bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A145: Study of mechanisms of immune evasion of oncogenic KRAS in NSCLC
Authors: Mugarza Edurne , Maldegem Febe van , Sopena Miriam Llorian , Arcas Miriam Molina , Downward Julian
Published: February 2019

Cancer immunotherapies such as immune checkpoint blockade have yielded long-term durable responses in some patients. Nevertheless, the majority of cancer patients do not respond to such therapies, which constitutes a large unmet need in the clinic. Tumors develop mechanisms by which they are able to evade the actions of the immune system, some of which may render them unresponsive to drugs aimed to boost antitumor immunity. Lung cancer is a highly immunogenic tumor type in which, if effective, cancer immunotherapies have proven to be superior to other treatment modalities. KRAS is an oncogene mutated in a third of lung cancer patients and has been previously shown to trigger immunosuppressive actions by tumour cells. We aim to study the immunosuppressive effects of KRAS mutations in vitro and in clinically relevant mouse models of lung adenocarcinoma. We have generated a tumor cell autonomous KRAS- dependent gene expression profile using in vitro systems. We have set a particular focus on genes playing a role in tumor immune evasion, whose function we are aiming to elucidate using immunogenic in vivo models. We have developed a derivative of the transplantable KRAS mutant murine Lewis lung adenocarcinoma (LLC) cell line in which KRAS activity can be specifically blocked using a small-molecule inhibitor. We aim to unravel the immune infiltration of such tumors and elucidate the specific role of KRAS in shaping its microenvironment. By combining simplistic in vitro models to unravel mechanisms of action and more complex mouse models to prove their clinical relevance, we aim to increase immune visibility of KRAS-mutated lung tumors to make them more susceptible to immune and other therapies.

Citation Format: Edurne Mugarza, Febe van Maldegem, Miriam Llorian Sopena, Miriam Molina Arcas, Julian Downward. Study of mechanisms of immune evasion of oncogenic KRAS in NSCLC [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 A145.
Abstract A155: Antibody-dependent cancer cell phagocytosis in macrophages induces immune escape by upregulating PD-L1 and IDO
Authors: Su Shicheng , Su An
Published: February 2019

Therapeutic antibodies can exert anticancer effects via antibody-dependenT-cellular cytotoxicity (ADCC). Also, they may trigger antibody-dependenT-cellular phagocytosis (ADCP) in tumor-associated macrophages (TAMs), but how ADCP influences TAM functions and antitumor immunity remains unclear. Here, we demonstrated that TAMs undergone ADCP of breast cancer cells and lymphoma cells mediated by trastuzumab and rituximab, respectively, suppressed the proliferation and cytotoxicity of NK cells and tumor-specific CD8+ T-cells against tumor cells by increasing PD-L1 and IDO. In vivo, inhibition of PD-L1 and IDO dramatically increases the infiltration of NK cells and CD8+ T-cells in Her2+ breast cancers and enhances the therapeutic effects of anti-Her2 antibody in both human Her2 knockin mice and humanized mice. Clinically, trastuzumab, but not chemotherapy alone, significantly increased the expression of PD-L1 and IDO in the TAMs of Her2+ breast cancer patients receiving neoadjuvant therapy. Furthermore, PD-L1+ IDO+ TAM infiltration was associated with poor trastuzumab response and reduced NK and CD8+ T-cells in tumors. Collectively, our findings unveil an unexpected role of ADCP mediated by therapeutic monoclonal antibodies in cancer immunosuppression, and suggest that antibody plus immune checkpoint blockade provide synergic therapeutic effects in cancer patients.

Citation Format: Shicheng Su, An Su. Antibody-dependent cancer cell phagocytosis in macrophages induces immune escape by upregulating PD-L1 and IDO [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 A155.
Abstract A200: Targeting ICOS receptor for development of cancer immunotherapy
Authors: Lo Yu-Hsun , Yu Cheng-Chou , Yu Shu-Han , Hseih Tsung-Hang , Chan Mei-Chi , Shih-Chong Tsai
Published: February 2019

Recently, checkpoint blockade-mediated immune reinvigoration acts as potential strategies to cure cancer. In addition to checkpoint blockade, a number of studies have shown that immune co-stimulators also act as crucial players in the immunotherapy. Inducible co-stimulator (ICOS), a homodimeric protein that belongs to CD28 superfamily, is expressed on activated T-cells and resting memory T-cells. Upon stimulation, ICOS and its ligand ICOSL (B7RP-1, B7H-2) have been shown to affect T-cell responses via ICOS-mediated PI3-kinase signaling to enhance the T-cells’ development and activity. In addition, previous studies have shown that ICOS/ICOSL pathway may play an important role in CTLA4 inhibitor-induced tumor immunity. In this study, we aim to develop and implement the Fc-fusion recombinant ICOSL proteins to induce T-cells’ activation for therapeutic use. Our data suggested that recombinant ICOSL-Fc can enhance the proliferation and cytotoxicity effect of human T-cells by increasing INF-γ and IL10 secretion. Moreover, ICOSL-Fc can also inhibit tumor growth in xenograft animal models. Based on our study, ICOS/ICOSL pathway could be a promising therapeutic target for the immunotherapy.

