bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5585: Tissue based next generation sequence is more accurate than ctDNA to detected pathogenic variants in MTAP wild type tumors
Authors: De Souza Andre Luiz 
Published: June 2023

Abstract
Next generation sequencing (NGS) of circulating tumor DNA (ctDNA) prevents invasive biopsies and captures tumor heterogeneity. In a prior report by Zhang et al (Nat Commun 2021), certain actionable mutations were more prevalent in ctDNA than tissue-based databases (e.g., EGFR 48% versus 25.2%). Our group investigated if discrepancies in patterns of pathogenic variants between liquid biopsy and tissue specimens in a subtype of metastatic urothelial carcinoma (MTAP deleted) can inform the best approach of utilizing tissue or blood. MTAP (methyl-adenosine phosphorylase) is an enzyme involved in salvage purine biosynthesis and its deletion confers sensitivity to pemetrexed and taxanes, but resistance to immune checkpoint inhibitors. The MTAP gene is deleted in 25% of urothelial carcinomas. We report herein the pattern of pathogenic variants from ctDNA in 17 patients with metastatic urothelial carcinoma, 10 with MTAP-deletion and 17 with MTAP wild-type. Among 10 patients with MTAP-deleted urothelial carcinoma with collected ctDNA, 3 had no detected pathogenic variant. The most common pathogenic variants in 7 patients were TP53 (4/7, 57%), TERT (4/7, 57%), ERBB2 (2/7, 28%); PIK3CA (2/7, 28%), and NFE2L2 (2/7, 28%). The mutations found in paired ctDNA and tissue based NGS were TP53 in 26.6 % (4/15), TERT in 21.0 % (4/19), ERBB2 in 66.6 % (2/3), PIK3CA in 50 % (2/4), and NFE2L2 in 100% (1/1) of patients. Three of the 10 patients with collected ctDNA had ELF3 frameshift loss-of- function alterations on tissue not found on ctDNA. Among 54 patients with MTAP wild-type urothelial carcinoma, 26 had collected ctDNA. Among these 26 patients, 9 had no detected pathogenic variants. Among the 17 patients with pathogenic variants, the most common mutations were TP53 (76%, 13/17), TERT (47%, 8/17), ERBB2 (24%, 4/17), RB1 (24%, 4/17), and BRCA1 or BRCA2 (24%, 4/17). Three of these 17 patients had no or insufficient tissue for NGS. The mutations found in paired ctDNA and tissue based NGS were TP53 in 100% (14/14), TERT in 64% (9/14), ERBB2 in 43% (6/14), RB1 in 29% (5/14), and BRCA1 or BRCA2 in 36% (5/14) of patients. MTAP wild-type patients had a higher frequency of TERT alterations (p=0.012), but not ERBB2, (p=0.453) than patients with MTAP-deleted type tumors. Ongoing evaluation of timing and location of pathogenic variants will inform where (primary tumor, metastatic site) and when (after chemotherapy, immune checkpoint inhibitors, antibody drug conjugates) to biopsy patients on progression after cancer therapies.
Citation Format: Andre Luiz De Souza. Tissue based next generation sequence is more accurate than ctDNA to detected pathogenic variants in MTAP wild type tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5585.
