bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6513: 3,3'-diindolylmethane enhances tumor regression after radiation through protecting normal cells to modulate anti-tumor immunity
Authors: Chen Renxiang , Li Lijun , Lin Yun-Tien , Humayun Arslon , Fornace Albert J. , Li Heng-Hong
Published: September 2020

Preclinical and clinical data indicate that radiotherapy acts as an immune modifier, having both immunostimulatory and immunosuppressive effects on the tumor immune microenvironment (TIME). 3.3'-Diindolylmethane (DIM), the acid-catalyzed dimer of the bioactive indole found in cruciferous vegetables, has long been known for its anticancer properties and has been proposed for use as a cancer prevention agent. The current study characterizes how DIM influences TIME and tumor regression after fractionated radiation treatment using preclinical breast cancer models. We first compared tumor graft models using immune-competent and immune-deficient mouse strains to find out whether immune cells are required for DIM's effects. Tumor targeted radiation was done using narrow-beam radiation with shielding. Tumor regression was monitored after DIM and radiation combined treatment and radiation alone. Our results indicated that DIM enhanced tumor regression after radiation treatment in immune-competent but not immuno-deficient mice. Data from nCounter® PanCancer immune profiling panel showed DIM increased intratumoral immune cells including cytotoxic T cells, neutrophils and macrophages after radiation and enhanced immunological processes such as adhesion and antigen processing. Expression of several MHC Class II molecules and CD74, a gene encoding chaperone and transport cofactor that assists MHC II molecules folding and presenting, significantly increased in the combined treatment of radiation and DIM. The results showing that DIM treatment alone does not affect tumor growth suggested that DIM's radioprotective effect on non-tumoral cells, including stromal cells and immune cells, plays a critical role in promoting a microenvironment that favors anti-tumor immunity. Additional experiments showed that DIM protected normal cells from radiation-caused immediate injuries in vitro and in vivo. In summary, DIM's radioprotective effects on immune cells and other normal cells are important in promoting a TIME that favors anti-tumor immunity. As a result, DIM increases the efficacy of radiation treatment on tumor regression. This study supports the development of DIM as an adjunct agent for radiation treatment.

Citation Format: Renxiang Chen, Lijun Li, Yun-Tien Lin, Arslon Humayun, Albert J. Fornace Jr., Heng-Hong Li. 3,3'-diindolylmethane enhances tumor regression after radiation through protecting normal cells to modulate anti-tumor immunity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6513.
Abstract 653: Enhancing therapies for MYC-overexpressing Non-Hodgkin's lymphoma: A role for MYC downregulation and new combination therapies
Authors: Psaras Alexandra Maria , Brooks Tracy Ann
Published: September 2020

Background: Non-Hodgkin's Lymphoma (NHL) is the fifth most common cancer in the United States. Up to 40% of NHL is diffuse large B-cell lymphoma (DLBCL); while only 3% of NHL is classified as mantle cell lymphoma, it is a particularly lethal disease. DLBCL and MCL patients that aberrantly express MYC, which occurs up to 20 and 50% of the time, respectively, have worse survival rates and a lack of sustained clinical response to the standard R-CHOP therapy. We sought to examine both the effect of MYC downregulation on the efficacy of standard of care drugs and enhanced anti-cancer activity with a novel NF-kB targeting steroid, in place of prednisone/prednisolone, and also under conditions of MYC modulation, in NHL cells.

Methods and Summary of Findings: The downregulation of MYC was achieved in two distinct manners: with siRNA and with our pioneered MYC G-quadruplex (G4)-stabilizing DNA interference (DNAi) oligonucleotide. This DNAi was optimized for stability, specificity, and in cell activity, from our previously work developing this approach (Hao, et al, NAR 2016). The optimization was done using EMSA, chemical (DMS) footprinting, cell viability assays, qPCR, and microscopy. The lead steroid compound, which is selective for NF-κB signaling inhibition over DNA binding and transcription effects, was more cytotoxic than prednisolone, as determined by cell viability assays in NHL cells. Moreover, its effects on cell growth were additive with doxorubicin, and the overall effect of both drugs on cytotoxicity were enhanced by MYC downregulation. The combination studies were also performed with prednisolone; effects on decreased cell viability were more notable with the novel steroid, as compared to prednisolone.

Conclusion: MYC-overexpressing NHL, particularly DLBCL and MCL, respond poorly to the standard R-CHOP therapy. The addition of a MYC-downregulating DNAi, a novel NF-kB targeting steroid, or both, have been noted to enhance the cytotoxic effects of standard drugs. Work is expanding to evaluate the utility of an updated R-CHOP regimen in order to enhance survival for patients with MYC-overexpressing NHL.

