bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract IA02: The role of aneuploidy during tumorigenesis
Authors: Davoli Teresa
Published: February 2019

Since Boveri’s postulates in 1914, aneuploidy has been recognized as a hallmark of human cancer; however, no comprehensive theory exists to explain its patterns and its role in tumor evolution. We have developed Tumor Suppressor and Oncogene (TUSON) Explorer, a computational method for the prediction of tumor suppressor genes (TSG) and oncogenes (OG) through the analysis of the pattern of somatic mutations in cancer. By integrating our prediction of TSGs and OGs with information of copy number alterations, we found that the distribution on chromosomes and the potency of TSGs and OGs can predict the frequency of arm-level and chromosome-level deletions and amplification (Davoli et al., 2013). We propose that it is the decrease or increase in the gene dosage of TSG and OG genes in deletion and amplification to determine the recurrent patterns of aneuploidy selected during tumor evolution. More recently, we have performed gene expression analysis on tumor samples, comparing tumors with different levels of aneuploidy (Davoli et al., 2017). We have found that tumors with high levels of aneuploidy show increased markers of proliferation as well as a strong decrease in infiltrating immune cells, especially CD8+ T cells. Notably, we show that aneuploidy predicts patients’ survival in two clinical trails of immunotherapy in cancer patients. Compared to neoantigen load, aneuploidy represents an independent and stronger predictor of survival. A combined score including aneuploidy and neoantigen load allows superior prediction of survival after immunotherapy. We are now investigating the mechanism by which aneuploidy affects cancer immune evasion. I will present novel data suggesting that aneuploidy may play a role in inhibiting and dysregulating antigen processing and presentation in tumor cells. Overall, our data indicate that aneuploidy is a driver event in human tumorigenesis.

Citation Format: Teresa Davo4li. The role of aneuploidy during tumorigenesis [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA02.
Abstract IA05: Early steps in lung oncogenesis
Authors: Janes Samuel M.
Published: February 2019

Lung cancer is the biggest cancer killer of men and women, and there has been no improvement in survival over the last 50 years. To reduce the mortality of lung cancer, we need to both detect and treat it earlier, ideally at a preinvasive cancer stage before progression into full-blown invasive cancer. This would allow us to initiate treatment in a timely manner, increasing the chances of cure and saving lives. Lung cancers arise from preinvasive lesions but, interestingly, not all these lesions progress to cancer. We believe that understanding the differences between the lesions that progress to invasive cancer and those that disappear will direct us to the key proteins and genes that are mis-expressed, or inappropriately switched on or off, that lead to invasive cancer formation. My talk will outline studies that shed new understanding on how lung cancer develops and identify novel biological markers that accurately predict whether a lesion will eventually grow into a cancer. This, I hope, will enable targeting potential therapies to those patients with lesions that are likely to progress and identify the key genes and proteins associated with cancer development, thereby opening the possibility of developing chemoprophylactic therapeutic approaches to prohibit cancer development.

Citation Format: Samuel M. Janes. Early steps in lung oncogenesis [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA05.
Abstract IA07: Influence of cancer initiation on tumor progression in SCLC
Authors: Yang Dian , Winslow Monte M. , Sage Julien
Published: February 2019

The vast majority of cancer patients die from metastatic disease, but the molecular and cellular mechanisms that drive metastatic progression often remain poorly understood. Small cell lung cancer (SCLC) is a neuroendocrine form of lung cancer and one of the most metastatic and lethal cancers. Most SCLC patients are usually first diagnosed when they already have metastatic disease, and SCLC tumors are thus thought to acquire metastatic ability early in the course of tumor development. However, how early events shape the evolution and metastatic progression of SCLC is largely unknown. We will present evidence, using genetically engineered mouse models of SCLC, that distinct mechanisms drive metastatic progression depending on the cell of origin. In one mouse model, we found that tumors gain metastatic ability through amplification of the transcription factor Nfib; this amplification is accompanied by a striking opening of the chromatin at many sites in the genome. In the second model, metastatic progression is not associated with Nfib-driven chromatin alterations. Gene expression profiling studies reveal distinct mechanisms of metastatic progression in the two groups, as well as markers predictive of the two metastatic paths. Our data indicate that Nfib-independent metastases arise from pulmonary neuroendocrine cells. These observations demonstrate that the identity of tumor-initiating cells can determine the molecular mechanisms of tumor evolution.

Citation Format: Dian Yang, Monte M. Winslow, Julien Sage. Influence of cancer initiation on tumor progression in SCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA07.
Abstract IA18: Evolution of acquired resistance in EGFR mutant NSCLC
Authors: Hata Aaron N.
Published: February 2019

Lung cancers harboring activating EGFR mutations are exquisitely sensitive to EGFR tyrosine kinase inhibitors; however, acquired drug resistance inevitably develops. Although genetic mechanisms of acquired resistance have been well characterized, less is known about how resistant clones evolve during treatment. Emerging data are beginning to illuminate the complex interplay of genetic clonal heterogeneity, adaptive signaling changes, epigenetic plasticity, and microenvironment factors that shapes the evolution of acquired resistance. Novel therapeutic strategies that specifically target these processes may prevent or delay the development of drug resistance.

