bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5635: The development to peptide vaccine targeting heat shock protein 90 to overcome resistance to HER-2 target drugs in breast cancer
Authors: Kang Jinho 
Published: August 2018

Abstract
HER-2 overexpression is observed in approximately 25% of all breast cancers and is associated with poorer overall survival and decreased time to relapse. Target therapies directed against HER-2 have been developed and used clinically, but many patients continue to develop resistance. Breast cancer is immunogenic and well suited to treatment via immunomodulation. HSP90 is a chaperon for most of the important signal transduction system in HER-2 type breast cancer; HER-2, ER / PR and Akt, the downstream protein of PI3K. Therefore, HSP90 is considered as a potential therapeutic target in order to improved treatment of HER-2 positive resistant breast cancer. Immunotherapy targeting HSP90 has been tried before, however, no clinically available vaccine due to limitation of autologous cell-based approach. We questioned whether HSP90 was an immune target in HER-2 positive breast cancer. First, HSP90-specific IgG antibody immunity was detected in the sera from HER-2 positive breast cancer patients. Next, potential MHC class II epitopes derived from HSP90 with high binding affinity across multiple human HLA genotypes were identified using in silico algorithms. Top 11 peptides were synthesized and Th1 vs Th2 immunity were assessed in human PBMCs. After IFN-γ and IL-10 ELISPOT assays, epitopes inducing Th1-directed immunity were selected for in vivo experiments. Immunogenecity of HSP90 peptides vaccine was evaluated in FVB mice model and showed strong antigen-specific T cell responses in IFN-γ ELISPOT assay. Then, we assessed the anti-tumor effect of immunization with HSP90 peptides vaccine in MMTV-neu-transgenic mouse model after autologous cancer cell implantation. Peptides vaccines derived from HSP90 significantly inhibited tumor growth compared with control group (mean ± SD; 1896 ± 1211 mm3 vs. mean ± SD; 774 ± 136 mm3, respectively; p &lt; 0.05). The tumor-inhibitory effect was associated with HSP90 peptide-specific IFN-γ-secreting T cell responses in immunization group. Also, immunohistochemical staining of tumors derived from immunized mice was performed to examine immune microenvironment and the protein expression of HER-2 pathways. Taken together, multi-epitope peptides vaccine derived from HSP90 is immunogenic in breast cancer patients and is a promising tumor antigen. Based on efficacies in tumor-rejection in vivo, further research in combination with immune modulating antibodies will be performed in the lapatinib-resistant tumor model.
Citation Format: Jinho Kang. The development to peptide vaccine targeting heat shock protein 90 to overcome resistance to HER-2 target drugs in breast 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 5635.
Abstract 5640: Development of a personalized pancreatic cancer vaccine
Authors: Cullinan Darren R. , McLellan Michael , Zhang Xiuli , Nywening Timothy M. , Miller Chris A. , Goedegebuure S. Peter , Hawkins William G. , Gillanders William E. 
Published: August 2018