Citation Format: Alexandra Maria Psaras, Tracy Ann Brooks. Enhancing therapies for MYC-overexpressing Non-Hodgkin's lymphoma: A role for MYC downregulation and new combination therapies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 653.
Abstract 6541: Accounting for immune escape mechanisms in personalized and shared neoantigen cancer vaccine design
Authors: Myronov Alexander , Niemiec Iga , Gruba Katarzyna , Mazzocco Giovanni , Sanecka-Duin Anna , Skoczylas Piotr , Drwal Michał , Kaczmarczyk Jan , Stepniak Piotr
Published: September 2020

The purpose of this study is to evaluate the importance of immune escape mechanisms (IEMs) when designing cancer immunotherapeutic strategies.

Cancer IEMs induced by negative selective pressure on tumor cells can have dramatic effects on immunotherapy treatment outcome. IEMs occurring during cancer evolution have been shown to facilitate loss of mutation-associated neoantigens (Anagnostou et al. Cancer Discov 2017). These mechanisms include: Loss of Heterozygosity (LOH), underexpression of HLA genes and mutations in the neoantigen presentation machinery.

During cancer evolution, the initially arising clonal neoantigens may be shared across many patients, followed by predominantly subclonal private neoantigens. The propensity of shared neoantigens to be clonal makes them promising candidates for the development of off-the-shelf cancer vaccines.

In order to optimize patient treatment strategies and qualify patients for either shared or private neoantigen-directed therapy, it is crucial to correctly assess the indication-specific IEMs and neoantigen landscape in both hot and cold tumors.

We carry out an extensive analysis of tumor neoantigen landscape from different indications based on TCGA, on Parkhurst et al. Cancer Discov. 2019 and other available data for selected indications (including MEL, NSCLC, CRC, and GBM). Using bioinformatics methods we investigate IEMs and their potential effects on the plasticity of neoantigen repertoires including enrichment of immunogenic neoantigens within the predicted vaccine composition, computed per patient. Immunogenicity is assessed using advanced deep learning models for neoantigen presentation and functional T-cell response prediction (Mazzocco et al., poster presented at SITC 2019).

We present the results of the comparison between different cancer indications including CRC, MEL, NSCLC and GBM using TCGA patient data and GI-tract cancer patients with validated T-cell responses. We present the frequency of particular immune evasion events, pointing out the differences in the number and quality of immunogenic neoepitopes (both shared and private) under those conditions and provide summary statistics.

As a result, we draw conclusions for vaccine design strategies, which are informed by the investigation of immune evasion events and are tested on selected datasets including experimentally-validated neoantigen responses.

Citation Format: Alexander Myronov, Iga Niemiec, Katarzyna Gruba, Giovanni Mazzocco, Anna Sanecka-Duin, Piotr Skoczylas, Michał Drwal, Jan Kaczmarczyk, Piotr Stepniak. Accounting for immune escape mechanisms in personalized and shared neoantigen cancer vaccine design [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6541.
Abstract 6551: Novel leads from Prosopis juliflora (Sw.) arrest the growth of B16F10 melanoma cancer cells by inducing apoptosis and down regulating the cell proliferating signalling pathways
Authors: Gacche Raju Nivarti
Published: September 2020

The evolving drug resistance and cancer heterogeneity is limiting the efficacy of current chemotherapy drugs. In the present state of the art, natural product and drug discovery has remained a significant hope for the identification of novel leads against series anti-cancer drug targets. The major issue is to convert the traditional knowledge into clinical reality by applying omics approaches. As a part of our continues efforts in exploring the efficacy of Prosopis juliflora as possible resource for the management of cancer, we have carried out the efficacy of P. juliflora against melanoma cancer using B16F10 as a melanoma model. The rational in selecting the melanoma lies in its aggressive metastatic phenotype and resistance to present chemotherapy drugs. Prosopis juliflora leaves methanol extract (PJLME) was assessed for its anticancer activity against B16F10 skin melanoma cancer cell line. Series of in vitro and in vivo experiments demonstrated that PJLME is cytotoxic (IC5017ug/ml), inhibited the migration ability of cells, inhibited the colony formation, arrested cell cycle at G0-G1 phase, induced apoptosis by up regulating the pro-apoptic markers like Bax & Bad, along with successful cleavage of Caspase-9 and PARP-1 and down regulated the anti-apoptotic marker Bcl2. The PJLME also suppressed the expression of Akt, mTOR and ERK signalling pathways. The in vivo xenograft studies in BALB/c mice model demonstrated impressive activity against the melanoma cancer. As a part of understanding the possible mechanism of action, our studies indicate that, PJLME induces cell death via apoptosis mechanism and by down regulating the cell proliferation signalling pathways. The HPLC-MS analysis of PJLME indicates the diversity of compounds, few of them are known for their anticancer effects. Our studies unraveled the significance of PJLME as a novel natural source for the management of melanoma cancer.

