bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4194: An in-silico approach to identify genes required for polyamine transport
Authors: Millington Victoria , von Kalm Laurence
Published: March 2024

The purpose of this study was to use an in-silico approach to identify genes required for polyamine transport. Polyamines are small positively charged molecules that control vital cellular processes including cell proliferation and growth. Cells obtain polyamines by biosynthesis or transport from the extracellular environment. Cancer cells require high levels of polyamines to sustain rapid growth, and therapies aimed at polyamine depletion are considered promising. The FDA approved drug difluoromethylorthinine (DFMO) blocks polyamine biosynthesis, however, in most cases malignant cells evade the biosynthetic block by increasing transport. Thus, a dual therapy that simultaneously targets polyamine biosynthesis and transport is needed. The mechanism of polyamine transport is poorly understood in multicellular eukaryotes and identification of genes involved in polyamine transport has largely relied on an inefficient hit-or-miss ‘educated guess’ approach. To increase the probability of identifying genes involved in polyamine transport, we adopted an in-silico approach comparing protein-protein interactions with the protein product of the human ATP13A3 gene across multiple databases. We used ATP13A3 because our work, and the work of others, has shown that ATP13A3 and its Drosophila ortholog ‘anne’ are required for polyamine transport. We searched for high confidence protein interactors with ATP13A3 in four databases, BioGRID, STRING, NextProt, and GPS-Prot, prioritizing hits that occurred in more than one database. We next asked if any of the high priority hits had orthologs in Drosophila. We chose to study the candidate genes in Drosophila because we have utilized the sophisticated genetic resources available in this organism to develop novel assays to identify positive and negative regulators of polyamine transport. Using the criteria described, we identified four candidates that occurred in three databases, and one that occurred in two databases. In addition, a very high confidence match to the human gene SLC15A was observed in one database and included in the group of candidate genes. To determine the validity of our candidate gene enrichment approach we are currently testing each gene for roles in polyamine transport.

Citation Format: Victoria Millington, Laurence von Kalm. An in-silico approach to identify genes required for polyamine transport [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 4194.
Abstract 4232: Exploring chemotherapy resistance in pancreatic cancer: Insights from a 3D organoid model
Authors: Lee Hee Seung
Published: March 2024

Pancreatic cancer is marked by a dismal prognosis, with a 5-year survival rate at approximately 10%. A key contributor to its lethality is the development of chemotherapy resistance, followed by early metastasis. However, studies elucidating the mechanisms behind chemotherapy resistance in pancreatic cancer are limited. Previous research has relied on 2D cell line models, which present limitations, such as uniform cell types that fail to capture tumor heterogeneity and an inaccurate representation of clinical realities, wherein resistance often develops gradually rather than through continuous exposure to high drug concentrations. In this study, we developed a more sophisticated organoid model of chemotherapy resistance. Six organoids from three patients were matched to study chemotherapy resistance in a personalized context. Comprehensive whole-exome sequencing and transcriptomic analyses were performed, along with an examination of chemotherapy resistance protein expression and EMT-related markers. Notably, differential expression levels of CK19 and Vimentin were observed between samples. Our analysis also focused on the expression of the ATP-Binding Cassette Subfamily G Member 2 (ABCG2) gene in chemoresistant organoids. Western blot analysis indicated a significant increase in ABCG2 expression in these organoids compared to controls. According to the Moffitt RNA signature, the primary and corresponding chemoresistant organoids retained their molecular subtype classifications both before and after developing chemoresistance. Gene set enrichment analysis uncovered significant upregulation of pathways related to DNA repair and cell cycle regulation, particularly the G2M checkpoint, in chemoresistant organoids. Furthermore, gene ontology functional analysis suggested a notable overrepresentation of activities related to amino acid transmembrane transport and extracellular matrix constituents, underscoring their potential role in the chemoresistance phenotype.

Citation Format: Hee Seung Lee. Exploring chemotherapy resistance in pancreatic cancer: Insights from a 3D organoid 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 4232.
Abstract 4240: A comprehensive in vitro tumor model: One-stop simultaneous isolation and culture of tumoroids, CAFs and TILs for advancing immuno-oncology research
Authors: KO YOO RI , Kim Sung Min , Park Hye Seon , Jang Se Jin
Published: March 2024

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 4247: Miniaturizing patient-derived organoid screening assays for predictive drug testing
Authors: Abouleila Yasmine , Verkerk Roel , Doorn Mayke , Voskuilen Timo , Harada Gakuro , Watanabe Masahiko , Smabers Lidwien , Kyan Hideaki , Kumagai Takahiko , Hikichi Yuichi , Overmeer Rene , Roodhart Jeanine , Matsuno Kiyotaka , Verissimo Carla , Boj Sylvia
Published: March 2024

