bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 614: VB4-845 tumor cell killing in a combination study with the anti-PD-1, Nivolumab
Authors: Dillon Rachelle Lee , Chooniedass Shilpa , Premsukh Arjune , MacDonald Glen , Cizeau Jeannick , Adams Gregory A. 
Published: July 2017

Abstract
VB4-845 is a Targeted Protein Therapeutic (TPT) comprised of a scFv fragment specific for the Epithelial Cell Adhesion Molecule (EpCAM) genetically fused to a truncated form of Pseudomonas exotoxin A (ETA), via a flexible linker. Due to the inherent immunogenicity of the ETA moiety, VB4-845 is only used for the treatment of loco-regionally accessible tumors and is currently in a Phase III clinical trial for the treatment of high grade, non-muscle invasive bladder cancer. In a Phase I study in late stage squamous cell carcinoma of the head and neck, direct injection of VB4-845 led to shrinkage of the principal injected tumor, as well as non-targeted tumors in some patients, suggesting the activation of a T cell-mediated anti-tumor response through cross-priming. Only cells undergoing immunogenic cell death, or ICD, are capable of stimulating cross-priming. ICD is characterized by distinct “eat-me” signals such as the release of ATP and HMGB1, and cell surface translocation of calreticulin, an endoplasmic reticulum chaperone protein. To evaluate whether VB4-845-mediated cell killing results in ICD events, treated tumor cell lines were assessed for these distinct signaling molecules. In vitro studies using flow cytometry and ELISA showed both translocation of calreticulin and release of ATP and HMGB1 by VB4-845-treated tumor cells. Immune T cell activation via an ICD pathway suggests a complimentary outcome when combined with checkpoint inhibitors. A study was performed in PDX tumor-bearing NOG mice reconstituted with a human immune system to assess the combination of intratumoral injection of VB4-845 with an anti-PD1 antibody, Nivolumab, given i.p. VB4-845 showed growth suppression of the injected tumor whereas the growth delay of the contralateral, non-injected tumor was more pronounced with the addition of Nivolumab. In summary, the data presented suggests that VB4-845 mediates tumor cell killing by an ICD pathway and that the resulting cross-priming effect can enhance the anti-tumoral activity of immune checkpoint inhibitors.
Citation Format: Rachelle Lee Dillon, Shilpa Chooniedass, Arjune Premsukh, Glen MacDonald, Jeannick Cizeau, Gregory A. Adams. VB4-845 tumor cell killing in a combination study with the anti-PD-1, Nivolumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 614. doi:10.1158/1538-7445.AM2017-614
Abstract 625: Eradication of cancer cells by T-cell receptor-engineered T cells targeting neoantigens/oncoantigens
Authors: Matsuda Tatsuo , Kato Taigo , Ikeda Yuji , Leisegang Matthias , Yoshimura Sachiko , Hikichi Tetsuro , Harada Makiko , Zewde Makda , Park Jae-Hyun , Schreiber Hans , Kiyotani Kazuma , Nakamura Yusuke 
Published: July 2017

