bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 7238: Exploring the potential of targeted DNA Nanobot delivery systems for gene delivery
Authors: Shahhoessini Melika , Spitzner Jeffrey R. , Lucas Christopher R. , Castro Carlos E. , Halley Patrick D. 
Published: March 2024

Abstract
Gene therapy is a cornerstone of modern medicine's quest for precision treatment to cure human disease including cancer. The current approach to gene delivery technology employs viral vector delivery systems. While effective, these vectors present significant challenges including immunogenicity, safety concerns due to off-target non-tissue specific delivery, payload limitations, and significant cost ultimately diluting their therapeutic potential. Thus, novel approaches to gene delivery are necessary. One such approach to address these critical limitations involves DNA Nanobots, a DNA-based nanotechnology that allows for a tissue-/target-cell specific gene delivery system. Utilizing DNA origami molecular assembly techniques, our DNA Nanobots offer a customizable and highly precise delivery platform, free from viral vector constraints. This innovative approach has the potential to transform the landscape of gene therapy by providing a safer, more efficient, and targeted alternative. Key technical advancements with our DNA Nanobots Gene Delivery Platform include: •CRISPR Cas-9 Integration: By incorporating CRISPR Cas-9 functional proteins, our nanobots were shown to enhance gene editing precision in primary human T cells, broadening therapeutic applications across various genetic conditions. •Targeted mRNA Delivery: Our nanobots revealed promising results in the targeted delivery of mRNA, vital for vaccine development and personalized treatments. •Efficient antisense/siRNA Delivery: Prior studies have overcome traditional challenges including endosomal escape and cytoplasmic entry, demonstrating effective siRNA delivery critical for gene silencing therapeutic development. In summary, DNA Nanobots mark a paradigm shift in gene therapy. Their ability to deliver various nucleic acids with high specificity and efficiency addresses many of the current methodological limitations especially off-target safety concerns and high cost. This advancement not only enhances the therapeutic index of existing treatments but also opens avenues for novel therapeutic strategies, potentially reshaping the future of molecular medicine and gene therapy.
Citation Format: Melika Shahhoessini, Jeffrey R. Spitzner, Christopher R. Lucas, Carlos E. Castro, Patrick D. Halley. Exploring the potential of targeted DNA Nanobot delivery systems for gene delivery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7238.
Abstract 7248: Simultaneous isolation and parallel analysis of genomic DNA and RNA for gene therapy
Authors: Wei Han 
Published: March 2024

Abstract
Introduction Viral vectors, such as adeno-associated vector (AAV), play a crucial role in delivering transgenes for gene therapy research. The success of vector transduction is vital for efficacy, which is measured through vector copy number (VCN) and transgene expression. In preclinical studies, both VCN and transgene expression are commonly tested from the same sample to ensure accuracy. We have reported a method for simultaneous high-quality genomic DNA and RNA extraction without splitting the sample, utilizing SPRI bead-based technology that has consistent performance across diverse tissue types and brain regions.
Methods AAV was administered to mouse and non-human primate (NHP) models. At the conclusion of each experiment, tissue samples from the adrenal gland, brain, gonads, heart, kidney, liver, lung, skeletal muscle, spinal cord, and spleen were harvested. All tissue samples that demonstrated around 15 mm3 were snap-frozen in liquid nitrogen before nucleic acid extraction. The extraction process was carried out manually or on an automated liquid handler. The quality and quantity of DNA and RNA were then assessed from all tested tissues before downstream assay.
Results Our study found that all mouse tissue types (n=72/tissue type) and NHP (n=11/tissue type) had an average gDNA and RNA yield that exceeded the minimum yield cutoff of 25 ng/μL for DNA and 6.25 ng/μL for RNA. We also analyzed DNA from tissues treated with two different AAV serotype-treated tissues in the mouse model, which showed that transduction across all the tissues was highly efficient for both AAV serotypes. Furthermore, we observed variations in transgene expression levels (copies/1 μg RNA) among different tissue types. Similar patterns of VCN and transgene expression were also observed in NHP models.
Conclusions Efficient gene therapy depends on a safe and effective viral vector. The simultaneous extraction of gDNA and RNA simplifies the process, saves time, ensures quality, and facilitates integration into existing lab automation. This leads to consistent and error-resistant performance in analyzing vector copy and transgene levels.
Citation Format: Han Wei. Simultaneous isolation and parallel analysis of genomic DNA and RNA for gene therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7248.
Abstract 7251: Surface-engineered extracellular vesicles to modulate antigen-specific T cell expansion for cancer immunotherapy
Authors: Lyu Xiabing , Yamano Tomoyoshi , Imai Shota , Van Le Toan , Hanayama Rikinari 
Published: March 2024