Colorectal cancer (CRC) ranks as the third leading cause of both cancer incidence and cancer-related mortality. A significant portion of CRC patients diagnosed with de novo metastatic disease face limited benefits from conventional treatment options, often accompanied by substantial side effects. This underscores the pressing need for more effective preclinical models to predict patient responses in clinical settings. Patient-derived organoids (PDOs or HUB Organoids®) represent a pivotal breakthrough in preclinical modeling. These organoids are directly derived from patient tissue, faithfully mirroring the patient's disease. While HUB Organoid Technology is currently applicable for preclinical drug screening, it is essential to expedite the transition from patient diagnosis to the delivery of PDO-based results to directly benefit patients. In a collaborative effort with Yamaha Motor, we have optimized the Yamaha CELL HANDLERTM for the automated transfer of organoids, offering enhanced precision and efficiency in handling a significantly reduced number of organoids per screening plate, compared to conventional methods. Moreover, we have developed an image-based readout system that enables precise quantification of organoid numbers, ensuring high assay quality. Utilizing this developed automated platform, we conducted a proof-of-concept investigation into PDO responses to chemotherapy in comparison to corresponding patient responses. The correlation between PDO and patient responses demonstrated a strong connection, highlighting the potential of the developed automated platform for predictive drug testing. In summary, this work signifies the development of an automated workflow that synergizes patient-representative HUB Organoids® with cutting-edge robotics from Yamaha Motor. The described workflow reduces the number of organoids needed per screening well, streamlining patient response prediction, potentially leading to faster diagnoses, and ultimately optimizing patient outcomes.

Citation Format: Yasmine Abouleila, Roel Verkerk, Mayke Doorn, Timo Voskuilen, Gakuro Harada, Masahiko Watanabe, Lidwien Smabers, Hideaki Kyan, Takahiko Kumagai, Yuichi Hikichi, Rene Overmeer, Jeanine Roodhart, Kiyotaka Matsuno, Carla Verissimo, Sylvia Boj. Miniaturizing patient-derived organoid screening assays for predictive drug testing [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 4247.
Abstract 4253: High expression of specific gene profiles in organoids from African American pancreatic cancer tumors
Authors: Lyn-Cook Beverly D. , Emamzaden Fatemeh Nouri , Word Beverly , Hammons George
Published: March 2024

Pancreatic cancer remains one of the leading causes of cancer-related deaths in the United States with limited therapies for advanced stages of this disease. African Americans have the highest morbidity and mortality rates of pancreatic cancer compared to other racial groups. Many factors are known to contribute to this disparity such as, socioeconomic and lifestyle factors. One of the major factors contributing to this disparity is the lack of African Americans with pancreatic cancer in clinical trials or genomic databases. In order to gain insight into the biology or genetic differences that may exist in signals driving the aggressiveness of this cancer in this population more studies are needed. Innovative in vitro models are needed to investigate possible differences in molecular changes that may exist in African Americans. Studies have shown that organoids developed from metastatic and primary tumors can give sights into genetic and epigenetic changes detected in several type of cancers. Using a Human Pancreatic Adenocarcinoma TagMan Array 96 (Applied Biosystems), which contained 76 genes known to be expressed in pancreatic cancer, pancreatic organoids from African American metastatic tumors revealed high expression levels of specific genes. Usually K-ras is highly expressed in pancreatic tumors but it was not significantly expressed in the organoids from African Americans metastatic tumors. However, preliminary results from organoids, compared to pancreatic cancer cell line spheroids, showed significantly increased gene expression of HSP90AA1 (13-fold), MMP1(36-fold), BRACA2 (20-fold), MDM2 (19-fold), RB1 (14-fold), Rel (12-fold), STAT1 (15-fold), STAT5B (5-fold), and TGFBR1 (1- fold). High expression of HSP90AA1 is related to poor prognosis, constitutively expression of STAT5B confers gemcitabine chemoresistance and promote invasiveness, and mutations in BRCA2 can increase pancreatic cancer risk. Further studies are being done to validate these findings in African American pancreatic tumors and to ascertain their relevance to the metastatic progression phenotype.