Citation Format: Raju Nivarti Gacche. Novel leads from Prosopis juliflora (Sw.) arrest the growth of B16F10 melanoma cancer cells by inducing apoptosis and down regulating the cell proliferating signalling pathways [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6551.
Abstract 6553: Plant power: Plant isolate dibenzyl trisulfide induces death of triple-negative breast cancer cells derived from an African American patient
Authors: Wooten Jonathan , Araújo Cristina , Wauchope Shaniece , Aja Joyce , Mavingire Nicole , Delgoda Rupika , Brantley Eileen
Published: September 2020

Triple negative breast cancer (TNBC), characterized by tumors that lack estrogen receptor, progesterone receptor, and human epidermal growth receptor expression, represents one of the most aggressive subtypes of breast cancer. TNBC carries a poor prognosis due, in part, to a lack of clinically available targeted therapy. Novel therapeutic strategies to combat TNBC primarily involve the use of synthetic small molecules. However, the World Health Organization reports that there is increased use of natural remedies and traditional medicine to treat diseases. Our lab has investigated the chemotherapeutic and chemopreventive effects of a variety of plant isolates. Dibenzyl trisulfide (DTS) is derived from Petiveria alliacea, a perennial shrub that grows in tropical regions of the world. Previous investigations surrounding DTS are limited to anticancer actions in European American breast cancer cells. The purpose of this study was to evaluate the anticancer actions of DTS in CRL-2335 cells which are derived from an African American patient with TNBC. We found that DTS inhibited TNBC cell migration and proliferation using wound healing and colony forming assays. Furthermore, we found DTS induced apoptotic body formation and nuclear fragmentation using relief contrast and fluorescence microscopy respectively. Moreover, using the Annexin V/PI assay we found that DTS induced early apoptosis, which was partially attenuated in cells pretreated with pan-caspase inhibitor zVAD-fmk. Finally, quantitative polymerase chain reaction analyses revealed that DTS induced the expression of pro-apoptotic genes BAK1, LTA and GADD45A. Our data suggest that DTS effectively induces caspase-independent death of TNBC cells derived from an African American patient and represents a promising agent to treat more refractory forms of breast cancer.

Citation Format: Jonathan Wooten, Cristina Araújo, Shaniece Wauchope, Joyce Aja, Nicole Mavingire, Rupika Delgoda, Eileen Brantley. Plant power: Plant isolate dibenzyl trisulfide induces death of triple-negative breast cancer cells derived from an African American patient [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6553.
Abstract 6560: Sann-Jhong-Kuey-Jian-Tang could inhibit glioblastoma cells through increasing TNF-α, Fas, Bax but decreasing Bcl-2, Mcl-1 expression
Authors: Su Chin Cheng
Published: September 2020

Glioblastoma is a highly malignant brain tumor and poor response to current chemotherapeutic medicine (such as Temozolomide). Glioblastoma remains a challenging disease and there is a need to identify new treatments. Sann-Jhong-Kuey-Jian-Tang (SJKJT), a traditional Chinese medicine prescription, has been prescribed as complementary medicine for patients with solid tumors in Taiwan. However, the anticancer effects of SJKJT on human brain tumor have not yet been elucidated. The present study focused on the anticancer effects and molecular mechanisms of SJKJT in human Glioblastoma by using DBTRG cells. In the present study, we evaluated the cytotoxic effects of SJKJT on DBTRG cells by MTT assay. The protein expression levels of tumor necrosis factor-α (TNF-α), Fas, Fas-associated Death Domain (FADD), Caspase-8, Caspase-9, Caspase-3, Bcl-2-associated X protein (Bax), Bcl-2 and myeloid cell leukemia 1 protein (Mcl-1) in the DBTRG cells were measured by western blotting. The cell cycles were analyzed by fluorescence-activated cell sorting (FACS). The protein expression of caspase-3 in DBTRG cells was analyzed by immunocytochemical (ICC) method. The results revealed that SJKJT inhibit the proliferation of DBTRG cells in a time- and dose-dependent manner. The protein expression levels of TNF-α, Fas, FADD, Caspase-8, Caspase-9, Caspase-3, Bcl-2-associated X protein (Bax) increased in the DBTRG cells treated with SJKJT; however, the level of Bcl-2 and Mcl-1 were decreased. These results indicated that SJKJT can inhibit DBTRG cells through both extrinsic and intrinsic pathway. The use of traditional Chinese medicine prescription SJKJT may become a feasible therapy option. Further studies are warranted to elucidate its mechanisms of action.

Citation Format: Chin Cheng Su. Sann-Jhong-Kuey-Jian-Tang could inhibit glioblastoma cells through increasing TNF-α, Fas, Bax but decreasing Bcl-2, Mcl-1 expression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6560.
Abstract 6569: Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation
Authors: Lopes-Ramos Camila M. , Kuijjer Marieke , Glass Kimberly , DeMeo Dawn , Quackenbush John
Published: September 2020