Abstract
Tumor immunotherapy, including immune checkpoint therapy, CAR T cell therapy, and TCR-T cell therapy, has made significant progress in the treatment of cancer. Recently, newly developed nanomaterials have also been applied to anti-tumor immunotherapy. Among them, extracellular vesicles (EVs) have been well-engineered in recent years due to their low immunogenicity, high stability, and wide distribution in biological fluids. Despite the recent development of several EVs-based cancer immunotherapies, their clinical efficacy remains limited. In this study, we have developed engineered EVs designed to mimic the function of antigen-presenting cells, which can co-deliver multiple immune-activation signals to tumor-associated T cells. We named these vesicles Antigen-presenting Extracellular Vesicles (AP-EVs). AP-EVs express a high level of MHC I-peptide complexes, costimulatory molecules, and surface-bound cytokines, allowing for the simultaneous presentation of multiple immune modulators to antigen-specific CD8+ T cells. AP-EVs promote the clonal expansion and differentiation of antigen-specific cytotoxic T lymphocytes, resulting in potent anticancer immune responses. Notably, our findings indicate that combination therapy involving AP-EVs and anti-PD-1 yields superior anticancer immunity against established tumors compared to anti-PD-1 monotherapy. This synergistic effect underscores the potential of our engineered EVs as a novel and highly effective strategy for cancer immunotherapy.
Citation Format: Xiabing Lyu, Tomoyoshi Yamano, Shota Imai, Toan Van Le, Rikinari Hanayama. Surface-engineered extracellular vesicles to modulate antigen-specific T cell expansion for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7251.
Abstract 7259: Effectiveness and comparison of CAR-T cell therapies for synovial sarcoma; HER2-targeted CAR-T and NKG2D-based CAR-T
Authors: Miyazaki Tomohiro , Imai Chihaya , Oike Naoki , Murayama Yudai , Ariizumi Takashi , Baba Minori , Kasahara Yasushi , Kawashima Hiroyuki 
Published: March 2024