Citation Format: Yu-Hsun Lo, Cheng-Chou Yu, Shu-Han Yu, Tsung-Hang Hseih, Mei-Chi Chan, Tsai Shih-Chong. Targeting ICOS receptor for development of cancer immunotherapy [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 A200.
Abstract A202: Lysophosphatidic acid impedes the effector function of CD8+ T-cells through LPA5R
Authors: Mathew Divij , Strauch Pamela , Pelanda Roberta , Torres Raul
Published: February 2019

Immunotherapies have demonstrated the utility of targeting the immune system for the eradication of tumors, yet a majority of patients remain refractory to such treatments. Therefore, further advances in our understanding of T-cell activation and inhibitory signals are required to find alternative combinational strategies to treat cancers. Lysophosphatidic acid (LPA) is a bioactive lipid that has been characterized to promote tumor growth via distinct mechanisms and thus displays multiple “hallmarks” of tumorgenesis, including enhancing tumor-promoting inflammation, metastasis, and angiogenesis. Despite LPA receptors (LPARs) being expressed on all immune cells, the impact of LPA on immune cells remains unclear. Work from our lab has previously shown that LPA signals via LPAR5 expressed by CD8+ T-cells to suppress TCR-mediated intracellular calcium mobilization. Thus, we propose that aberrant expression of LPA by diverse tumors serves also to dampen adaptive immune responses, thereby creating an immune suppressive tumor microenvironment. Here, we demonstrate that CD8+ T-cells express three of the six known LPA receptors, and that LPA signaling through LPA5R on CD8+ T-cells has not only a profound inhibition of Ca2+ release after TCR stimulation, but also impedes ERK and Nur77 TCR induced signaling pathway. Importantly we now demonstrate that LPA signaling also decreases the cytolytic function of CD8+ T-cells by inhibiting granule exocytosis. Both adoptive transfer of Lpar5-/- CD8+ T-cells and implantation of tumors into Lpar5-/- hosts leads to greater control of tumor growth, underscoring an immunosuppressive signal mediated by LPA through LPA5R on CD8+ T-cells. Finally, human CD8+ T-cells also express the same LPARs as in the mouse and similarly fail to efficiently release Ca2+ upon TCR stimulation in the presence of LPA. Pharmaceutical inhibition of the human LPA5 receptor restores Ca2+ flux, suggesting a similar mechanism seen in mice. Thus, our data illuminate a novel lipid-receptor interaction that suppresses CD8+ T-cell function in both human and murine cells.

Citation Format: Divij Mathew, Pamela Strauch, Roberta Pelanda, Raul Torres. Lysophosphatidic acid impedes the effector function of CD8+ T-cells through LPA5R [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 A202.
Abstract A203: Role of nonimmune functions of regulatory T-cells in inflammation and tissue homeostasis
Authors: Mendoza Alejandra
Published: February 2019

Regulatory T-cells (Treg) are a T-cell lineage vital to promoting tolerance to self antigens, commensal bacteria, and environmental antigens, as well as limiting responses to acute and chronic infections. Because of their critical role in immunosuppression in diverse biologic settings—including the tumor microenvironment—therapeutic targeting of Treg cells holds promise for cancer immunotherapy. In addition to dampening immune responses against tumor antigens and the associated inflammation, tissue-resident Treg cells may directly support tumor growth, homeostasis, and metastasis. Hence, understanding Treg cell functions independent from immunomodulation may provide novel targets for cancer therapy without the adverse side effects associated with immune checkpoint blockade. Studies of Treg cells found in non-lymphoid tissues have revealed transcriptional signatures and functions distinguishable from those found in Treg cells residing in secondary lymphoid organs, suggesting that Treg cells may perform a variety of specialized functions within non-lymphoid tissues. In addition, Treg cells can show distinct localization within non-lymphoid organs, raising the possibility that they may interact with different immune and non-immune tissue resident cells. In particular, we find frequent Treg cell localization in close proximity to peripheral neurons. Gene expression analysis has revealed expression of neuromodulatory molecules by Treg cells, further suggesting interplay between Treg cells and peripheral neurons. Interactions between Treg cells and the peripheral nervous system may play an important role in limiting immune responses and/or promoting tissue homeostasis. Understanding potential neuromodulatory activity of Treg cells and its effect on inflammation, tissue homeostasis and cancer could reveal novel strategies for therapeutic possibilities.

