bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4451: Combination of local mRNA immunotherapy with systemic immune checkpoint blockade demonstrates anti-tumor activity across a diverse range of preclinical syngeneic tumor models
Authors: Malkova Natalia V. , Tolstykh Tatiana , Levit Mikhail , Theilhaber Joachim , Hebert Andrew , Atchison Kevin , Maisonet Adalis , Hotz Christian , Sahin Ugur , Protopopov Alexei , Pollard Jack , Sidhu Sukhvinder , Wiederschain Dmitri , Wagenaar Timothy R. 
Published: September 2020

Abstract
Cancer immunotherapies with anti-PD-1/PD-L1 checkpoint blockade antibodies have revolutionized the treatment of a wide variety of malignancies. However, immunotherapy is ineffective in a significant subset of patients, or eventually results in the development of resistance with relapsed disease. Therefore, the future of immuno-oncology is identification of new agents that can be combined to increase the depth and breadth of anti-PD-1/PD-L1 therapies. Local intratumoral delivery of messenger RNA (mRNA)-based immunotherapies provides an opportunity to stimulate innate and adaptive immune responses against tumors and modulate tumor microenvironment, while limiting the side-effects related to systemic administration of immuno-modulatory therapeutics. We examined the local immunotherapy of synthetic mRNAs encoding immunomodulatory cytokines (single chain interleukin-12 (IL-12), interferon alpha (IFN-α), granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-15 sushi(IL-15)) alone and in combination with anti-PD-1 antibodies across 12 syngeneic mouse tumor models representing a diverse range of murine tumor types. Single agent treatment with cytokine mRNAs resulted in a significant anti-tumor response in 8 out of 12 tumor models. Combining cytokine mRNA with systemic anti-PD-1 immunotherapy further improved the anti-tumor response and resulted in tumor growth inhibition in two additional models otherwise unresponsive to single agent treatments. Transcriptome and cytokine analyses have been performed to understand factors which determine sensitivity to single agent and combination treatments with cytokine mRNA and anti-PD-1 antibodies. In summary, the combination of local cytokine mRNA immunotherapy with immune checkpoint blockade demonstrated improvement in the anti-tumor activity in a range of preclinical cancer models representing different murine tumor types. Based on these and other data, clinical testing of cytokine encoding mRNA mixture has recently been initiated (NCT03871348).
Citation Format: Natalia V. Malkova, Tatiana Tolstykh, Mikhail Levit, Joachim Theilhaber, Andrew Hebert, Kevin Atchison, Adalis Maisonet, Christian Hotz, Ugur Sahin, Alexei Protopopov, Jack Pollard, Sukhvinder Sidhu, Dmitri Wiederschain, Timothy R. Wagenaar. Combination of local mRNA immunotherapy with systemic immune checkpoint blockade demonstrates anti-tumor activity across a diverse range of preclinical syngeneic tumor models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4451.
Abstract 4474: A quantitative flow cytometry method for the measurement of HLA-DR expression level on monocyte subsets
Authors: Huang Wei 
Published: September 2020

Abstract
There is growing evidence that solid tumor cancer is often associated with a systemic immunosuppressive environment which correlates with poor responses to immunotherapy. The frequency of CD14+HLA-DRlo/neg monocytes, also called monocytic myeloid derived suppressor cells (M-MDSCs), is often used as a flow cytometry based biomarker for the measurement of the level of immunosuppression in cancer immunotherapy research. While this approach has been demonstrated to work in clinical investigation studies with well-controlled cytometer settings and analysis methods, it is difficult to produce consistent results and compare measurements from different laboratories due to lack of standardization. The BD Horizon™ Dri Monoset panel is designed to measure the absolute counts and relative frequency of classical, intermediate and nonclassical monocyte subsets for research use. The assay uses whole blood samples analyzed by flow cytometry using a consensus reagent panel and gating strategy published by an international organization. When used in combination with BD Quantibrite™ beads, the level of HLA-DR expression on each subset of monocytes can be quantified in antibody bound per cell (ABC) units independent of the cytometer used to perform the assay. Evaluating 10 normal blood donor samples, our data demonstrates using the BD Horizon™ Dri Monoset panel in combination with BD Quantibrite beads, quantification of HLA-DR expression level on monocyte subsets provides consistent flow cytometry results.
Disclaimers:
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
Class 1 Laser Product.
BD, the BD Logo, Horizon, and Quantibrite are trademarks of Becton, Dickinson and Company. © 2019 BD and its subsidiaries. All rights reserved.
Citation Format: Wei Huang. A quantitative flow cytometry method for the measurement of HLA-DR expression level on monocyte subsets [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4474.
Abstract 4475: Site-specific profiling of TCR signaling
Authors: Phyo Zaw , Verma Rohan , Ho Won J. , Jaffee Elizabeth M. 
Published: September 2020