Abstract
Introduction: In Japan since 2019, CAR-T cell therapy has been used to treat patients with relapsed or refractory B-cell acute lymphoblastic leukemia and diffuse large B-cell lymphoma and has shown excellent clinical results. Clinical studies of CAR-T cell therapies targeting various antigens, such as HER2, have been conducted, but the therapeutic outcome in sarcoma is still limited. We have previously reported that HER2-targeted CAR-T cells show antitumor effects for synovial sarcoma in vitro. The purpose of this study is to compare HER2-targeted CAR-T cells and NKG2D-based CAR-T cells in antitumor effect and specific responses for synovial sarcoma in vitro.
Materials and Methods: Surface expressions of HER2 and NKG2D ligands on three synovial sarcoma cell lines were detected by using recombinant human HER2 Fc chimeric protein and that of NKG2D, followed by staining with PE-conjugated anti-human IgG secondary antibody. We generated 4-1BB-type second generation CAR-T cells targeting NKG2D ligands and examined their antitumor effects and specific responses against synovial sarcoma cells. In addition, we compared the differences between HER2-targeted CAR-T cells and NKG2D-based CAR-T cells by co-culturing with synovial sarcoma cells using short-term assay (WST-8 assay), long-term assay (Real-time Cell Analysis) and CD107a assay.
Results: HER2 and NKG2D ligands were found to be expressed by flow cytometry in three synovial sarcoma cell lines. In vitro, NKG2D-based CAR-T cells showed antitumor effects against synovial sarcoma cells, including degranulation and cytokine production. Furthermore, NKG2D-based CAR-T cells showed stronger antitumor effects than HER2-targeted CAR-T cells in both short- and long-term assays and expressed higher levels of CD107a.
Conclusions: In this study, NKG2D-based CAR-T cells showed more antitumor effects than HER2-targeted CAR-T cells in vitro. Although the reason for this is not clear, we hypothesize that NKG2D ligands may be induced in synovial sarcoma cells by co-culture with CAR-T cells because HER2 is a cancer-specific antigen, whereas NKG2D ligands are ligands for activating receptors of natural killer cells. Further studies, including in vivo studies, will be conducted to verify the difference in anti-tumor effects between these CAR-T cells.
Citation Format: Tomohiro Miyazaki, Chihaya Imai, Naoki Oike, Yudai Murayama, Takashi Ariizumi, Minori Baba, Yasushi Kasahara, Hiroyuki Kawashima. Effectiveness and comparison of CAR-T cell therapies for synovial sarcoma; HER2-targeted CAR-T and NKG2D-based CAR-T [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7259.
Abstract 7265: ETS-005, a highly selective TEAD4 palmitoylation inhibitor with potent anti-tumor activity and brain penetrating capability
Authors: Lu Jiajun , Du Wenpei , Gao Ming , Fan Xiaofei , Li Jinping , Feng Lijian , Wang Mengya , Li Yingjie , Zhong Xiaofeng , Cui Wenqi , Zheng Qiangang , Zhu Jidong 
Published: March 2024

Abstract
The Hippo pathway is a highly conserved network that regulates cell proliferation, tissue regeneration, and organ size by orchestrating YAP/TAZ-TEADs, the core effectors of signaling. Aberrant activation of YAP/TAZ has been implicated in tumorigenesis, tumor progression, metastasis and the resistance to targeted therapeutics, including MAPK and RTK inhibitors. Among the four TEAD paralogs, TEAD4 is found widely overexpressed in various solid tumors and potentially less associated with YAP/TEAD-related renal toxicity. Here we reported the identification of ETS-005, a highly selective TEAD4 small molecule inhibitor that shows preference for binding to the palmitoylation pocket of TEAD4 than other TEAD paralogs over 15 folds. ETS-005 displayed low nanomolar inhibition of cell proliferation in NF2 or LATS1/2 mutant mesothelioma in vitro, and robust anti-tumor efficacy in vivo. ETS-005 showed favorable oral availability, high brain penetration capability and broad safety window. Moreover, ETS-005 had relative long projected T1/2 in human, supporting a more convenient clinical QD dosing schedule. Our study demonstrated that selective TEAD4 palmitoylation inhibitor ETS-005 exhibited potent anti-tumor activity as much as pan-TEAD palmitoylation inhibitors while may gain broader therapeutic index. Additionally, ETS-005 also exhibited profound synergistic effects in drug combination studies, offering broad opportunities combined with MAPK and RTK therapies. ETS-005 is currently in IND-enabling study and expected to enter Phase 1 in 2024.
Citation Format: Jiajun Lu, Wenpei Du, Ming Gao, Xiaofei Fan, Jinping Li, Lijian Feng, Mengya Wang, Yingjie Li, Xiaofeng Zhong, Wenqi Cui, Qiangang Zheng, Jidong Zhu. ETS-005, a highly selective TEAD4 palmitoylation inhibitor with potent anti-tumor activity and brain penetrating capability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7265.
Abstract 7351: Delineating the prostate cancer tumor microenvironment through scRNA-seq profiling at different timepoints
Authors: Valencia Itzel , Pakula Hubert , Omar Mohamed , Loda Massimo , Marchionni Luigi 
Published: March 2024