Abstract
Cytotoxic T lymphocytes (CTLs) play critical roles in cancer-immune responses, and functional characterization of CTLs and their cancer-specific antigens will facilitate cancer immunotherapies. Immunogenic peptides, which can be derived from oncogenic proteins specifically expressed in cancer cells but not expressed in normal organs except testis (oncoantigens), or from peptides with somatic nonsynonymous mutations (neoantigens), are known as good targets for CTLs to eradicate cancer cells. In this study, we aimed to establish a method to efficiently identify oncoantigen/neoantigen-specific CTLs. Firstly, we screened candidate HLA-A2402-restricted oncoantigen/neoantigen peptides by in silico prediction of their binding affinity to MHC class I molecules. We conducted an in-vitro stimulation of CD8 lymphocytes carrying HLA-A24:02 allele by each peptide, and then confirmed clonal expansion of the peptide-specific CTLs by TCR repertoire sequencing analysis, interferon-γ enzyme-linked immunospot (ELISPOT) and/or peptide-HLA multimer assays. After identification of TCR alpha-beta pairs, we conducted retroviral transduction and prepared the TCR-engineered T cells to evaluate their cytotoxic activities against cancer cells. As oncoantigens, we isolated the CTLs for FOXM1 and UBE2T from healthy donors, and found these CTLs showed strong cytotoxicity against HLA-A2402-positive cancer cells expressing target proteins, but not against HLA-unmatched cancer cells. Similarly, the TCR-engineered T cells for FOXM1 and UBE2T showed killing effects for only HLA-A2402-positive cancer cells. Neoantigen-specific TCR-engineered CTLs also exhibited the mutated peptide-specific response, but did not cross-react to the nonmutated peptide. In addition, neoantigen-specific cytotoxicity was observed against HLA-A2402-positive cancer cells expressing the proteins with target somatic mutations. In conclusion, we developed the pipeline to screen possible onconatigens/neoantigens and establish antigen-specific TCR-engineered CTLs from peripheral blood lymphocytes. Our approach provides a promising strategy to develop personalized immunotherapies using onconatigen/neoantigen-reactive TCR-engineered T cells to treat cancer.
Citation Format: Tatsuo Matsuda, Taigo Kato, Yuji Ikeda, Matthias Leisegang, Sachiko Yoshimura, Tetsuro Hikichi, Makiko Harada, Makda Zewde, Jae-Hyun Park, Hans Schreiber, Kazuma Kiyotani, Yusuke Nakamura. Eradication of cancer cells by T-cell receptor-engineered T cells targeting neoantigens/oncoantigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 625. doi:10.1158/1538-7445.AM2017-625
Abstract 645: Immunological landscape of non-small cell lung cancer (NSCLC): PD-1 expression in lung TILs correlate with co-expression of other checkpoint inhibitor molecules
Authors: Jeong Se W. , Bullock Timothy 
Published: July 2017

Abstract
Lung cancer is the leading cause of annual cancer related mortality in the United States. More than 150,000 people in the U.S. will die from lung cancer this year which will lead to roughly as many deaths as breast, prostate, colon, and pancreatic cancers combined. Lung cancer is also of global concern as tobacco and cigarette use, a significant known risk factor, in developing countries have risen significantly. Stage II and III non-small cell lung cancer (NSCLC) patients often have a 5-year disease free survival of less than 50% even after surgical resection and post-operative chemotherapy and a dismal 5% overall survival for patients with stage IV metastatic disease. Even with the advent of PD-1/PDL-1 checkpoint blockade immunotherapies, only about 20% of patients are responsive to the treatment. This limited scope of success may be due to our lack of understanding the immune landscape of NSCLCs. Therefore, we set out to characterize the immune composition from surgical lung resections via flow cytometry. We found that NSCLCs have a diverse set of checkpoint inhibitor and co-stimulatory molecules expressed by T cells, including PD-1, TIM-3, and TIGIT. Interestingly, even though PD-1 was elevated compared to a normal donor, the expression level was lower than either breast or melanoma tumor samples. We also discovered that PD-1 heavily correlates with co-expression of other checkpoint inhibitor molecules. In our regulatory T cell analysis, FoxP3+ populations have a profound presence in these lung tumors suggesting there is a highly suppressive environment for tumor infiltrating lymphocytes (TILs). Our lung resection screenings furthermore suggests a dynamic range of both frequency and proportion of CD3-CD56+ natural killer (NK) cells. Finally, our data indicates there is a large population of CD11b+CD33+ myeloid-derived suppressor cells (MDSCs) in the tumors, with varying degrees of arginase-1 expression, a functional marker for MDSCs. Altogether, these findings in concert suggest there are potential goldmine of opportunities to target molecules on different immune cell populations. This multi-modal approach, directing combination of immunotherapies that influences multiple immune compartments yet complement each other, may have significant implications for future clinical studies.
Citation Format: Se W. Jeong, Timothy Bullock. Immunological landscape of non-small cell lung cancer (NSCLC): PD-1 expression in lung TILs correlate with co-expression of other checkpoint inhibitor molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 645. doi:10.1158/1538-7445.AM2017-645
Abstract 647: Bortezomib enhances CD8+ T Lymphocyte antitumor effector function: Potential mechanism(s) via notch regulation
Authors: Renrick Ariana N. , Thounaojam Menaka C. , Thomas Portia , Pellom Samuel T. , Shanker Anil 
Published: July 2017