Despite pronounced sex differences in cancer incidence, severity, and response to treatment, most current approaches to clinical management, as well as therapeutics development and selection, are sex-independent. For most cancer types, including liver cancer, males have a higher risk of developing the disease and a lower survival rate than women. However, the molecular features that drive these sex differences are poorly understood. We inferred patient-specific regulatory networks of liver hepatocellular carcinoma using data from TCGA. By comparing the female and male networks, we found marked sex differences in transcriptional regulatory processes relevant to disease development, progression, and response to therapy. We found that oncogenes have significantly higher regulatory targeting in males, while tumor suppressor genes have significantly higher targeting in females. Many “hallmark” cancer pathways, including the HEDGEHOG, WNT, and TGF-β signaling pathways, were significantly more highly targeted in males, while drug metabolism and immune related pathways were enriched for genes highly targeted in females. We also evaluated sex-biased somatic mutation patterns using mutation and copy number alteration data in TCGA. By summarizing mutations found in genes into pathway mutation scores, we found sex-biased mutation profiles for many pathways, providing additional support for biological sex differences associated with WNT, NOTCH, TGF-β, and HEDGEHOG signaling pathways. Our analysis uncovered patterns of gene regulation that differentiate male and female liver cancer and may be associated with sex differences in prognosis and treatment response. These findings provide insight into the mechanisms that drive clinically observed sex differences and underscore the importance of considering sex as a factor influencing disease etiology and in developing and prescribing therapies. Our network approach can provide insights into why some therapies have differential effect in males and females, and suggest new ways to optimize drug response in each sex.

Citation Format: Camila M. Lopes-Ramos, Marieke Kuijjer, Kimberly Glass, Dawn DeMeo, John Quackenbush. Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6569.
Abstract 6576: DNA methylation reveals alternative promoter usage in genes critical to pediatric tumors
Authors: Williams Justin , Xu Beisi , Putnam Daniel , Chen Xiang
Published: September 2020

Transcriptional regulation is fundamental for cell identity and function, and it's deregulation is a defining feature for common diseases, including cancers. Besides directly modifying the canonical promoter activities, tumors frequently utilize alternative promoters to increase the isoform diversity, activate oncogenes when the canonical promoters are repressed, and to evade host immune attacks by immune-editing. However, fresh-tissue availability and technical challenges represent major obstacles in genomewide promoter activity assessment in patient tumors by ChIP-seq experiments. Here, we presented MethylToActivity (M2A), a deep-learning framework that reveals promoter activities (H3K4me3 and H3K27ac) from DNA methylation (DNAm) patterns, a relatively stable epigenetic regulatory mechanism that can be robustly and accurately profiled in various tissues, including retrospective tumor samples archived using the formalin-fixed paraffin-embedded (FFPE) method. Trained from a cohort of neuroblastomas (N = 6), we demonstrate that M2A 1) approaches the accuracies of ChIP-seq experiments in revealing promoter activities, 2) is generalizable to various pediatric and adult cancers, 3) captures changes of promoter activity associated with differentially methylated regions, and 4) faithfully recapitulates differential promoter usages among tumor subtypes. Importantly, M2A uncovers oncogenic activation of alternative promoters in genes critical for tumor survival while the canonical promoter remains inactive. These results substantiate that M2A is capable of accurately measuring promoter activities, which will be of great use not only to functionally interpret differential DNAm patterns, but to unveil alternative promoter usages in patient tumors, which will facilitate precision medicine by tailoring treatments based on both epigenetic deregulations and genetic variants.

Citation Format: Justin Williams, Beisi Xu, Daniel Putnam, Xiang Chen. DNA methylation reveals alternative promoter usage in genes critical to pediatric tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6576.
Abstract 6583: Systems scale characterization of malignant pleural mesothelioma to discover novel therapies
Authors: Wilferd Sierra F. , Hoang Chuong D. , Plaisier Christopher L.
Published: September 2020

We have built a platform integrating systems genetics and functional genomics for the discovery of therapies to eradicate residual microscopic tumor foci after surgical resection of the deadly cancer malignant pleural mesothelioma (MPM). Using our SYstems Genetics Network AnaLysis (SYGNAL) network inference pipeline we constructed a malignant pleural mesothelioma gene regulatory network to discover disease causing TFs and miRNAs regulatory interactions. We then overlaid the MPM gene regulatory network with significant hits from pooled CRISPR-Cas9 knock-out out growth functional genomics screens in low passage number MPM patient-derived cell lines. We then queried this integrated network to identify patient survival associated TFs and miRNAs that when knocked-down (siRNA) or over-expressed (miRNA mimic), respectively, are likely to have anti-proliferative effects in low passage number patient-derived cell lines. The perturbation of a majority of these TFs and miRNAs led to significantly lower proliferation in the patient-derived cell lines. Further, the expression of the regulator or its target genes should function as a biomarker(s) for whether therapy will be effective for a particular patient's tumor. We are currently working with our collaborator at the NCI to develop these siRNA and miRNAs into their existing miRNA mimic hydrogel delivery system and test them in orthotopic xenografts using the low passage number patient derived cell lines.