Citation Format: Alejandra Mendoza. Role of nonimmune functions of regulatory T-cells in inflammation and tissue homeostasis [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 A203.
Abstract A222: Exploiting mTORC1-independent protein synthesis in Tregs to boost antitumor immune response
Authors: Volta Viviana , Ernlund Amanda , Parra Columba De la , Gadi Abilash , Valeta-Magara Amanda , Schneider Robert J.
Published: February 2019

Regulatory T-cells (Tregs) maintain immune system homeostasis in the organism. In the tumor micro-environment, however, Tregs can hinder antitumor immune response. Treg maturation in peripheral sites (pTregs) requires inhibition of protein kinase mTORC1, which paradoxically blocks mRNA translation. mTORC1 phosphorylates (inactivates) 4E-BP1, a negative regulator of the translation initiation factor eIF4E. When mTORC1 is active, 4E-BP1 is hyperphosphorylated and releases eIF4E, which can then bind the mRNA cap structure and promote eIF4F complex assembly and ribosome recruitment. Inhibition of mTORC1 results in hypo-phosphorylation (activation) of 4E-BP1, which then binds and sequesters eIF4E, preventing its interaction with the cap and ribosome association to the mRNA. Using human CD4+ T-cells differentiated in vitro, we show that mTORC1 inhibition strongly impairs protein synthesis, yet with exposure to TGFbeta, is essential to mediate iTreg differentiation and immune suppression activity. We found that TGFbeta reprograms the T-cell transcriptome, while mTORC1 inhibition reprograms the translatome (genome-wide translation signature), mediating Treg differentiation. Genome-wide transcription and translation profiling identified TGFbeta-upregulated mRNAs resistant to mTORC1 inhibition, in part due to their 5’-untranslated regions, that induces Treg differentiation and immune suppression activity. These include canonical pTreg fate-determining mRNAs FOXP3, CTLA-4, CD101 and CD103, among others. Inhibition of mTORC1 alone or TGFbeta alone induces iTregs with poor immune suppression activity. Treg differentiation is therefore mediated by an mTORC1-independent privileged mRNA translation mechanism that converts activated CD4+ T-cells to Tregs. These findings are quite relevant in the tumor microenvironment, where mTORC1-inhibiting conditions such as hypoxia and deprivation of nutrients and energy are present. Investigation of molecular targets acting in this mTORC1/eIF4E-independent translation of Treg mRNAs is ongoing. These targets could be drugged to selectively inhibit Treg differentiation in the tumor microenvironment, thus allowing effector cells to mount the response against cancer cells.

Citation Format: Viviana Volta, Amanda Ernlund, Columba De la Parra, Abilash Gadi, Amanda Valeta-Magara, Robert J. Schneider. Exploiting mTORC1-independent protein synthesis in Tregs to boost antitumor immune 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 A222.
Abstract B009: New development of monoclonal antibodies targeting TRAIL agonist receptors
Authors: Dubuisson Agathe
Published: February 2019

Restoring programmed-cell death of cancer cells is a real challenge in oncology. To date, several monoclonal antibodies targeting TRAIL agonist death receptors have been developed, but none has been found to display significant clinical effects, so far. Efforts should be continued to develop novel DR4 and DR5 antibodies with improved properties. In this regard, novel monoclonal antibodies targeting DR4 and DR5 have been generated here using DNA-immunization in order to produce antibodies that can recognise DR4 or DR5 in their native forms. This cost- and time-effective technique allows the production of proteins of interest directly into the mice. Plasmids encoding DR4 or DR5 sequences have been injected into the tail veins of mice. Immunizations elicited significant humoral anti-DR4 and anti-DR5 responses and fusions of the corresponding spleens resulted in numerous hybridomas that can specifically recognise DR4 or DR5 in their native forms. After an intensive screening, anti-DR4 and anti-DR5 clones were selected for production and 4 to 5 were assessed for selectivity and affinity towards their respective targets by flow cytometry (FACS) and bio-layer interferometry (BLI). All antibodies efficiently bind to their targets with a very high affinity (nanomolar range). They were then characterized and tested for their capacity to induce apoptosis in a wide range of cancer cell lines. Of the four anti-DR4 antibodies of interest, one antibody displayed agonistic properties alone, one was able to inhibit and two were found to potentiate TRAIL-induced apoptosis. Similarly, one out of the four anti-DR5 antibodies behaved as an agonist whereas another one was found to enhance TRAIL. The most potent antibody was assessed in vivo, and preliminary results indicate that the latter is also able to inhibit tumor growth in animal models. In summary, this study is the first demonstration that DNA-based immunization method can be used to generate efficient therapeutic monoclonal antibodies targeting receptors of the TNF superfamily.

Citation Format: Agathe Dubuisson. New development of monoclonal antibodies targeting TRAIL agonist 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 B009.
Abstract B013: Site specific conjugation of engineered non-native amino acids in an anti-CD3 Fab-folate bispecific antibody significantly enhances its antitumor properties in gynecologic cancers
Authors: Gray Michael J. , Barkho Wisam , Tipton Barbara , Shastri Prathap , Jie Hyun-Bae , Steen Jeff , Frank Rik , Tian Feng , Jackson Dowdy , Zhang Shawn
Published: February 2019

Ovarian cancer is the seventh most commonly diagnosed cancer in women. Standard treatments typically include surgery followed by radiation and/or chemotherapy. However, currently 5-year survival rates are 44%, underlining the need for new effective therapies. The Folate receptor 1 (FOLR1, FRα) is expressed in 80% of ovarian tumors, making it an attractive target for CD3-based bispecific antibody therapies. Bispecific engagement of activated host T-cells in the tumor microenvironment is highly effective at eliminating tumor cells. We have developed an anti-CD3 Fab-folate bispecific antibody by engineering non-native amino acids (NNAAs) at a specific region within the Fab domain and conjugated a PEGylated folate molecule to these sites. Our data demonstrate that Ambrx’s proprietary site-specific conjugation technology provides significant advantages over non-PEGylated proteins.