Citation Format: Aaron N. Hata. Evolution of acquired resistance in EGFR mutant NSCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA18.
Abstract IA20: Immunotherapy: Biomarkers and checkpoint blockade in NSCLC
Authors: Carbone David P. , Sharpnack Michael , He Kai
Published: February 2019

Immunotherapy approaches targeting the PD-1 pathway have shown some clinical benefits in a fraction of patients with lung cancer, but expression of PD-L1 has proved to be an imperfect biomarker of efficacy. Recent studies have shown that tumor mutation burden (TMB) is also correlated with outcome and that it appears to be independent of PD-L1. TMB, however, only indirectly measures the number of neoantigenic peptides presented on tumor cell surface class I MHC, and predicted MHC matches may be an even better predictor of benefit. In addition, mutations in genes such as LKB1 may modulate the immune response, and mutations in the antigen presentation pathway may block it altogether. Mutations in DNA repair pathway genes may increase the number of potential neoantigens. Analysis of non-PD-1 pathway immunomodulators, immune cell infiltration, microenvironmental and microbiomic context, together with in-depth analysis of tumor somatic genomics, could lead to better patient selection for immunotherapy.

Citation Format: David P. Carbone, Michael Sharpnack, Kai He. Immunotherapy: Biomarkers and checkpoint blockade in NSCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA20.
Abstract IA23: Allele-specific HLA loss and immune escape in lung cancer evolution
Authors: McGranahan Nicholas , Rosenthal Rachel , Hiley Crispin T. , Rowan Andrew J. , Watkins Thomas B.K. , Wilson Gareth A. , Birkbak Nicolai J. , Veeriah Selvaraju , Loo Peter Van , Herrero Javier , Swanton Charles
Published: February 2019

In order to avoid immune predation, particularly in response to immunotherapy, tumors must acquire mechanisms to evade immune detection or withstand its activity. Disruption of human leukocyte antigen (HLA), which may lead to reduced neoantigen presentation, has been proposed as an immune escape strategy in many cancers, including lung cancer. A high proportion of cancer types have been found to downregulate HLA expression, potentially leading to the evasion of T cell-mediated destruction (Hicklin, 1999; Garrido, 2017) with reduced HLA expression associating with decreased overall survival and tumor progression (Mehta, 2008). Another irreversible means of HLA disruption is via loss of heterozygosity (LOH) at the HLA locus (Koopman, 2000). However, to date, the diversity of the HLA locus has impeded copy number analysis and determination of HLA loss. To investigate the prevalence, timing, and importance of HLA disruption, we developed LOHHLA (Loss Of Heterozygosity in Human Leukocyte Antigen), a computational tool to determine HLA allele-specific copy number from sequencing data. Supporting the notion that loss of antigen presentation may play an important role in immune evasion during tumor evolution, HLA LOH was identified in 40% of the NSCLC samples analyzed, frequently as a late event in tumor evolution and associated with a high subclonal neoantigen burden, increase in immune infiltration, and PD-L1 positivity. Characterizing HLA haplotype specific copy number with LOHHLA refines neoantigen prediction and may have implications for immunotherapeutic approaches targeting neoantigens.

Citation Format: Nicholas McGranahan, Rachel Rosenthal, Crispin T. Hiley, Andrew J. Rowan, Thomas B.K. Watkins, Gareth A. Wilson, Nicolai J. Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero, Charles Swanton. Allele-specific HLA loss and immune escape in lung cancer evolution [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA23.
Abstract IA27: MYC drives molecular and therapeutically distinct subtype of SCLC
Authors: Mollaoglu Gurkan , Guthrie Matthew R. , Bohm Stefanie , Bragelmann Johannes , Chalishazar Milind D. , Ireland Abbie S. , Huang Fang , Hu Zeping , Cardnell Robert J. , Sen Triparna , Gertz Jason , Johnson Jane E. , Gazdar Adi F. , Byers Lauren A. , DeBerardinis Ralph J. , Wechsler-Reya Robert J. , Sos Martin , Oliver Trudy G.
Published: February 2019

Small cell lung cancer (SCLC) has largely been treated in the clinic as a homogeneous disease for the last 40 years. However, it is become increasingly appreciated that SCLC exhibits both intra- and intertumoral heterogeneity. Genetic loss of the tumor suppressors RB1 and TP53 is nearly universal in SCLC, while amplifications in MYC family members including C-, L-, and N-MYC are mutually exclusive. Using genetically engineered mouse models (GEMMs), we show that MycT58A expression cooperates with Rb1 and Trp53 loss in the mouse lung to promote aggressive, highly metastatic tumors that are initially sensitive to chemotherapy followed by relapse, similar to human SCLC. Importantly, MYC drives a neuroendocrine-low ‘‘variant’’ subset of SCLC with low ASCL1 and high NEUROD1 expression corresponding to transcriptional profiles of human SCLC. The MYC-driven subset of SCLC is also low for other clinically relevant biomarkers such as TTF1/NKX2.1 and DLL3. Targeted drug screening reveals that SCLC with high MYC expression is vulnerable to Aurora kinase inhibition, which, combined with chemotherapy, strongly suppresses tumor progression and increases survival. These findings are consistent with the results of recent clinical trials in patients with relapsed SCLC who received paclitaxel with or without the AURKA inhibitor alisertib. Furthermore, recent preclinical studies demonstrate that the MYC-driven subset of SCLC is preferentially sensitive to CHK1 inhibition and other metabolic targets compared to MYCL-driven SCLC. These data identify molecular features for patient stratification and uncover potential targeted treatment approaches for MYC-driven SCLC.

