bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4042: Longitudinal monitoring of neoepitope-specific T cell repertoires in patient blood following cancer immunotherapy
Authors: Peng Songming , Yuen Benjamin , Tan Joanne , Yin Fangfang , Bao Robert , Pan Zheng , Dalmas Olivier , An Duo , Quach Boi , Yi Michael , Bethune Michael , Mandl Stefanie , Walters Matt , Jaen Juan , Franzusoff Alex 
Published: August 2019

Abstract
T cells targeting neoepitopes derived from mutations exclusive to the tumor are one of the main drivers of cancer immunotherapy efficacy. Tracking these neoepitope-specific T cells during cancer immunotherapy has been hampered by the impracticality of repeated sampling from the tumor, and by the low frequency of neoepitope-specific T cells in peripheral blood. An ultra-sensitive and high-throughput technology (imPACT) has been developed for the identification and isolation of neoepitope-specific T cells from peripheral blood. Subjects with colorectal cancer, endometrial adenocarcinoma, nasopharyngeal carcinoma and other solid tumors were treated with AB122 (anti-PD-1 antibody) as part of an ongoing dose-escalation clinical trial. Pre-treatment blood samples were analyzed to identify the basal repertoire of neoepitope-specific T cells. Evolution of this repertoire during AB122 treatment was monitored to enable immune phenotyping and correlation with clinical outcomes. In addition, transcriptional profile changes were monitored at the single-cell level for each neoepitope-specific T cell. These data will enable us to analyze T cells targeting neoepitopes and identify driver mutations that correlate with and may be responsible for therapeutic benefit. More broadly, this platform technology promises to significantly advance our understanding of T cell-mediated mechanisms of cancer immunotherapy.
Citation Format: Songming Peng, Benjamin Yuen, Joanne Tan, Fangfang Yin, Robert Bao, Zheng Pan, Olivier Dalmas, Duo An, Boi Quach, Michael Yi, Michael Bethune, Stefanie Mandl, Matt Walters, Juan Jaen, Alex Franzusoff. Longitudinal monitoring of neoepitope-specific T cell repertoires in patient blood following cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4042.
Abstract 4043: Application of high complexity flow cytometry for Monitoring activated T-cells, T and B regulatory subsets in combination immunotherapy trials, melanoma case study
Authors: Tsau Jennifer , Abadier Michael , Atzmiller Brittney , Vaupel Christine , Dakappagari Naveen , Sarikonda Ghanashyam , Tarhini Ahmad 
Published: August 2019

Abstract
Background
Ever increasing knowledge of the interplay between immune composition and a novel drugs’ treatment efficacy or the lack thereof leads to continual advancements in immunotherapies. Given the exponential increase in combination therapies, tools to determine the most promising regimens are critical.
Immunotherapeutic agents either reverse T-cell inhibitory pathways (e.g., PD-1) or activate the immune system to induce cytotoxic T-cell activation and proliferation through agonistic stimulation (e.g., Cytokines). These treatment strategies have proven to be efficacious by enhancing the balance between immune-effector and suppressive/regulatory cells that can directly affect the outcome of immunotherapy.
To concurrently monitor multiple immune cell subsets responsible for either immuno-suppression or activation, we developed a high-complexity (13-color) flow cytometry panel to reliably enumerate activated T-cells, Tregs (A & B subsets) and Bregs for clinical trial application.
Methods
The panel includes CD3, CD4, CD8, CD19, FoxP3, CD25, CD127, CD45RA, HLA-DR, CD38, CD24, and CD27 to monitor total Tregs, Treg-subsets, Bregs and T-cell activation. After robust analytical method validation following industry guidelines for exploratory biomarker assessments, we confirmed the clinical utility of this panel in stage III or IV melanoma patients (N= 14) enrolled in a randomized phase II clinical trial receiving high-dose of IL-2 with or without Afliberecept (VEGF inhibitor).
Results
We observed up-to 20-fold increase in activated CD8+ T-cells following treatment. Interestingly, while no discernible change was observed in the naive Treg-A cells (CD45RAhiFoxp3lo), a remarkable 5-fold expansion of effector Treg-B cells (CD45RAloFoxp3hi) was observed following treatment. Additionally, frequencies of Bregs (CD24hiCD38hi) remained unchanged after treatment.
Conclusions
In summary, we demonstrated the utility of a powerful high complexity clinical flow cytometry tool for precisely monitoring immune cell subsets involved in tumor escape such as Tregs and Bregs or those involved in tumor killing like CD8+ cytotoxic T-cells. More notably, this tool may be utilized to deprioritize agents that cause immunosuppression and focus on combination agents that lead to additive immune activation.
Citation Format: Jennifer Tsau, Michael Abadier, Brittney Atzmiller, Christine Vaupel, Naveen Dakappagari, Ghanashyam Sarikonda, Ahmad Tarhini. Application of high complexity flow cytometry for Monitoring activated T-cells, T and B regulatory subsets in combination immunotherapy trials, melanoma case study [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 4043.
Abstract 4046: Immune repertoire sequencing reveals tumor microenvironment and tracks clonally expanded B cell and T cell in blood
Authors: Song Chen , Liu Pingfang , Barry Andrew , Langhorst Bradley W. , Stewart Fiona J. , Russello Salvatore , Davis Theodore B. , Dimalanta Eileen T. 
Published: August 2019