Citation Format: Beverly D. Lyn-Cook, Fatemeh Nouri Emamzaden, Beverly Word, George Hammons. High expression of specific gene profiles in organoids from African American pancreatic cancer 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 4253.
Abstract 4265: ZEB1-regulated hyaluronan network in the lung tumor microenvironment
Authors: Lee Sieun , Park Jihye , Kim Eun Ju , Cho Seongran , Park Sungsoo , Kurie Jonathan M , Ahn Young-Ho
Published: March 2024

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 4267: Inflammation mediated expression of integrin αvβ3 potentiates KRAS driven PDAC oncogenesis
Authors: Shepard Ryan M. , Campos Alejandro D. , Ortega Zachary M. , Wettersten Hiromi I. , Von Schalscha Tami , Weis Sara M. , Cheresh David A.
Published: March 2024

Understanding how pancreatic epithelial cells respond to inflammation and why some become tumorigenic and aggressive could identify new methods of early detection and novel therapeutic targets to control disease progression. Here, we leveraged an in vivo model in which mice with pancreas-specific expression of mutant Kras progress from pre-malignant intraepithelial neoplasias (PanINs) to pancreatic ductal adenocarcinoma (PDAC) following caerulein-induced chronic pancreatitis. During the transition from PanINs to PDAC, we observe two classes of neoplastic lesions: classically-described PanIN tubular structures that are highly organized and previously uncharacterized atypical highly disorganized lesions that are marked by robust integrin αvβ3 expression, observations which are consistent with human pancreatitis and PDAC. In vitro, we report that immune-, stroma-, and tumor cell-derived inflammatory cytokines induce β3 expression in a STAT3-dependent manner leading to increased integrin αvβ3. Considering that we previously established αvβ3 as a driver of cancer cell stress tolerance, drug resistance, and a stem-like phenotype, the acquisition of αvβ3 during chronic inflammation may promote tumorigenesis. Indeed, using the spontaneous tumor mouse model and xenograft models of human PDAC, we find that cells with an inability to upregulate β3 during tumor initiation fail to form tumors. These findings implicate integrin αvβ3 as a critical driver of inflammation-mediated pancreatic tumorigenesis.

Citation Format: Ryan M. Shepard, Alejandro D. Campos, Zachary M. Ortega, Hiromi I. Wettersten, Tami Von Schalscha, Sara M. Weis, David A. Cheresh. Inflammation mediated expression of integrin αvβ3 potentiates KRAS driven PDAC oncogenesis [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 4267.
Abstract 4309: Establishment of intratumor heterogeneity using patient derived lung cancer cells
Authors: Funazo Tomoko , Ozasa Hiroaki , Tsuji Takahiro , Shima Yusuke , Suminaga Keiichiro , Hashimoto Kentaro , Yoshida Hiroshi , Ogimoto Tatsuya , Hosoya Kazutaka , Ajimizu Hitomi , Nomizo Takashi , Yoshida Hironori , Hirai Toyohiro
Published: March 2024

Overcoming cancer treatment resistance is a problem that must be solved to improve the prognosis of cancer patients. In recent years, genome analysis has revealed the existence of multiple subgroups with different properties within a single tumor, and intratumor heterogeneity is a cause of treatment resistance. It has also been reported that. However, the mechanism of intratumor heterogeneity remains unclear. Previous research on intratumor heterogeneity has mainly focused on analyzing patient cancer cells, classifying subgroups, and estimating characteristic factors. This method has two drawbacks. One is limitations in including all subgroups as research subjects, and other is lack of verification of whether characteristic factors are actually involved in intratumor heterogeneity in patients. Therefore, it is necessary to use a model of "early intratumor heterogeneity" in which monoclonal cells are divided into subgroups with different properties, and to verify the discovered factors using patient-derived cancer cell lines. In alectinib-resistant cell line (H2228-AR1S) created from monoclonal ALK-positive lung cancer cell line (H2228) by exposing to alectinib in vitro, existence of two fractions with different appearances. Using flow cytometry, it was revealed that H2228-AR1S bimodally expresses EpCAM, and the EpCAM-low fraction has high migration ability. In EpCAM-low fraction, epithelial markers were decreased, and mesenchymal markers were increased using immunoblotting. It suggests that EpCAM low subpopulation has undergone epithelial-mesenchymal transition (EMT). Additionally, we established a BRAF-positive lung cancer cell line (KTOR83) collected with consent from patients attending Kyoto University Hospital. Cells after in vitro dabrafenib exposure to KTOR83 showed bimodal EpCAM expression, and the EpCAM-low fraction has high migration ability. We established an intratumor heterogeneous model using commercially available cells and a patient-derived lung cancer cell line. Furthermore, we will explore factors common to the two models and examine factors involved in intratumor heterogeneity.