Citation Format: Gurkan Mollaoglu, Matthew R. Guthrie, Stefanie Bohm, Johannes Bragelmann, Milind D. Chalishazar, Abbie S. Ireland, Fang Huang, Zeping Hu, Robert J. Cardnell, Triparna Sen, Jason Gertz, Jane E. Johnson, Adi F. Gazdar, Lauren A. Byers, Ralph J. DeBerardinis, Robert J. Wechsler-Reya, Martin Sos, Trudy G. Oliver. MYC drives molecular and therapeutically distinct subtype of SCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA27.
Abstract IA38: Progress and unanswered questions in EGFR mutation-positive lung cancer
Authors: Sequist Lecia V.
Published: February 2019

A summary of the major advances in management of EGFR mutation-positive lung cancer will be provided, along with a discussion of missing pieces of information that could improve the care of patients.

Citation Format: Lecia V. Sequist. Progress and unanswered questions in EGFR mutation-positive lung cancer [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA38.
Abstract PR09: Alterations in cell junctions and neuroendocrine differentiation are key early steps in Crebbp/Ep300 mutation-driven SCLC development
Authors: Kim Dong-Wook , Kim Keebeom , Dunn Colin T. , Park Kwon-Sik
Published: February 2019

The abundance and heterogeneity of somatic alterations in small cell lung cancer (SCLC) present immense challenges in identifying key mechanisms of tumor development. Functional characterization of recurrent mutations is an essential step towards understanding the early stages of SCLC development, but this remains extremely difficult due to the scarcity of relevant and tractable models for defining oncogenic drivers and molecular pathways. In a previous study, we derived precancerous cells (preSCs) from the Rb/p53/Rbl2-mutant mouse model of SCLC and developed an engineered preSC-based model of early tumor development. In this model, activation of oncogenic drivers transforms preSCs into tumorigenic cells that form spheroid clusters characteristic of SCLC in culture and subcutaneous tumors in athymic nude mice. Using this streamlined approach, we found that both retroviral amplification of the Myc family members and CRISPR/Cas9-mediated mutation of Crebbp/Ep300 were sufficient to cause transformation of preSCs into SCLC cells. Notably, both sets of mutant preSC underwent a similar phenotypic change from adherent monolayers to spheroid aggregates, suggesting that the two different types of alterations interact with or converge on common molecular pathways. Comparative profiling of control preSCs and mutant preSCs carrying either a Myc family amplification or Crebbp/Ep300 mutation revealed that alterations in cell junctions and neuroendocrine differentiation are the most significant molecular changes during cellular transformation. The transformed preSCs exhibited decreased expression of adhesion-related genes, including Cdh1 and Dsp, but increased expression of mesenchymal genes Vim and Twist1. The transformed cells also showed reduced expression of neuroendocrine (NE) differentiation genes, including Ascl1, Chga, and Syp. Furthermore, these changes coincided with increased expression of Notch receptors and decreased expression of their ligands Dlls and Jags. Taken together, these novel findings suggest that a phenotypic switch from Dll/Jag-expressing NE cells to Notch-expressing non-NE cells is a key event in early SCLC development. This study also demonstrated that the preSC-based model can facilitate functional validation of recurrent mutations in SCLC and molecular pathways that will be further explored for mechanistic elucidation and development of targeted therapies.

This abstract is also being presented as Poster A09.

Citation Format: Dong-Wook Kim, Keebeom Kim, Colin T. Dunn, Kwon-Sik Park. Alterations in cell junctions and neuroendocrine differentiation are key early steps in Crebbp/Ep300 mutation-driven SCLC development [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr PR09.
Abstract PR13: MET copy number gain is associated with gefitinib resistance in leptomeningeal carcinomatosis of EGFR-mutant lung cancer
Authors: Nanjo Shigeki , Arai Sachiko , Wang Wei , Hata Akito , Katakami Nobuyuki , Yano Seiji
Published: February 2019

Leptomeningeal carcinomatosis occurs frequently in EGFR-mutant lung cancer, and develops acquired resistance to EGFR tyrosine kinase inhibitors (EGFR-TKIs). This study aimed to clarify the mechanism of EGFR-TKI resistance in leptomeningeal carcinomatosis and seek a novel therapeutic strategy. We examined EGFR mutations, including the T790M gatekeeper mutation, in 32 re-biopsy specimens from 12 leptomeningeal carcinomatosis and 20 extracranial lesions of EGFR-mutant lung cancer patients who became refractory to EGFR-TKI treatment. All 32 specimens had the same baseline EGFR mutations, but the T790M mutation was less frequent in leptomeningeal carcinomatosis specimens than in extracranial specimens (8% vs. 55%, P < 0.01). To study molecular mechanisms of acquired EGFR-TKI resistance in leptomeningeal carcinomatosis, we utilized our previously developed mouse model of leptomeningeal carcinomatosis with the EGFR-mutant lung cancer cell line PC-9/ffluc cells, in which acquired resistance to gefitinib was induced by continuous oral treatment. Compared with subcutaneously inoculated gefitinib-resistant tumors, the T790M mutation was less frequent in leptomeningeal carcinomatosis that acquired resistance to gefitinib. PC-9/LMC-GR cells were established from the gefitinib-resistant leptomeningeal carcinomatosis model, and they were found to be intermediately resistant to gefitinib and osimertinib (third-generation EGFR-TKI). Although EGFR-T790M was negative, gefitinib resistance of PC-9/LMC-GR cells was related to MET copy number gain with MET activation. Moreover, combined use of EGFR-TKI and crizotinib, a MET inhibitor, dramatically regressed leptomeningeal carcinomatosis with acquired resistance to gefitinib or osimertinib. These findings suggest that combination therapy with MET inhibitors may be promising for controlling leptomeningeal carcinomatosis that acquires resistance to EGFR-TKIs.

