tbuckley/cabot-search huggingface dataset:
Abstract 1303: Harness the power of data to improve cancer care - Understanding the complex landscape of health policies and regulations
Authors: Ying Huang, Heather Basehore, Emily S. Boja, Jaime M. Guidry Auvil
Journal: Cancer Research (2024)

Abstract In the era of big data and artificial intelligence, biomedical research and healthcare have been presented with unprecedented opportunities for improving the understanding of cancer biology. In addition, the Open Science Initiative aims to shift the current paradigm of research practice towards broad sharing and public access to research findings as the norm. Big data in oncology usually includes a combination of genomic sequencing, proteomics, medical imaging, electronic health records, payor records, and other data sources from pharmaceutical research, wearables, and medical devices. While combining, linking, and analyzing data from different sources across research and healthcare enterprises is key to realizing the promise of big data and a health learning system, it poses tremendous challenges for researchers and implementers to understand the nuances of relevant policies, laws, and regulations while striving for broad, equitable, timely and responsible data sharing, as well as tackling issues in data quality, harmonization, interoperability, and security. Herein, we aim to shine a light on the ever-evolving landscape of data privacy regulations, laws, and policies that govern different touch points of a patient's journey where data are collected for research and healthcare purposes throughout the lifecycle that would impact data-sharing outcomes. We hope the illumination of a complex landscape of data governance framework to consider for many data sources will facilitate broad community engagement including data scientists and technologists, patients and advocacy groups, and policymakers to maximize open data and science while protecting patient privacy and confidentiality. Citation Format: Ying Huang, Heather Basehore, Emily S. Boja, Jaime M. Guidry Auvil. Harness the power of data to improve cancer care - Understanding the complex landscape of health policies and regulations [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 1303.
Abstract 2343: Adapting gene set enrichment analysis to single cell data
Authors: Alexander T. Wenzel, John Jun, Jill P. Mesirov
Journal: Cancer Research (2024)

Abstract Gene Set Enrichment Analysis (GSEA) is a method for quantifying the activation of pathways and processes in gene expression data. GSEA works by ranking genes and testing if genes in annotated gene sets representing molecular pathways are overrepresented at the top or bottom of the ranked list. Standard GSEA assumes a gene-by-sample matrix with samples falling in two phenotype class labels and ranks genes based on correlation of expression and sample class labels. Single sample (ssGSEA) uses a similar approach to enrichment scoring but ranks genes in a single sample based on their expression. There has been recent interest in using the ssGSEA modality to measure pathway activity in individual cells from single cell RNA-sequencing (scRNA-seq) data. However, we have observed that ssGSEA scores in scRNA-seq cells are prone to uncertainty due to the characteristic sparsity of scRNA-seq data. This is because sparse data leads to large groups of tied genes, that is, genes with equal expression and subsequently equivalent positions in the ranked list. Because ssGSEA, which was designed for bulk gene expression technologies which yield much less sparse data, breaks ties arbitrarily, these ties can lead to variability in enrichment scores that is purely algorithmic and not a result of the underlying biology. To address this issue, we performed benchmarking to characterize the stability of scores using different enrichment scoring statistics, normalization methods, and aggregation of similar single cells. We have implemented the best practices identified using this analysis as Single Cell GSEA (scGSEA), a software tool which we will make freely available to researchers as open-source software to enable robust gene set enrichment scoring in scRNA-seq data. Citation Format: Alexander T. Wenzel, John Jun, Jill P. Mesirov. Adapting gene set enrichment analysis to single cell data [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 2343.
Abstract 5339: Establishment of a humanized IL5/IL5RA mouse model to evaluate modulators of eosinophilic inflammation <i>in vivo</i>
Authors: Suman Zhao, Shujin Zhang, Zhen Chen, Liya Yang, Mari Kuraguchi, Jiangfeng Yuan, Heiling Shen
Journal: Cancer Research (2024)

