSLs) represent a promising class of tumor markers. Indeed, cancer patients have altered GSL expression patterns on their tumoral cells compared to healthy tissue (Krengel et al., 2014). In a recent prioritization of cancer antigens by the National Cancer Institute at Rockville (USA), 4 out of 75 were GSLs (GD2, GD3, fucosyl-GM1, and GM3), with GD2 arriving already at the 12th position (Cheever et al., 2009). However, GSLs are only rarely addressed in the context of tumor targeting, obtaining GSL specific antibodies being a notorious difficult task. An exception is the anti-GD2 antibody, dinutuximab, which entered the market for the treatment of high-risk neuroblastoma patients, which is unfortunately associated to dose-limiting acute toxicity (Yu et al., 2010). This project aims at developing a novel class of therapeutic products for the delivery of therapeutic compounds by targeting tumor-specific GSLs. Our products are based on a naturally occurring GSL-binding lectin with intrinsic tumor targeting capacity. We will rely on a proprietary technology to derive products which are tuned to transport cytotoxic compounds specifically into cancer cells. As a proof of concept, we apply our technology to a tumor-specific GSL, GD2, to generate a therapeutic formulation against neuroblastoma, one of the most frequent cancer in children under 5 years old. Our technology has truly groundbreaking potential as, in principle, it can apply to any GSL to specifically target several common tumors.
Citation Format: Thomas Murarasu, Ludger Johannes. Engineered lectins to treat 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 5772.
Abstract 5773: Sequencing and cloning IDH1 R132H-targeted monoclonal T cell receptors from CD4+ T cells facilitated by opto-electric-positioning technology
Authors: Smith Duane , Watchmaker Payal , Stadler Guido , Marks Natalie , Bronevetsky Yelena , Chapman Keviin , Okada Hideho 
Published: August 2018

Abstract
Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) are enzymes that catalyze the conversion of isocitrate to α-ketoglutarate, while reducing NADH to NADPH. More than 80% of low-grade gliomas and secondary glioblastomas harbor point mutations in IDH. The R132H mutation is the most common mutation in IDH1, and vaccination with the mutant peptide elicited an MHC class II-specific antitumor response, suggesting mutant IDH1 as a potential target for immunotherapy (1). Discovering monoclonal T cell receptors (TCRs) that specifically recognize the R132H mutation is a key but challenging step towards viable immunotherapy for glioma/glioblastomas. Using opto-electric-positioning (OEP) technology in a chip-based, NanoPen culture environment, we have successfully identified and isolated a monoclonal T cell that specifically recognizes the R132H mutant IDH1 peptide. We cultured and identified monoclonal CD4+ T cells on chip, stimulated by monocyte-derived dendritic cells, pulsed with R132H IDH1 peptide. Activated, CD4+ T cells were selectively exported from the chip and their T-cell receptors (TCRs) were subsequently deep sequenced. The most likely pairs of alpha and beta TCR chains were cloned into mammalian expression vectors for functional validation in vitro, producing a TCR that specifically binds mutant IDH1 tetramer. Taken together, we show that the combined platform of the OEP and nanofluidic device provides a powerful solution to help identify cell type-specific, monoclonal T cells that can be exported and sequenced to reveal distinct TCRs, which in turn can be cloned, expressed and validated for future immunotherapies.
Reference: 1. Schumacher et al., Nature 2014;512:324-27.
Citation Format: Duane Smith, Payal Watchmaker, Guido Stadler, Natalie Marks, Yelena Bronevetsky, Keviin Chapman, Hideho Okada. Sequencing and cloning IDH1 R132H-targeted monoclonal T cell receptors from CD4+ T cells facilitated by opto-electric-positioning technology [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 5773.
Abstract 5778: Preclinical evaluation of TQB3616, a highly potent and selective small-molecule CDK4/6 inhibitor
Authors: Zhaobing Xu , Lihong Hu , Yingchun Liu , Ding Charles Z. , Zhu Xiaoyu , Chen Chen , Zhu Yusong , Wu Jiahu , Wu Dongdong , Chen Shuhui , Zhang Xiquan , Yang Ling , Tian Xin 
Published: August 2018

Abstract
Objective: The G1 restriction point is critical for regulating the cell cycle and is controlled by the retinoblastoma protein (Rb) pathway (CDK4/6-cyclin D1-Rb-p16/ink4a). Selective CDK4/6 inhibitors, such as palbociclib and ribociclib have been approved by US FDA in combination with letrozole to treat patients with HR+/Her2- breast cancer, and selective CDK4/6 inhibitor LY2835219 is in Phase 3 trials for the same and related indications. Here, we disclose TQB3616 for the first time, a novel selective, potent, oral inhibitor of CDK4/6.
Method: The anti-proliferative activity of TQB3616 was evaluated in a panel of 18 Rb-proficient cell lines in a 72-hour viability assay. Daily oral administration was used to evaluate in vivo antitumor activity of TQB3616 in the MCF-7 cell-derived xenograft (CDX) breast cancer model. Effect on CDK4/6-cyclin D1-Rb signaling was assessed by western blot analysis of downstream effector protein p-Rb. In vivo antitumor activity of TQB3616 was also tested in a patient-derived xenograft (PDX) lung cancer model LU-01-0393.
Result: TQB3616 displayed potent anti-proliferative activity in 8 of 18 Rb-proficient cancer cell lines (&gt;50% inhibition at 0.3 µM). Inhibition of p-Rb in the tumor samples was verified by western blot analysis. TQB3616 showed in vivo antitumor activity in the MCF-7 CDX model with TGI of 60% @7.5 mpk and 93% @15 mpk, better than palbociclib (TGI = 52% @20 mpk, 80% @40 mpk) and LY2835219 (TGI = 45% @7.5 mpk, 76% @15 mpk). TQB3616 also showed good in vivo antitumor activity in the LU-01-0393 lung cancer PDX model with 65% of TGI @35 mpk.
Conclusion: TQB3616 is a potent and selective CDK4/6 inhibitor and shows excellent antitumor activity in preclinical tumor models. These results warrant TQB3616 going to the clinic for exploration of its potential for treating HR+/Her2-/Rb+ breast cancer as well as other Rb+ cancer types.
Citation Format: Xu Zhaobing, Hu Lihong, Liu Yingchun, Charles Z. Ding, Xiaoyu Zhu, Chen Chen, Yusong Zhu, Jiahu Wu, Dongdong Wu, Shuhui Chen, Xiquan Zhang, Ling Yang, Xin Tian. Preclinical evaluation of TQB3616, a highly potent and selective small-molecule CDK4/6 inhibitor [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 5778.