Abstract
The immunosuppressive tumor microenvironment disturbs host antitumor immunity by multiple mechanisms including interference with the Notch system, which is important for various metazoan cell fate decisions and hematopoietic cell differentiation and function. We observed that treatment with the proteasome inhibitor bortezomib in mice bearing various solid tumors resulted in an upregulated expression of various Notch signaling components in lymphoid tissues, thereby increasing CD8+ T lymphocyte IFNγ secretion and expression of effector molecules, perforin and granzyme B, as well as the T-box transcription factor eomesodermin. Of note, bortezomib reversed tumor-induced downregulation of Notch receptors, Notch1 and Notch2, as well as increased the levels of cleaved Notch intracellular domain (NICD) and downstream targets Hes1 and Hey1 in tumor-draining CD8+ T cells. Moreover, bortezomib promoted CD8+ T cell nuclear factor-κB (NFκB) activity by increasing the total and phosphorylated levels of the IκB kinase and IκBα as well as the cytoplasmic and nuclear levels of phosphorylated p65. Even when we blocked NFκB activity by Bay-11-7082, or NICD cleavage by γ-secretase inhibitor, bortezomib significantly increased expression of Notch Hes1 and Hey1 genes as well as perforin, granzyme B and eomesodermin in activated CD8+ T cells. Data suggest that bortezomib can rescue tumor-induced dysfunction of CD8+ T cells by its intrinsic stimulatory effects promoting NICD-NFκB crosstalk. We are also elucidating components of microRNA regulation affecting NICD-NFκB crosstalk. Our preliminary data suggest that bortezomib is also able to positively regulate miR-155 expression in CD8+ T cells from mice bearing tumor. As well as, miR-155 suppression downregulates bortezomib-induced increase in Notch target genes in T cells. We are currently investigating alternative proteasome inhibitors in order to understand whether bortezomib’s effect on miR-155 expression in CD8+ T cells is specific to bortezomib or primarily conducive to a proteasome inhibition effect. These findings provide novel insights on using bortezomib not only as an agent to sensitize tumors to cell death, but also to provide lymphocyte-stimulatory effects, thereby overcoming immunosuppressive actions of tumor on antitumor T cell functions.
Citation Format: Ariana N. Renrick, Menaka C. Thounaojam, Portia Thomas, Samuel T. Pellom, Anil Shanker. Bortezomib enhances CD8+ T Lymphocyte antitumor effector function: Potential mechanism(s) via notch regulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 647. doi:10.1158/1538-7445.AM2017-647
Abstract 671: Prognostic importance of EGFR expression and Kras gene mutations in gallbladder carcinoma
Authors: Singh Anjali , Najmi Abul Kalam , Mishra Pramod , Talikoti Majid 
Published: July 2017

Abstract
Gallbladder carcinomas involve multiple cascades of oncogenes like EGFR and Kras. Activation of Kras downstream pathways predict the sensitivity to anti EGFR treatment. In 2012, for the first time it was established that GBC and cholangiocarcinomas have their unique somatic genomic landscape and thus be studied independently. This study evaluates whether EGFR is a prognostic factor in GBC and identifies the frequency of codon 12 and codon 13 Kras mutations along with its association with subject survival. Seventy two GBC curative resections from North India were immunostained with anti EGFR monoclonal antibody and assessed for codon 12 and 13 KRAS mutation by real time PCR. Strong EGFR expression was observed in 25.4percent cases. About 28/72; G12C, 17/72; G12R, 10/72; G12D and 18/72; G13D cases harboured point mutations in Kras gene, which was significantly higher as compared to control tissues. Multivariate analysis revealed that EGFR expression (p=0.01; HR=3.14; 95percent CI=1.28-7.71) and codon-13 mutation (p=0.001; HR=38.34; 95percent CI=4.90-300.01) had a significant impact on survival and were independent prognostic factors in GBC. Our study suggests that EGFR expression and codon 13 mutations are independent prognostic factors in the selected GBC cohort and showed a high frequency of Kras codon 12 mutations as well.
Citation Format: Anjali Singh, Abul Kalam Najmi, Pramod Mishra, Majid Talikoti. Prognostic importance of EGFR expression and Kras gene mutations in gallbladder carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 671. doi:10.1158/1538-7445.AM2017-671
Abstract 673: Exploration of tissue morphologies in breast cancer samples using unsupervised machine learning
Authors: Turkki Riku , Bychkov Dmitrii , Linder Nina , Isola Jorma , Joensuu Heikki , Lundin Johan 
Published: July 2017

