bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1299: Potential antitumor effects of a Golgi disrupting agent, M-COPA, via targeting cell-extracellular matrix interaction under the spheroid culture conditions
Authors: Ohashi Yoshimi , Takeuchi Kazuma , Okamura Mutsumi , Akatsuka Akinobu , Shiina Isamu , Yoshimatsu Kentaro , Dan Shingo 
Published: August 2019

Abstract
The Golgi apparatus plays an essential role in the transport, processing, and sorting of cell surface proteins. We previously demonstrated that a Golgi disrupting agent, 2-methylcoprophilinamide (M-COPA), exhibited antitumor effect in human cancer cells in vitro and in vivo; however, in vivo antitumor efficacy of M-COPA did not simply reflect its in vitro efficacy, probably due to the lack of microenvironmental features of tumor tissues in the monolayer culture conditions. To bridge the gap between in vitro and in vivo efficacies, we exploited 3-dimensional (3D) spheroid culture models, which can recapitulate physiological characteristics of tumor tissues; i.e., nutrient/oxygen gradient, cell-cell interaction and cell-extracellular matrix (ECM) interaction, if cancer cells synthesize their own ECM molecules. Interestingly, human gastric cancer MKN1 cells displayed hypersensitivity to M-COPA under the 3D culture conditions compared to those in the monolayer culture conditions. Especially, we found that M-COPA caused loss of spheroid integrity. We previously demonstrated that M-COPA exerted antitumor effects via inhibiting intracellular transport of receptor tyrosine kinases onto the cell surface. Therefore, we examined the involvement of cell adhesion molecules in the antitumor effect of M-COPA. As a result, we found that specific integrins, which serve as cell surface receptors responsible for cell-ECM adhesion, were overexpressed and their downstream signaling molecules such as Src, Akt and MEK/ERK were highly phosphorylated in the cells under the 3D culture conditions compared to those under the monolayer culture conditions. Upon exposure to M-COPA, cell surface expression of these integrins was efficiently decreased and the downstream signaling molecules were dephosphorylated along with loss of spheroid integrity. Moreover, expression knockdown or neutralizing antibody of the integrins clearly suppressed sphere formation of MKN1 cells. These results suggest that M-COPA exerted in vivo antitumor effects via targeting specific integrins that mediate cell-matrix adhesion and its downstream intracellular signaling pathway observed in 3D spheroid culture models.
Citation Format: Yoshimi Ohashi, Kazuma Takeuchi, Mutsumi Okamura, Akinobu Akatsuka, Isamu Shiina, Kentaro Yoshimatsu, Shingo Dan. Potential antitumor effects of a Golgi disrupting agent, M-COPA, via targeting cell-extracellular matrix interaction under the spheroid culture conditions [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 1299.
Abstract 1303: Targeted inhibition of galectin-1 suppresses glioblastoma growth
Authors: Cachia David , Chatterjee Arindam Rano , Vandergrift William Alex , Patel Sunil J. , Rabinovich Gabriel A. , Das Arabinda 
Published: August 2019

Abstract
Background: Galectin-1 (Gal1), a carbohydrate-binding protein is implicated in cancer cell proliferation, invasion and tumor angiogenesis. An earlier report from our laboratory demonstrated that glioblastoma (GB) cells express high levels of Gal-1, which promotes tumor progression through upregulation of CXCR4 viaNF-κB in in vitro GB models. Recently, several Gal1-targeting compounds have emerged. OTX008 is a calixarene derivative designed to bind the Gal1 amphipathic β-sheet conformation. Our study aimed to validate the effect of the non-peptidic galectin-1 inhibitor OTX008 in human GB in relevant pre-clinical models.
Methods: In vitro cell culture and in vivo GL261 murine models of GB were utilized to assess efficacy of treatment with OTX008 via Alzet osmotic pumps. To investigate the mechanistic effect of OTX008 on GB cells, we used RT-PCR and western blots techniques. Magnetic resonance imaging (MRI), and immunohistochemistry (IHC)-staining methods were used to detect tumor growth in in vivo GL261 murine model following OTX008 treatments.
