bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1603: Discover potent and functional human antibodies against a new B7-family member target for cancer immunotherapy
Authors: Wu Xiaodong , Wang Yongqiang , Lv Xiaocheng , Chen Fei , He Yun , Zhao Jiuqiao , Rong Yiping 
Published: July 2021

Abstract
Immunotherapeutics targeting immune checkpoints such as PD1/PD-L1 and CTLA4 offer effective treatment alternatives to the traditional cancer therapies. However, a considerable proportion of patients remain unresponsive to treatment indicating that a more complex immune suppressive tumor microenvironment is involved. Developing novel immune checkpoint inhibitors for combination with current approaches can provide more efficient therapies and expanded indications. A novel B7 family member B7y was recently reported to be highly expressed on a variety of human cancers such as colon, pancreas, breast, bladder, lung cancers and associated with metastatic disease and poor survival. Its co-inhibitory function makes it a new checkpoint and candidate for cancer immunotherapy other than PD-L1 or other immune checkpoints. Here we report the development of functional antibodies targeting this novel B7 family member with potent anti-tumor effect. Generated with H2L2 Harbour Mice® platform, these fully human anti-B7y antibodies specifically bind to cell lines that over-express human or cynomolgus B7y, as well as human tumor cell lines that express endogenous B7y, with high selectivity against other B7 family members. Antibodies that blocked the interaction between B7y and its receptors potently promoted T cell activation in vitro dependent on B7y expression on APC cells. Furthermore, these antibodies in ADCC null versions showed potent anti-tumor activity in humanized murine tumor model. In conclusion, we generated highly potent human antibodies targeting the new immune checkpoint B7 family member and showed good anti-tumor efficacy. Anti-B7y antibody presents a promising novel anti-tumor agent as monotherapy and/or combination therapy with currently established IO agents.
Citation Format: Xiaodong Wu, Yongqiang Wang, Xiaocheng Lv, Fei Chen, Yun He, Jiuqiao Zhao, Yiping Rong. Discover potent and functional human antibodies against a new B7-family member target for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1603.
Abstract 1609: Peripheral NK-cell immunophenotypes predict progression in nasopharyngeal carcinoma patients
Authors: Li Xiao-Yun , Lu Zi-Jian , Mai Hai-Qiang 
Published: July 2021

Abstract
Objective: The tumorigenesis is closely associated with the alteration in the expression of cell-surface proteins. As NK cells play a vital role in cancer immunotherapy, we thus conducted this study to characterize the immunophenotypes of circulating NK cells and to explore the association between NK phenotypes and disease prognosis.
Methods: 249 nasopharyngeal carcinoma (NPC) patients and 11 healthy individuals were recruited in the study, whose peripheral blood samples were collected before treatment. Multi-color flow cytometry analysis was performed. The expression of four inhibitory receptors, PD-1, TIGIT, LAG-3, TIM-3, and four stimulatory receptors, NKp46, NKp30, CD226, NKG2D, were measured in three NK subsets, identified by the co-expression of CD56 and CD16 when gated on CD3-. The LASSO (least absolute shrinkage and selection operator) logistic regression model was used to screen out potential prognostic NK subtypes and calculate the NK-function index.
Results: NPC patients exhibited distinct peripheral NK-cell distribution and altered expression of key receptors, as characterized by increased expression of PD-1 and TIGIT on CD56+CD16- cells and decreased expression of NKp46 on CD56+CD16- and CD56-CD16- cells. Four markers were selected from the LASSO model to calculate the NK-function index: PD1 and NKp46 on CD56-CD16+ NK cells, NKp46 on CD56+CD16- cells and NKG2D on CD56+CD16+ cells. Patients with low NK index had significantly shorter progression-free survival (PFS) and distant metastasis-free survival (DMFS), and the NK-function index was an independent prognostic factor for NPC patients.
Conclusions: The immunophenotype of peripheral NK cells and its association with survival outcomes of NPC patients revealed its potential as a strong prognosticator for PFS and DMFS, and highlighted the important role of circulating immune environment, especially for the application of immunotherapy.
Citation Format: Xiao-Yun Li, Zi-Jian Lu, Hai-Qiang Mai. Peripheral NK-cell immunophenotypes predict progression in nasopharyngeal carcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1609.
Abstract 164: Development of DeepCytoFlow: A novel deep learning pipeline enabling automated gating of flow cytometry data
Authors: Chandran Arjun , Tsau Jennifer , Gaddis Dalia , Sarikonda Shyam , Dakappagari Naveen , Laing Christian , Thomas Swetha Ann 
Published: July 2021

