bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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 &gt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.