Abstract
Distant metastasis remains the leading cause of death in patients with prostate cancer (PCa), however, the underlying mechanisms of this process remain unclear. Using samples from genetically-engineered mouse models (GEMMs) of PCa, we have identified eight different stromal cell states linked to epithelial mutations that may impact PCa progression to metastatic stages. To further investigate the unique intercellular interactions in the tumor microenvironment (TME) involved in mediating disease progression, we use single cell RNA sequencing (scRNA-seq) to profile primary PCa samples from different GEMMs including TRAMP, Hi-MYC, and FVBN, at different timepoints. Analysis of the scRNA-seq data revealed a significant enrichment of three clusters, designated as stromal c6 (s6), epithelial c7 (e7), and epithelial c10 (e10), exclusively in TRAMP, each expressing proliferative markers such as Mki67 and Top2a. To investigate the intercellular interactions among these clusters, we conducted ligand-receptor (LR) interaction analysis using CellChat. Notably, s6 is expressing the genes encoding ligands Bmp4, Fn1, and Igf1, which interact with the receptors Bmpr1b/Bmpr2, Itga3/Itgb1, and Igf1r, respectively expressed in e7. Subsequently, the transcriptomic profiles of these cells were used to build and validate a robust gene signature that can predict metastasis and survival in patients with PCa using a large cohort of 1239 samples, 930 of which were used for training while the remaining 309 samples were used for testing the model’s performance. In conclusion, these results underscore the role of the TME mediating PCa progression and highlight the potential of leveraging the TME to extract predictive and prognostic features which can be later employed to build predictive and prognostic models for patients with PCa.
Citation Format: Itzel Valencia, Hubert Pakula, Mohamed Omar, Massimo Loda, Luigi Marchionni. Delineating the prostate cancer tumor microenvironment through scRNA-seq profiling at different timepoints [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7351.
Abstract 7358: Role of noncoding genome architecture in esophageal cancer
Authors: Erkizan Hayriye Verda , Wadleigh Robert 
Published: March 2024

Abstract
Esophageal Cancer is a deadly disease with a tendency to be diagnosed at the later stages. Considered a rare disease, accounting for 1.1% of all cancers, EC comprises 2.6% of all cancer deaths. The survival rate for all stages is 21.7%. However, the survival rate decreases to 5.6 % for advanced-stage cancers. EC is more common in men and associated with older age and heavy alcohol and tobacco use. In the last 25 years, the death rate of EC has been decreasing slightly from 4.3 to 3.7. The death rates for lung, prostate, and colon cancers have decreased by half in the same time frame. Therefore, novel therapies and biomarkers are urgently needed to accelerate survival and reduce the death rates by at least half for patients with EC.We previously completed exome sequencing in a small sample size and observed that the mutations in the noncoding regions of the EC genome are highly affected. In this study, we perform exome sequencing in 110 paired esophageal tumors and normal tissues using an Agilent SSELXT HS Exon V8+UTR library enrichment kit. Twelve paired EC and normal tissues are sequenced using the PacBio Hifi system.In WES, we detected almost half of the noncoding region mutations in the 3UTR and 2kb downstream regions of the genome, significantly affecting 51 oncogenic or tumor suppressor genes. In addition, the involved genes are over-represented in critical signaling pathways and transcriptional regulation of pluripotent stem cells. The number of changes in the 5UTR and 2kb upstream are similar to the number of variations in the intronic regions. Apoptosis, stress response, and DNA double-strand break repair pathways are affected by 5UTR mutations. Mutations in the intronic regions frequently occurred in pro-tumorigenic immune regulation genes, such as IL-33 and IL-6, and oncogene-induced senescence.The combined effect of these genetic and coding region mutations on oncogenes, significant signaling pathways, cancer cell stemness, DNA damage repair pathways, and immune system regulation may significantly impact poor prognosis in EC patients. Further studies will verify the effectiveness of targeting these genes for developing candidate therapeutics.
Citation Format: Hayriye Verda Erkizan, Robert Wadleigh. Role of noncoding genome architecture in esophageal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7358.
Abstract 7385: Explainable AI model incorporating uncertainty estimation for enhanced MSI-H prediction and immunotherapy response in gastrointestinal cancer
Authors: Park Sunho , Kim Minj , Sung Ji-Youn , Park Jeong Hwan , Lee Sung Hak , Wang Sam C. , Cheong Jaeho , Hwang Tae Hyun 
Published: March 2024