Abstract
Background: T cell exhaustion is a hyporesponsive state commonly found in cancer and is characterized by overexpression of inhibitory receptors and secretion of immunosuppressive cytokines. Immune checkpoint inhibitors (ICIs) target inhibitory receptors such as PD-1 and CTLA-4 to reinvigorate exhausted T cells and promote anti-tumor responses. While ICIs have improved clinical outcomes, no biomarker to date reliably determines the extent of T cell exhaustion. Since robust T cell receptor (TCR) signaling is critical for effective antitumor immunity, we hypothesized that interrogating the phospho-signaling states within the T cells along with their functional states will enhance our understanding of T cell exhaustion and yield potential biomarkers.
Methods: In this study, we developed a validated mass cytometry panel of 24 markers to quantify phosphorylation states of 8 intracellular kinases involved in the TCR signaling within multiple CD8+ T cell subtypes. To identify potential differences between the local and peripheral immunological responses, we profiled CD8+ T cells derived from four sites (tumor, tumor draining lymph node, spleen and peripheral blood) in mice bearing MC38-induced flank tumors. We performed a clustering analysis of the dataset in aggregate using FlowSOM and visualized the results with UMAP, a dimensionality reduction algorithm, to compare the phospho-profiles of CD8+ T cell subtypes in all four sites.
Results: Bulk analysis of CD8+ T cells demonstrates site-specific concordance between phosphoprotein markers and T cell functional markers (i.e. Ki67 and Granzyme B) with the highest expression in tumor followed by tumor draining lymph node, spleen and peripheral blood. Based on the results from the clustering analysis, site-specific breakdown of CD8+ T cells revealed high prevalence of effector, memory, and exhausted memory T cells in tumors compared to other sites where naïve T cells predominated. Despite these variations in CD8+ T cell immunophenotypic distribution, TCR signaling profiles correlated strongly with specific T cell subtypes across all sites.
Conclusion: These data demonstrate that subtype-specific TCR signaling is preserved systemically and that phospho-immune subtyping of CD8+ T cells in the peripheral blood may be used to identify T cell exhaustion states that are found in the tumor microenvironment. Further studies will be conducted to investigate the changes in the TCR phospho-profiles in response to ICI treatment and their associated functions.
Citation Format: Zaw Phyo, Rohan Verma, Won J. Ho, Elizabeth M. Jaffee. Site-specific profiling of TCR signaling [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4475.
Abstract 4491: Characterizing long non-coding RNA expression of tumor-infiltrating lymphocytes across solid cancers
Authors: Dinalankara Wikum , Imada Eddie-Luidy , Jackson Christopher M. , Nirschl Thomas R. , Lim Michael , Drake Charles G. , Marchionni Luigi 
Published: September 2020

Abstract
Usually recognized as transcripts of length more than 200 bp and devoid of open reading frames, long non-coding RNAs (lncRNAs) span a vast range of the human genome. Once thought to be of relatively little biological importance, they have been shown to be involved in many biological processes and diseases, highlighting their important regulatory function, which is now gradually starting to be understood. For instance, the recent discovery of immune gene priming lncRNAs (IPLs) – a subset of lncRNAs that facilitate epigenetic priming of immune gene promoters – has demonstrated the hitherto unappreciated role of lncRNAs in orchestrating inflammatory and immune responses.
In this study we generated and analyzed bulk RNA sequencing data from a collection of purified cell populations obtained from patients with prostate cancer, glioblastoma, bladder cancer, and renal cell carcinoma. Each cohort was comprised of tumor infiltrating lymphocytes (TILs) and paired circulating lymphocytes, derived from matched peripheral blood samples, obtained by fluorescence-activated cell sorting (FACS).
The high depth of coverage in our data allowed the examination of expression patterns of CD4 and CD8 cell types at a level not possible with single cell sequencing, across relevant tumor phenotypes including T-cell exhaustion. To this end, we used the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) annotation, quantifying expression levels for over 100,000 coding and non-coding genes, encompassing enhancers and promoters recently characterized by the FANTOM consortium and examined their behavior with respect to immune function. We compared the behavior of coding genes and various categories of lncRNAs against each other, and identified important candidate lncRNAs for further functional study. Overall, our comprehensive study of TILs gene expression provides novel insights into lncRNA-directed networks controlling immune response mechanisms in cancer.
Citation Format: Wikum Dinalankara, Eddie-Luidy Imada, Christopher M. Jackson, Thomas R. Nirschl, Michael Lim, Charles G. Drake, Luigi Marchionni. Characterizing long non-coding RNA expression of tumor-infiltrating lymphocytes across solid cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4491.
Abstract 4493: Enhancer reprogramming contributes to anti-PD1 resistance in melanoma
Authors: Maitituoheti Mayinuer , Tang Ming , Terranova Christopher J. , Keung Emily , Tomczak Katarzyna J. , Wargo Jennifer , Rai Kunal 
Published: September 2020