Citation Format: Michael J. Gray, Wisam Barkho, Barbara Tipton, Prathap Shastri, Hyun-Bae Jie, Jeff Steen, Rik Frank, Feng Tian, Dowdy Jackson, Shawn Zhang. Site specific conjugation of engineered non-native amino acids in an anti-CD3 Fab-folate bispecific antibody significantly enhances its antitumor properties in gynecologic cancers [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 B013.
Abstract B028: Label-free Raman signatures of immune cells: A new tool for artificial intelligence in immunotherapy
Authors: Madathil Girish Chundayil , Nagareddy Raveena , Ramkumar Anjana , Krishnan Manu , Harish Vijay , Ashokan Anusha , Nair Shanti Kumar , Koyakutty Manzoor
Published: February 2019

In the emerging era of artificial intelligence mediated immune response analysis, post- imunotherapeutic interventions, monitoring of large pool of data related to different types of immune cells is a critical requirement. Several gold standard methodologies such as flow cytometry, cytoTOF, ELISPOT and other immune-imaging techniques are routinely used for quantifying the phenotypic behavior of immune cells. These techniques involve the use of antibodies for specifically labeling each cell types, which makes the procedure expensive and laborious. Here, we are presenting a novel approach for label free detection of various types of immune cells using their inherent vibrational Raman signatures and a method of using the same data for cluster analysis. Raman spectroscopy is a well-established tool that measures the vibrational fingerprints of the analytes. It has been extensively used in biologic research for differentiating cells and tissues based on their Raman spectral features. Since the basic building block molecules of the cells are the same, variations in the spectral features among cells and tissues are minimal. Mathematical tools such as multivariate statistical analysis and machine learning methods are adopted to identify the significant Raman spectral features that cause the variation among groups (DC, macrophage, NK, T-cell, B cell, neutrophils, etc.). In immunology, no studies have been reported so far in understanding and recording the inherent Raman spectral finger prints of all forms of immune cells, both in the naïve and active stage. In this study, we have created a spectral database of various immune cells such as T-cells, B cells, NK cells, dendritic cells, macrophages, neutrophils and their signature variations in activated and naïve forms. These spectral databases can be used in machine learning algorithms to predict the treatment response in clinical and preclinical settings.

Citation Format: Girish Chundayil Madathil, Raveena Nagareddy, Anjana Ramkumar, Manu Krishnan, Vijay Harish, Anusha Ashokan, Shanti Kumar Nair, Manzoor Koyakutty. Label-free Raman signatures of immune cells: A new tool for artificial intelligence in immunotherapy [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 B028.
Abstract B029: A novel media supplementation strategy for improved T-cell culture and preservation of naivety
Authors: Master Alyssa , O'Connor Roddy S. , Ghassemi Saba , Schneider Dina A. , Karimi-Naser Lisa
Published: February 2019

Recent advances in genetic engineering have resulted in exponential growth in cell therapy technologies. As an increasing number of CAR-T therapies are entering clinical trials, there is a scarcity of resources put into optimizing production strategies. This is largely due to the highly competitive timelines for these companies to advance their drug candidate. Yet, due to this pressure, there is a real need for advances in the cell culture media used to recover, sustain and expand these importanT-cells. Here we show that a novel xeno-free media supplement, PhysiologixTM XF serum replacement, results in improved human primary T-cell growth, preservation of naïve and central memory phenotype, and enhanced transduction efficiency when used in place of traditional media supplements. In the presence of this supplement, T-cell proliferation was nearly doubled in comparison to industry-leading serum free media. In a separate study, we compared PhysiologixTM XF to a control media containing the traditional 10% fetal bovine serum for bulk T-cell culture. We observed that T-cells in both control and test media had similar cell size and population doublings following 48 hours of CD3/CD28 activation. However, FACS analysis revealed thaT-cells grown in PhysiologixTM XF showed a 33% increase in beneficial naïve-like and central memory T-cell phenotypes after nine days in culture when compared to control media. Additionally, lentiviral transduction efficiency was increased from 74% to 94% in PhysiologixTM XF supplemented cells compared to control cells. Taken together, these data demonstrate that T-cell culture with PhysiologixTM XF results in improved growth characteristics, desirable cell phenotypes for patient infusion, and improved ease of transduction, all of which may prove beneficial in the CAR-T race from bench to bedside.

