bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract B025: Multiplex three-dimensional mapping of mRNA and protein in the tumor microenvironment
Authors: Lee Steve Seung-Young , Scholten David , Bindokas Vytautas P. , Kron Stephen
Published: February 2019

Detecting oncogenic protein-coding messenger RNA (mRNA) in tumor tissues is a key assay for accurate cancer diagnosis. Along with cancer protein biomarker analysis, mRNA identification is critical for matching the appropriate treatment to individual patients. Likewise, cytokine mRNA localization in on-treatment biopsies enables evaluation of the antitumor response to immunotherapy by identifying the types and functional states of lymphocytes, for example distinguishing activated cytotoxic T-cells from naive T-cells. To assess mRNA localization, a biopsy is typically formalin fixed and paraffin embedded (FFPE), thin sections are cut, and then are stained for mRNA by chromogenic In situ hybridization (CISH). Analyzing samples by mRNA CISH typically takes a few days and requires considerable technical expertise. Recent progress in multiplexed fluorescence In situ hybridization (FISH) has enabled simultaneous analysis of multiple mRNA types in a single tissue section. Nonetheless, even if fully characterized, individual tissue sections cannot adequately represent the complex three-dimensional (3D) architecture of the tumor microenvironment. There remains a pressing need for a rapid sample-to-answer technology for multiplex 3D imaging of mRNA at sub-cellular resolution that is able to fully characterize the tumor microenvironment in intact biopsy tissues for cancer diagnosis and immunotherapeutic response analysis. To address these challenges, we have adapted Transparent Tissue Tomography (T3), a simple and fast tissue clearing and multiplex 3D imaging method, to analyze mRNA distribution in the tumor microenvironment. With T3, oncogenic and immunoregulatory cytokine mRNAs are readily localized in the context of cell types and other features in murine, patient derived xenograft (PDX), and head and neck tumors. This work establishes T3 as a tool for a quantitative, 3D spatial analysis of mRNA and protein distribution in the tumor microenvironment.

Citation Format: Steve Seung-Young Lee, David Scholten, Vytautas P. Bindokas, Stephen Kron. Multiplex three-dimensional mapping of mRNA and protein in the tumor microenvironment [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B025.
Abstract B039: Peptide-MHC-directed expansion of multifunctional antigen-responsive T-cells
Authors: Rafa Vibeke Mindahl , Bodenhöfer Mona , Bentzen Amalie Kai , Tamhane Tripti , Donia Marco , Svane Inge Marie Stentoft , Jakobsen Søren Nyboe , Schmess Christian , Hadrup Sine Reker
Published: February 2019

Functional properties and antigen specificity of expanded T-cells are crucial for the efficacy of adoptive cell transfer-based therapies in cancer. Most current strategies involve nonspecific expansion of bulk tumor-infiltrating lymphocytes, often providing growth preference to co-infiltrated virus specific T-cells and driving an exhausted phenotype of the expanded T-cell product.A potential way to resolve this challenge, is the use of artificial antigen-presenting scaffolds providing both an antigen specific stimulation through peptide-MHC interaction and additional the required co-stimulatory and growth signals through associated stimulatory molecules and cytokines. We have designed such antigen-presenting scaffolds; build on a dextran-polysaccharide, carrying both peptide-MHC and relevant stimulatory molecules. The artificial antigen-presenting scaffolds interacts specifically with T-cells based on recognition of the peptide-MHC molecule and effectively expand and functionally stimulate specific T-cells in a peptide-MHC-directed fashion, while leaving all other T-cell specificities untouched. Results from in vitro experiments have showed that antigen specific CD8 T-cells stimulated with these artificial antigen-presenting scaffolds express a less differentiated phenotype and low PD-1 expression, associated with high proliferation potential and enhanced antitumor effect in vivo. Furthermore, this expansion strategy provides a high frequency of multifunctional antigen specific CD8 T-cells expressing IFN-γ, TNF-α, and CD107a upon target recognition and provide improved cancer cell killing over IL2-driven expansion of tumor-infiltrating lymphocytes. Furthermore, the current strategy allows for simultaneous expansion of numerous different T-cell populations, required to generate T-cell products with broad recognition profiles based on the personal cancer-antigen and mutational profile. All of these characteristics are of significant importance for in vivo tumor cell killing following adoptive transfer of expanded T-cell products. Thus, the present strategy represents an optimized method for expansion of cancer-restricted T-cells for adoptive cell therapy.

Citation Format: Vibeke Mindahl Rafa, Mona Bodenhöfer, Amalie Kai Bentzen, Tripti Tamhane, Marco Donia, Inge Marie Stentoft Svane, Søren Nyboe Jakobsen, Christian Schmess, Sine Reker Hadrup. Peptide-MHC-directed expansion of multifunctional antigen-responsive T-cells [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B039.
Abstract B045: Antigen-free cancer vaccine to treat poorly immunogenic tumors
Authors: Sobral Miguel C. , Wang Hua , Najibi Alexander J. , Li Aileen , Verbeke Catia S. , Mooney David J.
Published: February 2019

