tbuckley/cabot-search huggingface dataset:
Abstract 3580: Understanding and overcoming innate and acquired resistance to type I and II RAF inhibitors in anaplastic thyroid cancer using translational functional genomics
Authors: Peter Zeng, Jalna Meens, John Barrett, Matthew J. Cecchini, Sarah B. Ryan, Nachuan Pan, Amir Karimi, Laura Jarycki, Alice E. Dawson, Mushfiq Shaikh, David Palma, Eric Winquist, Paul C. Boutros, Laurie Ailles, Anthony C. Nichols
Journal: Cancer Research (2024)

Abstract Anaplastic thyroid cancer (ATC) is one of the most lethal human cancers, with some patients succumbing to the disease within weeks of diagnosis. Despite a subset of BRAFV600E mutant ATC patients responding to monomeric type I RAF inhibitor (RAFi) dabrafenib in combination with MEK inhibitor (MEKi) trametinib, almost all patients rapidly develop adaptive or acquired resistance. These patients, along with those who do not harbor the BRAFV600E alteration, have limited treatment options. To understand the mechanism of resistance to dabrafenib and trametinib, we utilized multi-region whole genome sequencing and single nuclei profiling of ATC patient tumors to unravel genomic, transcriptomic, and microenvironmental evolution during type I RAFi and MEKi therapy. Single-cell nuclei sequencing of matched primary and resistant ATC patient tumors identified transcriptomic reactivation of MAPK-pathway, along with immunosuppressive macrophage proliferation, underlie the development of acquired resistance. Our translation genomics led us to hypothesize that deeper inhibition of the MAPK-pathway can be efficacious in overcoming treatment resistance. Screening of a panel of type II RAFis revealed that ATC cell lines are exquisitely sensitive to the type II RAFi naporafenib. We further demonstrate that naporafenib in combination with MEKi trametinib can durably and robustly overcome both innate and acquired treatment resistance to dabrafenib and trametinib using ATC cell lines and patient-derived xenograft models, including in a PDX model from an ATC patient who developed acquired resistance to dabrafenib and trametinib. Finally, we describe a novel mechanism of acquired resistance to type II RAF inhibitor and MEK inhibitor through compensatory mutations in MAST1. Taken together, our work using translational and functional genomics have unraveled the differential mechanisms of treatment resistance to type I and type II RAFi in combination with trametinib, and rationalizes the clinical investigation of type II RAFi in the setting of thyroid cancer. Citation Format: Peter Zeng, Jalna Meens, John Barrett, Matthew J. Cecchini, Sarah B. Ryan, Nachuan Pan, Amir Karimi, Laura Jarycki, Alice E. Dawson, Mushfiq Shaikh, David Palma, Eric Winquist, Paul C. Boutros, Laurie Ailles, Anthony C. Nichols. Understanding and overcoming innate and acquired resistance to type I and II RAF inhibitors in anaplastic thyroid cancer using translational functional genomics [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 3580.