Abstract
Introduction: Cancer neoantigens result from mutations accumulated in an individual tumor. These mutations are usually private and yield high-affinity T-cells as they are not limited by mechanisms of self-tolerance. Neoantigens presented in the context of MHC class I can be recognized by anti-tumor CD8+ T-cells.
Methods: Three consecutive patients with confirmed pancreatic ductal adenocarcinoma (PDAC) had DNA and RNA isolated from areas of high tumor cellularity. Comparative normal DNA was isolated from peripheral blood mononuclear cells (PBMC). Nonsynonymous mutations were identified by tumor/normal whole exome sequencing and expression in the tumor was verified by cDNA capture. HLA typing was inferred from exome sequencing. Candidate neoantigens were identified using multiple epitope prediction algorithms for MHC class I. Matched patient PBMC were cultured in serum-free media for 48 hours with synthetic mutated short peptides to determine the baseline immune response by interferon-gamma (IFNγ) enzyme-linked immunospot assay.
Results: A KRAS driver mutation was identified in all three patients. Using KRAS variant allele frequency (VAF) as a surrogate for tumor purity, we achieved greater than 40% tumor purity for all three samples. This provides an adequate level of purity to proceed with neoantigen identification. In these samples, the mean number of nonsynonymous mutations identified was 27 (range: 18-32; DNA VAF cutoff 10%). Of these nonsynonymous mutations, a mean of 8.6 mutations (range: 7-10) were expressed (RNA VAF cutoff &gt;10% and FPKM &gt;1). Following confirmation of mutation expression, a mean of 5 mutations (range: 4-6) were predicted to bind to MHC class I using multiple prediction algorithms (binding affinity &lt;500nM). IFNγ immunospot assay revealed a baseline immune response to one neoantigen in each patient (Patient A - SDHA: 75 spot forming units per millions cells (SFU/M) vs Negative: 12.5 SFU/M, p=0.01; Patient B - ZRANB1: 588 SFU/M vs Negative: 17.5 SFU/M, p&lt;0.001; Patient C - ATAD3C: 340 SFU/M vs Negative: 75 SFU/M, p=0.002).
Conclusion: Utilizing advanced genomic and bioinformatics tools we have successfully characterized the cancer neoantigens in a series of three consecutive patients with PDAC. From this data, we plan to open a phase I clinical trial to assess the safety and immunogenicity of a neoantigen DNA vaccine.
Citation Format: Darren R. Cullinan, Michael McLellan, Xiuli Zhang, Timothy M. Nywening, Chris A. Miller, S. Peter Goedegebuure, William G. Hawkins, William E. Gillanders. Development of a personalized pancreatic cancer vaccine [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 5640.
Abstract 5645: Critical variables to reduce Western blot variability
Authors: Yukhananov Russ , Margulis Alex 
Published: August 2018

Abstract
Reliable immunodetection of proteins is a critical step in the discovery of new biomarkers and diagnostic. The immunodetection protocol consists of multiple steps including blocking of nonspecific binding sites, incubation using primary and secondary antibodies and extensive washing between steps that easily introduce bias and errors. The quality and reproducibility of results depends on multiple subjective and objective factors such as the qualification and technical skills of the personnel performing the assay and the accuracy of temporal and temperature control, especially during the immunodetection step. BlotCycler™, automated western blot processor, use fluidic control system that allows to eliminate the variability associated with immunodetection and to achieve higher sensitivity by optimized washing procedure. We used BlotCycler to analyze critical source of errors during immunodetection. Relatively small changes in duration and temperature of incubation significantly affect not only the intensity of signal but also the specificity of antibody interaction with antigen. Automated immunodetection at 4ºC significantly improve the specificity of detection and sensitivity that allows reproducible detection of low expressing proteins. Automated processing using BlotCycler allows optimization and control of critical variables leading to improved reproducibility and specificity of immunodetection and should be routinely used for new biomarker discovery and diagnostics, reliable protein quantification, primary antibody specificity testing, and optimization of primary and secondary antibodies concentrations.
Citation Format: Russ Yukhananov, Alex Margulis. Critical variables to reduce Western blot variability [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 5645.
Abstract 5646: Serum functional biomarker discovery with PEP technology
Authors: Wang Xing , Davies Michael 
Published: August 2018

Abstract
Proteins play essential roles in numerous biological processes and being able to pinpoint functional differences between cell or tissue samples can greatly aid in understanding disease processes and metabolic changes. The PEP technology allows systematic analysis of protein functions within a proteome. Hundreds of functional proteins can be separated and functionally assayed to generate a comprehensive three-dimensional landscape of protein families such as protein kinases, phosphatases, proteinases and oxido-reductases. This information can then be integrated into other genomic and proteomic knowledge bases to provide further insight of important biological processes such as cancer development and aging. Using the PEP technology, functional biomarker candidates have been identified from liver, lung and breast cancer patient serum. Both qualitative and quantitative differences of metabolic enzymes and proteases were observed when comparing the cancer patient serum and normal serum. Some of the active enzymes were identified by mass spectrometry and validated in selected bioassays. Deep mass spectrometry analysis revealed that some of the functional biomarkers are protein variants of important biological function. It is believed that this functional proteomics technology will provide a unique approach in the discovery of potential cancer biomarkers for diagnostic and prognostic applications. Further efforts are ongoing to develop a prototype of diagnosis kit for cancer detection based on the current discoveries.
Citation Format: Xing Wang, Michael Davies. Serum functional biomarker discovery with PEP 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 5646.
Abstract 5653: VMax™: A new platform for recombinant protein expression
Authors: Hesek Eric , Wilson Chris , Wolf Lindsey , Vasu Sanjay , Sturges Michael , Gibson Daniel , Weinstock Matthew 
Published: August 2018