Certain chemotherapeutic drugs can elicit immunogenic death of tumor cells and enhance antitumor immune responses. Here we explore whether immunogenic chemotherapy can be utilized for the development of antigen-free cancer vaccines, by combining it with peritumorally injected biomaterial scaffolds that recruit dendritic cells (DCs) for subsequent antigen presentation and T-cell priming. Pore-forming alginate gels containing granulocyte-macrophage colony-stimulating factor (GM-CSF) and a doxorubicin-iRGD conjugate were found to efficiently induce the apoptosis of 4T1 triple-negative breast cancer cells in vivo, while recruiting large numbers of DCs. The co-encapsulation of CpG oligodeoxynucleotides in the gel significantly enhanced the immunogenic death of 4T1 cells, increased systemic tumor-specific CD8+ T-cells and tumoral infiltration of CD8+ T-cells, repolarized tumor-associated macrophages towards an inflammatory M1-like phenotype, and resulted in significantly improved antitumor efficacy. This in situ antigen-free gel vaccine shows promise for the treatment of poorly immunogenic tumors, and more broadly, may serve as a facile platform to enable in situ personalized cancer vaccination without requiring identification of tumor-specific antigens and manufacturing of personalized vaccines.

Citation Format: Miguel C. Sobral, Hua Wang, Alexander J. Najibi, Aileen Li, Catia S. Verbeke, David J. Mooney. Antigen-free cancer vaccine to treat poorly immunogenic tumors [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B045.
Abstract B059: Synergistic activation of antitumor immunity by an oncolytic virus VG161 armed with multiple immune-stimulating genes
Authors: Zhao Ronghua , Ding Jun , Choujenko Dmitry , Murad Yanal , Lee Erica , Liu Guoyu , Bu Luke , Jia William
Published: February 2019

Oncolytic viruses (OVs) are among the most powerful approaches in cancer immunotherapy. OVs not only cause cancer cell lysis but more importantly, their infection in tumors induces anti-tumor immune response from the host, resulting in lasting anti-tumor immunity. It has been recognized that anti-tumor immune response requires multiple immune regulatory factors that act synergistically and tumor microenvironment is critical for tumor to grow. Herpes simplex virus type-1 (HSV-1) has been approved by FDA as an oncolytic viral drug to treat melanoma. One advantage of HSV-1 is its large genomic capacity for carrying multiple exogenous genes.A HSV-1 oncolytic viral vector (VG161) was constructed to simultaneously express IL12, IL15 with its receptor alpha unit and a PDL-1 blocking peptide. Antitumor activity of VG161 was tested in both immune competent mice (CT26 and A20 tumor models) and nude mice for human tumor models (LNCaP and U87). Since CT26 and A20 are poorly permissive for HSV-1 replication, the mouse tumor models were able to demonstrate the antitumor immune response induced by VG161 while oncolytic activity of VG161 was demonstrated in LNCaP and U87 models since the immune system is compromised in those models.VG161 completely inhibited tumors in all the models tested and the animals survived tumor-free for many months till sacrificed. VG161 induced tumor oncolysis in both LNCaP and U87 tumors. In the CT26 model, animals were protected from the second challenging with CT26 cells following previous virally induced tumor regression. Furthermore, in a A20 double tumor model, intratumoral injection into the tumor on one side caused tumor regression on both sides. Transcriptome analysis showed significant change in tumor microenvironment. Finally, tumor specific memory T-cells were evident in the treated animals. The anti-tumor immune response by VG161 was significantly stronger than similar viruses that did not express any immune stimulating gene or only express GM-CSF. These results showed that intratumorally expressed multiple immune regulatory factors by an oncolytic virus may significantly change the tumor immune microenvironment to enhance efficacy of the oncolytic virus.

Citation Format: Ronghua Zhao, Jun Ding, Dmitry Choujenko, Yanal Murad, Erica Lee, Guoyu Liu, Luke Bu, William Jia. Synergistic activation of antitumor immunity by an oncolytic virus VG161 armed with multiple immune-stimulating genes [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B059.
Abstract B065: Tracking adipose-tissue Treg provenance, dependencies, and activities via T-cell receptor transgenic mice
Authors: Li Chaoran , DiSpirito Joanna R. , Zemmour David , Spallanzani Raul German , Kuswanto Wilson , Benoist Christophe , Mathis Diane
Published: February 2019

Recent epidemiologic and animal model studies indicate that overweight and obese individuals have increased risk of type-2 diabetes, cardiovascular diseases and certain types of cancer. It was suggested that chronic, low-grade inflammation of the adipose tissue, and eventually systemically, is one of the major causes for obesity-associated metabolic abnormalities and cancer. Regulatory T (Treg) cells located within parenchymal tissues safeguard tissue homeostasis and suppress inflammation. A paradigmatic “tissue-Treg” population is that found in visceral- adipose tissue (VAT) of male mice. VAT-Treg cells have a unique transcriptome, are clonally expanded, and promote metabolic health through effects on local immunocytes and adipocytes. Because of their rarity and inaccessibility, cardinal questions such as what factors control their accumulation in fat and when/where/how do they adopt their distinctive phenotype remained unanswered. We addressed these issues using VAT- Treg T-cell-receptor (TCR) transgenic mice and reporter mice for the diagnostic VAT-Treg transcription factor, PPARγ. Accumulation of VAT-Tregs was driven by combined effects of TCR specificity, Foxp3 expression, and a cell-intrinsic response to interleukin-33. Their characteristic phenotype emerged in two stages: a minority of splenic Treg cells weakly up-regulated a slice of the VAT-Treg transcriptional signature, reflecting cell activation, but the definitive phenotype, arming cells for fat survival, was manifest only in VAT. This deeper understanding of tissue-Treg generation should facilitate precision-targeting strategies.