Results: In cultured human and mouse GB cells, OTX008 inhibited proliferation and invasion at micromolar concentrations. We also found that the anti-proliferative effects correlated with Gal1 expression in human and mouse GB cell lines. Furthermore, OTX008 inhibited Gal1 expression and AKT-dependent survival pathways, and decreased CXCR4 expression. In vivo, continued 100ng/kg OTX008 treatment via Alzet osmotic pumps over 14 days reduced tumor growth of GL261 murine model after 3 weeks of implantation. OTX008 treatment was associated with downregulation of Gal1 and Ki67 in treated tumors, as well as decreased micro-vessel density and VEGFR2 expression.
Conclusion: These findings suggest that targeting galectin-1 may be an effective approach in the treatment of GB patients.
Citation Format: David Cachia, Arindam Rano Chatterjee, William Alex Vandergrift, Sunil J. Patel, Gabriel A. Rabinovich, Arabinda Das. Targeted inhibition of galectin-1 suppresses glioblastoma growth [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 1303.
Abstract 1310: Abrogation of KRas-addicted tumors by GSK3 suppression-mediated upregulation of β-catenin and c-myc
Authors: Kazi Aslamuzzaman , Xiang Shengyan , Yang Hua , Delitto Daniel , Trevino Jose , Jiang Rays H. , Ayaz Muhammad , Lawrence Harshani , Kennedy Perry , Sebti Said M. 
Published: August 2019

Abstract
The significant involvement of mutant KRas in human cancer development underscores the need to develop approaches that disable mutant KRas-driven tumors. Targeting KRas directly is challenging, and such identifying vulnerabilities specific for mutant KRas tumors is an important alternative approach. In this study, we discovered that glycogen synthase kinase 3 (GSK3) is required for the in vitro and in vivo growth and survival of human mutant KRas-dependent tumors but not for mutant KRas-independent tumors. Pharmacological inhibition with the GSK3 inhibitor SB as well as siRNA depletion of GSK3 lead to tumor suppression that is mediated at least in part by inhibition of the phosphorylation of the GSK3 substrates c-Myc on T58 and β-catenin on S33/S37/T41. CRISPR/Cas9 targeted knock out studies demonstrated that c-Myc and β-catenin upregulation mediate the antitumor activity of SB. Importantly, GSK3 blockade inhibits the in vivo growth of G12D, G12V, and G12C mutant KRas primary and metastatic patient-derived xenografts from pancreatic cancer patients who progressed on chemo- and radiation therapies. This discovery warrants advanced pre-clinical and clinical investigations of GSK3 inhibitors in mutant KRas-dependent cancers.
Note: This abstract was not presented at the meeting.
Citation Format: Aslamuzzaman Kazi, Shengyan Xiang, Hua Yang, Daniel Delitto, Jose Trevino, Rays H. Jiang, Muhammad Ayaz, Harshani Lawrence, Perry Kennedy, Said M. Sebti. Abrogation of KRas-addicted tumors by GSK3 suppression-mediated upregulation of β-catenin and c-myc [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 1310.
Abstract 1329: Preclinical evaluation of TAS6417 as a highly effective, pan-mutation-selective EGFR tyrosine kinase inhibitor
Authors: Udagawa Hibiki , Hasako Shinichi , Ohashi Akihiro , Abe Naomi , Haruma Tomonori , Komori Toshiharu , Terasaka Miki , Fujita Ryoto , Funabashi Kaoru , Yasuda Hiroyuki , Miyadera Kazutaka , Goto Koichi , Costa Daniel B. , Kobayashi Susumu S. 
