tbuckley/cabot-search huggingface dataset:
Abstract 1074: Plasma EV profiling facilitates low abundance biomarker discovery in pancreatic cancer
Authors: Shivani Bansal, Shu Wang, Yaoxiang Li, Sunil Bansal, Jill Smith, John B. Tyburski, Keith Unger, Amrita Cheema
Journal: Cancer Research (2024)

Abstract The lack of reliable biomarkers for early detection of pancreatic ductal adenocarcinoma (PDAC) results in poor prognosis due to advanced disease at diagnosis. Biopsies for pancreatic cancer are known to be particularly difficult to perform because of the location of the pancreas and low volume of primary tumors that metastasize aggressively. Currently, there is no blood test or other screening modality in use, for stratification of individuals with higher-than-average risk (5-8-fold) of developing PDAC in their lifetime. Given this existing void in the US and worldwide, an FDA-compliant, minimally invasive, quantitative biomarker test for the early detection of PDAC would be critical for screening subpopulations with, a) inherent genetic or familial predisposition; history of chronic pancreatitis; c) precursor lesions of pancreas; and d) older patients (&amp;gt;50 years) with new onset diabetes or sudden weight loss. Extracellular vesicles (EVs) are shed by normal and cancer cells and carry a rich molecular cargo that can be leveraged for biomarker discovery. Whereas molecular profiling of bio-fluids poses intrinsic limitations for detection of low abundant, disease-specific biomarkers due to matrix effects; EVs, on the other hand, offer promise as a robust and minimally invasive biomarker resource. Mass spectrometry data were developed in our laboratory, based on multi-omics (proteomics, lipidomics and metabolomics) analyses of plasma EVs derived from patients diagnosed with early-stage PC (N=60), pancreatitis (N=39), precursor lesions of pancreas (N=45) as well as normal controls (N=50). These clinically annotated samples were made available by the Georgetown University Medical Center (GUMC) repository. Feature selection using a training-validation design allowed the development of a multiplexed biomarker panel comprising of 12-analytes (5-lipids, 2-metabolites and 5-proteins) that can robustly stratify early-stage PC from normal controls with high accuracy (AUC&amp;gt;95%). Availability of a FDA compliant, multi-analyte-based classification algorithm that can stratify patients with precursor lesions of the pancreas that are at potential risk of progression to PC with &amp;gt; 90% specificity and sensitivity is a critical clinical need. Refinement of panel to improve positive predictive value as well as identification of markers predictive of progression of precursor lesions to malignant transformation is ongoing. Citation Format: Shivani Bansal, Shu Wang, Yaoxiang Li, Sunil Bansal, Jill Smith, John B. Tyburski, Keith Unger, Amrita Cheema. Plasma EV profiling facilitates low abundance biomarker discovery in pancreatic 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 1074.
Abstract 4590: Antitumor effects of histone deacetylase inhibitors on breast cancer cell viability and mammosphere formation
Authors: Golnaz Asaadi Tehrani, Becca Kubick, Meenal Datta
Journal: Cancer Research (2024)

Abstract Histone deacetylases (HDACs) are overexpressed in various types of primary human cancer and have become attractive targets for cancer therapy. This study aimed to evaluate the cytotoxic properties of three HDAC inhibitors (suberoylanilide hydroxamic acid (SAHA, or Vorinostat), Valproic Acid (VPA) and CAY10603) and compare them to Paclitaxel (PTX), a chemotherapy agent used to treat Triple Negative Breast Cancers (TNBCs). In the present study, drug response in the MDA-MB-231, MDA-MB-468, and MCF-10A cell lines was evaluated by cell viability assays. Apoptosis and cell cycle distribution were analyzed by flow cytometry. Mammospheres generated from MDA-MB-231 and MDA-MB-468 breast cancer cells were also subjected to drug treatment; their response was assessed under both normoxic and hypoxic conditions. We found that SAHA and CAY10603 inhibited breast cancer cell viability without significantly affecting MCF-10A cells. SAHA, CAY10603, and VPA all arrested a significant percentage of MDA-MB-231 cells at G2/M phase after 24h compared to controls. TNBC cells experienced an increase in both early and late apoptosis following treatment with the most effective concentrations of SAHA, CAY10603, and VPA (1.8µM, 2µM, and 0.4mM, respectively). SAHA proved to be the most effective drug for induction of apoptosis compared to the control, followed by CAY10603 (8.26% and 6%, 3.67%). In both TNBCs and mammospheres under hypoxic conditions, SAHA and CAY10603 down regulated HIF-1α expression significantly, but PTX did not. In contrast, VPA and PTX down regulated CTNNB1 gene expression. This study indicates that epi-drugs exert an anti-tumor effect on TNBCs, suggesting a potential role for HDAC inhibitors as novel therapeutics for breast cancer patients. Citation Format: Golnaz Asaadi Tehrani, Becca Kubick, Meenal Datta. Antitumor effects of histone deacetylase inhibitors on breast cancer cell viability and mammosphere formation [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 4590.
Abstract 4221: Characterization and comparison of hypoxia inducing factors on tumor growth and metastasis in 2D and 3D tumor models
Authors: James McDonald, Leo Li-Ying Chan, Sarah Kessel, Bo Lin, Paul Weingarten
Journal: Cancer Research (2024)

