bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract B129: Human endogenous retroviruses as a potential reservoir for T-cell mediated cancer immunotherapy
Authors: Saini Sunil Kumar , Bjerregaard Anne-Mette , Ørskov Andreas D. , Unnikrishnan Ashwin , Holmberg Staffan , Anande Govardhan , Bentzen Amalie Kai , Szallasi Zoltan , Eklund Aron C. , Grønbæk Kirsten , Hadrup Sine Reker
Published: February 2019

Epigenetic modulation using DNA methyltransferase inhibitors (DNMTis), such as 5-azacytidine (5-aza-CR), have been shown to affect the cellular immunogenicity in vitro through upregulations of human endogenous retroviruses (HERV) leading to activation of the INFγ response pathway. HERVs comprise up to 8% of the human genome, and may hold a large reservoir of potential tumor antigens.We examined the in vivo efficacy of 5-aza-CR in terms of upregulations of HERV expression during standard treatment regimen, as well as the ability of such HERV transcripts to form T-cell antigens leading to measurable T-cell recognition upon treatment. We have studied 66 HERV genes that have been shown to be transcribed in human tissues. To identify HERV derived immune recognition, we generated a library of 1169 HERV derived potential antigenic peptides restricted to most abundant MHC class I molecules in the Caucasian population. Peripheral blood mononuclear cells (PBMCs) from a cohort of 19 patients and bone marrow samples from a cohort of 11 patients, treated with DNMTis for different hematological malignancies (MDS, AML, and CMML) were used to detect CD8+ T-cells reactive to ERV-derived peptides. We detected CD8+ T-cells specific to several HERV-derived peptides both in healthy and diseased individuals. Further, in an additional cohort of patients we examined expression level of these HERVs by RNA seq analysis and compared with healthy individuals demonstrating a disease associated upregulation of HERVs in hematological malignancies. Presence of T-cells reactive to HERV antigens and enhanced expression of HERVs in these malignancies suggest that HERVs may indeed provide a pool of shared tumor associated antigens. These antigens could potentially be enhanced through DNMTi treatment and may provide a target for T-cell mediated immunotherapy.

Citation Format: Sunil Kumar Saini, Anne-Mette Bjerregaard, Andreas D. Ørskov, Ashwin Unnikrishnan, Staffan Holmberg, Govardhan Anande, Amalie Kai Bentzen, Zoltan Szallasi, Aron C. Eklund, Kirsten Grønbæk, Sine Reker Hadrup. Human endogenous retroviruses as a potential reservoir for T-cell mediated 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 B129.
Abstract B146: The tumor necrosis factor superfamily member RANKL suppresses effector cytokine production in group 3 innate lymphoid cells
Authors: Bando Jennifer Kaoru , Gilfillan Susan , Song Christina , McDonald Keely , Huang Stanley C-C. , Newberry Rodney D. , Kobayashi Yasuhiro , Allan David S.J. , Carlyle James R. , Cella Marina , Colonna Marco
Published: February 2019

While signals that activate group 3 innate lymphoid cells (ILC3s) have been described, the factors that negatively regulate these cells are less well understood. Here we found that the tumor necrosis factor (TNF) superfamily member receptor activator of nuclear factor κB ligand (RANKL) suppressed ILC3 activity in the intestine. Deletion of RANKL in ILC3s and T-cells increased C-C motif chemokine receptor 6 (CCR6)+ ILC3 abundance and enhanced production of interleukin-17A (IL-17A) and IL-22 in response to IL-23 and during infection with the enteric murine pathogen Citrobacter rodentium. Additionally, CCR6+ ILC3s produced higher amounts of the master transcriptional regulator RORγt at steady state in the absence of RANKL. RANKL-mediated suppression was independent of T-cells, and instead occurred via interactions between CCR6+ ILC3s that expressed both RANKL and its receptor, RANK. Thus, RANK-RANKL interactions between ILC3s regulate ILC3 abundance and activation, suggesting that cell clustering may control ILC3 activity.

Citation Format: Jennifer Kaoru Bando, Susan Gilfillan, Christina Song, Keely McDonald, Stanley C-C. Huang, Rodney D. Newberry, Yasuhiro Kobayashi, David S.J. Allan, James R. Carlyle, Marina Cella, Marco Colonna. The tumor necrosis factor superfamily member RANKL suppresses effector cytokine production in group 3 innate lymphoid 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 B146.
Abstract B150: STING acquired species-specific motifs to control alternative immune responses
Authors: Mann Carina C. de Oliveira , King David S. , Kranzusch Philip J.
Published: February 2019