Published: August 2019

Abstract
Objectives: Three generations of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have developed to treat advanced non-small cell lung cancer (NSCLC) with EGFR mutations. However, each generation of TKI has different spectrum of activity against the different mutations. Currently, no EGFR TKIs are approved for NSCLC with EGFR insertion 20 mutation. Previously, we have shown that TAS6417, a novel EGFR TKI, is effective for cells harboring EGFR insertion mutations in vitro and in vivo. In this study, we asked whether TAS6417 is effective for tumors harboring other EGFR mutations observed in clinic.
Methods: Genetically engineered Ba/F3 cells expressing EGFR mutants, lung cancer cell lines including newly established cell lines established from tumors harboring EGFR insertion 20 were used to evaluate efficacy of erlotinib, afatinib, osimertinib, poziotinib, and TAS6417 by cell viability analyses. The selectivity indexes (the wild type EGFR/mutant EGFR ratio) were calculated to predict a therapeutic window for each TKI. Effects of each EGFR TKI on EGFR signaling and apoptosis were evaluated by western blotting. Finally, murine xenograft models were used to evaluate efficacy of TAS6417 and all generation of EGFR TKIs for the treatment of NSCLC with EGFR mutations.
Results: Cell viability assays demonstrate that TAS6417 was as potent as poziotinib against common EGFR mutations (L868R and exon 19 deletions) and the most potent against cells harboring the T790M resistant mutations. In addition, TAS6417 was effective in cells harboring EGFR rare mutations (G719X L861Q, and S768I). Even though IC50s were higher than those of poziotinib in cells harboring EGFR insertion 20, the selectivity indexes (the wild type EGFR/mutant EGFR ratio) were higher in TAS6417, indicating a wider therapeutic window. TAS6417 was effective in mice injected with cells harboring EGFR mutations with no body weight loss.
Conclusions: Our preclinical results confirm that TAS6417 is a potent EGFR TKI with a broader spectrum of activity and a wider therapeutic window and support clinical trials in the near future.
Citation Format: Hibiki Udagawa, Shinichi Hasako, Akihiro Ohashi, Naomi Abe, Tomonori Haruma, Toshiharu Komori, Miki Terasaka, Ryoto Fujita, Kaoru Funabashi, Hiroyuki Yasuda, Kazutaka Miyadera, Koichi Goto, Daniel B. Costa, Susumu S. Kobayashi. Preclinical evaluation of TAS6417 as a highly effective, pan-mutation-selective EGFR tyrosine kinase inhibitor [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 1329.
Abstract 1347: Peripheral blood TCRB chain convergence in chronic viral infection and cancer: Emerging trends from a novel immune repertoire biomarker
Authors: Looney Timothy J. 
Published: August 2019

Abstract
Background T cell receptor (TCR) convergence refers to the phenomenon whereby antigen-driven selection enriches for TCRs having shared antigen specificity but different nucleotide sequences. Previous work has demonstrated the potential utility of TCR convergence as a predictive biomarker for response to checkpoint blockade and dendritic cell based immunotherapy for cancer. The extent to which convergence arises owing to chronic viral infection is not yet established. Here we sought to identify features of chronic cytomegalovirus (CMV) infection using TCRB profiling of peripheral blood (PBL) total RNA.
Methods Total RNA from PBL was obtained from 35 blood donors of known CMV status, then used for TCRB sequencing via the Oncomine TCRB-LR assay (amplicon spanning CDR 1, 2 and 3) and the Ion Torrent S5. In parallel, we prepared libraries via the Oncomine TCRB-SR assay (CDR3 only). Data were used to identify TCRB repertoire features correlated with CMV status and compare repertoire features across the two assays. For context, we compare CMV-related convergence to previous reports detailing convergent T cell responses in individuals with cancer.
Results T cell clone evenness was reduced in CMV positive individuals irrespective of age, predictive of CMV status (AUC=.86, p=2E-4, Wilcoxon), and strongly correlated between LR and SR assays (Spearman cor=.96). TCR convergence was elevated in CMV positive individuals and uncorrelated with evenness (Spearman cor = -.03) such that the combination of convergence and evenness improved the performance of a logistic regression classifier (AUC= .93).