Citation Format: Tomoko Funazo, Hiroaki Ozasa, Takahiro Tsuji, Yusuke Shima, Keiichiro Suminaga, Kentaro Hashimoto, Hiroshi Yoshida, Tatsuya Ogimoto, Kazutaka Hosoya, Hitomi Ajimizu, Takashi Nomizo, Hironori Yoshida, Toyohiro Hirai. Establishment of intratumor heterogeneity using patient derived lung 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 4309.
Abstract 4312: KRAS oncogenic activation in Gramd2
+ AT1 cells form lung adenocarcinoma with distinct transcriptomic and tumor microenvironment signatures
Authors: Yang Minxiao , Castillo Jonathan , Gonzalez Edgar , Yan Chunli , Torres Evanthia Roussos , Borok Zea , Marconett Crystal
Published: March 2024

Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer and presents with a high degree of biological heterogeneity and distinct clinical outcomes. The current paradigm of LUAD etiology recognizes alveolar epithelial type II (AT2) cells as the primary cell of origin, while the role of AT1 cells in LUAD oncogenesis remains relatively unknown. Here, we examined transformation via activation of the oncogenic KRASG12D mutation in a Gram-domain containing 2 (Gramd2)+ AT1 cell lineage tracing model system, which resulted in multifocal LUAD, primarily of papillary histology. Spatial transcriptomic sequencing revealed significant differences of transcriptomic signatures and signaling activities between Gramd2+ AT1 cell-derived and Sftpc+ AT2 cell-derived LUAD. Single-cell RNA sequencing of macrodissected LUAD lesions demonstrated heterogeneous cell composition of the tumor microenvironment (TME), with Gramd2+ AT1 cell-derived LUAD fostering a proinflammatory, immunoreactive TME and Sftpc+ AT2-derived LUAD presenting with an immunosuppressive TME. Collectively, our study suggests that cell of origin for LUAD is associated with histologic subtype, transcriptomic aberrations, and immune cell composition within LUAD that may influence response to therapy.

Citation Format: Minxiao Yang, Jonathan Castillo, Edgar Gonzalez, Chunli Yan, Evanthia Roussos Torres, Zea Borok, Crystal Marconett. KRAS oncogenic activation in Gramd2 + AT1 cells form lung adenocarcinoma with distinct transcriptomic and tumor microenvironment signatures [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 4312.
Abstract 4317: The role of autophagy in triple negative breast cancer
Authors: Gamal Sameh , El-Nikhely Nefertiti A. , Nematallah Hesham , Saeed Hesham M.
Published: March 2024

Breast cancer (BC) remains a global health concern, being the most common cancer amongst women in the world, and the second-leading cause of cancer related death. Triple-negative breast cancer (TNBC) represents a challenging frontier in oncology, characterized by its aggressiveness and its unique molecular profile devoid of the known receptors. Its elusiveness lies in the inherent heterogeneity within its subtypes, contributing to diverse clinical behaviours and treatment responses. TNBC has also shown elevated basal autophagy level as a pro-survival mechanism to make up for the increased nutrients demand mandated by the high K-RAS signalling. To tackle such tumour, we chose an autophagy blocker in addition to multi-kinase inhibitor. The combination index calculated for the proposed drugs has shown promising results in reduction of cell viability more than each drug separately. Selectivity index proved the safety of our doses on normal fibroblast cells in contrast to two breast cancer cell lines (MDA-MB 231 & MCF7). To further complement the findings, cell cycle arrest was witnessed at S phase which lead to apoptosis seen by flowcytometry and other expression analysis studies. Finally, Imaging studies and expression analysis on protein level have documented the apoptotic effects rendered by autophagy inhibition.Research endeavours continue to unravel the intricate landscape of TNBC, seeking novel avenues for targeted treatments, immunotherapies, and personalized medicine, aiming to transform the paradigm of care for those affected by this enigmatic form of breast cancer. As evident from the results, our combination has also managed to reduce the cells migration effectively which reflects that it can be initiated with aggressive metastatic tumours like TNBC.

Citation Format: Sameh Gamal, Nefertiti A. El-Nikhely, Hesham Nematallah, Hesham M. Saeed. The role of autophagy in triple negative breast 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 4317.
Abstract 433: BCAT1 promotes HCC metabolic reprogramming and survival through HIF-1α stabilization
Authors: Zhang Misty Shuo , Kwan Kenneth Kin-Leung , Li Weixing , Papathanassiu Adonia E. , Ng Irene Oi-Lin , Wong Carmen Chak-Lui
Published: March 2024

