tbuckley/cabot-search huggingface dataset:
Abstract 3076: Unveiling the therapeutic potential of β-catenin inhibition in triple negative breast cancers: Targeting the Warburg effect
Authors: Sheikh Mohammad Umar, Shruti kahol, Arundhathi Dev JR, Akanksha Kashyap, Sandeep R. Mathur, Ajay Gogia, S.V.S Deo, Chandra Prasad
Journal: Cancer Research (2024)

Abstract Introduction: Triple Negative Breast Cancer (TNBC) exhibits increased glycolysis, known as the Warburg effect. Recent research, including our own Nanostring nCounter studies, identify β-catenin as an oncoprotein linked to elevated glycolysis in TNBC tumors. Our current research explores the impact of β-catenin inhibitors on glycolysis in TNBC cell lines and an in vivo CDX model. Method: We employed immunohistochemistry to assess 98 TNBCs for the presence of β-catenin, PFKP, LDH-A, and MCT1 proteins, exploring their correlation with clinicopathological factors. In in-vitro experiments using MDA-MB-231, MDA-MB-468, and 4T1 cell lines, we investigated how β-catenin inhibitors (XAV939 &amp; Axitinib) affected aerobic glycolysis components, and TNBC cell characteristics (proliferation, migration, invasion, and stemness). For in-vivo validation, 4T1 TNBC xenografts were employed to confirm our findings. Results: Among the 98 TNBC patients, 63 (64%) displayed cytoplasmic/or nuclear β-catenin staining. Additionally, cytoplasmic accumulation of PFKP was observed in 52/98 (53%), increased cytoplasmic LDH-A expression in 57/98 (58%), and membranous MCT-1 expression in 50/98 (51%) TNBC patients. Notably, significant positive correlations were found between nuclear/cytoplasmic β-catenin and cytoplasmic PFKP (p = 0.001) as well as membranous MCT1 (p = 0.014). Furthermore, β-catenin, PFKP, LDHA, and MCT1 proteins were overexpressed in all TNBC cell lines thereby supporting their glycolytic nature. Comparative analyses between XAV939 and Axitinib revealed that Axitinib significantly reduced various TNBC cell parameters, including migration, invasion, lactate production, colony-forming ability, and expression of aerobic glycolytic pathway proteins. In the in-vivo studies, 30mg/kg Axitinib in a female Balb/c-4T1 xenograft model resulted in a substantial reduction in tumor volume and weight. Conclusion: Our findings show that increased levels of β-catenin play an important role in regulating aerobic glycolysis in TNBCs. Furthermore, our findings also highlight Axitinib's potential as an effective therapeutic agent for the treatment of β-catenin-positive TNBCs. Citation Format: Sheikh Mohammad Umar, Shruti kahol, Arundhathi Dev JR, Akanksha Kashyap, Sandeep R. Mathur, Ajay Gogia, S.V.S Deo, Chandra Prasad. Unveiling the therapeutic potential of β-catenin inhibition in triple negative breast cancers: Targeting the Warburg effect [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 3076.