Citation Format: Chaoran Li, Joanna R. DiSpirito, David Zemmour, Raul German Spallanzani, Wilson Kuswanto, Christophe Benoist, Diane Mathis. Tracking adipose-tissue Treg provenance, dependencies, and activities via T-cell receptor transgenic mice [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B065.
Abstract B078: Unbiased identification of CD4+ T-cell epitopes using novel MHC-based chimeric receptors
Authors: Kisielow Jan , Obermair Franz-Josef , Kopf Manfred
Published: February 2019

αβT-cell receptors (TCRs) bind peptide-major histocompatibility complexes (pMHC) with low affinity, posing a considerable challenge for direct identification of αβT-cell cognate peptides (epitopes). Here, we describe a platform for the discovery of MHC class-II presented epitopes, based on screening of engineered reporter cells expressing novel pMHC-TCR (MCR) hybrid molecules carrying cDNA-derived peptides. This technology identifies natural epitopes of CD4 T-cells in an unbiased and efficient manner and allows detailed analysis of TCR cross-reactivity providing recognition patterns on top of discrete epitopes. We identify cognate peptides of virus- and tumor-specific T-cells in mouse disease models and present a proof of concept for human T-cells. Furthermore, we show that vaccination with a peptide naturally recognized by TILs can efficiently protect from tumor challenge. Thus, the MCR technology holds promise for basic research and clinical applications allowing personalized identification of T-cell antigens in patients.

Citation Format: Jan Kisielow, Franz-Josef Obermair, Manfred Kopf. Unbiased identification of CD4+ T-cell epitopes using novel MHC-based chimeric receptors [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B078.
Abstract B079: Evaluation of tools for predicting mutated tumor antigens from exome and RNA sequencing
Authors: Kodysh Julia , Finnigan John P. , Rubinsteyn Alex
Published: February 2019

Neoantigen vaccination is an emerging modality of cancer immunotherapy with many ongoing trials. One central question of neoantigen vaccination is the method for selecting which mutated tumor-specific antigens to include in a patient’s vaccine. Many in-silico pipelines for neoantigen selection have been published in the past few years, but no comprehensive evaluation has compared them directly on the same tumor/normal sequencing data. We evaluate several publicly available commonly used neoantigen pipelines (pVACtools [1], MuPeXI [2], TIminer [3], OpenVax [4]) on both murine and human cancer samples. Our evaluation highlights the salient differences between these pipelines and shows the divergent results they achieve. References: 1. Kiwala S, Hundal J, …, Griffith M. pVACtools: Computational selection and visualization of neoantigens for personalized cancer vaccine design. Cancer Genetics 2018. 2. Bjerregaard A-M, Nielsen M, ..., Eklund AC. MuPeXI: Prediction of neo-epitopes from tumor sequencing data. Cancer Immunology Immunotherapy 2018. 3. Tappeiner E, Finotello F, ..., Trajanoski Z. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. Bioinformatics 2017. 4. Rubinsteyn A, Kodysh J, …, Hammerbacher J. Computational pipeline for the PGV-001 Neoantigen Vaccine Trial. Frontiers in Immunology 2018.

Citation Format: Julia Kodysh, John P. Finnigan, Alex Rubinsteyn. Evaluation of tools for predicting mutated tumor antigens from exome and RNA sequencing [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B079.
Abstract B131: Live-attenuated LCMV-based vector for active immunotherapy of HPV16+ cancer
Authors: Schmidt Sarah , ElGazzar Ahmed , Bonilla Weldy V. , Pauzuolis Mindaugas , Reiter Andrea , Kleissner Theresa , Oeler Daniel , Stemeseder Felix , Berka Ursula , Kiefmann Bettina , Schulha Sophie , Matushansky Igor , Merkler Doron , Pinschewer Daniel , Orlinger Klaus
Published: February 2019

Active immunization against cancer requires the induction of exquisitely potent tumor-specific CD8+ T-cell (CTL) responses, which can be repeatedly boosted and reactivated. Hookipa Pharma engineered a replication-attenuated viral vector platform (TheraT®) based on the arenavirus lymphocytic choriomeningitis virus (LCMV), which meets these aforementioned criteria. Here, we present a preclinical data package of Hookipa´s lead immunotherapy product HB-201, targeting HPV16-driven head and neck cancer. It encodes a non-oncogenic version of the human papilloma virus 16 (HPV16) oncoproteins E7 and E6 (TheraT®-E7E6). Attenuation and safety of TheraT®-E7E6 were demonstrated by i) rapid viral clearance after systemic administration of the vector and ii) reduced neurovirulence in mice. TheraT®-E7E6 treatment was shown to induce substantial CD8+ T-cell expansion and high frequencies of E7- and E6-specific CTL responses with a balanced effector / central memory profile. These responses were boosted and reactivated upon TheraT®-E7E6 re-administration. TheraT®-E7E6 eradicated palpable TC-1 tumors, a syngeneic mouse tumor model of HPV-driven cancer. Even in mice with large tumors (~300mm3), TheraT®-E7E6 afforded significant tumor control and improved survival, with high frequencies of E7-specific CTLs persisting for several weeks. Furthermore, the efficacy of TheraT®-E7E6 can be potentiated in combination therapies, e.g., with PD-1 checkpoint inhibitors. In conclusion, replication-attenuated TheraT®-E7E6 is safe, highly immunogenic and shows excellent therapeutic efficacy as mono- or combination therapy in a preclinical model of HPV-induced cancer. Clinical trials for the treatment of HPV16+ cancers will be initiated in 2019.