This abstract is also being presented as Poster B29.

Citation Format: Shigeki Nanjo, Sachiko Arai, Wei Wang, Akito Hata, Nobuyuki Katakami, Seiji Yano. MET copy number gain is associated with gefitinib resistance in leptomeningeal carcinomatosis of EGFR-mutant lung cancer [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr PR13.
Abstract A014: Phase I clinical trial with PD-1/MUC1 CAR-pNK92 immunotherapy
Authors: Li Qiao , Wang Yi , Lin Ming , Xia Leiming , Bao Yangyi , Sun Xiang , Yang Lin
Published: February 2019

Mucin1 (MUC1) proteins represent a family of high molecular weight trans-membrane glycoproteins that protect epithelial cells and mediate signal transduction by communication with extracellular stimuli. On the other hand, MUC1 has been observed to be overexpressed and glycosylated in adenocarcinoma, making it an ideal molecular target for cancer treatment. MUC1 based antibody and specific chimeric antigen receptors (CARs) modified T/NK cells exhibit strong antibody-dependent or direct-cell cytotoxicity to MUC1 positive tumor cells. However, treatment failure with MUC1-targeted therapy was usually caused by tumor microenvironment (TME)-driven immune suppression. PD-L1 has been identified as a negative checkpoint molecule that promotes immune evasion of tumor cells. The interaction of PD-1 and PD-L1 inhibits the function of tumor-infiltrating lymphocytes (TILs) or infused T/NK cells while activating the negative immune-regulatory cells in TME, such as regulatory T-cells and MDSCs. To overcome these barriers, we engineered clinically applicable NK-92 cells by lentiviral gene transfer to express chimeric antigen receptors comprising an anti-MUC1 scFv antibody fusion protein with CD28-CD137 as a signaling moiety and truncated PD-1 peptide. NK92 cells expressing anti-MUC1 CAR specifically and efficiently lysed MUC1 positive tumor cells in vitro and in vivo. The safety of NK-92 cell administration has been demonstrated by numerous phase I clinical trials. In our study, 13 patients with different kinds of tumors (lung cancer, pancreatic cancer, colon cancer and ovarian cancer) with positive PD-L1 and MUC-1 expression were enrolled. CAR-NK cells were infused (1×109 cells/time) into these patients. Of 13 patients, 3 patients were withdrawn, 9 patients (69.2%) showed stable disease and 1 patient showed progressive disease. The cytokine level and hematologic changes were monitored to evaluate the safety. Severe cytokine storm and/or bone marrow suppression were not observed. From this phase I clinical trial we found that CAR-NK therapy has a broad prospect of application as a new cellular immunotherapy due to its stable clinical efficacy, mild side effects and ease of preparation.

Citation Format: Qiao Li, Yi Wang, Ming Lin, Leiming Xia, Yangyi Bao, Xiang Sun, Lin Yang. Phase I clinical trial with PD-1/MUC1 CAR-pNK92 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 A014.
Abstract A038: Effective rerouting of NK cell cytotoxicity against B-cell malignancies upon TCR gene transfer
Authors: Morton Laura T. , Wouters Anne K. , Remst Dennis F. , Hagedoorn Renate S. , Loenen Marleen M. Van , Boer Renate de , Falkenberg J. H.F. , Heemskerk Mirjam H.M.
Published: February 2019

T-cell receptor (TCR) gene transfer involves ex-vivo introduction of a tumour-reactive TCR into patient-derived CD8 T-cells enabling specific-targeting of tumour cells. Competition for expression with CD3 from the endogenous TCR and the potential for TCR mixed- dimer formation necessitate optimisation of cellular therapeutics with sustained potency and increased safety. NK-cells (CD3-CD56+) are potent short-lived effector cells that lyse abnormal or stressed cells independent of antigen. Efficacy and safety of adoptive NK therapy has been demonstrated in the treatment of hematologic malignancies in both the autologous and allogeneic setting. Here,we aimed to exploit NK-cell cytotoxicity and redirect it toward antigen-specific recognition of tumors without the limitation of TCR mixed- dimer formation and competition for CD3.Firstly, peripheral blood derived NK-cells were expanded and retrovirally transduced to express BOB1-specific TCR, restricted to HLA- B*07:02, in combination with CD3 alongside CD8 co-receptor.BOB1 is a B-cell restricted transcription factor, important for B-cell survival. Purified BOB1-TCR expressing NK-cells demonstrated antigen-specific binding of BOB1-specific pMHC-tetramer and proliferated upon co-culture with HLA-B*07:02 positive B-lymphoblastic cell lines (B-LCL) but not with HLA-B*07:02 negative B-LCL. Furthermore, BOB1-TCR expressing NK-cells demonstrated in vitro cytotoxicity against HLA-B*07:02 positive B-LCL, multiple myeloma and B-ALL cell lines. Conversely, these tumor cell lines remained resistant to NK-cell mediated lysis when co-cultured with mock transduced NK-cells. Finally, NK sensitive cell line K562 was comparably lysed by both BOB1-TCR or mock transduced NK-cells demonstrating retained NK-cell mediated activity.These data demonstrated that NK-cell cytotoxicity can be redirected toward antigen-specific recognition of tumors and is TCR-dependent. Retention of NK-cell function in genetically modified cells allows for a double-hit therapeutic approach that can offer advantages over current cellular approaches.