Abstract 97: A E2F6 ceRNA network suppresses dendritic cell function, via PBX1/IL-10 signaling, in ovarian cancer
Authors: Michael W.Y. Chan, Yin-Chen Chen, Ching-Wen Lin, Frank Cheng, Ching-Cher Sanders Yan, Chao-Ping Hsu, Yu-Min Chuang, Jie-Ting Low, Xiaojing Ma, Yao-Ting Huang, Chia-Bin Chang, Chin Li, Hung-Cheng Lai, Shu-Fen Wu, Shih-Hsun Hung, Je-Chiang Tsai
Journal: Cancer Research (2024)

Abstract It is reported that long-term use of estrogen could increase the risk of ovarian cancer. However, the role of estrogen in immunoevasion is not fully explored. We have previously demonstrated that estrogen-mediated upregulation of E2F6, and, c-Kit, by epigenetic silencing of miR-193a, and a competing endogenous (ceRNA) mechanism. In this study, we found that PBX1, a transcriptional activator of the immunosuppressive cytokine, IL-10, is also a target of miR-193a. Importantly, overexpression of the E2F6 3’UTR upregulates both E2F6 and, PBX1, as well as IL10 in ovarian cancer cell lines, suggesting that ceRNA mechanism exists between E2F6 and PBX1. These phenomena are further supported by our stochastic simulation of the estrogen-mediated E2F6 ceRNA network on the distribution of E2F6 and PBX1 mRNA in cancer cells, which is consistent with the TCGA ovarian cancer RNA-Seq dataset. Importantly, monocyte-derived dendritic cell activation of T-cell function was inhibited by pretreatment of conditioned media derived from ovarian cancer cells overexpressing E2F6 3’UTR; such inhibition was rescueable by an anti-IL-10 antibody. Clinically, IL10 level was higher in ovarian cancer patients with higher E2F6 and PBX1, and in ovarian cancer cell lines overexpressed with E2F6 3’UTR. Taken together, these results showed that E2F6 could suppress anti-tumor immune response of dendritic cell, E2F6 ceRNA network. Epigenetic intervention in restoring the expression of miR-193a may be able to enhance anti-tumor immune response against ovarian cancer. Citation Format: Michael W.Y. Chan, Yin-Chen Chen, Ching-Wen Lin, Frank Cheng, Ching-Cher Sanders Yan, Chao-Ping Hsu, Yu-Min Chuang, Jie-Ting Low, Xiaojing Ma, Yao-Ting Huang, Chia-Bin Chang, Chin Li, Hung-Cheng Lai, Shu-Fen Wu, Shih-Hsun Hung, Je-Chiang Tsai. A E2F6 ceRNA network suppresses dendritic cell function, via PBX1/IL-10 signaling, in ovarian 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 97.
Abstract 2348: A global multiscale map of protein assemblies from integration of protein interactions and images
Authors: Leah V. Schaffer, Mengzhou Hu, Edward L. Huttlin, Gege Qian, Abantika Pal, Neelesh Soni, Andrew Latham, Laura Pontano Vaites, Trang Le, Yue Qin, Christopher Churas, Dexter Pratt, Ignacia Echeverria, Andrej Sali, J Wade Harper, Steven P. Gygi, Emma Lundberg, Trey Ideker
Journal: Cancer Research (2024)

Abstract Cells regulate growth and function through a hierarchical structure of subcellular protein assemblies, in which alterations can result in cellular dysfunction leading to disease such as cancer. Much of this structure remains uncharted, resulting in recent efforts to map subcellular organization at different physical scales. Here, we report a global architectural map of human cancer cell protein assemblies spanning 10−9 to 10−5 nm, based on integration of near-proteome-wide affinity purification mass spectrometry-based protein interactions and immunofluorescent imaging in U-2 OS osteosarcoma cancer cells. The U-2 OS multi-scale integrated cell map places &amp;gt;5000 proteins into 270 distinct subcellular protein assemblies across biological scales, representing approximately half of expressed proteins. There are known organelles and protein complexes recovered in the map, as well as 152 putative assemblies, such as a putative interferon signaling complex consisting of a serine protease and STAT transcription factors. The map also incorporates 128 previously uncharacterized proteins into protein assemblies, such as C18orf21 association with a canonical RNAse complex. Protein subsystems in the U-2 OS map were evaluated for the potential for downstream integrative structural modeling, where available structural data (e.g. crosslinking, Protein Data Bank structures, AlphaFold predictions) are combined in a Bayesian framework to model the physical structures of protein complexes. Using this framework, we created an integrated structural model of new proteins interacting with the Rag-Ragulator complex, which regulates MAPK and mTOR signaling. In summary, the global proteome architecture map provides a resource for cellular biology discovery and the systematic determination of protein functions and structures. Citation Format: Leah V. Schaffer, Mengzhou Hu, Edward L. Huttlin, Gege Qian, Abantika Pal, Neelesh Soni, Andrew Latham, Laura Pontano Vaites, Trang Le, Yue Qin, Christopher Churas, Dexter Pratt, Ignacia Echeverria, Andrej Sali, J Wade Harper, Steven P. Gygi, Emma Lundberg, Trey Ideker. A global multiscale map of protein assemblies from integration of protein interactions and images [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 2348.