Citation Format: Sarah Schmidt, Ahmed ElGazzar, Weldy V. Bonilla, Mindaugas Pauzuolis, Andrea Reiter, Theresa Kleissner, Daniel Oeler, Felix Stemeseder, Ursula Berka, Bettina Kiefmann, Sophie Schulha, Igor Matushansky, Doron Merkler, Daniel Pinschewer, Klaus Orlinger. Live-attenuated LCMV-based vector for active immunotherapy of HPV16+ cancer [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B131.
Abstract B138: Cancer immunotherapy with APOBEC3B-induced heteroclitic library tumor cell vaccines and immune checkpoint blockade
Authors: Vile Richard , Evgin Laura , Kottke Timothy , Schuelke Matthew , Driscoll Christopher B. , Huff Amanda L. , Thompson Jill , Molan Amy , Harris Reuben S. , Pulido Jose S. , Wongthida Phonphimon
Published: February 2019

We have previously shown that a vesicular stomatitis virus-based cDNA library expressing xenogeneic altered self-epitopes led to T-cell mediated rejection of prostate cancer, glioma and melanoma. The use of a library of altered self-peptides which reflects the transcriptome of the tumor circumvents the necessity for a priori knowledge of which antigens may be immunogenic in a patient, and primes a polyclonal T-cell response that provides strong cumulative antitumor selective pressure. We have expanded this concept of altered-self library vaccination using tumor vaccines modified by the overexpression of APOBEC3B, a cytosine deaminase that generates C to T transition mutations. A freeze-thawed whole tumor cell vaccine prepared from B16 melanoma cells stably overexpressing human APOBEC3B treated established subcutaneous parental B16 tumors and, when combined with PD-1 checkpoint blockade, cured between 75%-100% of mice. T-cells from mice treated with the vaccine and anti-PD1 produced high levels of IFN-γ when restimulated with parental unmodified B16 melanoma cells in vitro. Whole-genome sequencing of B16APOBEC3B overexpressing cells identified 301 C to T or G to A missense mutations unique to the APOBEC3B line. Using an in silico MHC binding affinity algorithm, we identified and experimentally validated a short list of 10 APOBEC3B- induced heteroclitic peptides. We have also shown that this approach can be extended to an orthotopic brainstem model of high grade glioma. GL261 tumors stereotactically implanted into the brainstem were significantly responsive to treatment with an APOBEC3B- modified GL261 vaccine in combination with anti-PD-1 checkpoint blockade. In summary, when overexpressed in tumor cells, APOBEC3B generates a library of heteroclitic sequences that primes both CD4 and CD8 T-cells that have escaped central tolerance and that recognize both newly mutated antigens from the vaccine, and the corresponding unaltered self epitopes expressed on the tumor cells.

Citation Format: Richard Vile, Laura Evgin, Timothy Kottke, Matthew Schuelke, Christopher B. Driscoll, Amanda L. Huff, Jill Thompson, Amy Molan, Reuben S. Harris, Jose S. Pulido, Phonphimon Wongthida. Cancer immunotherapy with APOBEC3B-induced heteroclitic library tumor cell vaccines and immune checkpoint blockade [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B138.
Abstract B141: Anti-tumor immune responses elicited by mesothelin virus-like particles vaccine effectively controls pancreatic cancer in animal models
Authors: Yao Qizhi Cathy , Poteet Ethen , Liang Zhengdong , Lewis Phoebe , Yu Zhiyin , Chen Changyi
Published: February 2019

Pancreatic cancer is the 12th most common cancer, but is the 3rd leading cause of cancer death in America. This disparity is directly related to three factors: the difficulty in early detection of the disease, pancreatic cancer’s resistance to chemotherapy, and a tendency for the cancer to metastasize early and quickly. Here, we propose a novel immunotherapy to bypass pancreatic cancer’s resistance to standard chemotherapy. We have developed a virus-like particle (VLP) based on an HIV backbone Gag and pancreatic cancer-associated protein mesothelin (MSLN). Vaccination of C57BL/6 mice with MSLN VLP can efficiently activate the immune system and reduce and in some cases eliminate the host’s pancreatic cancer. Our results show that MSLN VLPs induce both humoral and cytotoxic specific response against MSLN in mouse pancreatic cancer models. Specifically, after vaccination with MSLN VLPs, significant increases in CD8+ MSLN specific T-cells and increases in serum anti-MSLN IgG were detected. Furthermore, we observed an increase in the serum of pro-inflammatory cytokine IFN-γ and B cell stimulator IL-5. Consistent with the increased IL-5, we observed a significant increase in tumor infiltrating B cells in the MSLN VLP immunized groups, but neither Gag VLP control nor unimmunized mice. Furthermore, while all tumor-bearing mice generated some antibodies towards MSLN, our MSLN VLP immunized mice had significantly higher serum titers of IgG1, IgG2B, and IgG3. Both Gag VLP and MSLN VLP immunized mice had a decreased tumor volume compared to control, but passive transfer of sera only from MSLN VLP immunized mice decreased tumor volume and increased survival of unimmunized tumor bearing mice, while Gag VLP immunized mice had much less effect. Overall, we have developed a promising vaccine for pancreatic cancer warranting additional studies with adjuvants and combination treatments with standard-of-care chemotherapy.