Abstract
We applied a machine learning approach for exploration of tissue morphology in hematoxylin and eosin (H&E) stained breast cancer tissue microarray (TMA) samples. We then investigated whether the morphological categories produced were associated with clinically relevant molecular biomarkers and 10-year overall survival.
The data set comprises digitized (0.22 µm/pixel) and H&E stained TMA spots from tumor samples of 490 women who were diagnosed with primary breast cancer within a Finnish breast cancer database (FinProg) collected in 1991 and 1992. In order to quantitatively describe the tissue morphologies of the TMA spots, we divided the tissue images into rectangular sub-images (224x224 pixels), and extracted features with a pre-trained convolutional neural network. We then clustered the sub-images (n=147,266) with a non-linear data embedding algorithm that creates a two-dimensional mapping of the tissue morphologies. Lastly, we defined a quantitative profile for each tumor, describing the morphologies within the tissue spot image by dividing the two-dimensional map of morphologies into 128 separate clusters with k-nearest neighbor clustering.
Visual inspection of the two-dimensional embedding of tissue spot images verified that the morphologies clustered coherently, i.e. similar looking sub-images formed distinct clusters in the map. Interestingly, some morphological patterns were strongly associated with tumor estrogen receptor content, progesterone receptor content, human epidermal growth factor receptor 2 status, and the proliferation marker Ki-67 status (p&lt;0.0001 for each comparison). In exploratory analyses we identified one morphological category that was associated with a favorable 10-year overall survival with a risk ratio of 0.68 (CI95% 0.53-0.89, p=0.002, power = 0.87).
Our work demonstrates that unsupervised machine learning can be applied to explore and better understand the role of morphological patterns in breast cancer. Methods that quantitatively assess the morphology of cancer tissue may complement molecular biomarkers and potentially reveal novel prognostic and predictive factors.
Citation Format: Riku Turkki, Dmitrii Bychkov, Nina Linder, Jorma Isola, Heikki Joensuu, Johan Lundin. Exploration of tissue morphologies in breast cancer samples using unsupervised machine learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 673. doi:10.1158/1538-7445.AM2017-673
Abstract 74: Discovery of new therapeutic monoclonal antibodies to challenging GPCRs, ion channels and transporters
Authors: Stafford Lewis J. , Chambers Ross , Willis Sharon H. , Hall Moniquetta , Screnci Brad , Mabila Manu , Tucker David , Barnes Trevor , Fong Rachel , Ettenger Andrew , Pfaff Jennifer , Sulli Chidananda , Molino Nicholas , Hudacek Andrew , Doranz Benjamin J. , Rucker Joseph 
Published: July 2017

Abstract
The objective of this work was to evaluate the ability to generate panels of monoclonal antibodies against a set of highly challenging targets including GPCRs (CB1, C5AR, CXCR5 and CGRPR), transporters (GLUT4), and ion channels (P2X3). Integral membrane proteins are important drug targets and monoclonal antibodies (MAbs) directed against them are highly sought for therapeutic purposes. However, the complex structure of multispan membrane protein targets makes the discovery of these MAbs especially challenging. To address this need, Integral Molecular has developed the MPS Discovery Engine® to enable the isolation, characterization, and engineering of monoclonal antibodies for GPCRs, ion channels, and transporters. MPS utilizes a collection of technologies to address each of the barriers to monoclonal antibody development against the native extracellular epitopes of multispan membrane proteins. These include, antigen engineering to attain high levels of surface expression, DNA and Lipoparticle immunization to present native epitopes to the immune system, diverse immunization host species to deal with highly conserved proteins, Lipoparticles (high concentration native membrane proteins) to enable phage display and microfludic B-cell isolation, and shotgun mutagenesis (comprehensive Alanine scanning) for epitope mapping. Using the MPS Discovery Engine® we were able to successfully generate large panels of antibodies to the targets that were able to bind to the native extracellular epitopes on cells by flow cytometry. A subset of the antibodies had antagonist activity. With this technology we have the ability to target intact, conformation specific, and functional antibodies to complex membrane proteins.
Citation Format: Lewis J. Stafford, Ross Chambers, Sharon H. Willis, Moniquetta Hall, Brad Screnci, Manu Mabila, David Tucker, Trevor Barnes, Rachel Fong, Andrew Ettenger, Jennifer Pfaff, Chidananda Sulli, Nicholas Molino, Andrew Hudacek, Benjamin J. Doranz, Joseph Rucker. Discovery of new therapeutic monoclonal antibodies to challenging GPCRs, ion channels and transporters [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 74. doi:10.1158/1538-7445.AM2017-74
Abstract 815: Using CRISPR/Cas9 to generate isogenic cell lines and reference standards for applications in cancer diagnostics
Authors: Jin Huanyu , Cheng Xin , Nguyen Nga , Zheng Qi , Shi Mi , Hilmer Andrew , Yuan Yuan , Chen-Tsai Ruby Yanru , Kong Ling-Jie 
Published: July 2017