Abstract IL-5/IL-5R signaling plays a key role in the maturation, activation, survival, and recruitment of eosinophils to sites of inflammation. Targeting this pathway is an attractive therapeutic strategy for certain inflammatory diseases, such as asthma. Here, we generated a novel humanized IL5/IL5RA model (B-hIL5/hIL5RA) to examine the utility of human IL-5/IL5R-targeting therapeutic candidates. Specifically, the entire murine Il5 coding region was replaced by the corresponding human IL5 sequence, and the human IL5RA sequence coding the extracellular domain was inserted to replace the corresponding murine sequence. Successful generation of the model was confirmed by expression of human IL-5 by ELISA and IL5RA by flow cytometry. Furthermore, the proportion of eosinophils in the blood of B-hIL5/hIL5RA mice increased after stimulation with human IL5 recombinant protein, indicating that the humanized IL5RA protein is functional. Next, the ability of the humanized mice to establish asthma-like disease was tested using ovalbumin: following a 14 day sensitization period, mice were challenged with nebulized OVA daily from day 21 until the endpoint; treatment with mepolizumab or benralizumab analog was performed. Flow cytometric analysis of the bronchioalveolar fluid indicates that treatment with mepolizumab or benralizumab analog significantly lowered the number of eosinophils when compared to the isotype control in homozygous B-hIL5/hIL5RA mice. Blood counts and quantification of lung H&amp;E sections also confirm that the treatments lowered the number of eosinophils in circulation and lung tissue, respectively. Taken together, these data indicate that B-hIL5/hIL5RA mice are a suitable preclinical model to test novel modulators of human IL-5/IL-5RA signaling. Citation Format: Suman Zhao, Shujin Zhang, Zhen Chen, Liya Yang, Mari Kuraguchi, Jiangfeng Yuan, Heiling Shen. Establishment of a humanized IL5/IL5RA mouse model to evaluate modulators of eosinophilic inflammation in vivo [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 5339.
Abstract 5324: Key antiviral response genes mediate the impact of chromosomal instability on breast cancer stemness
Authors: Shahnawaz A. Baba, Samson Mugisha, Shreyas labhsetwar, Richard klemke, Jay Desgrosellier
Journal: Cancer Research (2024)

Abstract Chromosomal instability (CIN) is a recognized hallmark of cancer, pivotal in tumor evolution and metastasis. Our research unveils CIN as a stress during tumor initiation, uniquely tolerated by activated breast cancer stem cells (aCSCs). Elevated CIN, specific to tumors from aCSCs, contrasts with baseline levels akin to non-stem cell types. This transient increase in CIN, observed in low burden aCSC tumors, diminishes in established disease, suggesting a dynamic induction during initiation. Consist wit this we have observed increase in CIN tolerance in stem-like vs basal-like cells suggesting heterogeneity in response. CIN triggers a specific response, activating proinflammatory cancer autonomous immune signaling. We identified several CIN-induced proinflammatory stem cell-specific genes from our overlap studies. Knockdown assays targeting RSAD2 and PLAU showed a significant decrease in tumorsphere properties, emphasizing their functional relevance for cancer progression. AXL did not show any effect on tumorsphere but was important to tolerate CIN induced due to reversine. Mechanistically, AXL expression was induced by c-Jun stress signaling activation in aCSCs. These antiviral CIN-induced proinflammatory markers, emerge as a vital player in breast cancer progression. This study establishes a foundation for investigating antiviral genes as crucial contributors to cancer. Citation Format: Shahnawaz A. Baba, Samson Mugisha, Shreyas labhsetwar, Richard klemke, Jay Desgrosellier. Key antiviral response genes mediate the impact of chromosomal instability on breast cancer stemness [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 5324.
Abstract 1391: Therapeutic salmonella induces long-term protective trained immunity in NK cells against metastasis
Authors: Li Rong, Jiandong Huang
Journal: Cancer Research (2024)

Abstract Immune memory is a trait commonly associated with adaptive immunity. Nevertheless, it has been observed that activation of the innate immune system can also result in enhanced responsiveness to subsequent triggers, a form of innate immune memory known as trained immunity. This phenomenon has been primarily explored in the context of host defense against infectious disease, where myeloid cells, including monocytes, macrophages, and their precursor cells, are conditioned by specific stimuli such as β-glucan, LPS, or the bacillus Calmette-Guιrin (BCG) to boost protection against microbial pathogens. However, the induction of trained immunity in innate lymphocytes, particularly through these known or yet-to-be-discovered stimuli and its explicit contribution to tumor immunity, remain insufficiently characterized. Metastasis accounts for 90% of cancer-related deaths, and no effective clinical therapies are currently available to halt the metastatic cascade. Based on multiple cancer metastasis mouse models and immunological analysis, we found that a single dose of therapeutic Salmonella YB1, an engineered oxygen-sensitive strain, provides extensive and persistent protection against metastasis by inducing protective trained immunity in NK cells, consistently observed irrespective of the mouse genetic background or cancer cell lines. Following inflammatory resolution, salmonella YB1-trained NK cells exhibit an enhanced capacity to release IFN-γ upon secondary stimulation and increased cytotoxicity towards cancer cells, which is associated with epigenetic changes. Further investigation using single-cell transcriptomic profiling indicates that the formation of long-term anti-metastatic trained immunity in NK cells by Salmonella YB1 is dependent on IL12 and IL18. Additionally, Salmonella YB1-trained NK cells outperform common immune checkpoint therapies like PD1 blockade and TIGIT blockade in suppressing metastasis. In summary, our results revealed a novel anti-metastatic function of trained NK cells induced by therapeutic Salmonella, suggesting the induction of trained immunity in NK cells as a potential anti-tumor strategy. Citation Format: Li Rong, Jiandong Huang. Therapeutic salmonella induces long-term protective trained immunity in NK cells against metastasis [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 1391.
Abstract 2717: Bifunctional fusion protein PDL1sFv/MICAe for cancer immunotherapy
Authors: Junyi Li, Yanzhang Wei
Journal: Cancer Research (2024)