Citation Format: Alyssa Master, Roddy S. O'Connor, Saba Ghassemi, Dina A. Schneider, Lisa Karimi-Naser. A novel media supplementation strategy for improved T-cell culture and preservation of naivety [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 B029.
Abstract B034: A novel immunomodulatory strategy of targeting glyco-immune checkpoints with EAGLE technology
Authors: Peng Li
Published: February 2019

Cancer therapy has been revolutionized by inhibiting immune checkpoints to harness the power of the immune system in fighting cancer. However, the majority of patients are resistant to the current immuno-oncology drugs. There is a strong need to identify novel mechanisms of cancer immune evasion and explore novel therapeutic modalities. Glyco-immune checkpoint axis plays a critical role in modulating innate and adaptive immune responses against cancer. However, this pathway is underexplored for therapeutic interventions of cancer, because the complexity and heterogeneity of glycan-ligands on tumor cells pose grand challenges for conventional therapeutic modalities. Here we described a novel multifunctional antibody-like therapeutic modality, named EAGLE (Enzyme-Antibody Glyco-Ligand Editing), which can overcome the heterogeneity and complexity problems and specifically edit tumor-specific glycans. We evaluated the efficacy of an EAGLE molecule and studied its mechanism of actions in a breast cancer EMT6 syngeneic tumor model. Systematic delivery of the EAGLE molecule decreased the expression levels of immunosuppressive glycan-ligands on tumor cell surfaces, and increased T-cell infiltration and activation in the syngeneic tumor models. EAGLE treatment led to 50% complete regressions of established tumors as a monotherapy and 100% cures in combination with an anti-PD1 mAb. Furthermore, cured mice from EAGLE treatment completely rejected the rechallenge of tumor cells, suggesting that EAGLE induced anti-tumor immunologic memory. In summary, the novel therapeutic modality, EAGLE, blocked the glyco-immune checkpoint pathway in the tumor microenvironment and potentiated innate and adaptive antitumor immunity, which offers a novel immunomodulatory strategy to treat cancer.

Citation Format: Li Peng. A novel immunomodulatory strategy of targeting glyco-immune checkpoints with EAGLE technology [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 B034.
Abstract B071: Validating sequence similarity-driven neoepitope fitness models via immunogenomics on TCGA and multiregional tumor data
Authors: Bubie Adrian , Akers Nicholas , Villanueva Augusto , Losic Bojan
Published: February 2019

Clonal fitness and survival models for checkpoint blockade response prediction have recently been proposed on the basis of ranking neoepitopes via an interaction between a proxy of T-cell recognition, a nonlinear function of neoepitope sequence similarity to known antigens, and neoantigen relative MHC binding affinity. In this work we examine the SKCM (n = 337) and NSCLC (n = 305) TCGA datasets to explicitly test if sequence similarity to known antigens from the IEDB is associated with tumor infiltrating lymphocyte (TIL) burden in patients, as measured by TCR sequencing and CDR reconstruction in RNA-seq data. We find that there is no statistically significant association between either the inferred clonality or magnitude of TIL response and neoepitope sequence similarity to known antigens. We do, however, find significant, moderate associations of TIL response to neoepitope burden. Further, we examined the LIHC (n = 193) and UCEC (n = 245) TCGA cohorts to explicitly derive tumor and virally derived epitopes (HepB, HPV respectively) and ranked their relative predicted MHC binding affinity profiles. We find a greater MHC binding affinity bias exists towards neoepitopes compared to virally derived peptides in a natural setting where both viral and tumor antigens are simultaneously present. Moreover, we find low and significant associations between TIL burden and overall neoepitope burden, but no association with overall viral epitope or expression burden. Finally, we used multiregionally sampled data (12 patients, 72 regions) from HepB-positive HCC liver cancer patients to confirm preferential MHC binding affinity and TIL response bias towards neoepitopes still holds and is significant. Our results suggest that neoepitopes dominate in their recruitment potential of, and association with, TIL burden compared to viral-cofactors. They also suggest that neoepitope sequence similarity to known antigens does not recapitulate patient TIL burden to first approximation.

Citation Format: Adrian Bubie, Nicholas Akers, Augusto Villanueva, Bojan Losic. Validating sequence similarity-driven neoepitope fitness models via immunogenomics on TCGA and multiregional tumor data [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 B071.
Abstract B076: Pan-cancer analysis to identify which cancers may benefit most from LAG-3 blockade
Authors: Ganesan Shridar , Panda Anshuman , Bhanot Gyan
Published: February 2019