Abstract
We are entering an era of precision medicine, in which there are significant initiatives to employ companion diagnostics and molecular profiling to inform clinical decisions in therapeutic treatment. In order for these initiatives to work as effectively as possible, there is a need for molecular reference materials that can help facilitate precision assay development. Cell-line based reference standards are ideal for such applications because they represent a reproducible and renewable source of control materials that can be employed for assay development, quality control, or lead compound discovery. With this in mind, we have used the CRISPR/Cas9 platform to engineer series of isogenic cell lines that feature 51 recurrent mutations in the MAPK signaling pathway. These cell lines contain footprint-free, homozygous mutations in the kinase domains of the EGFR, KRAS, and BRAF genes in HCT116 and RKO cancer cell lines, with 32 mutations in EGFR, 12 mutations in KRAS, and 7 mutations in BRAF. The mutations include precise deletions, point mutations and small fragment insertions, and these engineered cell lines have been further employed for the development of derivative reference materials, including genomic DNA (gDNA) and FFPE cell line blocks. Such materials can be employed as positive and negative controls in diverse assay platforms, including next generation sequencing (NGS), quantitative PCR (qPCR), in situ hybridization (ISH), and others. We present quality control data for these reference materials, which demonstrate excellent consistency and uniformity, as well as examples of the application of these materials in molecular assay validation. We conclude that using CRISPR/Cas9 technology to generate molecular reference standards is a very efficient and precise method in generating footprint-free, biorelevant mutations for companion diagnostic assays.
Citation Format: Huanyu Jin, Xin Cheng, Nga Nguyen, Qi Zheng, Mi Shi, Andrew Hilmer, Yuan Yuan, Ruby Yanru Chen-Tsai, Ling-Jie Kong. Using CRISPR/Cas9 to generate isogenic cell lines and reference standards for applications in cancer diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 815. doi:10.1158/1538-7445.AM2017-815
Abstract 893: Systematic assessment of spliceosome components as drivers of breast cancer progression
Authors: Koedoot Esmee , Dévédec Sylvia Le , Water Bob van de 
Published: July 2017

Abstract
Accumulating evidence indicates that RNA splicing is involved in different steps of carcinogenesis. Although the critical role of a limited number of splicing factors has been demonstrated in several cancer studies, the function of many spliceosome components is still unknown. In breast cancer samples higher expression levels of a subset of spliceosome components consistently correlated with more aggressive tumor types in patient microarray as well as RNA sequencing data from The Cancer Genome Atlas (TCGA). We further systematically evaluated the effect of siRNA-mediated knockdown of 244 individual splicing factors on both cell migration and proliferation in two aggressive breast cancer cell lines MDA-MB-231 and Hs578T using high throughput microscopy. Primary candidates were validated with four single siRNAs and classified based on their effects on migration and proliferation. Knockdown of validated spliceosome factors such as SNRPG and SNRPA1 affected the levels of small nuclear RNAs, the main catalyzers of the spliceosome. Moreover, high expression of these key candidate hits is associated with poor breast cancer metastasis free survival. To investigate the downstream mechanisms and splicing patterns controlled by our candidate genes we performed RNA sequencing on both control and siRNA mediated knockdown cells. Interestingly, knockdown of our hits affect extracellular matrix pathways that are essential in tumor cell migration and invasion. Altogether our data indicate a key role for spliceosome factors in the control of breast cancer progression which provide new leads for future therapeutic intervention.
Citation Format: Esmee Koedoot, Sylvia Le Dévédec, Bob van de Water. Systematic assessment of spliceosome components as drivers of breast cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 893. doi:10.1158/1538-7445.AM2017-893