Abstract
Immune checkpoint blockade therapy has improved clinical responses and long-term survival benefit for patients with advanced melanoma, however the response rate is modest and a large fraction of treated patients do not experience clinical benefits. Therefore, there is tremendous need to identify combination strategies to improve responses and to overcome resistance to therapy. Emerging data suggest that epigenetic drugs can improve the responses to immunotherapy. However, we have limited understanding of epigenetic mechanisms that characterize responses to Immune checkpoint blockade therapy. Therefore, we generated comprehensive epigenomic landscapes of 36 samples from anti PD-1 treated metastatic melanoma patients by profiling 6 histone markers. To determine correlation of epigenetic features with gene expression, we generated RNA-Access data for 12 matched samples. We determined chromatin states using ChromHMM and ChromHMM profiling consolidated using Epilogos. Analysis of chromatin state differences and associated individual mark profiles with response rate suggested that pre-treatment samples from anti PD-1 non-responsive patients contain higher active enhancer state (enriched for H3K27Ac) compared to responsive patients. Many of these enhancers targeted key regulators of pathways that are shown to mediate resistance to immune checkpoint blockade therapy. Importantly, aberrant expression of these genes correlated well with enhancer gains. Inhibition of enhancers with bromodomain inhibitor along with anti PD-1 significantly decreased the tumor volume by increased T cell infiltration. Together, these findings reveal that enhancer gains on key oncogenes associate with poor response to Immune checkpoint therapy which could be potentially used for stratifying responder and resistant lesions.
Citation Format: Mayinuer Maitituoheti, Ming Tang, Christopher J. Terranova, Emily Keung, Katarzyna J. Tomczak, Jennifer Wargo, Kunal Rai. Enhancer reprogramming contributes to anti-PD1 resistance in melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4493.
Abstract 4495: DNA demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells
Authors: de Cubas Aguirre A. , Dunker William , Hongo Rachel , Bhatia Anuj , Zaninovich Andrew , Panda Anshuman , Beckermann Kathryn E. , Bhanot Gyan , Ganesan Shridar , Karijolich John , Rathmell W K. 
Published: September 2020

Abstract
Recently, we reported that expression of endogenous retroviruses (ERVs), a class of transposable element, is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). Aberrant expression of ERVs can activate host antiviral responses, as well as produce neoantigens. ERV expression is repressed by DNA methylation and can be activated by DNA hypomethylating agents. Here, we investigate whether Decitabine, a DNA hypomethylating agent, can activate ERV expression and host antiviral defenses in RCC to potentially enhance response to ICB. Decitabine induced expression of ERV3-2 and ERV4700 in RCC cells lines, which was accompanied by activation of host antiviral defense genes and increased secretion of inflammatory cytokines. We validated this effect in primary human RCC cell lines. Knockout of RIG-I and MDA5 dsRNA sensors attenuated activation of antiviral responses associated with Decitabine treatment, and RIG-I and MDA5 immunoprecipitations showed increased ERV binding in RCC cells treated with Decitabine. Bioinformatic analysis of RNAseq data showed the Decitabine-induced gene signature could be associated with increased CD8 infiltration and response to ICB. Conditioned media from Decitabine treated RCC cells was capable of inducing host anti-viral defense in naïve RCC cells and could modestly improve activation of T-cells from healthy donors. Further, conditioned media from RCC cells treated with Decitabine significantly enhanced T-cell migration. In a small retrospective cohort of metastatic RCC patients treated with single-agent PD-1/PD-L1 blockade, activation of some host antiviral defense genes was significantly higher in responders compared with nonresponders. Thus, modulation of ERV expression by Decitabine to activate host antiviral defenses could represent a novel therapeutic strategy to enhance RCC patient response to immune checkpoint blockade.
Citation Format: Aguirre A. de Cubas, William Dunker, Rachel Hongo, Anuj Bhatia, Andrew Zaninovich, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W K. Rathmell. DNA demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4495.
Abstract 4497: A single-cell multiomics approach to study tumor-driven perturbations during hematopoiesis in mice
Authors: Kara Nihan , Shi Xiaoshan , Samusik Nikolay , Widmann Stephanie , Tyznik Aaron J. 
Published: September 2020