Stimulator of Interferon Genes (STING) is an adaptor protein critical for downstream signaling during recognition of mislocalized cytosolic DNA. STING activation requires recognition of a unique second messenger 2′–5′, 3′–5′ cyclic GMP–AMP (2′3′ cGAMP) synthesized by the pathogen recognition receptor cyclic GMP–AMP synthase (cGAS). Due to its broad expression in most tissues, and ability to respond to different endogenous and foreign small molecules, STING is emerging as a promising drug target for cancer immunotherapy and treatment of autoimmune diseases. However, it remains unknown how the single adaptor protein STING controls distinct transcriptional outputs leading to production of type I interferon, proinflammatory cytokine responses or autophagy. Here we present surprising evidence for the ancient origins of the cGAS-STING signaling pathway by discovery of bacterial cGAS-like enzymes and complete functional cGAS-STING pathways in lower metazoans. Our previous structural data demonstrate that human and metazoan STING proteins share a common architecture that couples ligand binding with conformational changes and allows signal activation. However, it remained unclear how alternative STING conformations control different downstream signaling outputs, and which motifs are responsible for recruitment of the downstream factors controlling each pathway. We have now combined a phylogenetic and biochemical approach to explain the conserved elements that regulate STING downstream signaling events. Our analysis identifies new immune pathway-specific regulatory motifs acquired by distinct STING species, and we are currently focused on identifying the recruited factors important for controlling human STING signaling. Together, our results explain the molecular basis for distinct STING downstream signaling, and provide new insights for the rational design of STING pathway-specific therapeutics.

Citation Format: Carina C. de Oliveira Mann, David S. King, Philip J. Kranzusch. STING acquired species-specific motifs to control alternative immune responses [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 B150.
Abstract B155: Impact of transcription initation on translation regulation by the mTOR pathway
Authors: Duttke Sascha H. , Chang Max , Glass Christopher K. , Berman Andrea , Benner Christopher
Published: February 2019

The two major processes of eukaryotic gene expression, transcription and translation, are spatially and temporally separated and commonly perceived to be independently regulated. Unexpectedly, the analysis of nascent transcription start sites (TSSs) genome-wide, proposes that alternative TSS can target mRNAs of the same gene to distinct modes of translational regulation.Our preliminary data found the TCT core promoter motif to function as a transcriptionally suboptimal Initiator (Inr) motif. Despite the rapid turnover of most regulatory elements, the TCT motif is remarkably conserved among the promoters of orthologous bilaterians genes. However, the translation of mRNAs starting from TCT but not Inr promoters is preferentially regulated by the Mammalian target of rapamycin complex 1 (mTORC1), likely via the La-related protein 1 (Larp1) that binds mRNAs starting on pyrimidine but not purines. These findings reveal a functional dependency between transcription initiation and translation regulation, and highlight the importance of TSS selection in promoters. Inhibitors of mTORC1, and more recently Larp1, are rapidly moving into clinical cancer therapy trials but did not live up to the expectations in patients. Markers for patient stratification and predicting mTOR inhibitor efficacy are needed. As TSSs reflect the integrated signals of gene regulatory pathways and also appear to impact translational regulation, our future research will address how far alternative TSSs facilitate acquired resistance to mTOR inhibitors in tumors and 2) TSSs can serve as a predictive marker for mTOR inhibitors efficacy.

Citation Format: Sascha H. Duttke, Max Chang, Christopher K. Glass, Andrea Berman, Christopher Benner. Impact of transcription initation on translation regulation by the mTOR 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 B155.
Abstract B168: A Radiosensitivity gene signature and PD-L1 status predict clinical outcome of patients with glioblastoma multiforme in The Cancer Genome Atlas Dataset
Authors: Kim Inah , Jang Bum Sup
Published: February 2019

Background: A combination of radiotherapy and immune checkpoint blockade, such as programmed death-1 (PD-1) or programmed death-ligand 1 (PD-L1) blockade, is being actively tested in clinical trial settings. Here, we tried to identify a subset of patients that could potentially benefit from this strategy using The Cancer Genome Atlas (TCGA) dataset for glioblastoma (GBM). Methods: A total of 399 cases were clustered into radiosensitive (RS) versus radioresistant (RR) groups based on radiosensitivity gene signature and were further stratified into PD-L1 high versus PD-L1 low groups according to the median expression of CD274 mRNA. Differential and integrated analyses with expression and methylation data were performed. CIBERSORT was used to enumerate the immune repertoire that resulted from transcriptome profiles. Results: We identified a subset of GBM patients, the “PD-L1 high-RR group” that had a worse clinical outcome compared to the other groups. In this group, differentially expressed genes (DEG) were highly enriched for an immune response and mapped into activation of PI3K-AKT and MAPK signaling pathways. Through integration of DEG and differentially methylated regions, kinase MAP3K8, which is involved in T-cell receptor signaling, was found to be upregulated, while BAI1, a factor that inhibits angiogenesis, was silenced. CIBERSORT showed that a higher infiltration of the immune repertoire, which included M2 macrophages and regulatory T-cells, contributed to an immunosuppressive tumor microenvironment. Conclusion: Looking at the results collectively, the “PD-L1-high-RR group” could potentially benefit from radiotherapy combined with PD-1/PD-L1 blockade and angiogenesis inhibition.