Citation Format: Sierra F. Wilferd, Chuong D. Hoang, Christopher L. Plaisier. Systems scale characterization of malignant pleural mesothelioma to discover novel therapies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6583.
Abstract 6587: Proteogenomic characterization of colorectal cancer using the IndivuType multiomics database
Authors: Krawczyk Margarita , Woodsmith Jonathan , Nutsoa Marcel , Corwin Thomas , von der Heyde Silvia , Piras Vincent , Whittaker Mark , Hergovich Alex , Frommolt Peter , Juhl Hartmut
Published: September 2020

Cancer is a highly heterogeneous disease, both intra- and inter-individually consisting of complex phenotypes and systems biology. Although genomic data has contributed greatly towards the identification of cancer-specific mutations and the progress of precision medicine, genomic alterations are only one of several important biological drivers of cancer. Furthermore, single-layer omics represent only a small piece of the cancer biology puzzle and provide only partial clues to connecting genotype with phenotype. A more integrated approach is urgently needed to unravel the underpinnings of molecular signatures and the phenotypic manifestation of cancer hallmarks. We have developed IndivuType, a knowledge and discovery platform that combines genomics, transcriptomics, and proteomics datasets to identify putative therapeutic targets in a colorectal cancer (CRC) cohort of 500 patients. We identified hundreds of proteins dysregulated in CRC that are dependent on the genetic background of the patient. Further, we characterized these proteins using clinical parameters from the IndivuType database to prioritize targets for precision medicine approaches. This project highlights the utility of moving beyond solely genomics approaches to better understand the molecular mechanisms underpinning cancer.

Citation Format: Margarita Krawczyk, Jonathan Woodsmith, Marcel Nutsoa, Thomas Corwin, Silvia von der Heyde, Vincent Piras, Mark Whittaker, Alex Hergovich, Peter Frommolt, Hartmut Juhl. Proteogenomic characterization of colorectal cancer using the IndivuType multiomics database [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6587.
Abstract 6589: Selecting clinical lead of TCRs targeting alpha-fetoprotein-positive liver cancer on balance of risk and benefit
Authors: Luo Xiaobing , Cui Huijuan , Cai Lun , Zhu Wei , Yang Wei-Chih , Patrick Michael , Zhu Shigui , Huang Jiaqi , Yao Xin , Yao Yihong , He Yukai , Ji Yun
Published: September 2020

Background: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with a poor prognosis and limited therapeutic options. Alpha-fetoprotein (AFP), an established clinical biomarker of HCC, has been employed as an attractive target for T cell-based immunotherapy against this disease given its high expression in the tumor and restricted expression in normal tissues. We have identified a number of T cell receptors (TCRs) recognizing the HLA-A*02:01 restricted AFP158-166 peptide FMNKFIYEI, providing a TCR candidate pool for identifying TCRs with optimal clinical benefit.

Methods: To select the ideal AFP TCR for clinical use, we evaluated the efficacy and safety profile of 7 TCRs on balance of their potency and specificity by testing their reactivity to normal and transformed cells covering a variety of primary cell types and HLA serotypes, and potential protein candidate in human genome by an extensive alanine scan (X-scan).

Results: We first selected three TCR candidates based on the in vitro anti-tumor activity. Next we eliminated two potential cross-reactive TCRs based on their reactivity against normal and transformed cells covering a variety of primary cell types and HLA serotypes, respectively. We then excluded the potential cross-reactivity of the selected TCR with protein candidate in human genome identified by X-scan.

Conclusion: Up to date we have selected a AFP TCR with the optimal affinity, function, and safety profile, bearing properties that are expected to allow AFP TCR redirected T cells to specifically differentiate between AFP levels on tumor and normal tissues. An early phase clinical trial using T cells transduced with this TCR to treat HCC patients (NCT03971747) has been initiated.

Citation Format: Xiaobing Luo, Huijuan Cui, Lun Cai, Wei Zhu, Wei-Chih Yang, Michael Patrick, Shigui Zhu, Jiaqi Huang, Xin Yao, Yihong Yao, Yukai He, Yun Ji. Selecting clinical lead of TCRs targeting alpha-fetoprotein-positive liver cancer on balance of risk and benefit [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6589.
Abstract 6599: Screening and characterization of AlloCAR T targeting DLL3 for the treatment of small cell lung cancer
Authors: Zhang Yi , Tacheva-Grigorova Silvia , Melton Zea , Smith Bryan , Sai Tao , Van Blarcom Tom , Amado Rafael , Sasu Barbra , Panowski Siler
Published: September 2020