Abstract
Cancer is associated with concomitant myeloid cell responses that are characterized by an expansion of tumor associated myeloid cells including, myeloid derived suppressor cells (MDSCs), tumor associated macrophages (TAMs) and neutrophils (TANs). These myeloid derived cells are known to modulate immune responses that enhance cancer cell stemness, angiogenesis, metastasis, invasion and immune escape. The prevailing paradigm is that cancer interferes with hematopoiesis and skews the host system to generate cells of myeloid origin with tumor-promoting functions. Intriguingly, tumor derived factors can perturbate normal bone marrow hematopoiesis and promote extramedullary hematopoiesis in organs such as the spleen. Advances in single cell multiomic technologies now enable the analysis of high dimensional protein and mRNA expression from thousands of cells simultaneously. Using the power of the BD Rhapsody™ Single-Cell Analysis system, we have carefully investigated melanoma associated extramedullary hematopoiesis in mice. To do this, we isolated four hematopoietic stem and progenitor cell populations simultaneously, including Lin- Sca-1+ c-Kit+ (LSK), common myeloid progenitor (CMP), granulocyte-macrophage progenitor (GMP) and megakaryocyte-erythrocyte progenitor (MEP) cells from the spleen and bone marrow of melanoma-bearing mice using the BD FACSMelody™ cell sorter in combination with a multiplex BD® AbSeq Oligos panel for surface protein expression and a single-cell whole transcriptome analysis. Using advanced analysis plugins in SeqGeq™ software, we were able to delineate the developmental trajectories of these hematopoietic stem and progenitor cells in this systemic immuno-suppressive myeloid environment. These advanced technologies are critical to uncover tumor mediated abnormalities in hematopoiesis.
Disclaimers: For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product. BD, the BD Logo, FACSMelody and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.
Citation Format: Nihan Kara, Xiaoshan Shi, Nikolay Samusik, Stephanie Widmann, Aaron J. Tyznik. A single-cell multiomics approach to study tumor-driven perturbations during hematopoiesis in mice [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4497.
Abstract 4524: Non-genetic generation of IgG-like immune cell-redirecting antibodies lacking effector function
Authors: van Delft Floris L. , van Geel Remon 
Published: September 2020

Abstract
Since the early approval of catumaxomab and blinatumomab, T cell-redirecting antibodies have emerged as a promising biologics in cancer treatment. New technologies are overcoming the limitations of the 1st generation T-cell redirecting bispecifics, especially extending half-life to allow intermittent dosing, reducing immunogenicity and improving the safety profile. Today, T cell-engagers are generated as a wide variety of molecular architectures, typically IgG-type. However, nearly without exception, these bispecifics are generated by genetic fusion of a cancer-binding and an anti-CD3 antibody, which inevitably requires genetic reengineering of an existing targeting antibody and/or extensive optimization of antibody format.
We have shown earlier that the native glycan of a monoclonal antibody provides a privileged site for controlled attachment of small-molecule cytotoxic drugs.1 The resulting antibody-drug conjugates (ADCs) were found to display significantly improved therapeutic index versus conventional technologies, while improving manufacturability. This proprietary technology, known as GlycoConnect™, has been adapted by various ADC developers, and entered clinical phase early 2019.
Here we present the adaption of GlycoConnect™ technology for the generation of immune cell-redirecting antibodies, without requiring prior protein reengineering. Instead, a two-stage chemoenzymatic process is applied that allows the conversion of any IgG isotype into a T cell-engager by selective attachment of anti-CD3 scFv to the antibody glycan. Studies are presented to precisely control conjugation stoichiometry, providing molecular architectures with defined 2:1 or 2:2 ratio (target-binding:CD3-binding), as well as functional studies to corroborate the biological activity of these GlycoConnect™ bispecifics. Finally, early results will be presented regarding extension of the concept to bispecifics designed to redirect natural killer (NK) cells, or to engage T-cells by activation of costimulatory molecules, such as CD137 (4-1BB).
1 van Geel et al. Chemoenzymatic Conjugation of Toxic Payloads to the Globally Conserved NGlycan of Native mAbs Provides Homogeneous and Highly Efficacious Antibody−Drug Conjugates. Bioconj. Chem. 2015, 26, 2233-2242.
Citation Format: Floris L. van Delft, Remon van Geel. Non-genetic generation of IgG-like immune cell-redirecting antibodies lacking effector function [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4524.