Citation Format: Inah Kim, Bum Sup Jang. A Radiosensitivity gene signature and PD-L1 status predict clinical outcome of patients with glioblastoma multiforme in The Cancer Genome Atlas Dataset [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 B168.
Abstract B171: Elucidating the mechanism of RAG tracking and its impacts on V(D)J recombination
Authors: Lee Cheng-Sheng , Hu Jiazhi , Alt Frederick W.
Published: February 2019

RAG endonuclease initiates V(D)J recombination by binding to the recombination signal sequences (RSSs), introducing DNA breaks between two V(D)J gene segments, and mediating their joining. This process is tightly regulated to generate diverse antigen receptor repertoires and prevent aberrant events that could cause genomic translocations/deletions and lymphoid cancer. RAG can track directionally over chromosomal loop domain in which they reside. Tracking is evidenced by cleavage/joining of short cryptic RSSs lying exclusively in convergent orientation to a bona fide RSS. However, the mechanism of RAG tracking and its impacts remain unknown. Here I established an unbiased assay system by utilizing allele-specific barcode and employing high throughput genome-wide translocation sequencing (HTGTS) to quantitatively evaluate RAG-mediated recombination frequency. I found that insertion of one single bona fide RSS is sufficient to initiate RAG tracking in the c-Myc domain and the recombination between the RSS and its cryptic RSSs seems to follow the 12/23 rule to some degree. When ectopically inserted bona fide RSS pair is 0.5kb apart, convergent configuration of the RSS pair is 4.8-fold more frequent than the tandem configuration. When the distance increases to 267kb, the difference increases to 14-fold, suggesting the contribution of RAG tracking over diffusion-based mechanism increases when the distance between RSS pair increases. In addition, the presence of CTCF-binding element promotes recombination by more than 10-fold. Depletion of Wapl, cohesin remover, to disrupt cohesin turnover reduces V(D)J recombination. The distal RSSs are much preferentially affected. The data suggest that RAG tracking may be driven by cohesin sliding along chromatin.

Citation Format: Cheng-Sheng Lee, Jiazhi Hu, Frederick W. Alt. Elucidating the mechanism of RAG tracking and its impacts on V(D)J recombination [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 B171.
Abstract B172: Molecular mechanisms of dual-specificity phosphatase 22 (DUSP22) in suppression of tumorigenesis: The potential involvement of the EGFR/PD-L1 axis
Authors: Lin Wen-Jye , Chang Cheng-Wei , Lin Hsiu-Ping , Ho Hui-Min
Published: February 2019

DUSP22, belonging to members of the dual-specificity phosphatases (DUSPs) family, can control the activity of various protein kinases and transcription factors through the dephosphorylation process. Many DUSP22-targeted proteins are involved in signaling pathways that are crucial for tumorigenesis, and inflammation. Genetic alteration of DUSP22 or DUSP22 downregulation was observed in some cancers. However, little is known about the roles of DUSP22 during tumor suppression. Here, utilizing TGCA databases, our analysis showed low DUSP22 expression is associated with shorter disease-free survival of lung and prostate cancer patients. The IL-6/STAT3 and EGFR/ERK1/2 axes are generally recognized as an important oncogenic and mitogenic pathway in prostate cancer. We found that DUSP22 expression markedly reduced p-STAT3 (Tyr705), and p-EGFR (Tyr1068)/p-ERK1/2 expression levels after IL-6 and EGF stimulation, respectively, in prostate cancer cells. Similarly, DUSP22 can inhibit the EGFR/ERK1/2 axis in lung cancer cells that harbor EGFR exon 19 deletion mutation, supporting a repressive role for DUSP22 in regulating growth receptor signaling pathways. In addition, we found the exogenous expression of DUSP22 significantly reduced the cell growth of prostate and lung cancer cells. More importantly, DUSP22 can serve as a negative regulator of androgen receptor in prostate cancer cells through reducing EGF-induced AR phosphorylation and inhibiting DHT-mediated nuclear AR translocation. Taken together, our current data indicate that loss of DUSP22 function or DUSP22 downregulation may accelerate lung and prostate tumorigenesis through EGFR-dependent pathways. Importantly, it has been reported that increased PD-L1 expression by EGFR activation mediates the immune escape in EGFR-driven lung cancer (NSCLC). We found that the inhibition of the EGFR signaling by DUSP22 can reduce PD-L1 expression in both lung and prostate cancer cells, suggesting that loss of DUSP22 function in cancer cells may not only enhance cell growth, but also potentially repress antitumor immunity through upregulation of PD-L1. Our findings implicate that anti-PD1/PD-L1 therapy could be a potential option if lung or prostate cancer patients are found with low DUSP22 expression. Currently, we are using multiple approaches to elucidate molecular mechanisms of DUSP22 ablation for accelerating lung and prostate tumorigenesis in vivo.

Citation Format: Wen-Jye Lin, Cheng-Wei Chang, Hsiu-Ping Lin, Hui-Min Ho. Molecular mechanisms of dual-specificity phosphatase 22 (DUSP22) in suppression of tumorigenesis: The potential involvement of the EGFR/PD-L1 axis [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 B172.
Abstract B181: Adenovirus, Semliki Forest virus and vaccinia virus-induced immunogenic cell death augments oncolytic virus immunotherapy
Authors: Ramachandran Mohanraj , Essand Magnus
Published: February 2019