Abstract 5663: Discovery and characterization of anti-LILRB2 antibody SPX-104
Authors: Haight Anthony , Chen Qian , Rodriguez Ernesto , Siekierzycki Martin , Hall Victoria , Williams Brandon , Shi Jun , Nguyen Dinh-Duc , Cai Robert , Ma Jichun , White Michael , Qin Jingdong , Shen Jadon , Zhao Chuanke , Rong Zhuona , Meng Lin , Shou Chengchao 
Published: June 2023

Abstract
T-cell based immunotherapies have produced durable remission in certain cancer patients, but owing at least partially to immunosuppression in the tumor microenvironment, response rates with current therapies remains challenging. Reversing the immunosuppression is a recognized pathway for enhancing the activity of existing IO therapies. LILRB2 (ILT4) is a key receptor for macrophage maturation and polarization and an emerging therapeutic target in immuno-oncology. This research aims to produce anti-LILRB2 antibodies to redirect the polarization of myeloid cells, specifically macrophages, in the tumor microenvironment. The LILRB2 antibodies were generated through the mouse hybridoma method. After humanization and maturation, potent and selective IgG4 anti-LILRB2 antibodies were obtained. Binding affinities were evaluated through ELISA and 293T-LILRB2 cell flow cytometry binding assays which demonstrated sub-nanomolar binding affinity as well as effective blocking of the interaction of LILRB2 with its ligands HLA-G and HLA-A2 for multiple antibodies. SPX-104 was shown to redirect macrophage polarization in primary cultured human PBMC and human monocyte derived macrophage (HMDM) models. SPX-104 treatment induced hTNFa expression and suppressed hIL10 expression in the LPS stimulated PBMC model. In the HMDM model, SPX-104 effectively induced pro-inflammatory cytokine hTNFα expression in M-CSF. Furthermore, an autologous mixed lymphocyte reaction (auto-MLR) assay to evaluate T cell response showed dose-dependent increases in hIFNγ and hGM-CSF expression following SPX-104 treatment. In a CD34-humanized hLILRB2 transgenic mouse efficacy model, SPX-104 in combination with an immune checkpoint inhibitor, effectively inhibited tumor growth. These results confirm enhanced T cell activity following macrophage redirected polarization. The in vitro and in vivo evaluation, of SPX-104 relative to other anti-LILRB2 antibodies will be presented.
Citation Format: Anthony Haight, Qian Chen, Ernesto Rodriguez, Martin Siekierzycki, Victoria Hall, Brandon Williams, Jun Shi, Dinh-Duc Nguyen, Robert Cai, Jichun Ma, Michael White, Jingdong Qin, Jadon Shen, Chuanke Zhao, Zhuona Rong, Lin Meng, Chengchao Shou. Discovery and characterization of anti-LILRB2 antibody SPX-104. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5663.
Abstract 5681: Tetra-specific antibody GNC-038: guidance and navigation gontrol (GNC) molecule development for treatment of CD19+ malignancies
Authors: Khalili Jahan Salar , Xiao Sa , Zhu Yi 
Published: June 2023

Abstract
B cell malignancies treated with CD19-directed immunotherapies can relapse, in some cases due to clonal selection for reduced CD19 antigen expression or enhancement of immunosuppressive phenotypes. Here we demonstrate that a Guidance and Navigation Control (GNC) tetra-specific antibody, GNC-038, binds to CD19, CD3, PD-L1, and 4-1BB and mediates cytolysis of human leukemia and lymphoma cells by T cells.
Redirected T cell cytolysis (RTCC) occurs in the presence of GNC-038 (Emfizatamab), resulting in the killing of CD19+ leukemia and lymphoma cell lines. The cytolytic functions induced by GNC-038 are similar to Blinatumomab in vitro, as indicated by T cell degranulation and production of IFN-gamma. Human T cells in PBMC exposed to GNC-038 in vitro proliferate in a dose-dependent fashion. Proliferation is further enhanced upon rechallenge with leukemic target cells. Proliferation of T cells from individuals with higher % PD-1+ and Effector polarized compartments is enhanced by GNC-038 compared to Blinatumomab. To evaluate the contribution of each binding domain of GNC-038 in mediating RTCC function, versions of GNC-038 were prepared, replacing each antigen binding domain with anti-FITC binding domains. Under assay conditions using PBMC for RTCC toward the CD19+ target cell line Nalm-6, the results demonstrate the contribution of each domain to the overall, anti-leukemic cytolytic activity.
To evaluate the potential for GNC-038 to mediate cytokine release syndrome, the molecule is evaluated in soluble, and plate bound formats in the presence of PBMC and CD19+ leukemic targets cells. In comparison to Blinatumomab, the production of cytokines is comparable, with some notable differences. PBMC exposed to soluble GNC-038 for 48 hours produced more IFN-γ, IL-2 and TNF-α, while showing no significant difference in production of IL-6. Based on these results, the primary indicator of CRS, IL-6, does not suggest increased risk compared to Blinatumomab, while the type of T cell activity induced by GNC-038 in PBMC with leukemia cells is distinct.
Collectively, the GNC-038 represents a class of multi-specific and multi-modal immune cell engagers with potential to mediate CD19+ cancer killing, while also increasing the T cell compartment’s therapeutic potential to respond to T cell redirection upon subsequent cycles of therapy. The clinical phase I-b study of GNC-038 is under way and the available data exhibit strong signals of efficacy with acceptable tolerability.