Hepatocellular carcinoma (HCC) is a highly lethal primary liver malignancy characterized by hypoxia, a common feature of solid tumors, particularly in HCC. Hypoxia-inducible factors (HIFs) play a pivotal role in mediating various cellular processes, such as metabolic adaptation, to support the survival of hypoxic cells. The cytosolic form of branched-chain amino transferase (BCAT1) is responsible for the reversible transamination reaction between branched-chain keto-amino acids (BCKAs) and branched-chain amino acids (BCAAs), facilitating the interconversion between α-ketoglutarate (α-KG) and glutamate. Interestingly, we found that in the context of HCC, BCAT1 consumes α-KG, thereby favoring the stabilization of HIF-1α through suppressing the α-KG-dependent prolyl hydroxylase (PHD). Knockdown (KD) or knockout (KO) of BCAT or BCAT inhibitor (ERG245) suppressed HIF-1 stability, as well as HIF-1 dependent transcriptomic and metabolic changes. Mass spectrometry (MS)-based isotopic carbon tracing showed that KD/KO or ERG 245 suppressed hypoxia/HIF-1-induced glycolytic flux. Interestingly, ERG245 effectively inhibited the proliferative output of hypoxic HCC cells and suppressed HCC growth. ERG245 also profoundly inhibited HCC growth in vitro and in vivo together with Sorafenib, a tyrosine kinase inhibitor (TKI) used in HCC by increasing the apoptotic cell death. Furthermore, we confirmed that the expressions of BCAT1 and the HIF-1α-targeted metabolic genes are positively correlated in human HCCs. Our findings unequivocally demonstrate that BCAT1 confers a growth advantage to HCC cells by stabilizing HIF-1α and orchestrating HIF-1α-mediated metabolic reprogramming. Consequently, targeting BCAT1 emerges as a promising therapeutic strategy for HCC patients.

Funding Support: This work was supported by the Centre for Oncology and Immunology under the Health@InnoHK initiative funded by the Innovation and Technology Commission, The Government of Hong Kong SAR, China and National Natural Science Foundation of China (NSFC) (82173123, C.C.-L.W.)

Citation Format: Misty Shuo Zhang, Kenneth Kin-Leung Kwan, Weixing Li, Adonia E. Papathanassiu, Irene Oi-Lin Ng, Carmen Chak-Lui Wong. BCAT1 promotes HCC metabolic reprogramming and survival through HIF-1α stabilization [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 433.
Abstract 4337: Illuminating the complex rearrangement landscape of sarcoma
Authors: Waise Sara , Lesluyes Tom , Demeulemeester Jonas , Tarabichi Maxime , Flanagan Adrienne , Pillay Nischalan , Van Loo Peter
Published: March 2024

Structural rearrangements and in particular, gene fusions, are key mutational processes in bone and soft tissue tumors, used for both disease classification and as biomarkers. However, the mutational processes and rearrangement processes underlying many of these events remain poorly characterized. Recent data indicate that sarcomas show particularly high frequencies of complex rearrangement events, including patterns which do not fit those of known mutational mechanisms. As the largest whole genome sequencing (WGS) cohort of sarcomas to date, the Genomics England (GE) 100,000 Genomes project represents a unique dataset in which to profile these events.

Structural variants (SVs) were identified in whole genome sequencing data for 978 samples from the Genomics England 100,000 Genomes Project using an optimized approach based on 5 specialized SV callers. SVs identified by at least 2 callers were filtered to retain only those which passed the quality filter, and to remove variants present in either matched germline samples or >1% of a panel of normal variants. Chromothriptic events, extrachromosomal DNA (ecDNA) and genes enriched for SVs were identified using established algorithms.

The prevalence of SVs varies across sarcoma, in keeping with previous reports, with particularly high rates observed in myxofibrosarcoma and liposarcoma. As described previously, liposarcomas showed the highest rates of chromothripsis. We have examined some tumor types at higher granularity than previously available, demonstrating directly that the rates of complex rearrangement events vary across subtypes. For example, chromothriptic events are identified in 100% of well-differentiated liposarcomas, but less than 10% of myxoid liposarcomas. Similarly, the presence of ecDNA varies by tumor type, with the novel observation of particularly high rates in angiosarcoma. Using these data, we have catalogued the rearrangement patterns generating canonical gene fusions in fusion-driven soft tissue tumor types.

Despite more recent advances in histological classification, survival for patients with sarcoma has remained largely unchanged for 40 years. Characterization of the mutational processes underlying these rearrangements will shed light on the pathogenesis of these tumors.

Citation Format: Sara Waise, Tom Lesluyes, Jonas Demeulemeester, Maxime Tarabichi, Adrienne Flanagan, Nischalan Pillay, Peter Van Loo. Illuminating the complex rearrangement landscape of sarcoma [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 4337.
Abstract 4344: Comprehensive analysis of LINE-1 transposable elements in colorectal cancer
Authors: de Wit Renske , Lakbir Soufyan , Buranelli Caterina , Meijer Gerrit A. , Abeln Sanne , Fijneman Remond J.
Published: March 2024

Background: Colorectal cancer (CRC) is the third most frequent cancer worldwide, and approximately a third of patients die from the disease. There is therefore an urgent need to better understand CRC biology. A particular feature in (colorectal) cancer is the activation of LINE-1 (L1) retrotransposons: DNA fragments which propagate to other places in the genome through an RNA intermediate. Per genome, about 100-150 genomic L1 copies are still retrotransposition-competent, but repressed in most somatic tissues. Their role in tumor development is currently unknown. Recently, the PCAWG consortium characterized the landscape of somatic L1 retrotranspositions in a series of primary cancers of different origin, and identified 124 recurrently active L1 source regions. However, only a limited number of these concerned CRC.