Oncolytic viruses represent new immunotherapy agents with therapeutic effects consisting of direct oncolysis of cancer cells and anticancer immune responses induced upon oncolysis. However, the exact pathways of cell death and the subsequent immune response initiations after oncolysis are not fully elucidated. We have examined the cell death pathways and immune-stimulatory pathways involved in adenovirus (Ad), Semliki Forest virus (SFV) and vaccinia virus (VV) infection. The three viruses activate distinct but different pathways but all of them induced immunogenic cell death (ICD), which is depicted by elevated cell surface exposure of calreticulin (CRT) and extracellular secretion of ATP. Oncolysis-mediated ICD grants dying cells to be phagocytosed and it promotes DC maturation and activation with a Th1-polarized cytokine secretion profile. As a proof of concept, we validated that when DCs are incubated with Ad- or SFV-, but not VV-infected tumor cells expressing a surrogate antigen (CMVpp65), they can efficiently process and cross-present peptides of this antigen to CD8+ T-cells, as shown by specific IFN-γ production. Mice immunized with SFV- or VV-infected murine glioblastoma cells (GL261) elicit a strong and specific T-cell response against GL261. This adaptive immune response can control tumor growth and prolong mice survival after GL261 rechallenge.

Citation Format: Mohanraj Ramachandran, Magnus Essand. Adenovirus, Semliki Forest virus and vaccinia virus-induced immunogenic cell death augments oncolytic virus 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 B181.
Abstract B186: Tumor cell-derived proteases contribute to antigen processing and enhance cross-presentation
Authors: Shields Nicholas J. , Young Katie A. , Jackson Christopher , Young Sarah L.
Published: February 2019

Tumor lysates (TLs) offer a source of both undefined tumor antigens and endogenous adjuvants, called danger-associated molecular patterns (DAMPs), to induce antitumor immune responses. TLs can therefore serve clinical applications for immunotherapy, including vaccination and as a platform for the expansion for tumor-specific T-cells for use in adoptive cell therapy. TL-based approaches offer the advantage of inducing antitumor immunity without the need to identify specific tumor antigens, a major challenge limiting the clinical application of immunotherapies for solid tumors. Immunogenic cell death (ICD) in tumor cells has proven crucial for the generation of robust antitumor immune responses, suggesting that the induction of ICD may improve the efficacy of TL-based immunotherapies. Here, we examined the immunogenicity of TLs prepared from tumor cells exposed to increasing levels of heat (37°C, 42°C and 56°C), using the MC38-OVA/OT-I system. Molecular correlates of ICD were assessed during the course of heat-treatment and in TL preparations. Notably, lethal heat-treatment (56°C) induced primary necrosis with concomitant caspase activation, calreticulin exposure, HMGB1 release and HSP upregulation. All TLs promoted maturation of bone marrow-derived dendritic cells (BMDC), as evidenced by CD80 and CD86 upregulation, and elicited protective antitumor immunity in vaccinated mice. However, only TLs prepared from lethal heat-treated tumor cells promoted cross-presentation in BMDC to elicit antigen-specific T-cell activation ex vivo. Marked proteolytic activity was observed in lethal heat-treated tumor cells, which were capable of processing antigen and binding resultant peptides. Interestingly, inhibition of broad protease activity in lethal heat-treated TLs markedly reduced cross-presentation. Selective inhibition of calpains, but not caspases, cathepsins or the proteasome, reduced antigen processing by heat-killed tumor cells.Together, this demonstrates that tumor-derived proteases can contribute to antigen processing and enhance cross-presentation. Our data suggest that in addition to DAMP release, antigenic processing by proteases in dying tumor cells can influence the immunogenicity of cell death.

Citation Format: Nicholas J. Shields, Katie A. Young, Christopher Jackson, Sarah L. Young. Tumor cell-derived proteases contribute to antigen processing and enhance cross-presentation [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 B186.
Abstract B195: Chemical probes for exploring muropeptide-pattern recognition receptor interactions in cells
Authors: Wang Yen-Chih
Published: February 2019

Peptidoglycan fragments from the bacterial cell wall activate innate immune signaling pathways and limits infections in animals. Indeed, recent studies from the Hang and Mucida laboratories have shown that E. faecium secreted peptidoglycan hydrolase (SagA) generates smaller peptidoglycan fragments, muropeptides, which can enhance host epithelial barrier integrity and enteric pathogen tolerance. However, the direct biochemical interactions of muropeptides with their proposed pattern recognition receptors have been challenging to characterize. Here, I report the chemical synthesis of photoaffinity probes for the analysis of muropeptide-pattern recognition receptor interactions in cells. These studies reveal direct biochemical interactions of muropeptide with pattern recognition receptors and other potential cofactors in mammalian cells. Further characterization of muropeptide-pattern recognition receptor and cofactor complexes will be important for elucidating fundamental mechanisms of innate immunity and inflammation-associated diseases and cancer.