Small cell lung cancer (SCLC) is an aggressive disease with very limited treatment options. SCLC responsiveness to immuno-oncology agents suggests this indication may be amenable to a T-cell based therapy. Genetically modified T cells that express chimeric antigen receptors (CARs) have shown impressive efficacy in multiple hematological malignancies. To translate this approach for SCLC treatment, we are exploring Delta-like ligand 3 (DLL3) as a therapeutic target. DLL3 is highly expressed in SCLC and several other types of neuroendocrine cancers, with limited normal tissue RNA expression in brain, pituitary and testis. A large panel of antibodies that bind to DLL3 were generated, formatted into CARs, and tested in in vitro short-term and long-term cytotoxicity assays using target cells that express high, medium or low levels of DLL3. A subset of CAR T cells were highly active and displayed long-term killing potential. These were tested in vivo and robust efficacy was seen in both subcutaneous and systemic SCLC models. To understand the potential for toxicity in pituitary and brain, subcutaneous or intracranial tumors expressing DLL3 were implanted in mice and human/mouse cross-reactive DLL3 CAR T cells were injected into the tumor-bearing animals. In both models, T cell infiltration into intermediate and posterior pituitary was detected. However, no tissue damage in brain or pituitary was observed and hormone-secretion function of pituitary was not ablated. We believe toxicity is significantly derisked but as an additional safety assurance, CAR T cells were further engineered to contain an off-switch, by which CAR T cells are eliminated upon administration of Rituximab. Multiple off-switch CAR formats were evaluated, and optimal formats determined independently for each CAR. In summary, DLL3 is a target for SCLC with limited normal tissue expression and toxicity. Multiple DLL3 CAR T cells have been characterized. A subset of these CAR T cells showed robust in vitro and in vivo activity and were chosen for further evaluation as potential clinical candidates.

Citation Format: Yi Zhang, Silvia Tacheva-Grigorova, Zea Melton, Bryan Smith, Tao Sai, Tom Van Blarcom, Rafael Amado, Barbra Sasu, Siler Panowski. Screening and characterization of AlloCAR T targeting DLL3 for the treatment of small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6599.
Abstract 6600: Rapid generation of TCR-engineered T lymphocytes by linking the single cell transcriptome to its corresponding T cell receptor in antigen specific T cells
Authors: Zhu Linnan , Wang Fei , Xu Qumiao , Sun Hai-Xi , Li Ziyi , Liang Yanling , Zhuang Zhenkun , Gu Ying , Chao Cheng-chi
Published: September 2020

Adoptive cell transfer of T-cell receptor (TCR)-engineered T cells has emerged as a powerful and potentially curative therapy for cancers and infectious diseases. However, how to rapidly identify and obtain therapeutic TCRs remains a major challenge in this field. Here, we simultaneously performed deep single-cell RNA and TCR V(D)J sequencing on 879 single T cells from in vitro stimulated CMV pp65NLV-specific CD8+ T cells. The correlation analysis of single-cell transcriptome and TCR V(D)J sequences revealed a differential distribution of T cell transcriptomic profiles among TCR clones. Two distinct cell types were identified in the T cell population. TYPE I T cell subtype, which represents the gene signatures of T cell activation and cytotoxicity, mainly includes TCR clone 1, 2 & 4, while TYPE II subtype, which represents the gene signatures of naïve status, mainly includes TCR clone 3 and other low frequency clones. Based on their temporal phases of T cell activation, the selected TCR sequences from clone 1 (TCRZWX1) and clone 3 (TCRZWX3) were functionally validated by constructing TCR-engineered T cells in vitro. The two clones showed distinct cell stages corresponding to their transcriptome patterns. TCRZWX1 transgenic T cells displayed effector functions including secretion of pro-inflammatory cytokines, IFN-γ and TNF-α, and cytotoxicity in response to CMV pp65NLV peptide. However, TCRZWX3 transgenic T cells displayed non-detectable levels of IFN-γ, which might correlate with a low affinity TCR. Our results provide a novel approach using correlative analysis of the single-cell transcriptome and TCR V(D)J sequences for rapidly identifying potential therapeutic TCRs for T cell therapy.

Citation Format: Linnan Zhu, Fei Wang, Qumiao Xu, Hai-Xi Sun, Ziyi Li, Yanling Liang, Zhenkun Zhuang, Ying Gu, Cheng-chi Chao. Rapid generation of TCR-engineered T lymphocytes by linking the single cell transcriptome to its corresponding T cell receptor in antigen specific T cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6600.
Abstract 6618: A database of potential T cell epitopes for cancer immunotherapy
Authors: Jiang Chongming , Chao Cheng-chi , Cheng Chao
Published: September 2020

Background: Adoptive immunotherapy with tumor-specific T cells is a promising treatment strategy for patients with malignancy. A key of adoptive T cell immunotherapy is to determine suitable immunogenic tumor antigens for targeting. The main challenges of T cell therapy are the relative lack of comprehensive information about proper antigens immunogenic to T cells, and excessive time-consumption to identify which kinds of peptides can be used for vaccine application and cancer immunotherapy. The objective of our work is to build a systematic database for those prospective tumor peptide antigens (dataset A), the documented promising immunogenic epitopes on cell surface having been experimentally validated (dataset B), and the antigens that have been tested in clinical studies (dataset C). The establishment of this database could overcome the prior inconvenience caused by the lack of collection data sets.

Finding: In the dataset A, we predicted a total of 4,999,192 neoantigen from 463 cancer patients across 10 main kinds of cancer types. The dataset B includes 118,564 T cell epitopes that were experimentally proved to exist on various cancer cell surfaces and could be immunogenic. In dataset C, 636 peptides from different stages of 121 clinical trials with 31 cancer types were collected. Finally, a clinical trial by using adoptive immunotherapy with tumor-specific T cells was designed to apply a similar method to identify suitable tumor antigens.