Citation Format: Jahan Salar Khalili, Sa Xiao, Yi Zhu. Tetra-specific antibody GNC-038: guidance and navigation gontrol (GNC) molecule development for treatment of CD19+ malignancies. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5681.
Abstract 5822: YAP inhibition via targeting MAP3K3-dependent lysosomal degradation pathway overcomes BRAF and CDK4/6 inhibitor resistance
Authors: Ryu Won-Ji , Park Sanghyun , Kim Tae Yeong , Hwang Yumi , Han Hyun Ju , Lee Jeong Dong , Kim Gun Min , Sohn Joohyuk , Kim Sang Kyum , Kim Joon , Kim Min Hwan 
Published: June 2023

Abstract
The Hippo-yes-associated protein (YAP) signaling pathway activation underlies the resistance to a wide range of molecularly targeted anti-cancer agents. However, strategies to block YAP activity in cancer by promoting YAP degradation have been largely unsuccessful despite rigorous investigations into canonical Hippo-YAP regulatory mechanisms. Here, we report a novel mechanism of YAP stability regulation by MAP3K3 independently of LATS-mediated proteasomal degradation. We observed that MAP3K3 depletion significantly reduced YAP protein levels in both normal and malignant cells, and mass spectrometry analysis revealed that MAP3K3 phosphorylates YAP at its serine 405 residue. MAP3K3-mediated serine 405 YAP phosphorylation polarizes YAP interaction with BTRC while hindering its interaction with FBXW7, collectively preventing both proteasomal degradation and the p62-mediated lysosomal degradation of YAP. We investigated the role of this mechanism in overcoming anti-cancer resistance and observed robust YAP activation in CDK4/6 inhibitor-resistant luminal breast cancer cells. Genetic and pharmacological MAP3K3 inhibition suppressed YAP-induced drug resistance. Moreover, increased MAP3K3 expression supported the pro-survival activity of YAP in BRAF inhibitor-resistant melanoma cells, and MAP3K3 depletion downregulated YAP-dependent cell cycle gene signatures. Accordingly, the combination of vemurafenib and ponatinib was effective in reducing the survival of BRAF inhibitor-resistant melanoma cells. Collectively, our study identified a novel phosphorylation-mediated YAP stability regulation mechanism and underscored MAP3K3 inhibition as a promising strategy to overcome BRAF and CDK4/6 inhibitor resistance by directly promoting YAP degradation.
Citation Format: Won-Ji Ryu, Sanghyun Park, Tae Yeong Kim, Yumi Hwang, Hyun Ju Han, Jeong Dong Lee, Gun Min Kim, Joohyuk Sohn, Sang Kyum Kim, Joon Kim, Min Hwan Kim. YAP inhibition via targeting MAP3K3-dependent lysosomal degradation pathway overcomes BRAF and CDK4/6 inhibitor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5822.
Abstract 5824: Human ovarian cancer cell seeding density as a mechanism of cisplatin resistance associated with expression of anti-apoptotic and autophagy proteins
Authors: Brown Thomas W. , Punyamurtula Ujwal , El-Deiry Wafik S. 
Published: June 2023

Abstract
Drug effects may vary depending on cancer cell density. We investigated discrepancies in phenotypes for high density and low-density cultured cancer cells and elucidated relevant variables that influence them. We assessed chemosensitivity as a function of tumor cell density by plating TOV-21G and OVMANA ovarian cancer cell lines in 96-well plates at various seeding densities per well and treated them with various concentrations of cisplatin. CellTiterGlo assays were performed at 72 hours of treatment to determine cisplatin dose response curves. We used ethidium homodimer fluorescence staining and imaging to quantify extent of cell death at differing cell densities of TOV-21G and OVMANA cells treated with cisplatin for 48 and 72hours in 48-well plates. We performed western blot analyses of apoptotic and autophagy proteins from TOV-21G and OVMANA cells that were seeded at high and low cell densities in 24-wellplates. TOV-21G and OVMANA cells plated at higher cell seeding densities displayed less cisplatin sensitivity than TOV-21G and OVMANA cells plated at lower seeding densities, as shown by cisplatin dose response curves. Ethidium homodimer staining of TOV-21G and OVMANA cells treated with cisplatin revealed that cells seeded at lower densities experience a greater amount of cell death that cells seeded at higher densities. Western blot analyses showed that high density TOV-21G cells may express greater amounts of BCL2 and c-FLIP and lower amounts of p62 and NOXA compared to low density cells when normalized for protein expression. Similarly, high density OVMANA cells express greater amounts of c-FLIP andBCL2 and lower amounts of NOXA compared to low density cells when normalized for protein expression. Our experiments reveal that human ovarian cancer cells display different phenotypic changes depending on cell density, causing higher density cells to require increased cisplatin to achieve the same level of effect seen in lower density cells. Ovarian cancer cell resistance to cisplatin is associated with alterations in autophagy and anti-apoptotic protein expression at high cell seeding density. These alterations may also affect chemosensitivity in vivo in settings of differential tumor density, such as single circulating tumor cells compared to clumps of tumor cells, and other settings, such as metastasis.