Abstract
Here we describe Vmax™, a next-generation protein expression platform based on the organism V. natriegens, an extremely rapidly growing gram-negative prokaryote capable of reaching high cell density. Vmax™ contains an IPTG inducible T7 expression system, enabling high levels of recombinant protein expression. By combining a robust expression system with a highly productive organism, Vmax allows researchers to perform experiments faster, shorten workflow times, and generate large amounts of recombinant protein.
Citation Format: Eric Hesek, Chris Wilson, Lindsey Wolf, Sanjay Vasu, Michael Sturges, Daniel Gibson, Matthew Weinstock. VMax™: A new platform for recombinant protein expression [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 5653.
Abstract 5655: Biophysics in the cell—CETSA to study drug binding and cellular processes in cancer therapy
Authors: Liang Ying Yu , Ramos Anderson , Laursen Henriette , Surova Olga , Lengqvist Johan , Lööf Sara , Langebäck Anette , Bacanu Smaranda , Bergh Jonas , Nordlund Pär 
Published: August 2018

Abstract
A key step of the action of most drugs is their binding (engagement) of the target protein(s). However, limitations in the available methods for directly accessing this critical step have added uncertainties in many stages of drug development. We have developed a generic method for evaluating drug binding to target proteins in cells and tissues (Martinez Molina et al. Science, 341:84). The technique is based on the physical phenomenon of ligand-induced thermal stabilization of target proteins; the method is therefore called the cellular thermal shift assay (CETSA). The technique allows for the first time to directly measure the biophysical interactions between a drug and protein target in non- engineered cells and tissues. We show that using CETSA a range of critical factors for drug action can be addressed at the target engagement level, including drug transport and activation, off-target effects, drug resistance as well as drug distribution in cells, patient and animal tissues.

Although CETSA was first developed for evaluating drug binding to target proteins in cells it is also useful for characterizing physiological interactions, including protein-protein, protein-metabolite and protein-nucleic acid interactions (Martinez Molina & Nordlund, Ann Rev Pharm Toxic 2016 56:141). In the proteome-wide CETSA experiment, interactions with more than 7000 proteins can be measured in parallel (Savitski, Science 2014 346;6205). This strategy therefore constitutes a novel mean for discovering key interactions determining the fate of cancer cells during therapy and resistance – interactions that can serve as biomarkers or candidates for novel drug targets in cancer therapy.
Citation Format: Ying Yu Liang, Anderson Ramos, Henriette Laursen, Olga Surova, Johan Lengqvist, Sara Lööf, Anette Langebäck, Smaranda Bacanu, Jonas Bergh, Pär Nordlund. Biophysics in the cell—CETSA to study drug binding and cellular processes in cancer therapy [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 5655.
Abstract 5667: High-throughput analysis of MAPK and JAK-STAT signaling in CT26 tumors using a combination of immunophenotyping and phospho-flow cytometry
Authors: Draper David , Wong Alden , Lapinski Philip , Barnes Sheri R. , Franklin Maryland Rosenfeld , Wise Scott C. 
Published: August 2018