Abstract The monocarboxylic acid transporter 4 (Mct-4), a downstream biomarker of hypoxia inducing factor (HIF)-1α, is involved in the cellular response to hypoxia, as indicated by the hypoxic response element in its promoter region. Using a tumorsphere assay as an in vitro 3-dimensional (3D) model generated using 384-well ultra-low attachment (ULA) plates for cell proliferation analysis using a plate-based image cytometer, we identify a hypoxic response in the tumorsphere model that is distinct from that of cells grown under 2-dimensional (2D) normoxic conditions and demonstrate a key role for Mct-4 in enabling 3D growth. The tumorsphere model yields evidence of an essential role for Mct-4 in multiple cell lines which were genetically modified to underexpress and overexpress Mct-4, evidence not apparent in a standard 2D model of growth in the same cell lines. In addition, we identify the effects of overexpressing Mct-4 in cancer cell migration using a transwell chamber assay. We also show that the response to hypoxia may be circumvented by transfection with a CMV promoter driven Mct-4, which confers constitutive 3D growth, wherein tumorsphere growth inhibition by small molecule HIF-1α inhibitors is mitigated. Finally, we demonstrate quantifiable gene/protein expression differences between 2D and 3D cancer models based on the normoxic and hypoxic conditions. Therefore, the tumorsphere 3D model generated using 384-well ULA plates in combination with high-throughput image cytometer is demonstrated to provide a convenient, robust, and reproducible tool and method for the elucidation of mechanisms of action underlying tumor growth and migration in the hypoxic tumor microenvironment. Citation Format: James McDonald, Leo Li-Ying Chan, Sarah Kessel, Bo Lin, Paul Weingarten. Characterization and comparison of hypoxia inducing factors on tumor growth and metastasis in 2D and 3D tumor models [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 4221.
Abstract 4217: An engineered breast tumor microenvironment model, with single-cell spatial resolution, to assess spatial dynamics of tumor evolution
Authors: Haylie R. Helms, Kody A. Oyama, Alexander E. Davies, Ellen M. Langer, Luiz E. Bertassoni
Journal: Cancer Research (2024)