Citation Format: Laura T. Morton, Anne K. Wouters, Dennis F. Remst, Renate S. Hagedoorn, Marleen M. Van Loenen, Renate de Boer, J. H.F. Falkenberg, Mirjam H.M. Heemskerk. Effective rerouting of NK cell cytotoxicity against B-cell malignancies upon TCR gene transfer [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 A038.
Abstract A098: SLC12A2 as a novel “brake” on immunogenic apoptotic cell clearance
Authors: Perry Justin Shaun Arnold , Morioka Sho , Medina Christopher , Raymond Michael , Ravichandran Kodi
Published: February 2019

Phagocytes face a key challenge during efferocytosis – they must engulf an apoptotic cell, often similar in size, while maintaining their own cell integrity, shape, and volume. Yet little is known about phagocyte volume homeostasis during apoptotic cell clearance. To this end, we performed an unbiased transcriptomics screen designed to reveal alterations of phagocyte gene expression after engulfment of apoptotic Jurkat lymphoma cells and identified several transcriptional programs distinctly modified in engulfing phagocytes. We identified a program involving cell volume regulation and potassium/chloride flux, the latter of which is thought to underlie immunogenic responses. Disruption of one member of this cell volume program, SLC12A2, resulted in “overeating” of apoptotic JurkaT-cells by individual phagocytes and a significant increase in cell size. Importantly, we demonstrate that SLC12A2-deficient phagocytes actively engulfing apoptotic JurkaT-cells led to a downregulation of the hallmark antiinflammatory efferocytosis program and robust upregulation of a proinflammatory program. In particular, we observed robust upregulation of immunogenic programs, including a type I interferon signature, in SLC12A2-deficient engulfing phagocytes that were not observed in phagocytes over-expressing the phosphatidylserine receptor TIM4, Mechanistically, we found that the chloride-sensing kinase WNK1 and downstream kinases OSR1 and SPAK function to regulate chloride flux into engulfing phagocytes via SLC12A2, and that this pathway regulates the apoptotic JurkaT-cell “overeating” observed in SLC12A2-deficient phagocytes. Collectively, these data elucidate a novel mechanism by which phagocytes protect themselves from potentially dangerous apoptotic cell-derived inflammatory ligands and suggest that SLC12A2 serves to actively suppress immunogenic responses by phagocytes and limits the rate of corpse uptake during efferocytosis.

Citation Format: Justin Shaun Arnold Perry, Sho Morioka, Christopher Medina, Michael Raymond, Kodi Ravichandran. SLC12A2 as a novel “brake” on immunogenic apoptotic cell clearance [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 A098.
Abstract A101: IDO2 host genetic status influences progression and radiotherapy response in pancreatic ductal adenocarcinoma
Authors: Prendergast George C. , Nevler Avinoam , Muller Alexander J. , Sutanto-Ward Erika , DuHadaway James B. , Nagatomo Kei , Londin Eric , O'Hayer Kevin , Cozzitorto Joseph A. , Lavu Harish , Yeo Theresa P. , Curtis Mark , Villatoro Tatiana , Leiby Benjamin E. , Winter Jordan M. , Yeo Charles J. , Brody Jonathan R.
Published: February 2019

Sporadic pancreatic ductal adenocarcinoma (PDAC) develops into a lethal disease that has remained refractory to different treatment approaches including recent advances in cancer immunotherapy. Variations in host genetic status affecting the inflammatory microenvironment can impact cancer susceptibility, malignant progression and clinical outcomes. In this study, we present genetic evidence from mouse and human genetic studies supporting a role for IDO2, an immunometabolic modifier of B cell-mediated autoimmune responses, in promoting pancreatic ductal adenocarcinoma (PDAC). In an established transgenic mouse model of KRAS-induced pancreatic cancer, IDO2 genetic inactivation markedly reduced malignant progression. In retrospective clinical analyses of PDAC patients (N=200), the biallelic occurrence of either of two inactivating polymorphisms in the IDO2 coding region trended with favorable disease-free survival. In PDAC tissues, an inactive IDO2 host genotype corresponded with changes in expression of genes involved in tryptophan catabolism and immune modulation, along with a reduced neutrophil to lymphocyte ratio. Notably, subset analysis revealed a striking association of inactive IDO2 status with improved disease-free survival in patients who had received adjuvant radiotherapy, a treatment modality that has been highly debated due to its variable efficacy in patients. Accordingly, our findings suggest that host IDO2 genetic status may offer a simple incisive marker to stratify PDAC patients who stand to gain the most from adjuvant radiotherapy, addressing the long-standing debate of its benefits.