Abstract 1307: Community-driven support platform BlueHQ: An innovative solution to address the needs of patients with colorectal cancer
Authors: Kimberly Lynn Newcomer
Journal: Cancer Research (2024)

Abstract Background: Colorectal cancer (CRC) is the third-most commonly diagnosed cancer and the second-leading cause of cancer death in men and women combined in the United States. To manage the disease, patients and caregivers turn to various tools and resources for financial assistance, information dissemination, emotional and peer support, and treatment planning, among other critical issues and needs they face. The Colorectal Cancer Alliance (the Alliance) created BlueHQ to provide patients and caregivers with a resource solution encompassing all potential areas of need. Methods: A survey aimed at understanding needs, barriers, and quality improvement opportunities was disseminated via the Alliance's Blue Hope Nation community for two weeks and by email. One hundred sixty-seven colorectal cancer patients and forty caregivers of colorectal cancer patients completed the survey. Results: Patients and caregiver respondents report reliance on external tools and resources to manage disease and support information. Of the support methods, patient respondents reported using social media (46.11%); notebooks, journals, and planners (45.41%); online articles (44.91%); the Blue Hope Nation Facebook group (41.32%); cancer discussion boards (35.33%); and spiritual or religious advice (29.94%). Patients sought financial assistance, local peer support and groups, and mental health help to minimize diagnosis-related stressors. To provide more efficient care and limit stress, the community suggested financial help, communication and support from other patients and caregivers, and informational resources. Conclusions: These survey results are consistent with other published learnings about patient and caregiver reliance on support tools and highlight the myriad resources that patients and caregivers currently use for managing CRC. BlueHQ is a support solution that provides patients and caregivers with access to information and resources tailored to users’ specified profiles, including molecular characteristics of the tumor. Users can also store documents and information from healthcare encounters, creating a longitudinal record and tracking disease progression. In the age of precision oncology, BlueHQ ensures patients and users are presented with personalized educational materials and multimedia resources to help manage their disease and bridge the gaps in patient support. BlueHQ was explicitly designed to connect the CRC community to the latest therapeutic and clinical research resources to improve outcomes and quality of life for all CRC patients. Citation Format: Kimberly Lynn Newcomer. Community-driven support platform BlueHQ: An innovative solution to address the needs of patients with colorectal 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 1307.
Abstract 1103: Molecular signature for treatment-responsive and recurrent Wilms tumors
Authors: Jieyun Jiang, Derek B. Allison, Ravshan Burikhanov, Saptadwipa Ganguly, Ryan A. Goettl, Jinpeng Liu, Chi Wang, Amanda F. Saltzman, Thomas Tucker, Peter H. Spielmann, Eric B. Durbin, John A. D’Orazio, Vivek M. Rangnekar
Journal: Cancer Research (2024)

Abstract Wilms tumor is the most common solid renal malignancy in children. To better understand the biology of Wilms tumors and develop drugs especially against tumors that relapse, we sought to identify mutations in the exome, differential gene expression patterns, and tumor suppressor expression status of Wilms tumors in Kentucky. The Kentucky Cancer Registry (KCR) Virtual Tissue Repository identified 29 cases of Wilms tumor diagnosed between 2015 and 2021 at hospitals across the Commonwealth of Kentucky. The Markey Cancer Center Biospecimen Procurement and Translational Pathology Facility prepared tumor microarrays (TMAs) using Wilms tumor and matching normal tissue cores for immunohistochemistry (IHC) analysis. RNA-Seq analysis performed at the Markey Cancer Center Oncogenomics Facility identified a gene signature that was further validated by IHC and reverse-transcription quantitative-PCR (RT-qPCR). Outcome data provided by KCR indicated that increased expression of an anti-apoptotic protein in the tumor counter-intuitively provided better prognosis and outcome to treatment, indicating that the treatments either directly or indirectly targeted this protein. Loss of function of the tumor suppressor proteins in Par-4/PAWR, WT1 and p53 did not explain the higher expression of the cell survival protein. Our multidisciplinary team approach involves basic science/translational researchers, population scientists, biomedical informaticists, and clinicians and has resulted in well-characterized, Wilms tumor tissue microarrays. The next phase of the study is generating patient derived xenografts (PDXs) for a better understanding of Wilms tumor biology in children. Citation Format: Jieyun Jiang, Derek B. Allison, Ravshan Burikhanov, Saptadwipa Ganguly, Ryan A. Goettl, Jinpeng Liu, Chi Wang, Amanda F. Saltzman, Thomas Tucker, Peter H. Spielmann, Eric B. Durbin, John A. D’Orazio, Vivek M. Rangnekar. Molecular signature for treatment-responsive and recurrent Wilms tumors [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 1103.