Citation Format: Yen-Chih Wang. Chemical probes for exploring muropeptide-pattern recognition receptor interactions in 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 B195.
Abstract IA14: Cell transfer immunotherapy targeting unique somatic mutations in cancer
Authors: Rosenberg Steven A.
Published: February 2019

Adoptive cell transfer (ACT) immunotherapy using T lymphocytes with antitumor activity is a living therapy that can be highly effective in patients with a variety of metastatic cancers. Naturally occurring tumor infiltrating lymphocytes (TIL) expanded in vitro and administered following a lymphodepleting preparative regimen mediated objective regression of metastatic melanoma in 55% of 194 patients including complete regressions in 24% of patients who remain ongoing disease-free 3 to 10 years later. To determine the antigens recognized by TIL we developed an approach based on deep exomic sequencing of the cancer and immunologic testing of TIL or peripheral lymphocytes to generate T-cells that recognized immunogenic mutations. TIL from 22 patients with metastatic melanoma recognized 54 random somatic mutations none of which were shared among different melanomas. We next extended these studies to patients with common epithelial cancers and showed that 81 of 99 (82%) patients with a variety human cancer types including esophageal, colorectal, bile duct, gastric, pancreatic, ovarian, cervical and lung cancer contained T-cells that recognized 197 neoantigens all of which were unique except for KRAS (2 patients). Targeting unique cancer mutations has extended the reach of ACT immunotherapy and was used to mediate objective regressions in selected patients with chemorefractory metastatic cancers of the bile duct, colon, cervix, and breast. In addition to the use of naturally occurring mutation-reactive cells, we have genetically engineered autologous lymphocytes to express shared antitumor T- cell receptors (TCR) or chimeric antigen receptors (CAR) for use in ACT immunotherapy that can mediate durable cancer regressions in heavily pretreated patients with refractory lymphomas, sarcomas and melanoma. Autologous T- cells can be used to provide a highly personalized immunotherapy for cancer patients refractory to conventional cancer treatments.

Citation Format: Steven A. Rosenberg. Cell transfer immunotherapy targeting unique somatic mutations in 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 IA14.
Abstract IA31: Measuring the emergence of non-self in tumors
Authors: Luksza Marta , Solovyov Alexander , Vabret Nicolas , Balachandran Vinod , Riaz Nadeem , Makarov Vladimir , Hellmann Matthew D. , Snyder Alexandra , Funt Samuel , Remark Romain , Merad Miriam , Gnjatic Sacha , Bajorin Dean F. , Rosenberg Jonathan , Leach Steven , Levine Arnold J. , Chan Timothy A. , Bhardwaj Nina , Wolchock Jedd , Greenbaum Benjamin D.
Published: February 2019

Molecules generated by mutational and epigenetic processes in tumors have been associated with recognition of tumors by the innate and adaptive immune system. For example, neoantigens have been implicated in response to checkpoint blockade therapies. Likewise, the display of pathogen-associated patterns by nucleic acids unsilenced by epigenetic alterations have been implicated in activation of the innate immune system. Here we determine molecular features which place a tumor at a selective advantage or disadvantage, and how these selective pressures depend on the tumor’s environment. We have proposed general frameworks to address these questions. In the case of tumor neoantigens, we present a fitness model of candidate immunogenic neoantigens distributed across a tumor’s subclonal structure in a given microenvironment. We show how our approach can be used to characterize response to checkpoint-blockade therapies and apply it to the general problem of immune-driven tumor evolution in a unique cohort of long-term survivors of pancreatic cancer. In the case of immunostimulatory RNA, we proposed a method of calculating entropic forces for determining the likelihood of tumoral RNA being recognized as pathogen-associated and characterizing classes of pathogen mimicry.

Citation Format: Marta Luksza, Alexander Solovyov, Nicolas Vabret, Vinod Balachandran, Nadeem Riaz, Vladimir Makarov, Matthew D. Hellmann , Alexandra Snyder, Samuel Funt, Romain Remark, Miriam Merad, Sacha Gnjatic, Dean F. Bajorin, Jonathan Rosenberg, Steven Leach, Arnold J. Levine, Timothy A. Chan, Nina Bhardwaj, Jedd Wolchock, Benjamin D. Greenbaum. Measuring the emergence of non-self in 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 IA31.
Abstract A12: Identification of resistance to immune checkpoint blockade
Authors: Gu Shengqing Stanley Gu , Li Ziyi , Bu Xia , Xing Xiaofang , Freeman Gordon , Brown Myles , Liu Xiaole Shirley
Published: February 2019

Despite its enormous success in treating several types of cancer, including melanoma, lung cancer, renal cancer, bladder cancer, and Hodgkin’s lymphoma, immunotherapy still only induces responses in a subset of patients. Understanding the response and resistance mechanisms are still open questions. Based on the reported heterogeneous response to targeted therapies in multiple cell lines, we hypothesize that significant heterogeneity might also exist regarding the response to immune checkpoint blockade (ICB), which may manifest the mechanisms of response/resistance to ICB. To this end, we applied the ClonTracer barcoding system to assess the heterogeneity of response to anti-PD1 and anti-CTLA4 in CT26 colorectal cancer model. Surprisingly, whereas significant heterogeneity exists in the cell line’s ability to initiate cancer in vivo, ICB treatment did not lead to dramatic clonal enrichment compared to control treatment. Therefore, the tumor microenvironment and/or the epigenetic programs in cancer cells may dictate the response to ICB.

Note: This abstract was not presented at the conference.