Immune checkpoint blockade using antibodies that target programmed-cell-death-1 (PD-1) or its ligand programmed-cell-death-ligand 1 (PD-L1), and/or cytotoxic-T-lymphocyte-associated-protein-4 (CTLA-4) have led to dramatic responses, but only in a subset of human cancers. An antibody targeting lymphocyte-activation-gene-3 (LAG-3), relatlimab (BMS-986016), recently showed significant clinical activity in melanoma, and early clinical data showed that LAG-3 expression is a biomarker of response to this agent. We performed a pan-cancer analysis of The Cancer Genome Atlas data to identify genomic and immunologic correlates of LAG-3 expression. Hyper-mutation, and exogenous (Epstein-Barr virus, human papillomavirus) or endogenous (endogenous retrovirus group 3 member 2) viral expression in tumor were associated with increased expression of LAG-3 in multiple cancer types. LAG-3 expression was also correlated with CD8A and PD-L1 expression in most cancer types; however, there were notable exceptions, including head-neck squamous-cell cancer (HNSC), renal cell cancer (RCC) and glioblastoma. In HNSC, LAG-3 expression, but not PD-L1, was significantly increased in HPV+ cancers. In RCC and gliobastoma, LAG-3 was more strongly associated with CD8A expression than PD-L1. These results may have implications on the design of future clinical trials of LAG-3 blockade.

Citation Format: Shridar Ganesan, Anshuman Panda, Gyan Bhanot. Pan-cancer analysis to identify which cancers may benefit most from LAG-3 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 B076.
Abstract B077: Signatures of T-cell dysfunction and exclusion predict cancer immunotherapy response
Authors: Jiang Peng , Gu Shengqing , Pan Deng , Fu Jingxin , Sahu Avinash , Hu Xihao , Li Ziyi , Traugh Nicole , Bu Xia , Li Bo , Liu Jun , Freeman Gordon J , Brown Myles A , Wucherpfennig Kai W. , Liu Xiaole Shirley
Published: February 2019

Cancer treatment by immune checkpoint blockade (ICB) can bring long-lasting clinical benefits, but only a fraction of patients responds to treatment. To predict ICB response we developed TIDE, a computational method to model two primary mechanisms of tumor immune evasion: inducing T-cell dysfunction in tumors with high infiltration of cytotoxic T lymphocytes (CTL) and preventing T-cell infiltration in tumors with low CTL level. We identified signatures of T-cell dysfunction from large tumor cohorts by testing how the expression of each gene in tumors interacts with the CTL infiltration level to influence patient survival. We also modeled factors that exclude T-cell infiltration into tumors using expression signatures from immunosuppressive cells. Using this framework and pre-treatment RNA-Seq or NanoString tumor expression profiles, TIDE predicted the outcome of melanoma patients treated with first-line anti-PD1 or anti-CTLA4 more accurately than other biomarkers such as PD-L1 level and mutation load. TIDE also revealed new candidate ICB resistance regulators, such as SERPINB9, demonstrating utility for immunotherapy research. TIDE source code and a web application are available at http://tide.dfci.harvard.edu.

Citation Format: Peng Jiang, Shengqing Gu, Deng Pan, Jingxin Fu, Avinash Sahu, Xihao Hu, Ziyi Li, Nicole Traugh, Xia Bu, Bo Li, Jun Liu, Gordon J Freeman, Myles A Brown, Kai W. Wucherpfennig, Xiaole Shirley Liu. Signatures of T-cell dysfunction and exclusion predict cancer immunotherapy 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 B077.
Abstract B088: Mapping tumoral and immune heterogeneity in PD-1 responsive glioblastoma
Authors: Restrepo Paula , Yong Raymund , Laface Ilaria , Tsankova Nadejda , Gnjatic Sacha , Hormigo Adilia , Losic Bojan
Published: February 2019

Clonal evolution and the immune microenvironment in glioblastoma (GBM) ultimately determine the potential benefit of checkpoint inhibition. In this case study of a patient who benefited from PD-1 blockade therapy, we characterize intratumoral heterogeneity from several primary and recurrent biopsies. We leveraged RNA-seq data from both the primary tumor and three recurrent biopsies to examine major components of the molecular landscape within the context of clonal evolution. Specifically, we surveyed tumor-immune interactions by computing the expressed mutational and neoepitope tumoral burden, along with the magnitude and clonality of infiltrating lymphocytes using VDJ-sequencing. We furthermore derived the regional gene expression landscape, and found significant differences between the primary and recurrent biopsies. We found significant heterogeneity in the predicted neoantigen and infiltrating lymphocyte landscape, with a pronounced shift towards lower predicted immunogenicity and lower immune infiltration in all recurrent biopsies. Notably, we also found evidence suggesting an outlier recurrent biopsy enriched in aberrant expression of the H19-IGF2 locus. Overall, this case study adds to existing knowledge of the molecular landscape and intratumoral heterogeneity within glioblastoma, in turn providing a starting point for future studies aimed at assessing the efficacy of checkpoint inhibition as a suitable treatment for this highly aggressive cancer type.