Conclusion: An informative database has been systemically built and tested in both theoretical and practical aspects, which enables a convenient and efficient approach for the selection of tumor antigens in vaccine design and cancer immunotherapy.

Citation Format: Chongming Jiang, Cheng-chi Chao, Chao Cheng. A database of potential T cell epitopes for cancer immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6618.
Abstract 6622: The identification of extranodal NK/T cell lymphoma-associated antigen for helper T cell-based immunotherapy
Authors: Kumai Takumi , Hayashi Ryusuke , Hayashi Tatsuya , Kobayashi Hiroya , Harabuchi Yasuaki
Published: September 2020

Extranodal natural killer/T-cell lymphoma, nasal type (NKTL) is a fatal destructive tumor that develops around the nasopharyngeal and nasal/paranasal areas. Although this disease was originally considered to be endemic to East Asia, Central and South America and was extremely rare in Europe and the United States, the incidence of NKTL has increased during the last several decades in countries where it was previously not epidemic. The combination of irradiation and chemotherapies such as SMILE and MPVIC-P are effective. However, these therapies cause severe and sometimes fatal adverse effects indicating that a novel strategy to treat NKTL is required. The positive results of clinical trials using immune checkpoint inhibitors in solid tumors proved that immune cells are capable of eliminating tumor. However, autoimmune diseases are inevitable adverse events in this type of therapy, which non-specifically activates T cells. Thus, the identification of epitope peptides in tumor has re-emerged as an attractive concept. I will describe our study to identify NKTL-derived T cell epitopes as a basis of cancer vaccine. The expression of c-Met and its ligand HGF plays a critical role in cell proliferation and is involved in numerous malignancies. Because c-Met expression and its role in NKTL remain unclear, we first studied the expression and function of c-Met in NKTL cells. As a result, we found that HGF and c-Met were expressed and contributed to the proliferation of cells in NK/T-cell lymphoma. Next, the helper epitopes were identified from c-Met protein using computer-based algorism. The identified epitope peptides could elicit peptide-specific helper CD4 T cells (HTLs), which showed antitumor responses in vitro. The addition of c-Met inhibitor suppressed TGF-β production from tumor followed by the augmentation of HTL responses. In summary, we identified novel c-Met HTL epitopes that can elicit effective antitumor responses against tumors expressing c-Met. Our results provide the rationale of combining c-Met targeting therapy and immunotherapy for NKTCLs and epithelial tumors.

Citation Format: Takumi Kumai, Ryusuke Hayashi, Tatsuya Hayashi, Hiroya Kobayashi, Yasuaki Harabuchi. The identification of extranodal NK/T cell lymphoma-associated antigen for helper T cell-based immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6622.
Abstract 6630: Synergistic immuno photothermal nanotherapy (SYMPHONY) for combination cancer therapy
Authors: Liu Yang , Maccarini Paolo , Palmer Gregory M. , Inman Brant A. , Fecci Peter E. , Vo-Dinh Tuan
Published: September 2020

Checkpoint inhibitor immunotherapy has been a revolutionary milestone in cancer treatment because it can counter the tumor immunosuppressive environment to improve patients' overall survival and even result in a durable complete response. However, only a fraction of patients benefit from checkpoint inhibitor immunotherapy. Improving the response rate and maximizing efficacy for immunotherapy are still unmet needs of great clinical significance. We have developed a novel combination cancer therapy referred to as Synergistic Immuno Photothermal Nanotherapy (SYMPHONY) by integrating plasmonic gold nanostars (GNS)-mediated photothermal therapy with anti-PD-L1 checkpoint inhibitor immunotherapy to improve the therapeutic efficacy of cancer treatment. GNS nanoparticles are superior photon-to-heat conversion transducers for photothermal therapy because they have tip-enhanced plasmonics from multiple sharp spikes and tunable plasmonic absorption in the near-infrared tissue optical window. Our in vivo experimental results with bladder cancer and brain cancer murine animal models have demonstrated that photothermal therapy with GNS in combination with anti-PD-L1 checkpoint inhibitor immunotherapy not only effectively ablates primary tumor with laser irradiation but also stimulates the immune response to treat distant tumors without laser irradiation. Furthermore, a rechallenge study performed three months later using cancer cells injected into long-term survivors demonstrates that SYMPHONY therapy can generate a long-term memorized immune response and prevent cancer recurrences in cured mice. The SYMPHONY combination therapy results in synergistic treatment surpassing what either single treatment can achieve, and shows the great promise for future translational medicine studies to treat aggressive metastatic cancer diseases.