Citation Format: Shengqing Stanley Gu Gu, Ziyi Li, Xia Bu, Xiaofang Xing, Gordon Freeman, Myles Brown, Xiaole Shirley Liu. Identification of resistance to immune checkpoint blockade [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 A12.
Abstract A73: Optogenetic regulation of T cell metabolism in the tumor microenvironment
Authors: Amitrano Andrea , Walling Brandon , Kim Kyun Do , Berry Brandon , Trewin Adam , Wojtovich Andrew , Kim Minsoo
Published: February 2019

The tumor microenvironment presents significant metabolic challenges to T cells by depleting oxygen and glucose, as well as limiting the uptake of key nutrients. Therefore, T cells and tumor cells engage in fierce metabolic competition, as the demand for both oxygen and glucose in the niche is extremely high. The transition from a resting naïve T cell into an activated and highly proliferative effector T cell requires substantial metabolic reprogramming from relying primarily on oxidative phosphorylation (OxPhos) to the rapid induction of aerobic glycolysis. However, evidence suggests that tumor infiltrating CD8+ T cells show defects in glycolytic functions. In addition, our data indicates that actively migrating effector CD8+ T cells have greater levels of OxPhos activity than stationary cells, imposing an increasing demand for oxygen during T cell migration to the tumor site. To overcome the glycolytic deficiency of the tumor-targeting T cells and boost anti-tumor effector functions at the tumor microenvironment, we developed a genetically encoded light-activated proton pump (fungal proton pump, “Mac”), namely photoactivatable OxPhos (PA-OxPhos) that is expressed in the inner mitochondrial membrane. During OxPhos, electrons enter the electron transport chain (ETC), causing protons to be pumped across the inner mitochondrial membrane to establish a proton gradient. The gradient is then used to generate ATP through complex V (CxV). Therefore, the outward proton pumping through the inner mitochondrial membrane by light stimulation of PA-OxPhos mimics the ETC function and boosts ATP generation in T cells, even in the presence of low levels of oxygen and substrates, giving T cells a metabolic competitive advantage in the tumor microenvironment. PA-OxPhos is tagged with GFP and is expressed in the mitochondria of transfected 293T cells and in activated mouse CD8+ T cells. When cells were treated with Rotenone (an inhibitor of complex I of the ETC), ATP production was decreased after 90 minutes. Importantly, light stimulation of 293T cells expressing PA-OxPhos successfully increased ATP production even in the presence of Rotenone. Our data suggests that PA-OxPhos can remotely provide a competitive metabolic advantage and boost T cell functions in the tumor microenvironment. The utilization of an alternative mechanism for ATP production in T cells could potentially dissipate the failures of T-cell-based cancer immunotherapies in destroying malignant cells of solid tumors.

Citation Format: Andrea Amitrano, Brandon Walling, Kyun Do Kim, Brandon Berry, Adam Trewin, Andrew Wojtovich, Minsoo Kim. Optogenetic regulation of T cell metabolism in the tumor microenvironment [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 A73.
Abstract B24: Digital signatures of T cell dysfunction predict immunotherapy response
Authors: Jiang Peng
Published: February 2019

Despite success in treating several cancer types, immunotherapy only shows response in a subset of patients. Predicting immunotherapy response and understanding the resistance mechanisms are still open questions. We present a computational framework, Tumor Immune Dysfunction and Exclusion (TIDE), which utilizes the vast amount of public clinical datasets to identify biomarkers of immunotherapy response. TIDE utilized the interaction test in multivariate model to identify the molecular features of tumors where high CD8 T cell infiltration does not associate with survival benefits. The top scored genes are enriched with drivers of T cell dysfunction identified by shRNA screen in mouse models, markers of T cell exhaustion in irreversible state, and reversely correlated with transcriptome profiles of cell types that drives T cell exclusion in tumors. The TIDE signatures from clinical data without immunotherapies can reliably predict the response to both anti-PD1 and anti-CTLA4 therapies in melanoma using pretreatment tumor profiles, with higher accuracy than mutation load, PDL1 expression level, and other biomarkers.

Citation Format: Peng Jiang. Digital signatures of T cell dysfunction predict immunotherapy response [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 B24.
Abstract B29: Multiplex three-dimensional optical mapping of tumor immune microenvironment
Authors: Lee Steve Seung-Young , Bindokas Vytautas , Kron Stephen
Published: February 2019

Recent advances in optical tissue clearing and microscopic imaging have facilitated three-dimensional (3D) visualization of large tissues and whole organs at a high resolution. However, to expand its applications to oncology, current challenges such as slow and complicated tissue clearing and uneven immunostaining must be addressed. Here we describe transparent tissue tomography (T3), a tool for rapid, three-dimensional, multiplex immunofluorescence tumor imaging. Cutting tumors into 400 μm macrosections enables simple and rapid immunofluorescence staining, optical clearing, and confocal microscope imaging. Registering and fusing macrosection images yields high resolution 3D maps of multiple tumor microenvironment components and biomarkers throughout a tumor. The 3D maps can be quantitatively evaluated by automated image analysis. As an application of T3, 3D mapping and analysis revealed a heterogeneous programmed death-ligand 1 (PD-L1) distribution in transgenic mouse mammary tumors, with high expression limited to Her2+ tumor cells at the periphery and to CD31+ vascular endothelium in the core. Also, strong spatial correlation between CD45+ immune cell distribution and PD-L1 expression at the tumor margin was determined by T3 analysis of the whole tumors. We also evaluate anti-tumor immune responses after PD-L1 blockade therapy using T3. We observe broad distribution of tumor infiltrating CD3+CD8+ cytotoxic T cells in 3D tumor section following combination therapy of radiation and anti-PD-L1 antibody compared to PBS, anti-PD-L1 antibody alone, or radiation alone treatment group. Moreover, we apply T3 to immunolocalization of cytotoxic lymphocytes in whole core needle biopsies obtained from mouse mammary tumors and human head & neck tumors. We spatially and quantitatively map granzymeB-producing CD3+CD8+ cytotoxic T cells and CD49b+CD31+ natural killer cells in pre-treatment and in-treatment core needle biopsies at cellular resolution and in three dimensions. Meanwhile, T3 analysis is nondestructive, allowing secondary analysis by chromogenic immunohistochemistry (IHC). We anticipate that T3 can be applied broadly to facilitate preclinical studies of tumor immunology and immunotherapy and also find use in spatial, multiparameter analysis of patient biopsies, particularly to improve predictive testing and analysis of immune responses to tumor immunotherapy.