Citation Format: Paula Restrepo, Raymund Yong, Ilaria Laface, Nadejda Tsankova, Sacha Gnjatic, Adilia Hormigo, Bojan Losic. Mapping tumoral and immune heterogeneity in PD-1 responsive glioblastoma [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 B088.
Abstract B095: Mapping the genetic features of immune checkpoint responsiveness using AAV-CRISPR mediated in vivo screen
Authors: Wang Guangchuan , Chow Ryan , Bai Zhigang , Ye Lupeng , Chen Sidi
Published: February 2019

Immune checkpoint blockade has achieved tremendous clinical success across many tumor types, but fails to induce clinical responses in many patients. The mechanisms underlying checkpoint resistance remain poorly characterized. Recent studies have applied next generation sequencing techniques to catalog the mutational burden of patient tumors, which provides a wealth of data to determine common mutations. To map the genetic features of response to checkpoint blockade immunotherapy as well as correlating the clinical efficacy with certain mutations, we developed a novel direct in vivo CRISPR screening approach for high-throughput profiling of functional cancer drivers in an autochthonous manner by injecting AAVs carrying an sgRNA library targeting the top 50 TCGA pan-cancer recurrently mutated tumor suppressor genes (mTSG) into the immunocompetent Cas9 transgenic mice. All mice that received the AAV-mTSG library developed liver cancer and died within four months. We then utilized MIP sequencing of sgRNA target sites to chart the mutational landscape of these tumors, revealing the functional consequence of multiple variants in driving liver tumorigenesis as well as identifying specific gene pairs that were co-occurring across mice. Using this approach, we also mapped the mutation landscape changes under the pressures of immune checkpoint inhibitors, anti-PD1 or anti-CTLA4. We monitored liver tumor growth in AAV-mTSG injected LSL-Cas9;LSL-Fluc mice by using intravital bioluminescent imaging system (IVIS) in combination with dissection check before drug administration. Using IVIS data, we grouped them into 3 size-matched cohorts to receive anti-PD1 or anti-CTLA4 treatments or PBS control. According to the survival data, the mice with mTSG-induced liver tumor benefit from anti-PD1 or anti-CLTA4 treatment. By comparing the mutation frequencies of liver tumors in the mice receiving either checkpoint inhibitors or PBS treatment, we mapped the mutation landscape changes associated with anti-PD1 or anti-CTLA4 treatment. We are performing validation studies on top targets such as Arid1a, Stk11, and B2M. Using this approach, we systematically mapped the correlation of these top 50 driver mutations with cancer immune evasion and immunotherapy responsiveness, providing a valuable reference for patient stratification when considering immunotherapy as well as novel targets for synergistic interventions.

Citation Format: Guangchuan Wang, Ryan Chow, Zhigang Bai, Lupeng Ye, Sidi Chen. Mapping the genetic features of immune checkpoint responsiveness using AAV-CRISPR mediated in vivo screen [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 B095.
Abstract B102: Pre-existing citrulline-specific CD4 T-cells can be efficiently harnessed for tumor therapy
Authors: Brentville Victoria A. , Symonds Peter , Cook Katherine W. , Daniels Ian , Atabani Suha , Choudhury Ruhul , Vaghela Poonam , Metheringham Rachael L. , Gijon Mohamed , Xue Wei , Durrant Lindy G.
Published: February 2019

Citrullination is the post-translational modification of arginine to citrulline mediated by Peptidylarginine deiminases (PADs), which are a family of calcium dependent enzymes found in a variety of tissues. Citrullinated proteins are known to play a significant role in the pathogenesis of autoimmune diseases and are presented in complex with MHC class II. We have previously shown that citrullinated peptides from vimentin and α-enolase are presented on HLA-DR4 in tumor cells and mediate strong anti-tumor responses (Brentville et al., 2016; Cook et al., 2017). Here we show that responses to these peptides are also restricted through HLA-DP4. These responses can be detected within 2 days of vaccination and can mediate rapid regression of tumors within 4 days in mice suggesting evidence of a pre-existing repertoire of T-cells specific for these citrullinated peptides. Evidence of CD4 T-cells specific to citrullinated antigens have been identified in a number of autoimmune disease patients in particular rheumatoid arthritis patients. These patients show an increase in frequency and change in phenotype of citrulline specific CD4 T-cells compared to healthy individuals (James et al., 2014). In this report we also demonstrate that a repertoire of CD4 T-cell responses to citrullinated peptides exists in healthy individuals and that this can be uncovered/enhanced by removal of CD25+ T-cells thus suggesting the existence of a regulatory mechanism keeping these responses in check. The responding populations appear to be oligoclonal and show an increase in effector memory and Temra phenotype. This suggests that a repertoire of CD4 T-cells exists to citrullinated peptides that could be targeted for cancer therapy.