Citation Format: Yang Liu, Paolo Maccarini, Gregory M. Palmer, Brant A. Inman, Peter E. Fecci, Tuan Vo-Dinh. Synergistic immuno photothermal nanotherapy (SYMPHONY) for combination cancer therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6630.
Abstract 666: A novel, highly selective PI3Kδ inhibitor for the treatment of solid malignancies that express high levels of target protein as assessed by immunohistochemistry
Authors: MacQueen Amy R. , Viticchie Giuditta , Niewola Karolina , Finotello Francesca , Powley Ian , Shah Pritom , van der Veen Lars , Lahn Michael , Johnson Zoe
Published: September 2020

The inhibition of PI3Kδ preferentially targets regulatory T cells and myeloid derived suppressor cells, breaking tumour-induced immune tolerance and restoring anti-tumour immunity. Bioinformatics and protein expression studies have shown that PIK3CD/PI3Kδ is also highly expressed in certain solid malignancies. IOA-244 is a novel, highly selective PI3Kδ inhibitor, with the unique property of being ATP non-competitive. In addition to the effects of PI3Kδ inhibition on the balance of CD8+ T cells and T regulatory cells in the tumour microenvironment, we have recently demonstrated that IOA-244 effectively controls the growth of tumour cells with high levels of PI3Kδ in vivo in T-cell deficient hosts.

Analysis of TCGA datasets shows that certain solid tumours express high levels of PIK3CD transcript, comparable to that of diffuse large B cell lymphoma. Of these indications, cutaneous and uveal melanoma are amongst the highest expressers. To support the clinical development of IOA-244, we demonstrate that patient-derived melanoma cells with a high expression of PIK3CD are susceptible to treatment with IOA-244 in a mouse patient-derived xenograft model. Furthermore, in vitro explant studies using clinical biopsy material demonstrates that PI3Kδ expression can be detected in tumour tissue and that IOA-244 has an anti-proliferative function when added to these samples.

Based on these and other supporting data, IOA-244 has received clinical trial approval in Europe and phase I clinical testing is underway in solid tumours with an anticipated high Treg:CD8 ratio and/or high protein expression of PI3Kδ.

Citation Format: Amy R. MacQueen, Giuditta Viticchie, Karolina Niewola, Francesca Finotello, Ian Powley, Pritom Shah, Lars van der Veen, Michael Lahn, Zoe Johnson. A novel, highly selective PI3Kδ inhibitor for the treatment of solid malignancies that express high levels of target protein as assessed by immunohistochemistry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 666.
Abstract 6707: Inhibition of proteolytic cleavage of NKG2D ligands increases immune cell-mediated cell killing of tumor cells in vitro
Authors: Yalcin Safak , Cicchini Vanessa , Du Xin , Wu Xin , Kaever Tom , Gibson Neil
Published: September 2020

Natural Killer Group 2, member D (NKG2D) is an activating receptor that is expressed on the key immune cells involved in the cytotoxic arm of the immune system. Ligands of NKG2D, such as MICA and MICB, are not normally expressed but are upregulated in response to stress, such as oxygen or nutrient deprivation, viral infection or oncogenic transformation. One mechanism that tumor cells, that express MICA and MICB, have adopted to evade the cytotoxic potential of NK and T cells, that express the NKG2D receptor, is to cleave MICA/B from the cell surface. Proteolytic cleavage of MICA/B occurs within the α-3 domain of MICA/B. In order to evaluate the therapeutic potential of blocking cleavage of MICA/B we have generated multiple antibodies that bind to the α-3 domain of MICA/B. The lead antibody, PDI-01, was found to bind to multiple recombinant human MICA alleles and human MICB and to recombinant MIC proteins derived from non-human primate sequences with low nM affinity. PDI-01 bound to target antigen on the surface of multiple cancer cell lines including HCT-116 colon carcinoma, HCC1534 lung carcinoma and PLC/PRF/5 liver cancer cell lines. Each of those tumor cell lines were positive for MICA and MICB expression. Low expression of other NKG2D ligands, known as UL-16 binding proteins 1-6 (ULBP 1-6), has been shown in those cell lines. PDI-01 was found to prevent cleavage of MICA from the surface of HCT-116, HCC1534 and PLC/PRF/5 cells via ELISA quantification of soluble MICA levels. Exposure of HCT-116, HCC1534 and PLC/PRF/5 tumor cell lines to PDI-01 increased surface MICA levels as measured by flow cytometry analysis. An increase in immune cell mediated killing of HCT-116, HCC1534 and PLC/PRF/5 cells was observed when tumor cells were incubated with NK-92 cells (NKG2D positive) in the presence of PDI-01. PDI-01 also enhanced antibody-dependent cell-mediated cytotoxicity (ADCC) against these three tumor cell lines. Co-culture of PBMCs, or purified NK cells, with PLC/PRF/5 cells in the presence of PDI-01 led to an increase in TNF-α, IFN-γ, CCL4, CCL5 and IL-6. PDI-01 is being advanced into clinical development and the Phase 1 program is scheduled to be initiated in the 2Q, 2020.

Citation Format: Safak Yalcin, Vanessa Cicchini, Xin Du, Xin Wu, Tom Kaever, Neil Gibson. Inhibition of proteolytic cleavage of NKG2D ligands increases immune cell-mediated cell killing of tumor cells in vitro [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6707.