Citation Format: George C. Prendergast, Avinoam Nevler, Alexander J. Muller, Erika Sutanto-Ward, James B. DuHadaway, Kei Nagatomo, Eric Londin, Kevin O'Hayer, Joseph A. Cozzitorto, Harish Lavu, Theresa P. Yeo, Mark Curtis, Tatiana Villatoro, Benjamin E. Leiby, Jordan M. Winter, Charles J. Yeo, Jonathan R. Brody. IDO2 host genetic status influences progression and radiotherapy response in pancreatic ductal adenocarcinoma [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 A101.
Abstract A112: OncoPeptTUME: A novel computational approach analyzes the tumor microenvironment to predict response to checkpoint inhibitors
Authors: Shi Xiaoshan , Manoharan Malini , Mandloi Nitin , Priyadharshini Sushri , Iyer Laxman , Gupta Rohit , Chakraborty Papia , Chaudhuri Amitabha , Gupta Ravi
Published: February 2019

Cancer immunotherapy is now an established treatment option for many cancers. Cancer immunotherapy boosts host antitumor immunity to provide long-term benefit; however, only a small fraction of the treated patients show a durable clinical response. The tumor microenvironment ecosystem, with its complex mixture of non-malignant and malignant cells, is a major contributor in regulating the response to checkpoint blockade and development of resistance. Ongoing efforts to characterize the tumor microenvironment to stratify patients for immunotherapy and find biomarkers of response often use methods that are limited by the availability of adequate tumor tissue from needle biopsy material and loss of tissue viability during sample processing that precludes the use of single-cell sequencing platforms. Therefore, genomic methods that use deconvolution to assess the relative proportion of different cell types and their phenotypes in the tumor microenvironment are desirable for clinical use. To this end, we have developed OncoPeptTUME, a novel computational approach that utilizes a proprietary minimal gene expression signature to assign immune scores for eight broad categories of immune cells present in the tumor microenvironment. To validate the approach, we used 9,640 TCGA gene expression datasets from 33 different tumors, defined their immune cell content, organized samples into clusters based on their immune cell content, and identified the molecular differences that predict survival in samples belonging to different clusters. We further performed a deeper analysis of samples enriched in infiltrating CD8+ T-cells to identify T-cell phenotype that correlated with a long-term survival benefit. A small set of genes associated with functional T-cell phenotype was used on a dataset of melanoma samples to show that higher expression of the genes discriminated responders from the nonresponders to nivolumab treatment. In conclusion, our analysis demonstrates that OncoPeptTUME is a powerful immunogenomic tool to predict patient prognosis, stratify patients who will benefit from cancer immunotherapy and identify pathways and novel biomarkers of long-term benefit from the use of cancer immunotherapy drugs.

Citation Format: Xiaoshan Shi, Malini Manoharan, Nitin Mandloi, Sushri Priyadharshini, Laxman Iyer, Rohit Gupta, Papia Chakraborty, Amitabha Chaudhuri, Ravi Gupta. OncoPeptTUME: A novel computational approach analyzes the tumor microenvironment to predict response to checkpoint inhibitors [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 A112.
Abstract A116: Lipid control of DNA-stimulated innate immunity
Authors: Tan Xiaojun , Zhang Conggang , Chen Zhijian J.
Published: February 2019

Type I interferon (IFN) plays essential roles in both spontaneous and iatrogenic tumor immunogenicity. Tumor-derived DNA is recognized by 2’,3’-cyclic GMP-AMP (cGAMP) synthase (cGAS) that is important in tumor immunogenicity. Upon DNA binding, cGAS produces the endogenous second messenger cGAMP that binds to and activates stimulator of IFN genes (STING), a signaling adaptor. cGAMP binding triggers STING trafficking from the endoplasmic reticulum (ER) to perinuclear compartments, with simultaneous activation of serine/threonine-protein kinase TBK1 that in turn phosphorylates the transcription factor IRF3, leading to upregulation of type I interferons. However, where and how TBK1 is activated by STING upon cGAMP stimulation is unclear. Our study focuses on the regulation of cGAMP-stimulated STING trafficking and activation by lipid messengers with essential roles in subcellular protein/membrane trafficking and signaling. Through in vitro signaling reconstitution, we identified a cellular lipid as an essential factor of STING signaling. We found both STING and TBK1 were lipid effectors. Lipid binding not only promotes STING trafficking but also stimulates TBK1 activation. These results reveal a new component of the STING-TBK1 complex that controls cytosolic DNA-stimulated innate immune signaling.