Abstract 4021: The development of CAR T cell therapeutics targeting tumor specific CD146
Authors: Erez Uzuner, Holly Mole, Chun W. Wong, Macarena L. Fernandez Carro, Rotem Leshem, Kieran Sefton, Helen Tovey, Andrew Picken, Marcel Blot-Chabaud, Adam F. Hurlstone
Journal: Cancer Research (2024)

Abstract Chimeric antigen receptor (CAR) T cells represent a promising class of "living drugs" for cancer treatment. These primary T cells are genetically engineered to express a synthetic antigen receptor, incorporating various domains to enhance their effector functions. While CAR T cells have shown success against liquid cancers, their application to solid cancers is hindered by significant "on-target/off-tumor" toxicities due to the absence of specific target proteins. In this study, we aim to enhance the tumor specificity of CAR T cells by targeting a tumor-specific version of CD146. CD146 is a glycoprotein widely expressed in several solid tumors, particularly melanoma and ovarian cancer. However, it is also expressed on benign cells, such as endothelial cells, pericytes, and smooth muscle cells. Nevertheless, a CD146 isoform exists that is enriched in cancer cells. We assessed CAR activity using flow cytometry to measure surface CD69 expression (an early activation marker) on CAR-expressing Jurkat cells co-cultured with various CD146-positive and CD146-negative human melanoma and ovarian cancer cell lines. The killing ability of primary CAR-T cells was evaluated by measuring the relative luciferase activity of target cells, and their effector functions were further analyzed by ELISA for the secretion of IFN-g and TNF-a. Through multiple rounds of protein engineering, we have developed a CAR construct capable of reprogramming T cells to respond to a tumour-enriched CD146 isoform. Our CAR demonstrated antigen-dependent activation of Jurkat cells when co-cultured with CD146-positive human melanoma and ovarian cancer cell lines, comparable to a CAR targeting pan-CD146. Moreover, primary CAR T cells exhibited proportional killing activity and other effector functions. We have successfully engineered a CAR with specificity for a tumour-enriched isoform of CD146. Our future work will involve rigorously evaluating the tumor selectivity of our CAR, as well as assessing the ability of primary CAR T cells expressing this CAR to control tumor growth in vivo. Citation Format: Erez Uzuner, Holly Mole, Chun W. Wong, Macarena L. Fernandez Carro, Rotem Leshem, Kieran Sefton, Helen Tovey, Andrew Picken, Marcel Blot-Chabaud, Adam F. Hurlstone. The development of CAR T cell therapeutics targeting tumor specific CD146 [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 4021.
Abstract 5325: Cytokine CCL9, new downstream target of oncogene Kras to modulate acinar-to-ductal metaplasia during pancreatic cancer initiation
Authors: Geou-Yarh (Stancy) Liou, Justin K. Messex, Crystal J. Byrd
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of cancer with a current five-year survival rate at 12% in the US, and is dominated by oncogenic Kras mutations. Accumulating evidence showed that PDAC can be originated from acinar-to-ductal metaplasia (ADM). In this process, pancreatic acini harboring oncogenic Kras mutations are transdifferentiated to a duct-like phenotype that further progresses to become pancreatic intraepithelial neoplasia (PanIN) lesions, giving rise to PDAC. Although ADM formation is commonly observed in KrasG12D transgenic mouse models of PDAC, the exact mechanisms of how oncogenic KrasG12D modulates this process remain unclear. Here, we unveil a new downstream target of oncogenic Kras, cytokine CCL9 during ADM formation. Either exogenously treating primary pancreatic acini with recombinant CCL9 or ectopically expressing CCL9 in primary pancreatic acini resulted in ADM formation in a 3D organoid culture system. Furthermore, knockdown of CCL9 in KrasG12D-expressed acini reduced KrasG12D-induced ADM. Higher levels of reactive oxygen species (ROS) were detected in the KrasG12D-expressed pancreatic acini, and knockdown of CCL9 in these acini decreased ROS levels. Overexpression of CCL9 in primary pancreatic acini elevated cellular ROS of pancreatic acinar cells. Furthermore, depletion of ROS in 3D organoid culture of CCL9-expressed acini reduced CCL9-induced ADM formation. In transgenic mice of p48cre:KrasG12D, blockade of CCL9 through its specific neutralizing antibody attenuated ADM formation as well as PanIN structures. Altogether, our results indicated oncogenic KrasG12D initiates PDAC through a new downstream target molecule, CCL9, to enhance ROS levels of pancreatic acinar cells. Citation Format: Geou-Yarh (Stancy) Liou, Justin K. Messex, Crystal J. Byrd. Cytokine CCL9, new downstream target of oncogene Kras to modulate acinar-to-ductal metaplasia during pancreatic cancer initiation [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 5325.