Aim: This study aims to perform a comprehensive analysis of L1 activity in a large cohort of metastatic colorectal cancer.

Methods: To this end, we retrieved data from the Hartwig Medical Foundation, comprising deep (106x) whole genome sequencing (WGS) data from metastatic CRC (n=745), to compare to breast (n=888) and lung cancer samples (n=640). We determined L1 activity as the number of somatic L1 insertions reported by the HMF DNA analysis pipeline and used the activity of each of the 124 L1 sources as previously reported by the PCAWG consortium.

Results: 99% of mCRC samples (n=741) displayed at least 1 somatic L1 retrotransposition, with at least 10 retrotranspositions in 89% of samples. L1 retrotransposition is more prevalent in mCRC than in metastatic lung and breast cancer, in which only 40% and 20% had at least 10 retrotranspositions per sample, respectively. Each cancer type showed a unique profile of active L1 sources. We did not observe a clear preference of L1 insertions for a single genomic region. However, in CRC, the gene most frequently affected in an exon was APC (n=13), an important tumor-suppressor gene. An analysis of somatic SNVs and SVs confirmed an association of mutations in some known L1 regulators such as TP53 with increased L1 activity, whereas mutations in others showed no change in the number of somatic retrotranspositions.

Conclusions: We conclude that somatic L1 retrotranspositions are highly prevalent in metastatic colorectal cancer. Presence of L1 insertions in APC suggests retrotranspositions start very early in CRC development and prompts further investigation into earlier CRC stages.

Citation Format: Renske de Wit, Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer, Sanne Abeln, Remond J. Fijneman. Comprehensive analysis of LINE-1 transposable elements in 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 4344.
Abstract 4387: Interplay of Notch1 and Notch3 signaling regulates pancreatic neuroendocrine tumor proliferation
Authors: Guenter Rachael , Chen Weisheng , Golivi Yuvasri , Robledo Mario , Adams Cole , Jaskula-Sztul Renata , Chen Herbert , Rose J. Bart
Published: March 2024

Background: The 5-year survival rate for patients with advanced pancreatic neuroendocrine tumors (pNETs) is less than 30%. Notch signaling is a transmembrane receptor pathway with four receptor isoforms and five different ligands. Binding between a receptor and ligand triggers pathway activation and is linked to cellular differentiation, cell fate, proliferation, and viability. Both Notch1 and Notch3 signaling have been shown to be dysregulated in pNETs. Notch3 activation has been shown to repress Notch1 activity in other cancers. We hypothesize that activation of Notch3 can reduce Notch1-mediated proliferation in pNETs.

Methods: Genetic deletion of Notch1 (N1-KO) in a pNET cell line (BON) was achieved using CRISPR/Cas9 to create a compound heterozygous knockout at exon 3. An inducible Notch1 overexpression cell line was generated by stably transfecting BON with a plasmid construct containing the Notch1 active form (N1ICD) under a Tet-On regulator. A constitutively active Notch3 cell line was generated by lentiviral transduction of BON with a plasmid overexpressing the Notch3 active form (N3ICD). Real-time quantitative PCR was used to measure mRNA transcript levels, and western blot was used to measure protein expression. Two-dimensional (2D) viability was measured by MTT assay, and three-dimensional (3D) proliferation was measured by spheroid size.

Results: Genetic knockout of Notch1 (N1-KO) reduced the expression of Notch3 at both mRNA and protein levels. N1-KO had reduced proliferation compared to (WT) BON. Increased cell density (ligand availability) or treatment with valproic acid (known Notch1 inducer) led to increased N3ICD in WT BON but not in N1-KO. Overexpression of N1ICD was associated with increased expression of a known downstream target Hes1, as well as Notch3. In contrast, forced overexpression of N3ICD led to increased Notch1 expression, but not Hes1 when compared to a BON cell line transfected with an empty vector. Functionally, N1-KO and N3ICD overexpression cells both had reduced proliferation in both 2D and 3D cell culture.

Conclusions: The Notch1 and Notch3 receptors produce signaling cascades that regulate growth in pNET cells through distinct mechanisms. Reduction of Notch1 signaling suppresses growth, while the same effect can be achieved with Notch3 overexpression. Thus, specifically upregulating Notch3 may be a strategy to block Notch1-mediated proliferation in pNET cells.