Abstract 6864: Tumor suppressor function of the ubiquitin ligase Siah1a in melanoma is mediated by myeloid derived suppressor cells
Authors: Marzia Scortegagna, Yuanning Du, Yongmei Feng, Ze'ev Ronai
Journal: Cancer Research (2024)

Abstract Growing evidence supports the important role of myeloid-derived suppressor cells (MDSC) in melanoma progression and response to therapy. MDSC contributes to a pro-tumorigenic phenotype, yet the mechanistic basis for the immune suppressor properties acquired by MDSC remains largely unknown. Mammals have two homologous Siah genes, Siah1 (Siah1a and Siah1b in mice) and Siah2. In the context of melanoma, the ubiquitin ligases Siah1a and Siah2 have melanoma-intrinsic and -extrinsic (immune) functions. Correspondingly, ablation of Siah1a/2 in melanoma or its microenvironment attenuates melanoma development in a number of mouse melanoma models. Given that number of macrophage clusters infiltrated into melanoma when grown in Siah2 KO mice, we set to assess macrophage function in melanoma. Selective ablation of Siah1a or Siah2 in macrophages, using Lyz2Cre, revealed that Siah1a but not Siah2 elicits a tumor suppressor function in melanoma. Inoculation of mouse melanoma Yummer1.7 cells (Braf mutated and Pten deleted) in mice lacking Siah1a in macrophages, resulted in bigger melanoma tumors compared to melanoma grown in either WT or mice in which macrophages were ablated of Siah2. FACS analysis of melanoma tumors grown in mice harboring Siah1a mutant macrophages revealed a significant increase in MDSC, which coincided with a decrease in CD4+ and CD8+ cells, compared with WT mice. These observations suggest that a lack of Siah1a in macrophages leads to an expansion of MDSC that affects surrounding immune cells, including T cells. RNA-seq analysis of MDSC that were differentiated in vitro from bone marrow cells of WT or Siah1a ablated macrophage mice revealed increased expression of genes involved in proliferation and alternative macrophage activation in MDSC lacking Siah1a when compared to the WT genotype. Mapping mechanisms underlying Siah1a tumor suppressor function is expected to reveal novel regulatory cues in melanoma control by the MDSC population while mapping novel means for stratifications of melanoma to therapy, and possibly new means for therapy of this tumor type. Citation Format: Marzia Scortegagna, Yuanning Du, Yongmei Feng, Ze'ev Ronai. Tumor suppressor function of the ubiquitin ligase Siah1a in melanoma is mediated by myeloid derived suppressor cells [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 6864.