Citation Format: Qizhi Cathy Yao, Ethen Poteet, Zhengdong Liang, Phoebe Lewis, Zhiyin Yu, Changyi Chen. Anti-tumor immune responses elicited by mesothelin virus-like particles vaccine effectively controls pancreatic cancer in animal models [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B141.
Abstract B179: The regulation of silent apoptotic cell-clearance in tissue-resident macrophages
Authors: Pestal Kathleen , Barton Gregory M.
Published: February 2019

When normal, healthy cells die by apoptosis, they must be cleared to ensure tissue homeostasis. Failure to clear apoptotic cells (ACs) efficiently enables the release of inflammatory stimuli, such as nucleic acids, leading to tissue injury and, ultimately, autoimmunity. Clearance of ACs is largely performed by tissue-resident macrophages. Despite expressing many innate immune receptors, these cells do not respond to the potentially stimulatory ligands within ACs. Recently, the Barton Lab has identified several populations of AC-engulfing macrophages with many common features. These features include the expression of AC-recognition receptors and reduced TLR responsiveness to nucleic acids. The transcription factors KLF2 and KLF4 appear to contribute to this expression program both in vitro and in vivo in distinct AC-clearing macrophage populations. Macrophages that are removed from their environments lose this program and the program can be adopted by transferring TLR responsive macrophages into environments where endogenous silent residents are maintained. This coordinated silent immune program allows tissue-resident macrophages to maintain homeostasis while efficiently clearing ACs.

Citation Format: Kathleen Pestal, Gregory M. Barton. The regulation of silent apoptotic cell-clearance in tissue-resident macrophages [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B179.
Abstract B187: Origins of neoantigens for the major histocompatibility complex class I pathway
Authors: Sroka Ewa Maria , Martins Rodrigo Prado , Daskalogianni Chrysoula , Apcher Sebastien , Fahraeus Robin
Published: February 2019

Neoantigens are antigens generated by somatic mutations that can be recognized by the host immune system, firstl described as differentiating or tumor antigens back in 80s and 90s in research related to mice melanoma and breast cancers carried out by Houghton’s and Cheever’s teams, respectively. Now, during the era of potent immunotherapies, cancer vaccines and checkpoint inhibitors (CTLA-4, PD-1), neoantigens again attract much of scientists’ attention. With the use of cutting-edge technologies like next-generation sequencing, mass spectrometry, and predictive algorithms, more is known about antigen presentation and the links between occurrence of somatic mutations in cancer cells and antigen recognition by CD8+T-cells. Interestingly, discoveries of alternative sources of antigenic peptides (e.g., DRIPs and PTPs) challenged the notion about full-length proteins being the main supplier of material for MHC class I pathway and shifted focus of search for new sources to ribosomal scanning during pioneer round of translation. Despite the fact that pathways involved in processing and presentation of peptides have been thoroughly studied, there is still more to be learned about the sources of peptide material for the endogenous and exogenous MHC class I pathways. Based on works related to Epstein-Bar virus, it has been shown that MHC class I immune surveillance is directly correlated with the mechanism that regulates protein synthesis. Together with other results, it highlights the importance of pre-mRNA and mRNA processing in providing antigenic peptides for MHC class I surveillance. Here we revise some significant research related to the production of alternative antigenic peptides, their importance in cancer research, immunosurveillance and generation of tolerance. The lack of animal models to study the origin of alternative antigenic peptides hinders research in the field of neoantigens. I will describe results of the presentation of intron-derived antigenic peptides in mice model developed by our team.

Citation Format: Ewa Maria Sroka, Rodrigo Prado Martins, Chrysoula Daskalogianni, Sebastien Apcher, Robin Fahraeus. Origins of neoantigens for the major histocompatibility complex class I pathway [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B187.
Abstract B197: Translational control in macrophages during inflammatory response
Authors: Xiang Kehui , Bartel David P.
Published: February 2019

Translational control has been increasingly appreciated as a critical gene-regulatory mechanism during immune responses. Previous studies suggested that translation of select cytokines could be regulated by mRNA poly(A)-tail lengths in memory T-cells and macrophages. We carried out transcriptome-wide analysis with mRNA sequencing, ribosome-footprinting profiling as well as poly(A)-tail length profiling in both RAW264.7 cells and mouse thioglycollate-elicited peritoneal macrophages. No coupling between poly(A)-tail length and translational efficiency (TE) was observed in either cell type, arguing against a global translational-regulatory regime mediated by poly(A)-tail lengths. Immune activation with the treatment of lipopolysaccharides (LPS) to these cells did not change the uncoupled regime. Moreover, gene expression landscape in LPS-treated macrophages was dominated by mRNA level changes, with little contribution from TE changes. The up- or down-regulation of TE was not accompanied by concerted lengthening or shortening of poly(A) tails, implying existence of yet unclear translational control mechanisms in these immune cells. Finally, our studies in other biologic systems, including HeLa cells, Xenopus oocytes and yeast suggest that saturating levels of poly(A)-binding proteins might suppress poly(A) tail length-mediated translational control in various uncoupled systems, including immune cells.