Abstract
The study of complex immunological diseases and tumor microenvironments has progressed through recent developments on sequencing of the immune repertoire. Using this approach, the interrogation of disease progression is facilitated through analysis of millions of V(D)J combinations from B cell antibodies (Igs) and T cell receptors (TCRs). One major challenge of immune repertoire sequencing is to accurately capture the structural and sequence complexities of antibodies and TCR genes. We have developed a method for accurate sequencing of full length immune gene repertoires of B cells and T cells. RNA extracted from tumor tissues containing tumor infiltrating lymphocytes, as well as matched peripheral blood mononuclear cells (PBMCs) were used to generate full length Ig and TCR libraries. Unique molecule index (UMI) was used to discretely barcode each mRNA molecule, enabling absolute quantitative ranking of antibody/TCR clone abundance. Full length immune repertoire sequencing facilitates detection of distinct and shared clones in tissue and blood samples, enabling identification of disease specific clones to evaluate immunotherapy effects. Highly expanded clones in tumor samples are also found in blood samples. RNA-seq libraries were also constructed from the same RNA for Ig and TCR libraries. The expression level of IGH/IGL/IGK and TRA/TRB in the immune sequencing libraries highly correlates with the RNA-seq data. In addition, both Ig and TCR libraries can be constructed in one tube to obtain a whole immune repertoire profile.Our immune repertoire sequencing approach allows accurate clonal determination for both Ig and TCR. This technique is applicable for investigation of lymphocytes infiltration of tumor microenvironments, tracing expanded B cell and T cells in blood samples, and monitoring of minimal residual disease.
Citation Format: Chen Song, Pingfang Liu, Andrew Barry, Bradley W. Langhorst, Fiona J. Stewart, Salvatore Russello, Theodore B. Davis, Eileen T. Dimalanta. Immune repertoire sequencing reveals tumor microenvironment and tracks clonally expanded B cell and T cell in blood [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 4046.
Abstract 4048: REAlease® technology: Controlled release of antibody-fluorochrome conjugates for maximal flexibility in flow sorting and fluorescence microscopy applications
Authors: Pankratz Jennifer , Schmachtenberg Sabine , Jansen Nicole , Hansen Marie , Krauthäuser Susanne , Kinkhabwala Ali , Schlegel Karolina , Meiler Svenja , Siewert Christiane , Bartholomäus Alina , Yushchenko Dmytro A. , Dose Christian 
Published: August 2019