Citation Format: Steve Seung-Young Lee, Vytautas Bindokas, Stephen Kron. Multiplex three-dimensional optical mapping of tumor immune microenvironment [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 B29.
Abstract B35: Class IIa HDAC inhibition promotes an antitumor macrophage phenotype that induces breast tumor regression and inhibits metastasis
Authors: Guerriero Jennifer L. , Sotayo Alaba , Ponichtera Holly E. , Castrillon Jessica A. , Pourzia Alexandra L. , Schad Sara , Johnson Shawn F. , Carrasco Ruben D. , Lazo Susan B. , Bronson Roderick T. , Davis Scott P. , Lobera Mercedes X. , Nolan Michael A. , Letai Anthony
Published: February 2019

Tumor macrophages generally promote tumorigenesis and are associated with increased vascular density, resistance to chemotherapy and a worse clinical outcome in the majority of human tumors. Therefore, significant pharmaceutical effort has focused on inhibiting the immunosuppressive effects of tumor macrophages by depleting or inhibiting them. However, macrophage types also exist that can promote tumor clearance. Shifting tumor macrophages to an anti-tumor phenotype offers great hope given their plasticity and high numbers in a variety of solid tumors. We recently reported that a novel, first in class, specific class IIa HDAC inhibitor, TMP195, significantly alters the gene expression signature of human monocytes and promotes their polarization to an anti-tumor phenotype in vitro. Here, we demonstrate that a first in class, class IIa histone deacetylase (HDAC) inhibitor, TMP195, can activate tumor macrophages in vivo to induce tumor regression and inhibit pulmonary metastases in a mouse model of breast cancer. We find that TMP195 induces macrophage recruitment and differentiation of highly phagocytic cells within the tumor, which increases tumor cell death while decreasing angiogenesis. Strikingly, we find that TMP195 enhances chemotherapy and immunotherapy to induce durable tumor reduction. These data reveal a novel role for harnessing the anti-tumor potential of macrophages to enhance cancer therapy.

Citation Format: Jennifer L. Guerriero, Alaba Sotayo, Holly E. Ponichtera, Jessica A. Castrillon, Alexandra L. Pourzia, Sara Schad, Shawn F. Johnson, Ruben D. Carrasco, Susan B. Lazo, Roderick T. Bronson, Scott P. Davis, Mercedes X. Lobera, Michael A. Nolan, Anthony Letai. Class IIa HDAC inhibition promotes an antitumor macrophage phenotype that induces breast tumor regression and inhibits metastasis [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 B35.
Abstract B37: Clinical relevance of tumor-infiltrating immune cells in neuroblastoma
Authors: Melaiu Ombretta , Boldrini Renata , Chierici Marco , Furlanello Cesare , Fruci Doriana
Published: February 2019

The presence of tumor-infiltrating T cells is crucial for the development of immunotherapies and the prediction of clinical response for many human cancers. Recently, we have shown that tumor-infiltrating T cells have a prognostic value greater than, and independent of, the criteria currently used to stage neuroblastoma, the most common pediatric extra-cranial solid tumor accounting for 15% of childhood cancer-related death. We demonstrated that expression of PD-L1 in tumor cells is inversely correlated with that of HLA class I, and that when combined they represent a promising prognostic biomarker in neuroblastoma.

To further dissect the immune heterogeneity of neuroblastoma microenviroment, we evaluated the density of infiltrating dendritic cells (iDC), which are crucial for drug-induced anticancer immune response, in the same cohort of NB samples characterized for type, density, and composition of tumor T lymphocytes and expression of tumor PD-L1 and HLA class I. As for T cells, high density of iDCs was correlated with the presence of infiltrating T cells, expression of tumor HLA class I and favorable clinical outcome, suggesting that iDCs may be critical for robust tumor control by improving prediction of patient survival.