Abstract
Introduction
Following the advent of cellular therapies, flow cytometry has become a central tool for simultaneous assessment of drug levels and disease burden due to its ability for high dimensional cellular analysis. However, identification and monitoring of myriad immune- and leukemic cell phenotypes requires a manual gating process by subject matter experts. Although this process is the current gold standard for flow data analysis, it is slow, tedious, and prone to subjectivity. Herein, we describe our approach to automate flow data analysis using novel strategies that reduces the reliance on clustering methods that are unable to filter challenging noisy data sets inherent in flow data.
Methods
We developed DeepCytoFlow, a novel deep learning framework adapted for flow cytometry data analysis. DeepCytoFlow utilizes a convoluted neural network structure to analyze flow cytometry data files to generate appropriately gated cell populations in a matter of minutes significantly reducing the time required for manual analysis. The neural networks were first trained using a unique data set generated manually by multiple operators and tested using an independent data set to establish concordance in assessments. In addition, we evaluated the performance of our method using both accuracy and F1-score.
Results
Our integrated DeepCytoFlow pipeline employing neural network design shows promise on clustering-based analysis methods in terms of accuracy, precision and recall. More specifically, DeepCytoFlow is capable of correctly classifying various immune cell lineages (e.g., CD4 and CD8 T-cells). However, a limitation was observed on its ability to classify rare cell populations with a very limited prevalence. In an effort to improve performance, we are currently designing a new network architecture, and increasing our training and test dataset's size and quality.
Conclusions
DeepCytoFlow provides proof of concept of the applicability of deep learning for automation of gating in flow cytometry. The high adaptability of deep learning to a large set of problems suggests that this technique can be broadly applied to a larger set of biomarkers for the purpose for automated gating. With additional improvements, we believe DeepCytoFlow can enable a fast, accurate, and robust platform for analysts to perform consistent and, repeatable flow analysis for biomarker monitoring in clinical trials investigating novel immunotherapies.
Citation Format: Arjun Chandran, Jennifer Tsau, Dalia Gaddis, Shyam Sarikonda, Naveen Dakappagari, Christian Laing, Swetha Ann Thomas. Development of DeepCytoFlow: A novel deep learning pipeline enabling automated gating of flow cytometry data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 164.
Abstract 1645: Cell-based reporter bioassays for the development of Fc-functional and Fc-silent SIRPα/CD47 checkpoint inhibitors
Authors: Mitchell Jonathan , Grailer Jamison , Hartnett Jim , Fan Frank , Cong Mei , Cheng Zhijie Jey 
Published: July 2021