Conclusions We identify reduced T cell evenness and elevated TCR convergence as features of chronic CMV infection. CMV infection appears to significantly alter the T cell repertoire, suggesting that CMV status may be required for proper interpretation of T cell expansion in the context of immunotherapy for cancer. TCR convergence may detect T cell responses to a broad range of viral and tumor neoantigens and thus may serve as a particularly useful biomarker for the identification of immunogenic tumors having few genetic alterations.
Citation Format: Timothy J. Looney. Peripheral blood TCRB chain convergence in chronic viral infection and cancer: Emerging trends from a novel immune repertoire biomarker [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 1347.
Abstract 1360: MMP-degraded vimentin is elevated in serum from patients with non-small cell lung cancer - development and biological validation of a new serum biomarker
Authors: Nissen Neel I. , Karsdal Morten , Willumsen Nicholas 
Published: August 2019

Abstract
Background: Non-small cell lung cancer (NSCLS) accounts for 85% of lung cancers. The five-year survival rate decreases from 47% in stage I to 1% in stage IV, emphasizing the need for early detection. In lung cancer, the intermediate filament protein vimentin has been shown to be applicable for clinical pathology and associate with epithelial-to-mesenchymal transition. Vimentin has been found extracellularly and may be a target for proteolytic cleavage by matrix metalloproteases (MMPs). In fact, a MMP-degraded and citrullinated vimentin fragment (VICM) has shown biomarker potential in serum from patients with NSCLC. The aim of this study was to determine whether (un-citrullinated) MMP-degraded vimentin (VIM) can serve as a biomarker in patients with NSCLC.
Methods: A monoclonal antibody was raised against a MMP-generated vimentin fragment identified by mass spectrometry. A competitive enzyme-linked immunosorbent assay (ELISA) was developed and technically validated. Levels of VIM were measured in serum from patients with NSCLC (n=40) and healthy controls (n=20) and compared to the equivalent citrullinated vimentin fragment (VICM).
Results: The VIM ELISA assay was highly specific to MMP-degraded vimentin and with no cross-reactivity to VICM and the full-length vimentin. VIM was significantly elevated in serum from patients with NSCLC (p=0.0003) compared to controls whereas VICM was not (p=0.0741). In support, the diagnostic accuracy (AUROC) for VIM was 87.1% (p=&lt;0.0001) vs 64% (p=0.0685) for VICM.
Conclusion: The newly developed VIM assay detected significantly elevated levels of MMP-degraded vimentin in serum from patients with NSCLC compared to controls. Furthermore, this non-citrullinated vimentin fragment (VIM) shows stronger accuracy in separating NSCLC patients from healthy controls than the citrullinated equivalent (VICM), suggesting its biomarker potential and biological relevance in NSCLC. Future studies are needed to validate and expand on these findings.
Citation Format: Neel I. Nissen, Morten Karsdal, Nicholas Willumsen. MMP-degraded vimentin is elevated in serum from patients with non-small cell lung cancer - development and biological validation of a new serum biomarker [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 1360.