Abstract Many cancer cells upregulate the expression of programmed death ligand 1 (PD-L1) to surpass T-cell mediated immune response. Immune checkpoint blockers targeting PD-L1 or its receptor PD1 have been shown to suppress the inhibitory signals and enhance T cell function. As a new immunotherapy, immune checkpoint blockers have been used to treat multiple cancers. However, most clinically available blockers only engage with one type of immune cell: the T cells. Natural killer (NK) cells, on the other hand, play a significant role in anti-cancer immune responses. It will represent an advancement in anti-cancer immunotherapy if NK cells are engaged with immune checkpoint blockers. In this study, we designed a unique bifunctional fusion gene, PDL1sFv/MICAe, consisting of the variable regions of an anti-PD-L1 antibody and the extracellular domain of stress protein MICA and hypothesized that fusion protein PDL1sFv/MICAe will simultaneously bind to PD-L1 on tumor cells to block the inhibitory signal and extend T cells activity, and to NKG2D to activate NK Cells. cDNA sequence of fusion gene PDL1sFv/MICAe was designed based on the variable region of an established clinically used antibody, Atezolizumab, and the extracellular domain of MICA with linkers in between. After a computational confirmation of its structure and binding affinities, the fusion gene was synthesized and cloned into an expressing vector, and the fusion protein was produced for evaluation. Western blotting and fluorescent microscopic analyses confirmed that the protein binds to PD-L1 of human tumor cells, including MCF7 and MDAMB231, and NKG2D of KHYG1 cells. Preliminary results also show that the fusion protein enhances NK cell cytotoxicity against tumor cells. Studies on confirming the fusion protein’s activities on other tumor cells, NK cell IFN-γ production, T cell function, etc., are underway. In summary, fusion protein PDL1sFv/MICAe represents an improved version of the immune checkpoint blockers and could treat cancer patients quickly and effectively. Citation Format: Junyi Li, Yanzhang Wei. Bifunctional fusion protein PDL1sFv/MICAe 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 2717.
Abstract 3066: Lung cancer cells overcome nutrient stress by upregulating an integrin αvβ3/AMPK/OXPHOS axis
Authors: Arin Nam, Shashi Jain, Alejandro Campos, Ryan M. Shepard, Tami von Schalscha, Sara M. Weis, Hiromi I. Wettersten, David A. Cheresh
Journal: Cancer Research (2024)

Abstract Tumor cells are exposed to various forms of stress within the tumor microenvironment, and those cells that adapt often gain stem-like properties that facilitate tumor initiation and metastasis. Here, we show that lung cancer cells exposed to nutrient stress adapt and survive by converting their metabolism from glycolytic to oxidative phosphorylation (OXPHOS). This is based on the cell’s ability to upregulate expression of integrin αvβ3, a driver of tumor initiation, progression, and drug resistance. Mechanistically, integrin αvβ3 recruits and activates c-Src, promoting sustained AMPK activity leading to activation of PGC-1α, which promotes the expression of mitochondrial OXPHOS complexes. In fact, ectopic expression of integrin β3 was sufficient to drive OXPHOS-dependent metabolism even in the absence of stress. Furthermore, pharmacological targeting of this pathway not only rendered integrin αvβ3+ cells sensitive to nutrient depletion but also prevented their ability to undergo tumor initiation. These findings reveal that targeting integrin αvβ3 or its pathway can prevent cancer cell metabolic flexibility and their capacity to adapt to stress within the tumor microenvironment. Citation Format: Arin Nam, Shashi Jain, Alejandro Campos, Ryan M. Shepard, Tami von Schalscha, Sara M. Weis, Hiromi I. Wettersten, David A. Cheresh. Lung cancer cells overcome nutrient stress by upregulating an integrin αvβ3/AMPK/OXPHOS axis [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 3066.
Abstract 3764: Spatially resolved immune landscape revealed sex-biased T-cell infiltration in glioblastoma
Authors: Yue Hao, George Reid, Angela Baker, Karen L. Fink, George J. Snipes, Bruce E. Mickey, Andrew E. Sloan, Jill S. Barnholtz-Sloan, Michael Berens
Journal: Cancer Research (2024)