Abstract
Background: Microsatellite instability-high (MSI-H) tumors respond well to immune checkpoint blockade and oftentimes not to chemotherapeutics. Despite value of determining MSI status to guide therapy, many patients’ samples are not untested. Deep learning models may be able to predict MSI status by analyzing hematoxylin and eosin (H&E) stained whole-slide images (WSIs). Validation of this tool will provide another tool to increase MSI testing. However, to be deployed into clinical routine care, prediction models need be externally validated in large and diverse patient cohorts. In addition, these models should provide uncertainty of prediction to help clinicians make informed decisions.
Results: In this study, we introduce a novel Bayesian prediction model using whole-slide images (WSIs) and deep Gaussian processes (DGPs) in a weakly supervised learning context. Extensively tested on large datasets (n=3,146) from multiple centers, our model not only demonstrated superior performance but also showed that incorporating uncertainty into predictions significantly improves MSI prediction accuracy, achieving AUROC of &gt;0.91 in colon cancer and &gt;0.94 in gastric cancer. Additionally, an in-depth analysis within the gastric cancer cohort indicated a significant correlation between predicted MSI-H regions and immunotherapy response. Patients who responded to immune checkpoint inhibitors had a higher proportion of MSI-H regions (P-value &lt; 0.05). This correlation was also observed in patients categorized as MSS but responsive to ICIs, highlighting the potential of our model to identify MSI-H patterns not detected through standard laboratory tests. This advancement could lead to more precise patient selection for ICI therapy, enhancing personalized treatment strategies in gastrointestinal cancer.
Citation Format: Sunho Park, Minj Kim, Ji-Youn Sung, Jeong Hwan Park, Sung Hak Lee, Sam C. Wang, Jaeho Cheong, Tae Hyun Hwang. Explainable AI model incorporating uncertainty estimation for enhanced MSI-H prediction and immunotherapy response in gastrointestinal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7385.
Abstract 7473: Flotillin-2 ablation in T cells enhances antigen sensitivity and functionality
Authors: Moon Sookjin , Karmaus Peer W. , Fessler Michael B. 
Published: March 2024

Abstract
The membrane scaffolding protein flotillin-2 (Flot2) has been proposed to support receptor signaling, but its involvement in T cell receptor (TCR) signaling and T cell responses remains unclear. Here, we show that the deletion of Flot2 increases antigen sensitivity along with changes in surface TCR clustering, resulting in enhanced TCR signaling and effector function to weak TCR stimulation. T cell-specific Flot2-deficient mice showed enhanced proliferation and effector cytokine production in both CD4+ and CD8+ T cells, resulting in better control of tumor growth and infection. However, in vitro TCR stimulation with plate-bound anti-CD3 and soluble anti-CD28 showed increased TCR signaling and early activation of CD4+, but not CD8+ Flot2-deficient T cells upon weak stimulation. In addition, Flot2-deficient CD4+ T cells showed better in vitro polarization toward T helper 1 cells upon weak TCR stimulation, likely due to increased sensitivity of the TCR-triggering threshold. Changes in TCR clustering on the membrane have been suggested to influence the early detection of foreign stimuli and the formation of immune synapses. Flot2 ablation indeed increased the number of membrane TCR nanoclusters on naïve CD4+ T cells. Collectively, this study suggests a mechanism for increasing T cell functionality to weak TCR stimulation by modulating the membrane protein Flot2, which affects surface TCR clustering. These results may have important implications for improving T cell reactivity in diseases with poor antigenicity, such as anti-tumor immune responses.
Citation Format: Sookjin Moon, Peer W. Karmaus, Michael B. Fessler. Flotillin-2 ablation in T cells enhances antigen sensitivity and functionality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7473.