Citation Format: Kehui Xiang, David P. Bartel. Translational control in macrophages during inflammatory response [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B197.
Abstract IA05: From the clinic to the lab: Investigating response and resistance mechanisms to immune checkpoint therapy
Authors: Padmanee Sharma
Published: February 2019

Immune checkpoint therapies, including anti-CTLA-4, anti-PD-1 and anti-PD-L1, have led to significant clinical responses in cancer patients. To investigate immunologic changes and mechanistic pathways that are elicited by these therapies, we conducted pre-surgical and tissue-based clinical trials, which permit access to tumor tissues for laboratory studies. To compare and contrast data, we chose one tumor type that responds well to immune checkpoint therapy and one that does not. The first pre-surgical trial was conducted with anti-CTLA-4 (ipilimumab) in a cohort of patients with localized bladder cancer. The second pre-surgical trial was conducted with anti-CTLA-4 (ipilimumab) in patients with localized prostate cancer. In addition, we evaluated data from patients with melanoma who received immune checkpoint therapy. These data enabled us to identify the ICOS/ICOSL pathway as relevant for anti-tumor immune responses in the setting of anti-CTLA-4 therapy. We also identified resistance mechanisms including expression of other immune inhibitory pathways, such as VISTA, and loss of the IFNg signaling pathway in tumor cells. These data will be discussed in greater details.

Citation Format: Sharma Padmanee. From the clinic to the lab: Investigating response and resistance mechanisms to immune checkpoint therapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr IA05.
Abstract IA11: The immunotherapy faces of Interleukin-8 and CD137
Authors: Melero Ignacio
Published: February 2019

IL-8(CXCL-8) is a chemoattractant factor for myeloid leukocytes, that is produced in large quantities by many solid tumors. Interestingly its concentration in serum is a negative prognostic and is predictive of lack of response to the anti-PD-1 mAb nivolumab, as confirmed in large series of patients. As a neuthrophil chemoattractant, IL-8 produced in cancer tissue attracts myeloid-derived suppressor cells and correlates with poor T-cell infiltration and weak gamma-interferon gene signatures. An IL-8 blocking mAb is being developed in combination with PD-1 blockade for cancer therapy focusing on cases with high circulating levels of IL-8. CD137 (4-1BB) is a costimulatory receptor expressed on primed NK and T cells whose activation with agonists antibodies invigorates CTL responses to fight cancer. CD137 agonists are highly synergistic with adoptive T-cell therapy. Recent evidence shows that CD137-costimulation reprograms chromatin, modifying DNA methylation in the loci of immune –relevant genes and potently enhances the size and respiratory functions of mitochondria in human and mouse CD8 T cells. Metabolic and epigenetic effects of CD137 agonists are critical for the antitumor therapeutic effects. In combination immunotherapy, strategies of CD137 costimulation can be used to potentiate radiotherapy in a synergistic fashion. Multiple constructs based on CD137 agonists are being developed clinically by the pharmaceutical and biotech industries.

Citation Format: Ignacio Melero. The immunotherapy faces of Interleukin-8 and CD137 [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr IA11.
Abstract PR04: A natural killer–dendritic cell axis defines checkpoint therapy–responsive tumor microenvironments
Authors: Barry Kevin C. , Krummel Matthew F.
Published: February 2019

Intratumoral stimulatory dendritic cells (SDCs) play an important role in stimulating cytotoxic T-cells and driving immune responses against cancer. Understanding the mechanisms that regulate their abundance in the tumor microenvironment (TME) could unveil new therapeutic opportunities. We find that in human melanoma, SDC abundance is associated with intratumoral expression of the gene encoding the cytokine FLT3LG. FLT3LG is predominantly produced by lymphocytes, notably natural killer (NK) cells in mouse and human tumors. NK cells stably form conjugates with SDCs in the mouse TME, and genetic and cellular ablation of NK cells in mice demonstrates their importance in positively regulating SDC abundance in tumor through production of FLT3L. Although anti-PD-1 “checkpoint” immunotherapy for cancer largely targets T-cells, we find that NK cell frequency correlates with protective SDCs in human cancers, with patient responsiveness to anti-PD-1 immunotherapy, and with increased overall survival. Our studies reveal that innate immune SDCs and NK cells cluster together as an excellent prognostic tool for T-cell–directed immunotherapy and that these innate cells are necessary for enhanced T-cell tumor responses, suggesting this axis as a target for new therapies.