Abstract 1364: A Non-Small Cell Lung Cancer Reference Material
Authors: Tomson Farol L. , Huang Catherine , Clement Omo , Garlick Russell , Anekella Bharathi 
Published: August 2019

Abstract
Lung cancer is the leading cause of cancer death in the United States as well as globally. The major diagnosis (~85%) of lung cancer patients is non-small cell lung carcinoma (NSCLC). About 10-50% of NSCLCs have several activating EGFR driver mutations which have been clinically validated as therapeutic biomarkers for anti-EGFR drugs. Identifying these driver mutations through liquid biopsies is a promising alternative to traditional biopsies; however, the precision of mutation analysis for some of these targets, e.g., T790M, especially in advanced-stage metastatic NSCLC patients remains a challenge. To address this, we developed a platform of single and low complexity, highly patient-like circulating tumor DNA (ctDNA) EGFR reference standards designed for PCR assays that are used for EGFR-based patient testing. We mixed genomic DNA from the highly characterized human cell line (GM24385) with four synthetic EGFR variant-containing DNA sequences: T790M, L858R, G719S, and an ex19 deletion, in both individual and combined format. Using digital PCR we were able to precisely blend the material at the defined variant allele frequencies of 1% and 0.1%. In addition, wild-type reference material without any synthetic EGFR variants was also created as a comparable negative control. The materials were size-selected (160-170bp) after fragmentation for more patient-like ctDNA size characteristics. After size-selection the material is further refined to improve conversion efficiency. In order to make the material comparable to native ctDNA, such as that isolated from cancer patients, we encapsulated the DNA fragments into a synthetic plasma matrix. The process of DNA size selection followed by encapsulation and formulation into a synthetic plasma matrix enhances the commutability of these reference standards and improves the long-term stability of the samples to at least two years. The allele frequencies of the reference materials were confirmed by both dPCR and NGS. The Archer Reveal ctDNA 28 Kit was used for NGS library preparation while an Illumina MiSeq, using v2 (2x150 bp) PE chemistry reagents, was used for sequencing. Additional evaluation of these materials was conducted by laboratories that provide EGFR RT-PCR tests for patient anti-EGFR therapy stratification. The data from the dPCR, NGS and RT-PCR assays were comparable and highlight the broad compatibility of these EGFR ctDNA reference standards on a variety of assay testing platforms for NSCLC.
Citation Format: Farol L. Tomson, Catherine Huang, Omo Clement, Russell Garlick, Bharathi Anekella. A Non-Small Cell Lung Cancer Reference Material [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 1364.
Abstract 1379: Insights into analytical factors impacting variant concordance of plasma-tumor NGS testing
Authors: Stetson Daniel 
Published: August 2019

Abstract
Next generation sequencing (NGS) of circulating free DNA (cfDNA) is transforming the treatment paradigm in oncology. Sensitive non-invasive cfDNA assays could revolutionize clinical trial design with improved patient safety. However, there are substantial challenges to working with cfDNA, particularly in an early-stage setting. It has been shown that solid tumors from early stage disease shed less DNA into the bloodstream making the detection of somatic variants difficult. Because of this, the current landscape of commercial cfDNA assays are focused on advanced stage patients and may lack the sensitivity and specificity to interrogate early stage samples. To understand the limitations of the currently available cfDNA assays on early-stage oncology samples, we have designed several studies to examine the factors that impact the concordance of plasma-tumor testing and hinder the ability to detect low frequency somatic variants. Three comparison studies have been completed examining both the inter- and intra- variability of commercially available plasma-based NGS assays. Two inter-vendor studies utilized matched sets of 24 tumor-plasma samples purchased from a commercial bio-banking company. The plasmas were aliquoted into 2 ml volumes and sent to the commercial vendor for sequencing with the currently available cfDNA assay, while the tumor-normal tissues were sequenced by an external tumor sequencing vendor. The unique study design allowed for confident determination of true positive, false positive and importantly, false negative variants from the reported plasma variants. The third comparison study also used commercially purchased early-stage patient and normal samples to examine the intra-vendor assay reproducibility. Summarizing the results from all three studies, we found that the majority of discordant variants were from technical rather than biological factors. The technical factors identified include mutational bias, bioinformatic filtering, and variant annotation, while the biological factors found were clonal hematopoiesis and tumor heterogeneity. Through a detailed examination of the discordant variants from the first inter-vendor comparison, we believe that less than 15% of discordance was from biological sources. Overall these findings differ from the current literature which suggests that the sub-clonal nature of a tumor is the cause of most discordance in plasma testing. We have begun to establish guidelines to identify these technical factors in our current and past datasets, with the hope of liquid biopsy testing improvement for early-stage cancer patients.
Citation Format: Daniel Stetson. Insights into analytical factors impacting variant concordance of plasma-tumor NGS testing [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 1379.