Abstract
CD47, a membrane glycoprotein commonly overexpressed in human cancers, interacts with its cognate receptor SIRPα on myeloid cells to deliver a “don't eat me” signal that inhibits phagocytosis. This SIRPα/CD47 interaction has emerged as a critical and potentially druggable immune checkpoint. Blockade of SIRPα/CD47 interaction promotes phagocytosis of tumor cells in vitro, and SIRPα/CD47 inhibitors exhibit anti-tumor activity, including synergistic activity with other tumor-targeted mAbs (e.g. rituximab), in vivo. These encouraging pre-clinical data have sparked widespread development of SIRPα/CD47 inhibitors and driven a need for robust functional assays to measure the activity of these therapeutic candidates. Biological activity of SIRPα/CD47 inhibitors is typically assessed via in vitro phagocytosis assays based on imaging or flow cytometry. These low-throughput assays often use primary monocyte-derived macrophages and are inherently prone to donor variability. Additionally, many SIRPα/CD47 inhibitors under development are designed to minimize Fc function to enhance safety and are thus incapable of driving phagocytosis directly. To overcome these limitations, we have developed a pair of reporter-based bioassays for measuring the biological activity of Fc-functional and Fc-silent SIRPα/CD47 inhibitors. These assays utilize a SIRPα-positive monocytic effector cell-line that expresses multiple Fc gamma receptors (FcγRs) and encodes a FcγR-responsive NanoLuc luciferase reporter that is inhibited by SIRPα/CD47 interaction upon co-culture of SIRPα effector cells with CD47-positive target cells. Addition of Fc-functional inhibitors simultaneously disrupts the SIRPα/CD47 interaction and engages FcγRs on the SIRPα effector cells, resulting in NanoLuc reporter activation. To enable testing of Fc-silent inhibitors, we have engineered a second CD47 target cell-line which provides a constitutive activating stimulus to SIRPα effector cells that is restricted by SIRPα/CD47 interaction. Addition of Fc-silent SIRPα/CD47 blockers releases inhibition by SIRPα/CD47, resulting in NanoLuc reporter activation. These newly developed reporter bioassays provide a robust, high-throughput platform to facilitate discovery and development of diverse SIRPα/CD47 checkpoint inhibitors.
Citation Format: Jonathan Mitchell, Jamison Grailer, Jim Hartnett, Frank Fan, Mei Cong, Zhijie Jey Cheng. Cell-based reporter bioassays for the development of Fc-functional and Fc-silent SIRPα/CD47 checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1645.
Abstract 1650: MoA-based reporter bioassays enable quantitative potency determination for therapeutic biologics targeting co-stimulatory and co-inhibitory immune checkpoint receptors
Authors: Grailer Jamison , Gilden Julia , Stecha Pete , Garvin Denise , Wang Jun , Beck michael , Hartnett Jim , Fan Frank , cong mei , Cheng Zhi-Jie Jey 
Published: July 2021

Abstract
Immune checkpoint (IC) receptors play critical roles in maintaining immune homeostasis and are emerged as promising drug targets for the treatment of various cancers and autoimmune disorders. Monoclonal antibodies designed to block immune inhibitory receptors PD-1 and CTLA-4 have been approved and showed unprecedented efficacy in cancer treatment. This led to rapid expansion of drug development to many more IC receptors targeted individually or in combination. However, due to the novelty and fast speed, one of the bottleneck during immunotherapy drug development is the lack of quantitative and reproducible functional assays for potency determination when existing methods heavily rely on primary immune cells and the process are labor intensive and highly variable.
To address this need, we developed a panel of cell-based reporter bioassays that can quantitatively measure the potencies of biologics targeting individual IC receptor (e.g. PD-1, LAG-3, BTLA, CTLA-4, TIGIT, TIM-3, ICOS, 4-1BB, CD40), or bispecific molecules targeting two IC receptors spontaneously (e.g. PD-1xTIGIT, PD-1xLAG-3, PD-1xCTLA-4, PD1x4-1BB). These bioassays each consist of an engineered T effector cell line that expresses T cell receptors and IC receptors of interest, and an engineered artificial antigen presenting cells (aAPC) expressing the corresponding ligands for the IC receptors. The T effector cell line also expresses a luciferase reporter driven by response elements/promoter specifically responding to TCR activation which can be co-stimulated or inhibited by the signal from the IC receptors. These bioassays are designed to reflect the mechanisms of action for the drug candidates designed for each IC receptor and the assay signals are specific. They are prequalified according to ICH guidelines and show the precision, accuracy and linearity required for relative potency determination and product stability study under cGMP environments. Therefore, these MoA-based bioassays can serve as value tools for early drug discovery, potency determination and stability study throughout immunotherapy drug development.
Citation Format: Jamison Grailer, Julia Gilden, Pete Stecha, Denise Garvin, Jun Wang, michael Beck, Jim Hartnett, Frank Fan, mei cong, Zhi-Jie Jey Cheng. MoA-based reporter bioassays enable quantitative potency determination for therapeutic biologics targeting co-stimulatory and co-inhibitory immune checkpoint receptors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1650.
Abstract 1657: Tumor selective immunotherapy to overcome checkpoint blockade resistance
Authors: Jiang Lingxiang , Hergenrother Paul J. , Huang Xiumei 
Published: July 2021