Citation Format: Rachael Guenter, Weisheng Chen, Yuvasri Golivi, Mario Robledo, Cole Adams, Renata Jaskula-Sztul, Herbert Chen, J. Bart Rose. Interplay of Notch1 and Notch3 signaling regulates pancreatic neuroendocrine tumor proliferation [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 4387.
Abstract 4392: Neuropeptide Y system in glioblastoma
Authors: Abualsaud Nouran , Tilan Jason , Alrfaei Bahauddeen M. , Glor Harrison , Polk Taylor , Izycka-Swieszewska Ewa , Kitlinska Joanna
Published: March 2024

Gliomas constitute the most common primary cerebral tumors of the central nervous system (CNS), with glioblastoma (GBM) representing the most aggressive subtype. Neurotransmitters are important players in maintaining physiological processes in CNS and abnormal levels of their expression is pathogenic, leading to different processes, including neoplasia. Neuropeptide Y (NPY) is one of the neurotransmitters that is found to play a pivotal role in several malignancies. NPY, acting via its cognate receptors Y1, Y2 and Y5 (Y1R, Y2R and Y5R), has been shown to stimulate cancer cell proliferation, migration, invasiveness and dissemination, as well as tumor vascularization in various malignancies including neuroblastoma, Ewing sarcoma, colon, breast, prostate and liver cancers. Thus, the goal of this study was to determine if the NPY system is involved in glioma biology. Our immunohistochemistry staining of NPY, Y1R, Y2R, and Y5R in human GBM tissues revealed positive staining for NPY and Y2R in GBM cells. No expression of Y1R and Y5R was detected in GBM neoplastic population. To further elucidate the association between NPY and its receptors with GBM tumor stage and patients' survival, we used the available clinical data from the Cancer Genome Atlas Program (TCGA) database to analyze the gene expression of the NPY system. Y2R expression was increased in high-grade gliomas, while mRNA levels of NPY, Y1R and Y5R inversely correlated with the degree of glioma malignancy. Moreover, high Y2R expression was associated with worse survival in GBM patients. Importantly, endothelial Y2R is also responsible for angiogenic effects of NPY, suggesting its role in GBM vascularization. Altogether, these data suggest the involvement of NPY/Y2R axis in glioma progression toward more aggressive phenotype. Further functional studies are required to determine the role of the Y2R axis in this process.

Citation Format: Nouran Abualsaud, Jason Tilan, Bahauddeen M. Alrfaei, Harrison Glor, Taylor Polk, Ewa Izycka-Swieszewska, Joanna Kitlinska. Neuropeptide Y system 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 4392.
Abstract 4417: Development of biochemical screening assays to facilitate drug discovery in RNA m6A modification regulators
Authors: AbdulSalam Safnas F. , Oh Sung Won , Lee Brenna P. , Ferry Joseph J. , Ries John R. , Horiuchi Kurumi Y.
Published: March 2024

Over the recent years, knowledge of RNA modifications and their regulation has expanded extensively, providing novel insights and strategies to explore potential therapeutics for pathogenesis of various diseases, including cancer. Several chemical modifications in RNA have been identified so far, among these N6-methyladenosine (m6A) modification is the most abundant and well-studied epitranscriptomic marker found in mRNA and long noncoding RNA. Abnormal m6A expression is proven to be associated with tumorigenesis, cancer stemness and drug resistance of cancers. Methylation in 6-Adenosin of RNA is a dynamic and reversible process tightly regulated by its writer, m6A methyltransferase complex and erasers, FTO and ALKBH5. m6A methyltransferase complex contains METTL3-METTL14-WTAP as core components. METTL3 is the catalytic component, which is activated by heterodimer formation with METTL14. High METTL3 expression is found in several cancers such as breast, lung, liver, gastric, colorectal, AML and a METTL3 catalytic inhibitor is found to delay AML progression in mouse models. Protein that binds RNA m6A modification to execute it signaling are known as m6A readers. Readers are categorized into three main classes, YTH domain proteins, IGF2 mRNA-binding proteins and heterogeneous nuclear ribonucleoproteins. YTH family readers are found to have oncogenic roles in several cancers including AML, breast, lung, CRC and glioblastoma. Recent studies suggest inhibition of m6A binding of individual YTH family proteins is a promising therapeutic strategy however, potent inhibitors are yet to be identified. This poster summarizes current assays we have developed to facilitate cancer therapeutic discovery in m6A related protein targets. We present development and validation of an assay suitable identify in METTL3 catalytic inhibitors using our proprietary hotspot technology. We also show development of HTRF based biochemical assays for all five YTH family protein YTHDF1-3 and YTHDC1-2, to screen for molecules that disrupt protein-m6A interaction. We further study the selectivity of an FDA approved drug Tegaserod, a reported YTHDF1 inhibitor by a structure based virtual screening, between YTH family proteins.