Abstract Cellular heterogeneity is a prominent feature of the tumor microenvironment, and the organization of these cells has been linked to clinical outcomes such as disease progression and drug resistance. While retrospective analysis of patient tumors has produced a myriad of insights, samples are limited and highly complex making it challenging to validate causality. Here we present an engineered breast tumor microenvironment model, with single cell spatial resolution, to systematically identify which cell phenotypes and their spatial arrangements may be driving ductal carcinoma in situ disease progression. A microfluidic dispenser (Biopixlar, Fluicell) was optimized to enable the spatial patterning of single cells to replicate native histology. To demonstrate the high spatial precision of our method, we first replicated an annotated 2D section of a breast tumor biopsy region of interest (ROI) using MCF10A, MDA-MB-231, primary mammary fibroblasts, THP-1 derived macrophages, and primary mesenchymal stem cells. The XY coordinate of each cell was identified to create a print map matching the original biopsy. Deposited cells adhered to their intended target with an average print fidelity of 2.4 µm. Next, the stromal compartment of the ROI was altered to include phenotypes associated with tumor promoting microenvironments (i.e. cancer associated fibroblasts, M2 macrophages) and the core of the MCF10A ring filled with MDA-MB-231. Each deposited cell contained a fluorescent tag corresponding with its cell type to facilitate real time spatial tracking and annotation. The tumor microenvironments were live cell imaged for 24 hours at 5 minute intervals. MCF10A cells spread to form their junctions and create a cohesive ring, MDA-MB-231 cells proliferated and rapidly moved around within the confined space, and the cells of the stromal compartment spread to create a dense tissue like structure. The microenvironments were cultured for an additional 2-6 days, fixed, and stained for markers of proliferation, phenotype shifts, cell-cell junctions, and morphology. Unlocking the relative contributions of the specific cell types in ductal carcinoma in situ tumor microenvironment to the overall evolution of invasive breast cancer may hold the answer for many questions in early detection, treatment, and cancer avatar models. Citation Format: Haylie R. Helms, Kody A. Oyama, Alexander E. Davies, Ellen M. Langer, Luiz E. Bertassoni. An engineered breast tumor microenvironment model, with single-cell spatial resolution, to assess spatial dynamics of tumor evolution [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 4217.
Abstract 3609: Chimeric cytokine receptors increase memory phenotypes and improve expansion and efficacy of CAR-T cell therapies
Authors: John R. Newcomb, Jun Ren, Sakeena Syed, Zachary Caruolo, Lindsay Webb, Craig McKay, Stephanie Kwei, Carl Novina, Fred Mermelstein
Journal: Cancer Research (2024)

Abstract Cytokine activation of T cells can promote T cell proliferation, memory and improve T cell function in driving tumor cell killing. However, systemic administration of cytokines at therapeutic doses is also associated with unacceptable toxicities. To overcome this limitation, we have engineered a system of private cytokine signaling to affect T cell homeostasis, identity, and function. Specifically, we have engineered chimeric cytokine receptors (CCRs) composed of single-chain variable fragments (scFvs) that bind specifically to small molecules such as fluorescein or DOTA. These scFvs are fused to transmembrane and intracellular domains of all members of the common gamma-chain (γ-chain) family of cytokine receptors. CCRs that permit private cytokine signaling were introduced into known CAR-T cell therapies and their impact on CAR-T cell phenotype, function, and anti-tumor activity was tested. First, CCR-containing T cells were tested for activation-induced changes in phenotype and expansion following stimulation with small molecule conjugates in vitro. The most promising results were obtained using either the IL-7Rα- or IL-2Rβ/γ-containing CCR’s. CCR-containing constructs were then transduced into one of two different anti-BCMA CAR-T constructs, ide-cel or cilta-cel, using a lentiviral transduction system. CAR-T cells containing each CCR were then compared with CAR-T cells lacking CCRs for phenotype and function in vitro. Results indicated that engineering the IL-7Rα CCR with both of these CAR-T’s led to increased expansion, cytokine secretion and improved tumor cell killing. Next, CAR-T cells expressing the IL-7Rα CCR were compared to CAR-T cells lacking CCR for efficacy and durability in a mouse model of human multiple myeloma. IL-7Rα CCR-expressing CAR-T cells demonstrated improved long-term tumor control compared to ide-cel and cilta-cel alone. In addition, IL-7Rα CCR-expression increased T cell numbers in blood, spleen and bone marrow of tumor-bearing mice. These increases were particularly evident in the CD8+population of CAR-T cells in vivo. These results demostrate that private cytokine signaling using small-molecule activatable CCRs can improve efficacy and durability of CAR-T cells. We are testing these CCRs in mouse models of human solid tumors to assess their ability to overcome the immunosuppressive microenvironment. Citation Format: John R. Newcomb, Jun Ren, Sakeena Syed, Zachary Caruolo, Lindsay Webb, Craig McKay, Stephanie Kwei, Carl Novina, Fred Mermelstein. Chimeric cytokine receptors increase memory phenotypes and improve expansion and efficacy of CAR-T cell therapies [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 3609.
Abstract 4240: A comprehensive i<i>n vitro</i> tumor model: One-stop simultaneous isolation and culture of tumoroids, CAFs and TILs for advancing immuno-oncology research
Authors: YOO RI KO, Sung Min Kim, Hye Seon Park, Se Jin Jang
Journal: Cancer Research (2024)