Abstract
Most patients are resistant to PD-1/PD-L1 blockade therapy but mechanisms are not well defined. Defective innate sensing limits reactivation of T cells after the blockade. Patients with well-established solid tumors often generate complicated immunosuppressive networks and are generally refractory to immunotherapy. NAD(P)H:quinone oxidoreductase 1 (NQO1) is a two-electron oxidoreductase elevated (more than 100-fold) in most solid cancers and has emerged as a promising target for direct tumor-killing. Here, we demonstrate that novel NQO1 targeting drug-Isobutyldeoxynyboquinone (IB-DNQ) causes tumor-selective innate sensing leading to T cell dependent tumor suppression. IB-DNQ treatment increases PD-L1 expression in the tumor microenvironment. Upregulated PD-L1 within TME contributes to tumor relapse and provides therapeutic window for combination therapy of IB-DNQ with immune checkpoint blockade. We demonstrate that IB-DNQ or PD-1 blockade treatment alone leads to tumor rejection in mice bearing small but not large established tumors. However, combination therapy of IB-DNQ with anti-PD-L1 eradicates well-established and checkpoint blockade refractory tumors.
Citation Format: Lingxiang Jiang, Paul J. Hergenrother, Xiumei Huang. Tumor selective immunotherapy to overcome checkpoint blockade resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1657.
Abstract 1676: A comprehensive whole blood CyTOF immune monitoring panel with expanded surface and intracellular markers using the Maxpar Direct Immune Profiling Assay
Authors: Mujib Shariq , Li Stephen K. , Zabinyakov Nick , Loh Christina 
Published: July 2021

Abstract
In-depth monitoring of the immune response to cancer and infection is vital to ascertain disease status and to assess immunotherapeutic options. Time-of-flight technology, the basis of CyTOF® mass cytometry, enables multiplex proteomic cellular phenotyping with 50 or more markers, making it ideal for comprehensive immune profiling. Unlike fluorescence-dependent approaches, which require signal compensation that makes the development of larger panels more challenging, CyTOF utilizes monoisotopic metal-tagged antibodies that exhibit minimal background signal, enabling the highest-resolution multiparametric landscape of a single cell. The Maxpar® Direct™ Immune Profiling Assay™ is a pre-titrated dried-down 30-antibody cocktail preparation for immune profiling of human whole blood or PBMC. This assay is used with Maxpar Pathsetter™ software, which resolves whole blood into 37 immune populations comprising major lineage populations and their subsets, such as CD4 Th subsets and B and T cell memory cells, as well as stratifications of myeloid populations. The resulting system is a simple sample-to-answer solution for immune monitoring studies. Here, we expanded the 30-marker assay with 14 additional antibodies comprising pertinent targets of immunotherapy, including the exhaustion markers PD-1, PD-L1, Tim-3 and CTLA-4, and co-stimulation markers 4-1BB and ICOS. We also demonstrated the compatibility of the assay with downstream intracellular staining for cytoplasmic markers IFN-γ, TNF-α, IL-2, perforin and granzyme B for assessment of cellular function in 4h PMA/ionomycin-stimulated whole blood cultures. Next, we modified the existing Pathsetter model to automate the analysis of whole blood stained with the expanded panel to generate reports on key immune cell populations, percentages of exhausted cells and cell subsets producing cytokines. Last, to demonstrate the ability of this expanded panel to identify antigen-specific T cell subsets accompanied by their in-depth phenotypic assessment, we tested this panel against CMV peptide-stimulated whole blood samples. We demonstrated the flexibility of the Maxpar Direct Immune Profiling Assay in panel customization and a streamlined workflow for automated analysis to enable comprehensive immune profiling of human whole blood. For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Shariq Mujib, Stephen K. Li, Nick Zabinyakov, Christina Loh. A comprehensive whole blood CyTOF immune monitoring panel with expanded surface and intracellular markers using the Maxpar Direct Immune Profiling Assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1676.
Abstract 168: Computational model for prediction of actionable drug combinations in cancer
Authors: Pentaparthi Sairahul , Burgman Brandon , Yi S. Stephen 
Published: July 2021