Citation Format: Kevin C. Barry, Matthew F. Krummel. A natural killer–dendritic cell axis defines checkpoint therapy–responsive tumor microenvironments [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr PR04.
Abstract PR13: A new high-performance HLA ligand identification strategy enables prediction of T-cell tolerance to neoepitopes
Authors: Klatt Martin G. , Gejman Ron S. , Moon Sung S. , Korontsvit Tatyana S. , Dao Tao , Scheinberg David A.
Published: February 2019

T-cell responses against neoepitopes presented by human leukocyte antigen (HLA) complexes represent a critical effector of anticancer immunity. However, detection of neoepitopes by mass spectrometry is still challenging as is identification of the fraction of neoepitopes that elicit immune responses in vitro and in vivo. To address these problems, we developed a strategy to identify HLA ligands combining the peptide identification algorithm Byonic with the epitope binding predictor netMHCpan. We obtained up to 4-fold increases in unique HLA ligand identifications compared to standard approaches, false discovery rates below 0.6% and over 17,000 unique HLA ligand identifications in a single experiment. Even with only 10 million cancer cells we were able to detect over 5,000 unique HLA ligands, which allows our approach to be applied to small tumor samples in a clinical setting. Of note, phosphorylated as well as glycosylated HLA ligands were identified with the same accuracy and allowed a better characterization of the rules for presentation of post-translationally modified HLA ligands. Furthermore, by reanalyzing mass spectrometry samples with our novel approach, we confirmed high-confidence, rejected low-confidence and identified additional neoepitopes including the first-time detection of a phosphorylated neoepitope. Finally, we used our broadened knowledge of the immunopeptidome to create rules for prediction of non-immunogenicity of neoepitopes based on high biochemical similarity with unmutated HLA ligands, which showed high specificity and positive predictive value when validated with two datasets derived from neoepitope-based clinical studies. Altogether, our methods substantially improved sensitivity and specificity for detection of native, modified and mutated HLA ligands, propose an explanation for tolerance to neoepitopes, and should in combination facilitate the design of neoepitope-based therapies.

Citation Format: Martin G. Klatt, Ron S. Gejman, Sung S. Moon, Tatyana S. Korontsvit, Tao Dao, David A. Scheinberg. A new high-performance HLA ligand identification strategy enables prediction of T-cell tolerance to neoepitopes [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr PR13.
Abstract A23: Anti-PD-1 antibody scFv producing recombinant Bifidobacterium exerts antitumor effect in a larger fraction of the treated mice compared to full-length anti-PD-1 antibody
Authors: Shioya Koichiro , Wang Li , Matsumura Tomio , Shimizu Hitomi , Kanari Yasuyoshi , Seki Yuji , Shimatani Yuko , Taniguchi Shun’ichiro , Kataoka Shiro
Published: February 2019

Anti-PD-1 therapy has improved therapeutic outcomes of patients in multiple cancer types. However, the therapy has demonstrated clinical benefits in only a small fraction of patients. The reason of the limited response in clinical practice is not fully understood.

In an aim to improve anti-cancer drug delivery and potency, we have been developing in situ delivery and production system (i-DPS) by modifying a non-pathogenic anaerobic bacterium, Bifidobacterium, which localizes and proliferates only in the hypoxic environment like solid tumors after intravenous administration, produces anticancer proteins, enzymes or other pharmacologically active molecules selectively at the tumor site. Here we present anti-human PD-1 antibody scFv producing i-DPS in cancer immunotherapy, which could be specifically delivered to and amplified only at the hypoxic sites of solid tumors. A series of in vitro assays has been performed to confirm the stable expression and secretion of anti-human PD-1 scFv by recombinant Bifidobacterium, the binding inhibition of PD-1/PD-L1 interaction and elevated IFN gamma production in mixed lymphocyte culture by anti-human PD-1 scFv secreted from recombinant Bifidobacterium.

Anti-murine PD-1 scFv producing Bifidobacterium as surrogate systemically administered to the syngeneic mice model demonstrated significant tumor growth inhibition. Of particular interest, the suppression of tumor growth was observed in a larger fraction of the treated mice while the control anti-PD-1 antibody showed the effect on only a few mice. The analysis of tumor infiltrating lymphocytes and myeloid cells will be presented as well. Taken together, i-DPS for anti-PD-1 antibody provides a new promising immune-therapeutic modality to target hypoxic solid tumors and also provides a unique insight for antibody drug delivery in cancer immunotherapy.

Citation Format: Koichiro Shioya, Li Wang, Tomio Matsumura, Hitomi Shimizu, Yasuyoshi Kanari, Yuji Seki, Yuko Shimatani, Shun’ichiro Taniguchi, Shiro Kataoka. Anti-PD-1 antibody scFv producing recombinant Bifidobacterium exerts antitumor effect in a larger fraction of the treated mice compared to full-length anti-PD-1 antibody [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A23.
Abstract A52: Vaccine cells derived from cancer stem cells expressing interleukin-15 and its receptor inhibit tumor growth
Authors: Toukam Donatien Kamdem , Steel Jason C. , Carwell Christian , Eldessouki Ihab , Morris John C.
Published: February 2019

Background: Interleukin-15 (IL-15) is a powerful activator and inducer of NK cells and cytolytic CD8+ T cells. IL-15 also activates and expands CD8+ memory T cells without stimulating immunosuppressive CD4+CD25+ T regulatory cells. As such, IL-15 may be useful as an immunotherapy for cancer. In an effort to enhance antitumor activity and reduce systemic side effects, we studied an approach using a tumor vaccine enriched for cancer stem cells (CSCs) expressing murine (m) IL-15 and its receptor (mIL-15Rα).