Citation Format: Safnas F. AbdulSalam, Sung Won Oh, Brenna P. Lee, Joseph J. Ferry, John R. Ries, Kurumi Y. Horiuchi. Development of biochemical screening assays to facilitate drug discovery in RNA m6A modification regulators [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 4417.
Abstract 4425: Metabolic vulnerabilities of dedifferentiated liposarcoma
Authors: Brett Jamie O. , Han Ji Seul , Kim Choah , Kelley Liam P. , Han SeongJun , Boone Dylan , Crowley Joseph , Joshi Shakchhi , Raut Chandrajit P. , Greka Anna , Haigis Marcia C.
Published: March 2024

Dedifferentiated liposarcoma (DDLPS) is a rare, life-threatening malignancy in the family of adipocytic sarcomas. DDLPS, which usually arises in the retroperitoneum of middle-aged adults, has a poor prognosis. This is due to the propensity of DDLPS to metastasize and recur locally, combined with a dearth of effective systemic therapies. A longstanding curiosity is that DDLPS has non-lipogenic morphology and no lipid droplets, while its less aggressive sister sarcoma, well-differentiated liposarcoma (WDLPS), resembles benign adipose tissue and contains large lipid droplets. How DDLPS metabolizes lipids and the metabolic vulnerabilities of DDLPS in patients, which may form new therapeutic targets, are unknown. In our project, we investigate the metabolism of DDLPS versus WDLPS using patient samples and cell lines. Snap-frozen tissues from patients were obtained from the Dana-Farber/Harvard Cancer Center specimen bank of DDLPS and WDLPS. We performed metabolomics and lipidomics on these samples. We complemented these results with publicly available transcriptional profiles of separate cohorts of DDLPS, WDLPS, and other cancers. In vitro, we made use of a panel of multiple DDLPS-derived cell lines, WDLPS-derived cells, benign preadipocytes, and benign adipocytes. We measured mitochondrial function and the cellular effects of perturbing various metabolites in screens in culture. Overall, our initial results indicate strong alterations in mitochondrial metabolism in DDLPS in patients. In culture, DDLPS is susceptible to multiple metabolic perturbations related to mitochondrial dysfunction. These metabolic vulnerabilities of DDLPS provide potential therapeutic opportunities. Work is ongoing to optimize the targeting of these vulnerabilities in vivo, elucidate the molecular roles of specific metabolites, and complete a blueprint of DDLPS metabolic weaknesses in patients.

Citation Format: Jamie O. Brett, Ji Seul Han, Choah Kim, Liam P. Kelley, SeongJun Han, Dylan Boone, Joseph Crowley, Shakchhi Joshi, Chandrajit P. Raut, Anna Greka, Marcia C. Haigis. Metabolic vulnerabilities of dedifferentiated liposarcoma [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 4425.
Abstract 4452: The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle
Authors: Manceau Ambroise , Galenkamp Koen M. , Galapate Cheska M. , Commisso Cosimo
Published: March 2024

As an integral aspect of the metabolic reprogramming that occurs in cancer, oncogenic KRAS mutations drive the stimulation of macropinocytosis, a type of endocytosis that mediates nonselective fluid-phase uptake. Using KRAS-driven models of pancreatic ductal adenocarcinoma (PDAC), we were the first to demonstrate that macropinocytosis functions in tumor cells as a nutrient acquisition pathway. Macropinocytosis triggers the internalization of extracellular proteins via discrete endocytic vesicles called macropinosomes. The incoming protein cargo is targeted for lysosome-dependent degradation, causing the intracellular release of amino acids. These protein-derived amino acids support metabolic fitness by contributing to the intracellular amino acid pools, as well as to the biosynthesis of central carbon metabolites. In this way, macropinocytosis represents a novel amino acid supply route that tumor cells use to survive the nutrient-poor conditions of the tumor microenvironment. While the tenets of the signal transduction events that drive macropinocytosis in cancer have emerged, a detailed picture of the macropinosome itself is not yet available. With the aid of nanotechnology, we have developed a methodology to isolate a pure fraction of macropinosomes from PDAC cells. Using a large-scale proteomic approach, we have been able to generate a list of proteins that reside in macropinosomes. The specificity of this approach was confirmed through the identification and validation of proteins known to specifically localize to these organelles in different contexts, such as Rab5 or SDC1. Thanks to this innovative method, we have demonstrated the involvement of two calcium channels, ATP2B1 and ATP2B4, in the formation of macropinosomes. By elucidating the molecular anatomy of KRAS-driven macropinosomes, we will gain further insight into the regulation and function of macropinocytosis in cancer. Moreover, having a clearer picture of the macropinosome will make us better positioned to exploit this pathway therapeutically and deliver breakthroughs to patients.

Citation Format: Ambroise Manceau, Koen M. Galenkamp, Cheska M. Galapate, Cosimo Commisso. The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle [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 4452.