Abstract
The development of robust platforms that enable the analysis of cell signaling proteins is crucial for small molecule drug development. Analysis of phospho-proteins in solid tumors is one area that remains a challenge due to the complex nature of the tissue. The most common approaches used to measure the effects of in vivo therapy are immunoblot and ELISA-based assays. However, these bulk analysis methods have drawbacks. This is primarily due to their inability to distinguish between phospho-protein levels in different cell subsets that exist in the tumor. Using the CT26 syngeneic model for colorectal cancer, we describe a novel high-throughput phospho-flow platform that can simultaneously analyze the phosphorylation status of up to 6 signaling proteins in both tumor cells and immune cells. To first validate the phospho-flow assay, splenocytes from naïve mice were treated in vitro with various stimuli that preferentially target distinct signaling proteins. We then tested the platform in vivo. To this end, CT26 tumor-bearing mice were dosed with the MEK inhibitor trametinib or vehicle. At the appropriate time point post-dosing, tumors were harvested and dissociated into single cell suspensions. Live tumor cells and CD8+ T cells were first identified by flow cytometry using antibodies against CD45, CD3, and CD8. Following fixation, MAPK and JAK-STAT signaling activity was analyzed by measuring the levels of phosphorylated MEK, ERK1/2, STAT1, STAT2, STAT5, and STAT6 proteins using phospho-flow. Our results demonstrated that trametinib triggered a reduction in both pMEK and pERK1/2 levels in tumor cells that was evident 24 hours after the final trametinib dose. We also found phosphorylated STAT1, STAT3, and STAT5 was readily detectable in tumor cells, while STAT6 phosphorylation was not obvious. In contrast, we found that the CD8+ T cell levels of pMEK and pERK1/2 were not affected by trametinib. Furthermore, when JAK-STAT signaling was analyzed, only phosphorylation of STAT3 was detected in CD8+ T cells, which was also unaffected by trametinib. These results demonstrate successful combination of immunophenotyping and phospho-protein analysis in solid tumor-derived cells using flow cytometry. This platform is a tool that can be used to provide valuable insight into the effects that small molecule inhibitors may have on distinct cell subsets within a heterogenous tumor microenvironment.
Citation Format: David Draper, Alden Wong, Philip Lapinski, Sheri R. Barnes, Maryland Rosenfeld Franklin, Scott C. Wise. High-throughput analysis of MAPK and JAK-STAT signaling in CT26 tumors using a combination of immunophenotyping and phospho-flow cytometry [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 5667.
Abstract 5670: Systemic lymphoid architecture response assessment (SYLARAS): Application to system-wide immunophenotyping of glioblastoma
Authors: Baker Gregory J. , Palaniappan Sucheendra K. , Moore Jodene K. , Davis Stephanie H. , Sorger Peter K. 
Published: August 2018

Abstract
Interactive flow cytometry analysis software allows users to make binary decisions on immunomarker status of single cells through arbitrary placement of one- and two- dimensional gates. However, manual gating through a point-and-click graphical user interface (GUI) is impractical for large datasets. Here we describe SYLARAS, a suite of experimental and computational tools for the systematic and chronological evaluation of lymphoid tissue architecture. SYLARAS takes multiplex single-cell data as input, bins cells in n-dimensional orthant space, and returns schematized summary statistics on immunophenotypes of interest. We programmatically curated data on 33 immunophenotypes constituting primary and secondary lymphoid tissue of immunocompetent mice bearing syngeneic, orthotopic glioblastoma (GBM) at 3 stages of tumor growth. SYLARAS permitted the discovery of tumor-induced immune signatures whose divergence from mock engrafted, age-matched controls was quantified and statistically analyzed. By integrating information on peripheral immune composition with the levels of 111 blood cytokines of the same mice, we uncovered novel cell types, cytokines, and correlation networks perturbed by the mouse GL261 glioma model. SYLARAS facilitates the discovery of immune regulatory mechanisms and their response to therapy and is broadly applicable to the fields of immuno-oncology, autoimmunity, and infectious disease.
Citation Format: Gregory J. Baker, Sucheendra K. Palaniappan, Jodene K. Moore, Stephanie H. Davis, Peter K. Sorger. Systemic lymphoid architecture response assessment (SYLARAS): Application to system-wide immunophenotyping of glioblastoma [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 5670.
Abstract 5677: Establishment and application of a panel of PBMC-humanized mouse tumor models in immune-oncology and targeted cancer immunotherapy
Authors: Zhang Lan , Wu Haochen , Chen Fei , Zhao Lianqi , An Xiaoyu , Tan Weibin , Fu Xiaoyan , Qiao Meng , Shi Qian , Yang Wenqing 
Published: August 2018