Citation Format: Ombretta Melaiu, Renata Boldrini, Marco Chierici, Cesare Furlanello, Doriana Fruci. Clinical relevance of tumor-infiltrating immune cells in neuroblastoma [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 B37.
Abstract B46: Roles for LKB1 at the immune synapse during B-cell activation and antitumor responses
Authors: Jimenez Laura , Waters Lynnea , Kim Diane N.H. , Walsh Nicole , Teitell Michael A.
Published: February 2019

Defense from infection or cancer is provided by coordinated actions of the innate and adaptive immune system, including B lymphocytes that generate antibodies (Abs) against pathogens or tumor antigens. B cells establish immune synapses with antigen-presenting cells during activation to initiate Ab-production, which may include entrance into a germinal center (GC) reaction to generate very high-affinity Abs. Establishment of an immune synapse requires polarity proteins to coordinate uptake and processing of external antigens. For this, there is a highly conserved family of partitioning defective (Par) proteins that mediates cell polarity in multiple cell types. In particular, Par-3, a member of the Par polarity complex (Par-3, aPKC, Par-6), is a key protein that localizes to the immune synapse and is required for B cell polarization and immune synapse formation. Recently, we showed that LKB1, the mammalian homolog of Par-4 and a regulator of energy metabolism, controls B cell activation, GC formation and differentiation into Ab-producing plasma cells. However, roles for LKB1 in B cell polarity, immune synapse formation and anti-tumor immunity are unknown. Based on previous studies showing that LKB1 induces cell polarity and co-localizes with Par-3, we hypothesize that LKB1 is required for Par complex assembly and controls immune synapse formation during B cell activation. Subcellular analysis of LKB1 by immunofluorescence microscopy in mouse primary B cells reveals LKB1 co-localization with aPKC in membrane protrusions required for immune synapse formation. Interestingly, B cell specific LKB1 knock out (BKO) mice exhibit mislocalization of aPKC/Par complex, loss of lymphoid tissue polarity and spontaneous B cell activation that results in the formation of giant GCs and secretion of proinflammatory cytokines and chemokines. Similar inflammatory profiles with T cell chemoattractants are known to recruit CD8+ cytotoxic T lymphocytes (CTLs) into solid tumors, such as melanoma. These similarities suggest that LKB1 inactivated B cells in the tumor microenvironment could stimulate T cell infiltrates into solid tumors. Our studies suggest that physiologic inactivation of LKB1 in B cells controls B cell activation, GC formation and potentially infiltration of T cells in the tumor microenvironment during anti-tumor responses. We are currently utilizing an exciting genetic mouse melanoma model to examine the role of LKB1 in promoting anti-tumor immunity. Together, our studies assess LKB1 as a target for augmenting adaptive immunity against cancer.

Citation Format: Laura Jimenez, Lynnea Waters, Diane N.H. Kim, Nicole Walsh, Michael A. Teitell. Roles for LKB1 at the immune synapse during B-cell activation and antitumor responses [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 B46.
Abstract B53: Intra-tracheal delivery of low-dose bacterial lipopolysaccharides protects against tumor formation in the KP lung adenocarcinoma model
Authors: Sriram Ganapathy , Milling Lauren , Irvine Darrell J. , Yaffe Michael B.
Published: February 2019

While genetically engineered mouse models (GEMM) of lung adenocarcinoma (LUAD) recapitulate some aspects of the histopathology of human LUAD, they poorly reflect the inflammatory components of human LUAD. In this study, we performed repeated weekly intra-tracheal dosing with bacterial lipopolysaccharides (LPS) after adenoviral-Cre (AdCre) delivery into K-RasLSL-G12D/+; p53fl/fl mice to examine the effect of inflammation on lung adenocarcinoma progression. LPS has been historically used to study the acute inflammatory response both locally and systemically in animal models. The typical response involves recruitment and activation of innate immune cells, mainly neutrophils and macrophages, to the site of delivery and/or production of pro-inflammatory cytokines including TNF-alpha, IL-6 and IL-1. Repeated long-term conditioning with low-dose LPS results in alveolar wall thickening as observed by uCT and the accumulation of lymphoid aggregates in the lung. However, surprisingly, LPS conditioning drastically reduced tumor incidence from 75% in the control group to 25%. Furthermore, starting LPS delivery four weeks after AdCre instillation, to eliminate any possible LPS effects on adenoviral delivery and K-Ras induction/p53 loss, still resulted in drastically reduced lung tumor formation suggesting that the effect results from an LPS-induced immune response. Two LPS instillations were sufficient to elicit this effect. Short-term antibody-mediated depletion of neutrophils or CD8+ T cells also did not abrogate the effect of LPS on tumor formation. In vitro re-stimulation of CD8+T cells (from blood or spleen) from tumor-free animals with KP tumor cells did not elicit interferon-gamma production, as assayed by intra-cellular cytokine staining and ELISPOT, suggesting that a cell type other than CD8+ T-cells or neutrophils mediates the effect. Interestingly and consistent with the inhibitory effect of LPS on tumor formation, multiple pneumonia diagnoses in COPD patients/smokers has been associated with a lower odds ratio of developing lung cancer in humans. Identifying the cell-type (s) and mechanisms mediating the anti-tumor effect of LPS will help in defining the aspects of immune response that inhibit LUAD progression.

Citation Format: Ganapathy Sriram, Lauren Milling, Darrell J. Irvine, Michael B. Yaffe. Intra-tracheal delivery of low-dose bacterial lipopolysaccharides protects against tumor formation in the KP lung adenocarcinoma model [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 B53.