Abstract The tumor microenvironment (TME), composed of a diverse array of cells, jointly participates in tumor formation and has attracted attention as a direct or indirect therapeutic target. Among the tumor-forming cells, cancer cells, cancer-associated fibroblast (CAF), and tumor-infiltrating lymphocytes (TILs) comprise major proportion and players in tumor biology. Therefore, an in vitro tumor model composed of at least above three major cellular players better mimics a patient’s tumor. Here, we developed a patient-derived tumor model containing tumoroids, CAFs and TILs isolated from the patient’s tumor tissue by using one-stop isolation culture system. Our one-stop culture system utilizes a Transwell-based method that concurrently segregates cancer cells, CAFs, and TILs based on distinct characteristics such as cell size, migration speed, and growth. Lung tumoroids, fibroblasts, and TILs segregated in Matrigel-coated upper Transwell chamber, Transwell pores and in the lower chamber, respectively. Lung tumoroids maintain the patient’s lung cancer tissue characteristics and genetic features during extended in vitro cultivation. Fibroblasts extracted from the Transwell pores exhibit significant similarity to CAFs found in patient tissue. TILs in the lower part of the Transwell chamber closely resemble those found in the original cancer tissue analyzed by FACS. We have also refined the functionality of TILs through a two-week expansion process. Patients’ tumor composed of 0.15 to 95.3 % of EpCAM positive tumor cells, 0.14 to 19.4 % of CD90 positive fibroblasts and 3.98 to 91.2 % of immune cells in FACS analysis. By reassembling three main cellular components of the tumor in a proper proportion, we developed a co-culture platform for a patient-derived tumor model reproducing patient-specific TME conditions. The co-culture platform showed a potential not only for an experimental model but also to use a predictive test of personalized immunotherapy responses for lung cancer patients. Citation Format: YOO RI KO, Sung Min Kim, Hye Seon Park, Se Jin Jang. A comprehensive in vitro tumor model: One-stop simultaneous isolation and culture of tumoroids, CAFs and TILs for advancing immuno-oncology research [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 4240.
Abstract 3748: Evaluation of immune cells from patient-derived tumor tissue and peritoneal washing cytology in correlation with immunohistochemical markers in endometrial cancer
Authors: Changmin Shin, Seungmee Lee, Hyewon Chung, Jin Young Kim, Eunyoung Ha, Ji Hae Seo, Sojin Shin
Journal: Cancer Research (2024)

Abstract Background This study aims to evaluate the characteristics and clinical correlations of tumor-infiltrating lymphocytes (TILs) in endometrial cancer, derived from fresh tumor tissue and peritoneal washing cytology. Furthermore, it seeks to explore the correlation between TILs and immunohistochemical markers in endometrial cancer. Methods In this study, we investigated the nature of TILs extracted from endometrial tissue and peritoneal washing cytology, along with their correlation with immunohistochemical markers. Samples collected from endometrial cancer patients during surgery, with informed consent, were analyzed for immune cell composition using flow cytometry. We examined the association between pathological findings, a range of immunohistochemical markers (including LVSI, PD-L1, ER, P53, HER2, MLH1, MSH2, MSH6, PMS2, MSI), and the status of tumor-infiltrating immune cells (such as CD3-CD19+ B Cells, CD3-CD16+CD56+ NK Cells, CD4+CD25+ regulatory T cells (Treg), and CD3+CD8+ cytotoxic T cells). Results Our analysis encompassed 25 endometrial cancer-derived samples. Notable observations include an increase in CD3-CD19+ B cells in the LVSI-positive group and a decrease in the ER-positive group (p&amp;lt;0.05, respectively). CD3-CD16+CD56+ NK Cells decreased in the ER-positive group, while CD3+CD8+ cytotoxic T cells were decreased in the HER2-positive group (p&amp;lt;0.001, p&amp;lt;0.05, respectively). Other immunohistochemical markers showed no significant differences. Conclusion The study suggests that tumor-infiltrating immune cells from patient-derived tissue and peritoneal washing cytology may reflect the molecular and clinical characteristics of endometrial cancer. However, further research with an expanded sample size and correlation with oncologic outcomes is warranted to validate these findings. Citation Format: Changmin Shin, Seungmee Lee, Hyewon Chung, Jin Young Kim, Eunyoung Ha, Ji Hae Seo, Sojin Shin. Evaluation of immune cells from patient-derived tumor tissue and peritoneal washing cytology in correlation with immunohistochemical markers in endometrial 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 3748.
Abstract 1674: Inhibition of oncogenic nras signaling in acute myeloid leukemia cell lines through directed transcriptome alterations
Authors: Michael Roberts, Sophia Kovatsis, Amelia Harper, Megan Cravinho, Kishan Mangru, Sher Bahadur, Keagan Hesse, Katy Meta, Cuong Nguyen
Journal: Cancer Research (2024)