Citation Format: Thomas W. Brown, Ujwal Punyamurtula, Wafik S. El-Deiry. Human ovarian cancer cell seeding density as a mechanism of cisplatin resistance associated with expression of anti-apoptotic and autophagy proteins. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5824.
Abstract 5833: Crosstalk between cancer-associated fibroblasts and CD8 T cells leads to improved T cell activation in head and neck cancer
Authors: Graves Diana , Obradovic Aleksandar , Schares Henry , Korrer Michael , Bachmann Brian , Kim Young , Park Ben , Hurley Paula 
Published: June 2023

Abstract
Cancer-associated fibroblasts (CAFs) have been shown to modulate immune responses in the tumor microenvironment (TME), however, the extensive heterogeneity of these cells has precluded rigorous understanding of their immunoregulatory role in the head and neck TME. To gain a better understanding of the relationship between CAFs and the immune environment in head and neck cancer, we leveraged protein activity inference tools to analyze single-cell RNA sequencing of advanced-stage head and neck squamous cell carcinoma (HNSCC) patients pre- and post-treatment with the αPD-1 therapy, nivolumab. From this analysis, we identified a novel CAF population predictive of patient response to αPD-1 therapy. Utilizing in vitro co-culture assays with primary human CD8 T cells, we discovered that this novel CAF population was able to elicit features associated with enhanced CD8 T cell function, namely the reduction of PD-1+TIM-3+ exhaustive phenotypes and induction of CD103+NKG2A+ tissue-resident memory phenotypes and cytotoxicity. Due to their unique ability to stimulate T cells in this manner, we termed this novel CAF population T cell-stimulating CAFs (tsCAFs). In efforts to elucidate the mechanism behind this pro-inflammatory function, we determined that tsCAFs secrete a heat-sensitive small molecule/s in order to alter CD8 T cell behavior. However, tsCAFs will only secrete this factor in the presence of activated T cells demonstrating crosstalk between T cells and CAFs in the head and neck TME. This pro-inflammatory crosstalk between CAFs and T cells represents a novel finding that further contributes to the idea of immunoregulatory pleiotropy among CAFs. Accordingly, our findings highlight the functional importance of distinct CAF subsets in modulating the immunoregulatory milieu of human HNSCC and warrant more extensive characterization of CAF-T cell interactions in human squamous cell carcinoma.
Citation Format: Diana Graves, Aleksandar Obradovic, Henry Schares, Michael Korrer, Brian Bachmann, Young Kim, Ben Park, Paula Hurley. Crosstalk between cancer-associated fibroblasts and CD8 T cells leads to improved T cell activation in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5833.