Citation Format: Xiaojun Tan, Conggang Zhang, Zhijian J. Chen. Lipid control of DNA-stimulated innate immunity [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 A116.
Abstract A125: Pulsatile MEK inhibition improves antitumor immunity and T-cell function in Kras mutant lung cancer
Authors: Choi Hyejin , Deng Jiehui , Li Shuai , Silk Tarik , Brea Elliott J. , Boiarsky Jonathan , Akbay Esra A. , Smith Paul D. , Merghoub Taha D. , Wong Kwok-Kin , Wolchok Jedd D.
Published: February 2019

KRAS is one of the most commonly identified driver oncogene in non-small cell lung cancer (NSCLC) and is commonly associated to NSCLC that is refractory to current available modalities of treatment. Targeted therapy to inhibit MEK has shown promising tumor growth control, but is followed by quick rebound of tumor growth. Recently, cancer immunotherapy has shown great promise by activating T-cells that are suppressed in the tumor microenvironment, especially through targeting co-inhibitory molecules and their counterparts. We sought to identify the most effective therapy for the treatment of KRAS mutant NSCLC patients by targeting cancer cells and activating immune infiltrates at the same time, by studying the impact of MEK inhibition on the immune microenvironment. We utilized Kras mutant lung cancer cell lines and Kras mutant transgenic lung cancer animals. We found that pulsatile treatment of MEK inhibitors activates T-cells and releases their proliferation suppression ex vivo and in vivo. Both selumetinib and trametinib showed highly increased CTLA-4 expression and mild increase of PD-1 in T-cells in pulsatile treatment, compared to continuous treatment in vivo. In addition, the pulsatile schedule alone showed superior antitumor effect and delayed drug resistance, in contrast with continuous dosing schedule. Based on the above observations, we combined pulsatile MEK inhibitor treatment and anti-CTLA-4 and found that it showed most prolonged survival of Kras tumor-bearing mice. All together, our findings will set the foundation for a combinatorial therapeutic strategy using pulsatile targeted therapy together with immunotherapy in patients, to optimally enhance tumor apoptosis and promote long-term immune response simultaneously.

Citation Format: Hyejin Choi, Jiehui Deng, Shuai Li, Tarik Silk, Elliott J. Brea, Jonathan Boiarsky, Esra A. Akbay, Paul D. Smith, Taha D. Merghoub, Kwok-Kin Wong, Jedd D. Wolchok. Pulsatile MEK inhibition improves antitumor immunity and T-cell function in Kras mutant lung 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 A125.
Abstract A159: Agonistic CD40 antibody therapy induces formation of tertiary lymphoid structures in glioma and inhibits the response to immune-checkpoint blockade
Authors: Hooren Luuk van , Vaccaro Alessandra , Georganaki Maria , Ramachandran Mohanraj , Huang Hua , Lau Joey , Smits Anja , Essand Magnus , Dimberg Anna
Published: February 2019

Cancer immunotherapy of glioma, the most common primary brain tumor in adults, is constrained by an immunosuppressive microenvironment. Tertiary lymphoid structures (TLSs) are ectopic lymphoid structures that mediate immune responses and provide a local site for tumor antigen presentation. Here, we show for the first time that TLSs are present in human low-grade glioma and that they can be induced in murine glioma models. Agonistic CD40 antibodies induced lymphotoxin α expression in B cells and enhanced the formation of TLSs in mice bearing orthotopic GL261 or CT-2A gliomas. TLSs consisting of B cells, T-cells and antigen presenting cells formed around CD31+ vessels proximal to the tumor tissue and adjacent to the meninges. Agonistic CD40 antibody treatment improved the CD8+ T-cell / Treg ratio in tumor-bearing mice, but there was no survival benefit. A decreased CD69 activation status on CD8+ T-cells, an increase of B cells with a CD1d+CD5+ regulatory phenotype and a high infiltration of Tregs in TLSs indicate that agonistic CD40 antibodies induce an immunosuppressive microenvironment in glioma. Consistent with this, the efficacy of both PD-1 and CTLA-4 checkpoint blockade was significantly decreased by co-administration of agonistic CD40 antibodies. These results demonstrate that TLSs are present and can be induced in glioma, but that they at least under certain conditions are associated with immunosuppression, shedding light on new mechanisms of immune regulation in the brain microenvironment.

Citation Format: Luuk van Hooren, Alessandra Vaccaro, Maria Georganaki, Mohanraj Ramachandran, Hua Huang, Joey Lau, Anja Smits, Magnus Essand, Anna Dimberg. Agonistic CD40 antibody therapy induces formation of tertiary lymphoid structures in glioma and inhibits the response to immune-checkpoint blockade [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A159.
Abstract A175: Memory T-cells targeting unique and shared oncogenic mutations detected in peripheral blood of epithelial cancer patients
Authors: Cafri Gal , Yossef Rami , Pasetto Anna , Deniger Drew , Gartner Jared J. , Prickett Todd , Robbins Paul F. , Rosenberg Steven A.
Published: February 2019

T-cells targeting shared oncogenic mutations can induce durable tumor regression in epithelial cancer patients. These T-cells can be detected in tumor-infiltrating lymphocytes, but whether such cells can be detected in the peripheral blood of patients with common metastatic epithelial cancer is unknown. Using a highly sensitive in vitro stimulation and enrichment of peripheral memory T-cells from six metastatic cancer patients, we identified and isolated memory T-cells targeting the mutated KRASG12D and KRASG12V variants, in three patients. In an additional two metastatic colon cancer patients, we detected CD8+ neoantigen-specific cells targeting the unique mutated SMAD5 and MUC4 proteins. Therefore, memory T-cells targeting KRAS and neoantigens can be detected in the peripheral blood of epithelial cancer patients and can potentially be used for the development of effective personalized T-cell-based cancer immunotherapy across multiple patients.