Abstract 3765: Single cell spatial proteomics analysis and computational evaluation pipeline
Authors: Behnaz Bozorgui, Zeynep Dereli, Guillaume Thibault, John N. Weinstein, Anil Korkut
Journal: Cancer Research (2024)

Abstract Resolving tissue and proteomic heterogeneity is critical to decoding the structure and function of tumor-immune microenvironment (TIME). Such understanding requires profiling of tumor and immune cell proteomic features with spatial resolution at the single-cell level. Although such spatially resolved methods and data sets are becoming increasingly available, analytical and computational methods that can extract the highly complex features and interactions within TIME are lacking. To address that problem, we have developed a computational pipeline we call the Spatial Proteomics Analysis and Computational Evaluation Pipeline (SPACE). The SPACE pipeline is composed of many analysis modules for processing and mining highly multiplexed imaging-based data types to explore TIME composition, organization, and heterogeneity. The pipeline generates and interprets biomarker expression and positional information from multiplexed images using algorithms for image indexing, image registration, quality control, segmentation, identification and removal of non-specific signals, data normalization, automatic identification of missing data, and adjustment for left-over signals. The accurate intensity measurements at single cell level are then used to calculate the proposed spatial features that represent cellular interactions in TIME. A hierarchical decision tree of cell markers is used to annotate types and identities for individual cells. The SPACE enables statistical and differential analyses of complex spatial features as well as cell types/identities with respect to clinical annotations and genomic alterations. The visualization of spatial and imaging data is made possible through an open-source OMERO image repository and spatial maps that integrate diverse markers in a single representation. Here, we demonstrate the applications of our pipeline in diverse gastrointestinal tumor types (e.g., small bowel adenocarcinoma) and validate the importance of integrating tissue heterogeneity at spatial and single-cell level. The framework is applicable to nearly all highly multiplexed imaging data platforms, including but not limited to, CycIF, CODEX, and imaging mass cytometry. Citation Format: Behnaz Bozorgui, Zeynep Dereli, Guillaume Thibault, John N. Weinstein, Anil Korkut. Single cell spatial proteomics analysis and computational evaluation pipeline [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 3765.
Abstract 530: The effect of cardamonin on PD-L1 expression in triple-negative breast cancer cells
Authors: Patricia Mendonca, Bhonessa Kirpal, Sukhmandeep Kaur, Karam F. A. Soliman
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer (TNBC) accounts for about 10% of all breast cancers and does not express estrogen, progesterone, or HER2 receptors. It has an aggressive nature, it is highly metastatic, and because of the lack of therapies, it continues to be a challenge. These cancer cells employ mechanisms to escape the immune system that induce the upregulation of PD-L1 expression, a ligand encoded by the CD274 gene. Because cancer cells tend to produce higher levels of PD-L1 compared to normal cells, therapies that inhibit PD-L1 may be helpful. Evidence also shows that high levels of oxidative stress and inflammation may participate in both the initiation and progression of cancer. Cardamonin, an aromatic enone flavonoid, has displayed an array of pharmacological activities, including modulation of different signaling molecules involved in the development and progression of cancer. This work investigated the cardamonin’s ability to modulate PD-L1 expression and NF-KB in genetically distinct MDA-MB-231 (Caucasian) and MDA-MB-468 (African American) TNBC cell lines. The methodology included cytotoxic assays, ELISA, Real Time-Polymerase Chain Reaction (RT-PCR) assays, and Wes analysis. The results showed that cardamonin treatment caused a dose-dependent decrease in cell viability in both cell lines, ranging from 3.12 µM to 200 µM. The RT-PCR and ELISA data showed that even though IFN-γ stimulated MDA-MB-231 cells showed a higher expression of PD-L1, cardamonin reduced mRNA and protein expression of PD-L1 in both cell lines. As a possible molecular mechanism for PD-L1 inhibition, cardamonin modulated MUC-1, STAT3, and JAK, which are genes that activate the PD1/PD-L1 mechanism. Moreover, data also show that cardamonin modulated NF-KB1 and NF-KB2 genes involved in activating NF-KB signaling. NF-KB is a transcription factor of inflammation and immunity, emerging as a key positive regulator of PD-L1 expression in cancer. Therefore, cardamonin may have the potential utilization as a checkpoint inhibitor that acts by blocking PD-L1 protein, allowing the immune system to recognize and attack the TNBC cancer cells, providing a novel cancer therapy. (Supported by a grant from NIH-NIMHD U54 MD 007582) Citation Format: Patricia Mendonca, Bhonessa Kirpal, Sukhmandeep Kaur, Karam F. A. Soliman. The effect of cardamonin on PD-L1 expression in triple-negative breast cancer cells [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 530.