Abstract
Synthetic essentiality presents an effective approach towards finding connected genetic targets in cancer by identifying genes that produce an inviable phenotype upon joint inactivation. However, it is less studied how synthetic lethal gene pairs may be contextualized with respect to deregulation of different cell functions and how these pairs act in different cell types and tissues. To study cancer-specific synthetic essentiality, we devised an integrated network-based algorithm to analyze relationships between tumor gene expression and patient survival in The Cancer Genome Atlas (TCGA) and expression data from the Genotype-Tissue Expression (GTEx) project. In particular, we identify gene pairs in each cancer cohort that exhibit upregulation in tumors but are associated with improved survival for patients whose tumors feature reduced expression of the gene pair. Our findings reveal variability in synthetic lethal pair activity across different cancer types, and the identified pairs connect distinct signaling and metabolic cellular pathways to different cancer types. Altogether, our findings present a pan-cancer reference for gene expression-based synthetic lethal gene pairs as well as a nuanced perspective on changes in synthetic essentiality across different cellular and tissue contexts, pointing to a new avenue for drug combination discovery oriented on targeting key pathways based on the cancer type.
Citation Format: Sairahul Pentaparthi, Brandon Burgman, S. Stephen Yi. Computational model for prediction of actionable drug combinations in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 168.
Abstract 1686: Host intrinsic STING is a promising biomarkerfor predicting clinical efficacy of anti-PD-1 inhibitors in lung cancer
Authors: Zhou Li , Xu Qiuli , Huang Litang , Zhan Ping , ye mingxiang , Lv Tangfeng , Song Yong 
Published: July 2021

Abstract
Background: The stimulator of IFN genes (STING) signaling pathway plays an important role in anti-tumor immune responses. However, the mechanistic contribution of host and tumor STING signaling to the therapeutic efficacy of anti-PD-1 inhibitors in lung cancer remains unknown.
Methods: We analyzed the association of STING with immune makers in TCGA datasets; we evaluated the efficacy of anti-PD-1 inhibitors by coculturing spleen cells with LLC cells in vitro, and inoculating wild type/STING knockdown LLC cells into the flank of wild-type/STING knockout mice in vivo. Furthermore, we measured the expression of STING by multiple immunohistochemistry and immunohistochemistry in lung cancer patients, and analyzed the relationship between expression level of STING in different cells and treatment efficacy of DCB(Durable clinical benefit : CR or PR or SD lasting longer than 6 months) and NDB(No durable clinical benefit : PD or SD that lasted ≤ 6 months) patients receiving immunotherapy.
Results: Here we first demonstrated that STING signaling pathway activation was associated with better immunotherapy efficacy in lung cancer patients. Next, we identified two distinct STING expression pattern and found that STING in host cells not in tumor cells was positively correlated with infiltration of CD8+ T cells. More importantly, we demonstrated a loss of therapeutic efficacy of anti-PD-1 inhibitor in STING KO spleen cells and STING KO mice. In contrast, knock down of STING expression in tumor cells had no effect. Furthermore, expression of STING on host cells not in tumor cells was correlated with the efficacy of Anti-PD-1 inhibitors in lung cancer patients.
Conclusion: Together, these findings demonstrate that STING expressed in host cells, rather than on tumor cells, plays an essential role in anti-PD-1 inhibitor therapy, suggesting that host intrinsic STING could be predictive of sensitivity to anti-PD-1 inhibitors.
Citation Format: Li Zhou, Qiuli Xu, Litang Huang, Ping Zhan, mingxiang ye, Tangfeng Lv, Yong Song. Host intrinsic STING is a promising biomarkerfor predicting clinical efficacy of anti-PD-1 inhibitors in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1686.