Abstract 6031: Fasting associated microbiota contributes to small intestinal radioprotection by modulating the epigenome
Authors: Praveen Barrodia, Emre Arslan, Sabrina Jeter-Jones, Robert R. Jenq, Kunal Rai, Helen Piwnica-Worms
Journal: Cancer Research (2024)

Abstract Normal tissue toxicity often restricts the administration of effective radiation doses for optimal tumor cell elimination. We identified a novel host-protective effect conferred by short-term fasting when treating mice with high dose radiation. We showed that fasting mice for 24h induces epigenetic and transcriptional changes in small intestinal epithelial cells (siECs) and confers protection to small intestinal stem cells from high dose radiation. Here we report that fasting induces changes in the gut microbiome favoring bacteria producing metabolites, specifically short-chain fatty acids, that induce epigenetic changes in siECs. 16S rRNA sequencing of feces isolated from the small intestines of fed and fasted mice revealed a marked enrichment of Akkermansia muciniphila (AKK) in fasted relative to fed mice. Specific depletion of AKK through antibiotic treatment impaired the ability of fasting to provide organismal radioprotection whereas both organismal and OLFM4+ stem cell protection was restored in fasted animals upon reintroduction of AKK. AKK produces short chain fatty acids (SCFAs) including propionate which is able to induce histone modifications and our metabolomic analysis of feces isolated from the ileums of mice demonstrated a significant increase in propionic acid levels in fasted mice compared to fed mice. Importantly, we showed that AKK conditioned medium as well as its metabolite (propionate) are able to induce histone acetylation in Lgr5+ stem cell enriched epithelial spheroids cultured in vitro. We are currently employing high-dimensional analysis techniques, including single cell analysis, Cut&amp;Tag and RNAseq to determine how the epigenetic and transcriptional changes induced by fasting provide organismal and SI radioprotection. Citation Format: Praveen Barrodia, Emre Arslan, Sabrina Jeter-Jones, Robert R. Jenq, Kunal Rai, Helen Piwnica-Worms. Fasting associated microbiota contributes to small intestinal radioprotection by modulating the epigenome [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 6031.
Abstract 5527: Spatiotemporal analysis of growth factor regulation of osteosarcoma AKT and ERK signaling dynamics in an <i>ex vivo</i> lung metastasis model
Authors: Rawan Makkawi, Ryan D. Roberts, Jeremy Copperman, Alexander E. Davies
Journal: Cancer Research (2024)

Abstract In the present study, we investigated the relationships between spatiotemporal distribution of growth factors in the lung microenvironment, metastatic osteosarcoma cell signaling, and intratumoral gene expression heterogeneity. Osteosarcoma is an aggressive bone malignancy that commonly metastasizes to the lungs, resulting in significant patient mortality. During metastasis, disseminated cancer cells are exposed to microenvironment-derived growth factors that result in signaling pathway activation. Two such pathways are MAPK/ERK and PI3K/AKT, which regulate complex transcriptional programs underlying cell proliferation and survival decisions. In this study, we utilized precision cut lung slices (PCLS) obtained from mice with established osteosarcoma metastases to ex vivo model associations between the spatiotemporal distributions of growth factors in the lung, osteosarcoma signaling dynamics, and intratumoral gene expression heterogeneity, with single cell precision. To accomplish this, we engineered osteosarcoma cells that co-expressed genetically-encoded ERK and AKT sensors, engrafted them into PCLS tissues, then recorded sensor dynamics via live-cell microscopy. These tissues were subsequently fixed and immuno-stained for measurement of growth factor expression in resident lung cells and spatial correlation with observed tumor cell ERK-AKT signaling dynamics. Using this approach, we found that growth factor expression was diffusely increased within areas bordering osteosarcoma metastases. FGF2 and IGF1, which we have previously demonstrated to potently induce ERK signaling in osteosarcoma cells, were both significantly upregulated in these regions. However, despite relatively uniform overexpression of growth factors adjacent to tumors, individual osteosarcoma cells displayed stochastics patterns of ERK and AKT signaling, and downstream gene targets. These findings revealed that upregulation of lung growth factors, and the inherent systems-level properties of osteosarcoma signaling networks, can converge to promote intratumoral signaling and gene expression heterogeneity. Together, our results, using a novel PCLS and live-cell biosensor imaging approach, provide new insight into how spatial and temporal changes in microenvironmental signaling composition are integrated by metastatic osteosarcoma cells to promote heterogeneity. Citation Format: Rawan Makkawi, Ryan D. Roberts, Jeremy Copperman, Alexander E. Davies. Spatiotemporal analysis of growth factor regulation of osteosarcoma AKT and ERK signaling dynamics in an ex vivo lung metastasis model [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 5527.