Abstract Glioblastoma (GBM) multiforme is the most aggressive type of brain cancer. These lethal brain tumors are characterized by the inter- and intra-tumor molecular heterogeneity and demonstrated cell plasticity. A male:female distribution of 1.6:1; survival outcome from treatment (debulking, radiation, and temozolomide) benefits females nearly twice that for males. Through spatial transcriptomics, we interrogated the immune landscape of GBM, seeking to tease out whether distinct biological and therapeutic niches in GBM were evident, and to understand how the tumor microenvironments contributed to the heterogeneity of GBM. We designed a set of RNA hybridization probes specifically for portraying the cell identities and cell functional states within GBM tumor. The probe set was used to profile six human GBM samples from male and female cohorts on the Vizgen MERSCOPE platform. An integrated analysis of 505,614 cells from the six samples yielded a rich and varied spatial cell atlas of glioblastoma. Our preliminary findings depict distinct spatial niches of different tumor cell subpopulations that are associated with local environmental factors such as hypoxia. We identified a small cluster of cells that are in neuronal-like state, which could potentially drive invasion. We found spatial proximity of CD4+ cells and cells that express HIF1A, suggesting the dynamic interactions between tumor cells, regulatory T cells and tumor microenvironment. We also observed significant difference in the degree of CD8+ T-cell infiltration in female samples versus male samples. The average CD4+/CD8+ T-cell ratio in males is twice as high as that of females, suggesting intrinsic sex-based differences in immune response to tumor. Expansion of these studies in additional specimens will further illuminate microenvironmental influences on glioma progression and may instruct specific interventions leading to more effective and predictable immune-oncology of this disease. Citation Format: Yue Hao, George Reid, Angela Baker, Karen L. Fink, George J. Snipes, Bruce E. Mickey, Andrew E. Sloan, Jill S. Barnholtz-Sloan, Michael Berens. Spatially resolved immune landscape revealed sex-biased T-cell infiltration in glioblastoma [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 3764.
Abstract 304: The role of DDR1 mediated E-cadherin stability in collective colon cancer cell migration
Authors: Hui-Chun Chen, Yu-Chun Wang, Yu-Chien Ching, Chun-Pu Cheng, Chia-En Ku, Shin-Ru Lee, Wei-Ting Chao
Journal: Cancer Research (2024)

Abstract In cancer metastasis, the mechanism of single cell migration and collective cell migration are investigated. The dynamics of E-cadherin is critical in collective cell migration as the important mechanism of metastasis. DDR1 (Discoidin Domain Receptor 1) has been shown to promote E-cadherin stability at adherens junction in epithelial cells by regulating endocytosis of E-cadherin. However, in the growth of epithelial cell cluster and collective cell migration, the role of DDR1 in the cell-cell contacts is not clear. In this study, HT-29 colon cancer cells with epithelial phenotype were used in the experiments. Cells were treated with epidermal growth factor to stimulate E-cadherin turnover or applied with lysosome inhibitor chloroquine to interfere cellular vesicle transport. DDR1 and E-cadherin were revealed by immuno-confocal microscopy. The immunostaining results showed DDR1 was localized at cell-cell contacts and co-localized with E-cadherin. When cells were treated with epidermal growth factor, the phosphor MAPK activity was increased and DDR1 was localized at cell-cell contacts intensively. When lysosome activity was blocked by chloroquine treatment. The cellular vesicle transport and collective cell migration was reduced and furthermore inhibited DDR1 translocation to the cell-cell contacts. This study demonstrated DDR1 co-localized with E-cadherin is responsible for epidermal growth factor stimulation in cell cohort. Lysosome activity is required for E-cadherin turnover and affected DDR1 translocation. Chloroquine maybe the potential drug to suppress tumor nest growth and collective cell migration by interfere DDR1 mediated E-cadherin stability. Citation Format: Hui-Chun Chen, Yu-Chun Wang, Yu-Chien Ching, Chun-Pu Cheng, Chia-En Ku, Shin-Ru Lee, Wei-Ting Chao. The role of DDR1 mediated E-cadherin stability in collective colon cancer cell migration [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 304.