Abstract
Multi-parameter immunofluorescent labeling is the method of choice for the flow-based sorting of targeted cell populations from heterogeneous samples. However, existing antibody-fluorochrome conjugates used for flow sorting limit the types of downstream analyses that can be applied to the isolated cells, as their continued presence on the cells blocks specific cellular epitopes and restricts the choice of downstream fluorescence detection channels. Herein, we present a new type of antibody-fluorochrome conjugates that facilitates a highly specific multi-parameter cell staining for flow sorting as well as subsequent complete release of the conjugate probes from the sample. These new conjugates rely on recombinantly engineered antibody fragments that individually possess low epitope binding affinities. A tailor-made covalent conjugation chemistry allows for their multimerization as well as fluorochrome labeling, generating fluorescent probes comparable to conventional antibody conjugates. Importantly, upon addition of a release reagent, the antibody-fluorophore conjugates can be rapidly released from the cell surface. Accordingly, previously blocked epitopes are free for re-labeling, which provides maximal flexibility for renewed epitope targeting in downstream applications. As many targeted cell populations require multi-parameter detection of several antigens for their isolation, the recombinant engineered antibodies were conjugated with different fluorochromes. The versatility of this technology is presented in multi-parameter panels enabling clear distinction and discrimination of different cell populations of different starting material, e.g. peripheral blood and tumor cells. The applicability of the new REAlease® antibody fluorochrome conjugates is also demonstrated by flow sorting of human naïve regulatory T cells. In addition, we show that the fast and efficient releasability of the new conjugates can serve as an optimal basis for cyclic immunofluorescence microscopy using a new MACSima™ imaging platform, which permits cell analysis with potentially unlimited number of parameters.
Citation Format: Jennifer Pankratz, Sabine Schmachtenberg, Nicole Jansen, Marie Hansen, Susanne Krauthäuser, Ali Kinkhabwala, Karolina Schlegel, Svenja Meiler, Christiane Siewert, Alina Bartholomäus, Dmytro A. Yushchenko, Christian Dose. REAlease® technology: Controlled release of antibody-fluorochrome conjugates for maximal flexibility in flow sorting and fluorescence microscopy applications [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 4048.
Abstract 4054: Mass cytometry approaches to biomarker discovery via high-dimensional antigen-specific T cell identification and profiling
Authors: Cobbett Mathew , Fehlings Michael , Newell Evan 
Published: August 2019

Abstract
immunoSCAPE leverages the high-dimensional immune profiling capabilities of mass cytometry combined with a unique technology for the identification of antigen-specific T-cells to support the development of immunotherapy strategies in cancer and immune-related diseases. In cancer, there is now strong evidence that immunotherapy-mediated tumor rejection can rely on tumor-specific (neoantigen-specific) CD8+ T-cells. Consequently, the discovery of neoantigens becomes valuable for personalized cancer immunotherapies. Although in silico pipelines exist, that are capable of predicting non-synonymous mutations potentially giving rise to tumor-specific neoantigens, it is not clear how accurate these methods are in identifying immunogenic and therapeutically relevant epitopes, since T-cell epitope usage can be influenced by many factors. Moreover, analysis of T-cells in cancer patients is challenging as it requires detecting rare antigen-specific T-cell populations in samples that are usually limited in volume and availability.
By applying cytometry by time of flight in conjunction with combinatorial peptide-MHC tetramer staining and high-performance dimensional analysis tools, we are able to map broadly MHC-class I epitope with a high sensitivity for rare antigen-specific T-cells and perform concurrently in-depth characterization of these cells. We will show here the application of this technology in the context of immunotherapy, through the example of a murine in vivo tumor model responsive to checkpoint blockade inhibitors, as well as through the analysis of different human cancer samples.
Together, by providing insights into the nature of neoantigen-specific T-cells, immunoSCAPE’s unique target discovery and high-dimensional immune profiling platform is a valuable tool for the development of novel diagnostic biomarkers and therapeutic strategies at different stages of drug development.
Citation Format: Mathew Cobbett, Michael Fehlings, Evan Newell. Mass cytometry approaches to biomarker discovery via high-dimensional antigen-specific T cell identification and profiling [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 4054.
Abstract 4073: Novel BETi NHWD-870 synergizes with immune checkpoint inhibitor in preclinical model of non-small cell lung cancer
Authors: Zhang Yongchang , Sun Ziyi , Yang Nong 
Published: August 2019