Citation Format: Gal Cafri, Rami Yossef, Anna Pasetto, Drew Deniger, Jared J. Gartner, Todd Prickett, Paul F. Robbins, Steven A. Rosenberg. Memory T-cells targeting unique and shared oncogenic mutations detected in peripheral blood of epithelial cancer patients [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 A175.
Abstract A186: A new strategy to identify and expand tumor-reactive CD8 TILs in human solid tumors
Authors: Duhen Thomas , Duhen Rebekka , Montler Ryan , Moudgil Tarsem , Bulk Jitske van den , Fox Bernard A. , Chang Shu-Ching , Grunkemeier Gary , Verdegaal Els M.E. , Miranda Noel F. de , Leidner Rom , Bell Richard B. , Weinberg Andrew D.
Published: February 2019

The immune system can recognize and destroy tumor cells through T-cell mediated mechanisms. Hence, identifying tumor antigen-specific T-cells from cancer patients and expanding them in large numbers in vitro has important implications for immunotherapy diagnostics and therapeutics. Here we show that tumor-reactive T-cells are enriched in a subset of tumor-infiltrating CD8 T-cells (CD8 TILs) identified by co-expression of CD103 and CD39 both in primary and metastatic tumors. The CD103+CD39+ CD8 TILs are present at high frequencies in melanoma and mismatch repair-deficient colon cancer but at low frequencies in microsatellite stable (MSS) colon cancer and colorectal liver metastasis. This cell population displays a distinct T-cell receptor (TCR) repertoire, with T-cell clones expanded in the tumor but present at low frequencies in the periphery. Importantly, we show in a MSS colon cancer patient that a very low number of CD103+CD39+ CD8 TILs can be expanded in vitro and that those cells recognize tumor-specific neoantigens. Finally, patients with head and neck cancer whose CD8 TILs contained a higher frequency of CD103+CD39+ cells experienced a greater overall survival. Our work suggests that CD103+CD39+ CD8 TILs are key players in the patient’s antitumor response and describe an approach for detecting and expanding those cells, which will help improve adoptive TIL therapy for cancer patients.

Citation Format: Thomas Duhen, Rebekka Duhen, Ryan Montler, Tarsem Moudgil, Jitske van den Bulk, Bernard A. Fox, Shu-Ching Chang, Gary Grunkemeier, Els M.E. Verdegaal, Noel F. de Miranda, Rom Leidner, Richard B. Bell, Andrew D. Weinberg. A new strategy to identify and expand tumor-reactive CD8 TILs in human solid 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 A186.
Abstract A196: Systematic identification of markers and drug targets on exhausted CD8+ T-cells
Authors: Hudson Will H. , Gensheimer Julia L. , Kissick Haydn T. , Ahmed Rafi
Published: February 2019

CD8+ T-cells are responsible for detection and killing of hosT-cells expressing non-self proteins. Upon antigen persistence, as in cancer or chronic viral infection, antigen-specific CD8+ T-cells lose their effector function, a phenomenon known as T-cell exhaustion. This process is concomitant with increased surface expression of negative regulatory proteins such as PD-1 and CTLA-4. Blockade of these molecules has become a widespread and successful clinical strategy for the treatment of malignancies. Unfortunately, not all tumor types are responsive to checkpoint molecule blockade, nor do all patients with susceptible tumor types exhibit clinical responses. These failures highlight the need for identification of additional negative regulators on exhausted, tumor-specific CD8+ T-cells. Here, we perform a systematic approach to identify surface proteins expressed on exhausted murine and human CD8+ T-cells. Using RNA-sequencing data from antigen-specific CD8+ T-cells from the mouse lymphocytic choriomeningitis virus (LCMV) infection model as well as data from human tumor-infiltrating CD8+ T-cells, we show high cross-species concordance of genes encoding membrane proteins in T-cell exhaustion. These expression profiles not only include many known checkpoint molecules such as PD-1, but also several proteins that negatively regulate T-cell receptor signaling but are largely unexplored in the process of CD8+ T-cell exhaustion. We validate these results performing by flow cytometry on both mouse and human CD8+ T-cells, including on T-cells obtained from resected human tumor tissue. To substantiate the importance of these markers, we further explore the function of one identified surface protein, CD101, in the murine LCMV infection model. We demonstrate that CD101 is induced on antigen-specific of CD8+ T-cells weeks after infection, in contrast with the early expression of canonical exhaustion markers such as PD-1. We show that antigen-specific CD101+ cells arise from CD101- precursors and that this differentiation process results in a loss of effector function, cytokine production, and proliferative capacity with simultaneous large transcriptomic changes. Together, these results demonstrate that exhaustion-associated surface protein expression patterns are largely conserved between humans and mice and provide a comprehensive catalog of phenotypic markers and potential drug targets for CD8+ T-cell-directed immunotherapy.

Citation Format: Will H. Hudson, Julia L. Gensheimer, Haydn T. Kissick, Rafi Ahmed. Systematic identification of markers and drug targets on exhausted CD8+ T-cells [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A196.