Abstract Oncogenic mutations in genes involved in proliferative signaling are hallmarks of malignant transformation. The Ras family of signal transducing proteins are involved in the activation of several proliferative pathways and therefore are found to be oncogenically mutated in a variety of cancer types. The NRAS-directed pathways resulting in Erk1/2 activation are dysregulated in a significant percentage of acute myeloid leukemia (AML), metastatic melanoma, Hodgkin lymphoma, and thyroid cancers. The consequence of oncogenic NRAS signaling is the establishment of a transcriptome commanding constitutive proliferation and survival. It has long been known that phorbol ester treatment of AML cell lines, resulting in activation of protein kinase C (PKC), causes phenotypic changes that include cell cycle arrest, myeloid differentiation, and apoptosis. The paradox is that numerous studies identify PKC as an activator of RAS/ERK signaling. Here we show that phorbol ester treatment of NRAS-driven AML cell lines results in the transcriptional upregulation of genes encoding negative regulators of RAS signaling including DUSP1,2,4,5,6, SPRY2, SPRED1, RASA1, PEA15, RPS6KA1, and RASSF5. Additionally, phorbol ester treatment eventually results to ERK1/2 inactivation through dephosphorylation. Several of these negative regulators, when overexpressed in AML cell lines, dampen proliferation, and induce senescence. We propose that the induction of RAS negative regulators alters the AML transcriptome to a non-proliferative state in part through the transcriptional regulation of genes such as CDKN1A, CDKN2B, ZFP36L1, and MYC. As gene therapy strategies develop, designed to provide negative regulators of proliferative signaling pathways that are repressed in the malignant cell, we imagine the RAS/ERK pathway as a target for transcriptome reprogramming. Citation Format: Michael Roberts, Sophia Kovatsis, Amelia Harper, Megan Cravinho, Kishan Mangru, Sher Bahadur, Keagan Hesse, Katy Meta, Cuong Nguyen. Inhibition of oncogenic nras signaling in acute myeloid leukemia cell lines through directed transcriptome alterations [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 1674.
Abstract 274: Cancer-associated fibroblasts exhibit increased motility under hypoxic conditions via interaction with cancer cells
Authors: Jihye Park, Sieun Lee, Jonathan M. Kurie, Young-Ho Ahn
Journal: Cancer Research (2024)

Abstract Cancer-associated fibroblasts (CAFs) are key components of the tumor microenvironment, playing various roles through interactions with cancer cells and other stromal cell types. In a 3D co-culture system of CAFs and lung cancer cells, a specific subgroup of CAFs exhibited increased motility, while another subgroup of CAFs remained stationary. Using the photoconvertible fluorescent protein Dendra2, we isolated these distinct CAF subgroups and conducted RNA sequencing. Gene set enrichment and gene ontology analysis revealed that upregulated genes in motile CAFs are associated with hypoxia and glycolysis. Conditioned medium from mesenchymal-like cancer cells enhanced the expression of genes related to hypoxia and glycolysis in CAFs. Among these genes, Aldoa and Ldha were chosen for knockdown in CAFs, resulting in a reduction in CAF motility. We confirmed that mesenchymal-like cancer cells promoted CAF motility and intensified hypoxic conditions within the co-culture system, which was monitored using a hypoxia reporter. Ceruloplasmin (CP) was identified as a secretory protein from mesenchymal-like cancer cells through mass spectrometry. Knockdown of CP led to the inhibition of CAF motility. In conclusion, the motility of CAFs is enhanced under hypoxic conditions facilitated by the secretion of CP from mesenchymal-like cancer cells in the lung tumor microenvironment. Citation Format: Jihye Park, Sieun Lee, Jonathan M. Kurie, Young-Ho Ahn. Cancer-associated fibroblasts exhibit increased motility under hypoxic conditions via interaction with 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 274.