Abstract
Background: Monoclonal antibodies and checkpoint blocking approaches have achieved remarkable success in cancer immunotherapy in clinical practices. Besides the success of anti-PD-1 and anti-PD-L1 antibodies (such as Keytrude and Tecentriq), two bispecific antibodies, Catumaxomab and Blinatumomab have been approved to treat cancer patients, and many more bispecific antibodies are currently in pre-clinical or clinical development. To meet the increasing market needs for fast, reliable and cost effective mouse tumor model systems, we developed a panel of humanized tumor models, designated as MiXenoTM platform. MiXenoTM could be used in a broad spectrum of applications in immuno-oncology drug discovery, including targeted cancer immune-therapy.
Method: CrownBio has a collection of about 200 xenograft models, including subcutaneous, orthotropic and systemic models, which covers majority of cancer type. Gene expression and mutation status are often profiled in these models. To engage both host immune system and tumor antigens, we have developed some specific MixenoTM tumor models by inoculating tumor cells over-expressing specific anti-tumor antigens (e.g. EGFR, CD47, Braf or PD-L1) into PBMC-humanized immunocompromised mice. Reconstitution of human immune component with human PBMCs in these tumor-bearing mice provides a useful tool to evaluate the targeted immune-therapeutics including bispecific T cell engagers.
Results: To validate the MiXenoTM models for targeted cancer immunotherapy, several xenograft models have been profiled and selected based on their tumor antigens or gene expression. Models with over-expression of a variety of tumor antigens (e.g. EGFR, CD47, Braf, PD-L1, etc.) were used to develop specific MixenoTM tumor models. The immune and tumor cells were engrafted either simultaneously or sequentially. Graft versus host disease (GvHD) can be managed by optimizing the immune cell constitution and tumor cell engraftment. Some models were also validated using stand of care I/O drugs and characterized by immune-phenotyping.
Conclusions: MiXenoTM tumor models with specific tumor antigen targeting strategy are valid model systems to evaluate the human immuno-modulatory drugs including bispecific antibodies. Further studies are needed to expand model collections and to extend their applications in I/O space.
Citation Format: Lan Zhang, Haochen Wu, Fei Chen, Lianqi Zhao, Xiaoyu An, Weibin Tan, Xiaoyan Fu, Meng Qiao, Qian Shi, Wenqing Yang. Establishment and application of a panel of PBMC-humanized mouse tumor models in immune-oncology and targeted cancer immunotherapy [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 5677.
Abstract 5689: Characterization of immune infiltrate and checkpoint protein expression patterns in murine syngeneic tumors via multiplex immunohistochemistry
Authors: Ziello Jennifer , Klein Sarah , Crosby Katherine 
Published: August 2018

Abstract
Murine syngeneic tumor models are increasingly utilized for preclinical immuno-oncology studies as immunotherapeutic strategies continue to make clinical strides. However, the immunologic features of the tumor microenvironment (TME) in these models remain largely undefined. In this study, we applied a 7-color multiplex immunohistochemistry panel to visualize and quantify the immune infiltrate within formalin-fixed, paraffin-embedded RENCA, CT26.WT, and LL/2 tumor tissues derived from subcutaneous mouse models of renal cell carcinoma, colon carcinoma, and lung carcinoma, respectively. Additionally, we applied this panel to a 4T1 orthotropic primary mammary tumor and lung metastasis formed via tail vein injection. The multiplex panel included antibodies detecting CD3 and CD8 as T cell markers, F4/80 as a myeloid cell marker, the immunosuppressive receptor PD-1 as well as its ligand PD-L1, pan-keratin as a tumor mask, and DAPI as a nuclear counterstain. We characterized the tissue localization of tumor-infiltrating immune cells and analyzed the trends in co-expression and frequency patterns of immunosuppressive proteins. This study strives to better understand the underlying differences in the immunologic landscapes of these tumors, which in turn has implications for researchers studying responses to immunotherapeutic approaches and combination strategies.
Citation Format: Jennifer Ziello, Sarah Klein, Katherine Crosby. Characterization of immune infiltrate and checkpoint protein expression patterns in murine syngeneic tumors via multiplex immunohistochemistry [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 5689.