Citation Format: Victoria A. Brentville, Peter Symonds, Katherine W. Cook, Ian Daniels, Suha Atabani, Ruhul Choudhury, Poonam Vaghela, Rachael L. Metheringham, Mohamed Gijon, Wei Xue, Lindy G. Durrant. Pre-existing citrulline-specific CD4 T-cells can be efficiently harnessed for tumor 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 B102.
Abstract B109: Broadly neutralizing antibodies against HCV use a CDRH3 disulfide motif to recognize an E2 glycoprotein site that can be targeted for vaccine design
Authors: Flyak Andrew I. , Ruiz Stormy , Colbert Michelle , Luong Tiffany , Crowe James E. , Bailey Justin R. , Bjorkman Pamela J.
Published: February 2019

Hepatocellular carcinoma is the most common type of liver cancer and is responsible for approximately one million deaths each year. In the United States, persistent infection with hepatitis C virus (HCV) is among the leading causes of hepatocellular carcinoma. HCV vaccine efforts are hampered by genetic diversity of HCV envelope glycoproteins E1 and E2. Structural studies of broadly neutralizing antibodies (bNAbs) (e.g., HEPC3 and HEPC74) isolated from individuals who spontaneously cleared HCV infection will facilitate immunogen design to elicit antibodies against multiple HCV variants. However, challenges in expressing HCV glycoproteins previously limited bNAb-HCV structures to complexes with truncated E2 cores.New expression and purification techniques allowed us to produce bNAb complexes with full-length E2 ectodomains for structural studies. We solved crystal structures of HEPC3 and HEPC74 alone and complexed with E2 ectodomains. We measured the binding and neutralization potency of HEPC3/HEPC74-like germline precursors. Despite derivation from different individuals, HEPC3 and HEPC74 use the same germline heavy chain gene segments and possess a limited number of somatic mutations. We describe a shared CDRH3 disulfide motif that exhibits common interactions with a conserved epitope in the front layer of E2. The germline-encoded CDRH3 motif plays a critical role in initial recognition of HCV by naïve B cells. The structures of E2 ectodomain reveal regions (including a target of immunogen design) that were truncated or disordered in E2 core. We also identify candidate immunogens: E2 variants that bind to HEPC3/HEPC74-like germline precursors. These data reveal unusual structural features relevant to the fundamental understanding of antibody-antigen interactions. The identification of common genetic signatures of HCV bNAbs will facilitate lineage-targeted immunogen design to raise bNAbs against the conserved epitope in the E2 front layer.

Citation Format: Andrew I. Flyak, Stormy Ruiz, Michelle Colbert, Tiffany Luong, James E. Crowe, Jr., Justin R. Bailey, Pamela J. Bjorkman. Broadly neutralizing antibodies against HCV use a CDRH3 disulfide motif to recognize an E2 glycoprotein site that can be targeted for vaccine design [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 B109.
Abstract B125: Targeting human CD141+ DC using CLEC9A antibodies for cancer immunotherapy
Authors: Radford Kristen , Pearson Frances , Masterman Kelly-Anne , Tullett Kirsteen , Haigh Oscar , Walpole Carina , Daraj Ghazal , Rojas Ingrid Leal , Lahoud Mireille
Published: February 2019

Dendritic cells (DC) are a heterogeneous cell population, with specialist subtypes driving specific immune responses. In mice, the cDC1 subset (also referred to as Batf3-dependent DC, XCR1+ DC, CD8+ DC in lymphoid tissues and CD103+ DC in peripheral tissues) is essential for the induction of tumor immune responses and for the efficacy of checkpoint inhibitor blockade and adoptive T-cell immunotherapies. Vaccines that can deliver antigens (Ag) directly to DCs in vivo are more effective than cell-based therapies in mouse models and are promising approaches to translate to humans. CD141+ DC are the human cDC1 equivalent and specifically express the C-type lectin-like receptor CLEC9A, that facilitates cross-presentation of dead cell Ag. Targeting tumor-associated Ag (TAA) to human CD141+ DC using CLEC9A antibody (Ab) is therefore an attractive strategy to induce or boost tumor immune responses. NYESO1 and WT1 are well characterised, highly immunogenic TAA expressed by a broad array of tumor types. We developed recombinant human chimeric IgG4 Ab specific for human CLEC9A genetically fused to NYESO1 or WT1. For comparison we developed TAA fusions with chimeric IgG4 Ab specific for human DEC-205, which is expressed by many human leukocytes, and β-galactosidase as an irrelevant isotype control. CLEC9A-NYESO1 and CLEC9A-WT1 Abs retained their binding specificity for CD141+ DC. Following uptake of CLEC9A-WT1, CD141+ DC cross-presented a WT-1 HLA-A24-restricted epitope for recognition by specific CD8+ cytotoxic T-cells. Likewise, a HLA-A2-restricted NYESO1 epitope was cross-presented Ag specific CD8+ T-cells by CD141+ DC following uptake of CLEC9A-NYESO1. For both TAA, the CLEC9A Abs were more efficient at delivery of Ag for cross-presentation than DEC-205 or isotype control Abs. Moreover, using a humanized mouse model in which functional human CD141+ DC and Ag-specific T-cells develop, CLEC9A-TAA Ab induced priming of Ag-specific T-cells. Our data advocate further development of human CLEC9A targeting Abs as cancer vaccines.

Citation Format: Kristen Radford, Frances Pearson, Kelly-Anne Masterman, Kirsteen Tullett, Oscar Haigh, Carina Walpole, Ghazal Daraj, Ingrid Leal Rojas, Mireille Lahoud. Targeting human CD141+ DC using CLEC9A antibodies for cancer immunotherapy [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 B125.