Abstract 6244: Design, synthesis, and structure-activity relationships of substituted pyrido[3,2-d]pyrimidines as microtubule targeting agents and anti-cancer agents
Authors: Shah Yesha Vijaykumar , Bai Ruoli , Hamel Ernest , Gangjee Aleem 
Published: June 2023

Abstract
Microtubules (MTs) are composed of αβ-tubulin heterodimers and are essential components of the cellular cytoskeleton involved in critical cellular functions, including mitosis, cell migration and signaling, intracellular trafficking, and angiogenesis. Microtubule targeting agents (MTAs) are highly successful chemotherapeutic agents because they target MT dynamics and interfere with MT-dependent cellular processes. The clinical efficacy of MTAs is limited by multidrug resistance due to expression of the P-glycoprotein (Pgp) drug efflux pump or increased expression of βIII-tubulin. This necessitates the development of novel MTAs effective against cell lines expressing these forms of drug resistance, which could offer potential advantages in patients who fail to respond to current MTAs, such as paclitaxel. Previously, we reported colchicine site (CS) binding compound 1 with a pyrido[3,2-d]pyrimidine scaffold and a 2-H substitution and N4-4’-methoxyaniline substitution inhibited colchicine binding and tubulin assembly (87% inhibition at 5 µM and IC50 = 1.3 µM, respectively). Compounds 2-9 were designed with a 2-CH3 substitution to evaluate the structure-activity relationships at the 4-position by using conformational restriction and isosteric replacements. Compounds 2-9 were synthesized, and the biological evaluation showed that compounds 2-9 inhibited tubulin assembly (7, IC50 = 0.72 μM) and binding of colchicine to tubulin (7, 97% inhibition at 5 µM, 81% at 0.5 µM). Compound 7 was found to be highly potent in the MCF-7 breast cancer cell line with an IC50 of 2.5 nM which was ~3.5-fold better than combretastatin-A4 (CA4). Compound 7 inhibited the growth of the human ovarian cancer cell line OVCAR-8 with an IC50 = 3.0 nM. For the Pgp overexpressing cell line NCI/ADR-RES, 7 was equally potent (IC50 = 3.0 nM), whereas paclitaxel was almost inactive (IC50 = 1,500 nM). Thus, we have identified 2-CH3 substituted pyrido[3,2-d]pyrimidines as a novel structural scaffold for inhibition of tubulin assembly and colchicine binding that have potent cytotoxic activity against the breast cancer cell line MCF-7 and against both the parental ovarian cancer cell line OVCAR-8 and its derivative Pgp overexpressing cell line NCI/ADR-RES. These compounds thus merit further study as potential cancer chemotherapeutic agents.
Citation Format: Yesha Vijaykumar Shah, Ruoli Bai, Ernest Hamel, Aleem Gangjee. Design, synthesis, and structure-activity relationships of substituted pyrido[3,2-d]pyrimidines as microtubule targeting agents and anti-cancer agents. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6244.
Abstract 6257: Developing HDAC inhibitors as immunomodulators
Authors: Colligan Sean , Shen Li , Rupert Christopher , Bard Jonathan , Pili Roberto 
Published: June 2023

Abstract
Immune checkpoint inhibitors (ICIs) are standard of care for several solid tumor types, including renal cell carcinoma (RCC). However, the clinical success of these therapies is dampened by the fact that the majority of patients demonstrate either inherent resistance to treatment or develop secondary resistance following an initial response. One key mechanism of tumor-driven ICI resistance is the generation and recruitment of suppressive immune cell types, including regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs), which coordinate to suppress anti-tumor T cell responses. Thus, there is a critical need for the development of novel combination strategies aimed at mitigating the presence and function of suppressive immune cells to improve the efficacy of ICIs in the clinic. Our laboratory has previously demonstrated that histone deacetylase inhibition (HDACi) is associated with a decrease in both the number and function of tumor-infiltrating Tregs and MDSCs in the RENCA tumor model. Thus, the overall goal of these studies both preclinically and clinically is to investigate the impact of the immunomodulatory effects of HDACi in combination with ICI therapy, with the overall hypothesis that HDACi will improve the efficacy of anti-PD1 therapy in RCC. Our pre-clinical data support this hypothesis by demonstrating increased tumor control and survival in RENCA tumor-bearing mice when treated with a combination of anti-PD1 and HDACi compared to single agent therapy. These increases were also associated with an increase in the activation state of anti-tumor immune cells, as demonstrated by increased surface expression of MHC Class II molecules on macrophages and a decrease in phenotypically defined monocytic MDSCs. ATACseq and RNAseq data generated from combination-treated animals also outline a gene expression signature associated with both myeloid and T cell activation. Interestingly, our clinical studies also afforded us the opportunity to investigate potential biomarkers associated with responder status, which will allow us to better predict patient outcomes and administer therapies accordingly. Accumulating evidence from two independent clinical trials run by our group suggests that high levels of suppressive CD11b+HLA-DRlo MDSCs at baseline in the peripheral blood is associated with lack of clinical response to the combination of HDACi and ICI. Overall, these data support the rationale for the combination of ICI and HDACi in the clinic, and provide a potentially useful biomarker through which we can predict the success of combination therapy.
Citation Format: Sean Colligan, Li Shen, Christopher Rupert, Jonathan Bard, Roberto Pili. Developing HDAC inhibitors as immunomodulators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6257.