Abstract 4265: ZEB1-regulated hyaluronan network in the lung tumor microenvironment
Authors: Sieun Lee, Jihye Park, Eun Ju Kim, Seongran Cho, Sungsoo Park, Jonathan M Kurie, Young-Ho Ahn
Journal: Cancer Research (2024)

Abstract In the tumor microenvironment, hyaluronan surrounds neighboring cells as one of the major components of the extracellular matrix and stimulates the epithelial-mesenchymal transition (EMT) of various epithelial cancer cells. However, the mechanism of how the hyaluronic network is formed by cancer cells and regulates cancer progression and metastasis has not been known in detail. Therefore, we investigated the role of the hyaluronan network built-up by cancer cells in regulating cancer progression and metastasis in the tumor microenvironment. Our study demonstrated that ZEB1, an EMT-inducing transcription factor, reconstructs the hyaluronan network to induce the expression of ITIH2, a hyaluronan-binding protein, and hyaluronic acid synthase-2 (HAS2), ZEB1 was also shown to control the isoform switching of CD44, a hyaluronan receptor. ITIH2 knockdown and HAS inhibition reduced the formation of hyaluronan cables and inhibited cancer cell migration and invasion. In addition, the treatment of a specific ITIH2 inhibitor identified through deep learning-based screening suppressed the formation of hyaluronan cables, cell migration, and metastasis. These findings suggest that targeting the hyaluronan network could be a novel strategy for suppressing lung cancer progression and metastasis in the tumor microenvironment. Citation Format: Sieun Lee, Jihye Park, Eun Ju Kim, Seongran Cho, Sungsoo Park, Jonathan M Kurie, Young-Ho Ahn. ZEB1-regulated hyaluronan network in the lung tumor microenvironment [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 4265.
Abstract 1489: The role of EPAS1 and TEAD1 in gastric cancer liver metastasis
Authors: DONG KI Lee, Hyun Woo Park, Jae-Ho Cheong, Heon Yung Gee
Journal: Cancer Research (2024)

Abstract Gastric cancer ranks fifth in incidence and fourth for cancer-related mortality worldwide. While the liver is widely recognized as the leading site of metastasis in gastric cancer, the intricate mechanisms underpinning its tropism toward the liver and the hematogenous metastasis process remain poorly understood and demand further investigation. Hematogenous metastasis encompasses the generation of circulating tumor cells from the primary tumor site and their subsequent attachment to the metastatic niche. This process involves the transition between adherent and suspension states. In our investigation of anchorage dependency, we identified 20 transcription factors upregulated in suspension cells compared to adherent cells and 18 transcription factors upregulated in adherent cells relative to suspension cells, respectively. To investigate factors involved in gastric cancer metastasis, RNA sequencing of paired primary and metastatic tissue samples obtained from 15 patients diagnosed with advanced gastric cancer was conducted, which disclosed the selective upregulation of EPAS1 and TEAD1 in metastatic liver tissue compared to the matched primary tumor tissue and the metastatic tissue originating from other sites. Through in vitro analysis, we observed a portion of adherent cells transitioning into suspension cells when subjected to a hyperdense environment. We also observed cell reattachment upon harvesting and replating these suspension-state transited cells. Comparing EPAS1 and TEAD1 expression in these states unveiled increased expression of EPAS1 and TEAD1 in reattached cells relative to suspension-state cells. We established a gastric cancer metastasis mouse model introducing gastric cancer cells into the mouse circulatory system via intracardiac injection to validate our findings. In vivo imaging was utilized to confirm systemic metastasis. After fluorescence-based cell sorting, EPAS1 and TEAD1 expression in cancer cells collected from the blood, liver, and ovary were assessed. We detected higher expression of EPAS1 and TEAD1 in liver metastasis compared to the circulating tumor cells. Furthermore, EPAS1 and TEAD1 were upregulated in liver metastatic cancer cells compared to ovarian metastatic cancer cells. Our findings underscore EPAS1 and TEAD1 as pivotal factors governing gastric cancer liver tropism and metastasis, offering insights that may contribute to targeted interventions in the clinical landscape. Citation Format: DONG KI Lee, Hyun Woo Park, Jae-Ho Cheong, Heon Yung Gee. The role of EPAS1 and TEAD1 in gastric cancer liver 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 1489.