Methods: Lentiviral vectors expressing the wild type or optimized (opt) cDNA sequences for mIL-15 and/or mIL-15Rα under the control of the human EF-1 promoter were generated and used to transduce TC1 mouse lung cancer cells. The TC1 cells were cultured under low serum conditions to generate tumor spheroids enriched for CSCs.

Results: The transduced TC1 cells demonstrated the expected mRNA transcripts. On flow cytometry only the cells transduced with mIL15Rα in combination with mIL-15 showed surface expression of mIL-15, while cells transduced with mIL-15 or mIL-15Rα constructs did not. When co-cultured with the transduced tumor spheroids or incubated with supernatants from these TC1 cells, CTLL-2 murine T cells demonstrated proliferation indicating that the cloned cDNAs expressed functional proteins. The vector demonstrating the greatest stimulation of CTLL-2 cells expressed both the mIL-15Rα and mIL-15opt sequences and demonstrated suppressed TC1 tumor growth in vivo.

Conclusion: CSCs expressing mIL-15Rα and mIL-15 stimulated proliferation of T cells in vitro and demonstrated inhibited tumor growth in mice. In vivo tumor vaccination studies are in progress.

Citation Format: Donatien Kamdem Toukam, Jason C. Steel, Christian Carwell, Ihab Eldessouki, John C. Morris. Vaccine cells derived from cancer stem cells expressing interleukin-15 and its receptor inhibit tumor growth [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A52.
Abstract B06: Enhancement of checkpoint inhibitor efficacy by combination treatment with a novel COX2/sEH dual inhibitor
Authors: Zimmermann Maike , Hwang Sung Hee , Hammock Bruce D. , Cimino George , Henderson Paul T.
Published: February 2019

It has been shown that the COX2/PGE2 pathway is involved in the regulation of PD-L1 expression in tumor-infiltrating myeloid cells, and that angiogenesis inhibitors alter tumor stroma in a pro-immunogenic fashion. We recently developed Oomnicoxib, a compound that concurrently inhibits COX2 and soluble epoxide hydrolase (sEH), which work together to modulate expression a variety of prostaglandins of importance to inflammation and cancer. Oomnicoxib potently inhibits tumor angiogenesis in several tumor types via this mechanism of action that is unique compared to approved anti-angiogenesis drugs, which includes downregulation of COX2 and PGE2. Importantly, the compound is nontoxic to human PBMC. Accordingly, we hypothesize that Oomnicoxib modulates tumor stroma to favor immune cell infiltration and can potentiate immune activation of check point inhibitors. Progress towards comprehensive Oomnicoxib immune profiling and efficacy enhancement of a checkpoint inhibitor in mice will be presented.

Note: This abstract was not presented at the conference.

Citation Format: Maike Zimmermann, Sung Hee Hwang, Bruce D. Hammock, George Cimino, Paul T. Henderson. Enhancement of checkpoint inhibitor efficacy by combination treatment with a novel COX2/sEH dual inhibitor [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr B06.
Abstract B19: Modulation of cytotoxic effects of vemurafenib by chloroquine in malignant melanoma cells G-361: Role of dermcidin
Authors: Neyra Jennifer Montoya , Belizario Jose
Published: February 2019

Dermcidin (DCD) is a candidate oncogene localized at 12q13.1 and co-amplified with multiple oncogenes in many tumor cells, including breast carcinomas and melanomas. DCD is one of the 100 gene signature for melanomas. To further understand the role of DCD on growth, survival and progression of melanoma cells, we selected G-361 melanoma cell clones expressing shRNA to DCD and established in vitro and in vivo models. In this study we evaluated the pharmacologic effects of vemurafenib (BRAFV600E inhibitor) and chloroquine (autophagy inhibitor) in cell viability and tumor growth of two melanoma cell lines identified as G-361 pLKO, which expresses DCD and BRAFV600E, and G-361 IBC I which express shRNA to silence DCD constitutively. Vemurafenib induces features of stress-induced senescence in addition to apoptosis. G-361 melanoma cells responded to vemurafenib (1-2 μM) alone or combined with chloroquine (50-100 μM) which increased apoptosis rates, while decreasing senescent cells expressing β-galactosidase enzyme. Vemurafenib (50 mg/kg / 21 days) inhibited melanoma growth in immunodeficient mice dependent on DCD expression. Chloroquine (30 mg/kg) in combination with vemurafenib, accelerated (given at 24-hour interval), and reduced (given at 72 hours interval), melanoma growth. Tumor cells resistant to vemurafenib and chloroquine displayed atypical cell morphology and nuclear histological patterns and diferential expression of melanocytic differentiation biomarkers S100, HMB-45, Melan-A and pancytokeratins. This work confirms the efficacy of vemurafenib and suggests potential adjuvant effects of chloroquine. It also confirms the role of dermcidin as growth factor and oncogene for melanoma cells.

Citation Format: Jennifer Montoya Neyra, Jose Belizario. Modulation of cytotoxic effects of vemurafenib by chloroquine in malignant melanoma cells G-361: Role of dermcidin [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr B19.