Abstract
Background: Small molecular inhibitors targeting bromodomain and extraterminal domain (BET) protein is promising in cancer therapy. NHWD-870 was a highly selective BETi and has been proved effective in lung cancer according to our previous findings. Combination of immune checkpoint inhibitors with BETi is now under investigation for lung cancer treatment.
Method: We set up a fast track preclinical model with C57 mouse. Growth rate and survival data were measured in subgroups receiving single NHWD-870, single PD-1 antibody and combined treatment respectively. Finally, pathology sections, immunohistochemistry and inflammatory cell infiltration was applied to evaluate the pathological response.
Result: Millions of mouse lung cancer cells were harvested and injected to the lateral leg. Lung cancer xenografts were visible in 3-5 days. And the total survival time was within 30 days without any treatment. Tumor volume was measured for effective evaluation. During the three groups, NHWD-870 combined with anti-PD-L1 showed robust efficacy in inhibiting tumor growth. And the survival time was also prolonged significantly. Pathological examination showed the lung cancer cells were filled with necrosis. Inflammatory cell infiltration and immunohistochemistry showed that PD-L1 was down regulated and CD4+/ CD8+ positive lymphocyte cells increased significantly.
Conclusion: We established a useful method to evaluate tumor response to immune checkpoint inhibitor. And our data proved BETi plus immune checkpoint inhibitor to be a promising treatment of NSCLC.
Citation Format: Yongchang Zhang, Ziyi Sun, Nong Yang. Novel BETi NHWD-870 synergizes with immune checkpoint inhibitor in preclinical model of non-small cell lung cancer [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 4073.
Abstract 4077: ATOR-1144 is a tumor-directed CTLA-4 x GITR bispecific antibody that acts by depleting Tregs and activating effector T cells and NK cells
Authors: Fritzell Sara , Levin Mattias , Åberg Ida , Johansson Maria , Winnerstam Magnus , Smith Karin Enell , Ellmark Peter , Furebring Christina , Norlén Per , Kvarnhammar Anne 
Published: August 2019

Abstract
ATOR-1144 is a human CTLA-4 x GITR bispecific IgG1 antibody generated by fusing a high affinity CTLA-4 binder, derived by FIND® optimization of the CTLA-4 binding domain of CD86, to an agonistic GITR antibody isolated from the human antibody library ALLIGATOR-GOLD®. CTLA-4 and GITR are highly expressed on Tregs in the tumor microenvironment, and GITR is also expressed on NK cells and certain tumor cells. ATOR-1144 was designed to induce a tumor-directed immune activation for treatment of solid tumors and hematological malignancies. The in vitro activity of ATOR-1144 in terms of Treg depletion and activation of T cells and NK cells was investigated using purified cells from healthy human donors. ATOR-1144 induced depletion of primary Tregs in an ADCC assay with NK cells. T-cell activation in terms of IL-2 and IFN-γ release was demonstrated in the presence of CTLA-4 and Fcγ receptor crosslinking. NK cells treated with ATOR-1144 released IFN-γ, perforin and granzyme B, and displayed enhanced cytolytic killing of tumor cells. Moreover, NK cell-mediated depletion of CTLA-4-expressing cells was significantly improved upon stimulation with ATOR-1144 compared to monospecific anti-CTLA-4, indicating that NK cells activated via GITR acquire an enhanced capacity to induce ADCC. In conclusion, ATOR-1144 is a first-in-class bispecific tumor directed antibody targeting CTLA-4 and GITR. ATOR-1144 acts through several mechanisms, including depletion of Tregs, activation of effector T cells and activation of NK cells for enhanced Treg depletion and tumor cell killing.
Citation Format: Sara Fritzell, Mattias Levin, Ida Åberg, Maria Johansson, Magnus Winnerstam, Karin Enell Smith, Peter Ellmark, Christina Furebring, Per Norlén, Anne Kvarnhammar. ATOR-1144 is a tumor-directed CTLA-4 x GITR bispecific antibody that acts by depleting Tregs and activating effector T cells and NK cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4077.
Abstract 4084: Radiation enhances efficacy of TEM1-specific cancer vaccination
Authors: Pierini Stefano , Uribe-Herranz Mireia , Perales-Linares Renzo , Beghi Silvia , Costabile Francesca , Pustylnikov Sergei , Facciabene Andrea 
Published: August 2019