Abstract 542: Development of novel syngeneic tumor models with intrinsic or extrinsic resistance mechanisms to PD-1 blockade
Authors: Xiaomin Wang, Ziwei Zhang, Longzhou Liu, Xue Zhang, Dong Wang, Nengwei Xu, Xiangnan Qiang, Qingyang Gu, Jian Xiang, Zhixiang Zhang
Journal: Cancer Research (2024)

Abstract Programmed cell death-1 (PD-1) blockade has demonstrated remarkable clinical efficacy across various tumor types. However, the current PD-1 blockade monotherapy benefits only a small proportion of patients, and primary or acquired resistance can ultimately lead to cancer progression in clinical settings. Understanding the underlying mechanisms of resistance is both necessary and urgent to enhance clinical outcomes. Increasing evidence suggests that resistance to PD-1 therapy can arise from both tumor-cell-intrinsic and tumor-cell-extrinsic factors. Loss-of-function mutations in the antigen presentation pathway and downstream elements represent intrinsic mechanisms, while tumor-infiltrating immunosuppressive cells such as regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and tumor-associated macrophages (TAMs) contribute to immune tolerance as extrinsic factors. Currently, the rational design of combination therapies based on these resistance mechanisms remains to be achieved. In this study, we developed two types of anti-PD-1 antibody-resistant models based on the intrinsic anti-PD-1 treatment-sensitive MC38 models. These models include genetically engineered resistant models with B2M or STK11 knockout (KO) and induced resistant models through in vivo progressive drug selection. STK11 KO mutations resulted in reduced expression of PD-L1 on tumor cells and a lower infiltration of CD8+ cytotoxic T lymphocytes in the tumor microenvironment, while B2M KO led to a lack of antigen presentation on the tumor cell surface, blocking the binding of the anti-PD-1 antibody. In terms of the induced anti-PD-1 resistant models, a higher proportion of immunosuppressive cells, including Tregs, MDSCs, and TAMs, were observed in the tumor microenvironment compared to the parental counterparts, contributing to immune escape from PD-1 blockade. These models simulate extrinsic and intrinsic mechanism-based anti-PD-1 resistance, allowing for the identification of combination therapies to overcome resistance to anti-PD-1. Our study enhances our understanding of the biological basis of anti-PD-1 resistance and supports the discovery of mechanistically-designed combination therapies to overcome resistance to anti-PD-1 therapy, potentially broadening its clinical applicability. Citation Format: Xiaomin Wang, Ziwei Zhang, Longzhou Liu, Xue Zhang, Dong Wang, Nengwei Xu, Xiangnan Qiang, Qingyang Gu, Jian Xiang, Zhixiang Zhang. Development of novel syngeneic tumor models with intrinsic or extrinsic resistance mechanisms to PD-1 blockade [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 542.