Abstract
Tumor endothelial marker 1 (TEM1 or CD248) is a protein found in both tumor vasculature and stroma. In prior experiments, we showed that immunizing with Tem1-TT plasmid-DNA (Tem1 cDNA fused to the minimal domain of the C fragment of tetanus toxoid) was effective in controlling tumor progression in three mouse tumor models in a T cell-dependent manner. Moreover, effective Tem1-TT vaccination reduced tumor vascularity without impacting normal angiogenesis. Radiation therapy (RT) is an established curative and palliative cancer treatment regimen which uses high-energy radiation to kill cancer cells. RT modulates the tumor microenvironment - by increasing MHC-I expression, inducing immunological cell death, and damaging the tumor-associated vasculature - potentially synergizing with anti-cancer immunotherapies. Here, we combined RT and Tem1-TT heterologous vaccination and showed that combination of the two therapies was more effective in controlling CT26 and TC1 tumor progression than either single therapy alone. Interestingly adding RT to Tem1-TT vaccine resulted in a stronger vaccine-specific immune response and increased epitope spreading toward gp70, a TAA expressed by CT26 tumor cell line. Further analysis of the tumor microenvironment revealed a significant increment of PD-L1 expression in both tumor cells and tumor vasculature after single or either combination therapy. This led us to test whether blocking the PD1/PD-L1 axe would further improve the efficacy of RT plus Tem1-TT therapy. Our results demonstrate that administration of anti-PD-L1 antibody further synergized with RT plus Tem1-TT and improved mice survival. In conclusion, triple combination of Tem1-TT vaccine, RT and anti-PD-L1 can offer a therapeutic advantage for TEM1-positive tumors which also express PD-L1.
Citation Format: Stefano Pierini, Mireia Uribe-Herranz, Renzo Perales-Linares, Silvia Beghi, Francesca Costabile, Sergei Pustylnikov, Andrea Facciabene. Radiation enhances efficacy of TEM1-specific cancer vaccination [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 4084.
Abstract 4095: Adding fuel to the fire: Augmenting the efficacy of adoptive T-cell therapy with pro-oxidants
Authors: Aboelella Nada , Zhou Gang , Fesenkova Kateryna , Ding Zhi-chun 
Published: August 2019

Abstract
Cancer cells face increased oxidative stress driven by oncogene activation, tumor suppressor gene mutation and increased metabolism. Even though cancer cells can resist this redox imbalance by activating various antioxidant defense mechanisms, they are more susceptible to further redox disruption by pro-oxidants. Our previous study indicated that adoptive T-cell therapy (ACT) leads to heightened oxidative stress in tumor cells reflected by depletion of cellular antioxidant glutathione (GSH), accumulation of reactive oxygen species (ROS), and presence of oxidative DNA damages. Based on this observation, we propose that intensifying oxidative stress in tumor with pro-oxidants can sensitize cancer cells to ACT and lead to improved therapeutic outcomes. In this study, we used clinically relevant ACT models to screen a panel of pro-oxidant agents for their ability to potentiate the antitumor effects of ACT. We identified several clinically applicable pro-oxidants, including some commonly used non-steroidal anti-inflammatory drugs (NSAIDs), that can benefit the infusion of tumor-specific CD4+ T cells or CD19-targeting CAR T cells. Our data provide a rationale for combining selected pro-oxidants with ACT to achieve synergistic antitumor effect.
Citation Format: Nada Aboelella, Gang Zhou, Kateryna Fesenkova, Zhi-chun Ding. Adding fuel to the fire: Augmenting the efficacy of adoptive T-cell therapy with pro-oxidants [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 4095.