tbuckley/cabot-search huggingface dataset:
Abstract 429: A novel regulatory role of FLT3/ITD mutation in lipid metabolism of leukemia cells: The mechanism and therapeutic implications
Authors: Yumin Hu, Feng Yin, Mingyue Zhao, Wenhua Lu, Tiantian Yu
Journal: Cancer Research (2024)

Abstract Internal tandem duplication in FMS-like tyrosine kinase 3 (FLT3/ITD), is a common type of activating mutation and frequently detected in AML. FLT3/ITD is associated with poor prognosis of AML. In this study, we investigated the regulation of FLT3/ITD mutation on sterol regulatory element-binding protein (SREBP) and the therapeutic vulnerabilities of lipid metabolism in FLT3/ITD leukemia. With the transcriptomics analysis we found that FLT3/ITD controlled lipid metabolism via the transcription factor SREBP. The analysis of TCGA_LAML dataset revealed that a gene signature involved in fatty acid and cholesterol metabolism, which is regulated by SREBP, was upregulated in FLT3/ITD patients compared with FLT3/wild-type patients. The upregulation of SREBP protein expression in FLT3/ITD leukemia was confirmed using a genetically engineered mouse model. We further demonstrated that FLT3/ITD regulates the protein degradation of SREBP through the PI3K/AKT-GSK3β axis. The metabolomics analysis further showed that FLT3/ITD primarily regulates glycerophospholipid synthesis, which contribute to the key structure lipid in the membrane, specifically, the cardiolipin. Moreover, pharmacologic inhibition of SREBP activation and its downstream enzyme fatty acid synthase (FASN) sensitized FLT3-ITD AMLs to the treatment of FLT3 inhibitor quizartinib. Collectively, our findings reveal a novel regulation of FLT3-ITD in metabolic reprogramming and indicate a targetable vulnerability in a subset of refractory leukemia. Citation Format: Yumin Hu, Feng Yin, Mingyue Zhao, Wenhua Lu, Tiantian Yu. A novel regulatory role of FLT3/ITD mutation in lipid metabolism of leukemia cells: The mechanism and therapeutic implications [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 429.
Abstract 4311: The interplay of SYNCRIP deficiency, APOBEC activity, and extrachromosomal DNA in castration-resistant prostate cancer drug resistance
Authors: Xiaoling Li, Su Deng, Choushi Wang, Yunguan Wang, Ping Mu
Journal: Cancer Research (2024)

Abstract Background: Prostate cancer, particularly in its castration-resistant form (CRPC), frequently develops resistance to androgen receptor (AR)-targeted therapies. This resistance involves complex factors, including tumor mutational burden and heterogeneity. APOBEC proteins, associated with mutagenesis and DNA damage, are implicated in this process. Our study centers on SYNCRIP, a key regulator of APOBEC activity, and investigates its influence on extrachromosomal DNA (ecDNA) in CRPC. Objective: This research aims to explore how SYNCRIP deficiency leads to increased APOBEC activity, and to examine its possible implications for ecDNA formation and its contribution to drug resistance and tumor heterogeneity in CRPC. Methods: Genomic and transcriptomic analyses, such as whole exome sequencing and single-cell RNA-seq, were performed on CRPC cell lines and patient-derived samples, with an emphasis on SYNCRIP-deficient models. The study focused on understanding the relationship between elevated APOBEC activity due to SYNCRIP deficiency and potential ecDNA changes, evaluating their effect on AR-targeted drug sensitivity and overall tumor behavior. Results: SYNCRIP was identified as a critical factor in resistance to AR therapy in both in vitro and in vivo models. Its deficiency resulted in increased therapy resistance and amplified APOBEC-mediated mutagenesis. Functional CRISPR screening identified eight key drivers of resistance in SYNCRIP-deficient tumors. Single-cell RNA sequencing revealed APOBEC-driven mutagenesis as a key factor in promoting intratumoral heterogeneity and resistance. Notably, in SYNCRIP-deficient CRPC samples, increased APOBEC activity and significant DNA damage were observed, prompting an investigation into a possible correlation between resistance and ecDNA presence. Conclusion: The study uncovers a significant link between SYNCRIP deficiency and increased APOBEC activity in CRPC. While it also hints at a potential connection with ecDNA alterations, further research is necessary to establish this relationship firmly. This interplay contributes to the complexity of drug resistance in CRPC, highlighting the need for novel therapeutic targets. The dynamics among SYNCRIP, APOBEC activity, and ecDNA offer valuable insights into the molecular underpinnings of therapy resistance in prostate cancer, suggesting new directions for treatment strategies. Citation Format: Xiaoling Li, Su Deng, Choushi Wang, Yunguan Wang, Ping Mu. The interplay of SYNCRIP deficiency, APOBEC activity, and extrachromosomal DNA in castration-resistant prostate cancer drug resistance [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 4311.
Abstract 4273: Genetically engineered mesenchymal stromal cells degrade hyaluronic acid to disrupt the ECM and enhance cancer therapy outcomes
Authors: Alice T. Browne, Miranda Clements, Wei Ju, Rosandra Kaplan
Journal: Cancer Research (2024)

Abstract The extracellular matrix (ECM) is a vital component of cancer pathophysiology. However, little is known about how to modulate the ECM for therapeutic benefit effectively. Hyaluronic acid (HA) is a polysaccharide component of the ECM with increased deposition during tissue injury or inflammation. HA in the tumor microenvironment (TME) has been linked to aggressive cancer progression. We have found enhanced ECM remodeling behavior linked to pre-metastatic niche formation and metastatic progression. To remodel this ECM-enriched microenvironment, we developed HA-targeting genetically engineered mesenchymal stromal cells (GEMesys) expressing hyaluronidase (Hyal), the enzyme responsible for HA degradation. We examined the impact of Hyal-GEMesys in osteosarcoma (F42010), rhabdomyosarcoma (M-3-9M), and pancreatic cancer (Panc02) syngeneic murine models. Hyal-GEMesys delivered to tumor-bearing mice homed to primary tumor sites and successfully degraded HA in the TME. The degradation of HA also resulted in a significant remodeling of collagen. T cells in Hyal-GEMesy treated tumors display an activated CD4+CD44+ phenotype with a reduction of LAG3+PD1+ exhaustion markers. Additionally, Hyal-GEMesy treatment results in a significant decrease in hypoxic regions within tumors and reorganization of the tumor vasculature to a more normalized phenotype, marked by diminished CD31 expression. Hyal-GEMesy treatment reduces tumor volumes in osteosarcoma, rhabdomyosarcoma, and pancreatic cancer models and enhances chemotherapeutic efficacy. These findings suggest that reorganizing the tumor ECM with Hyal-GEMesys holds the potential to dismantle the protective stroma of the tumor, which often shields malignant cells from therapeutic reach, and combining anti-cancer and anti-stroma agents can enhance anti-tumor efficacy and patient outcomes. Citation Format: Alice T. Browne, Miranda Clements, Wei Ju, Rosandra Kaplan. Genetically engineered mesenchymal stromal cells degrade hyaluronic acid to disrupt the ECM and enhance cancer therapy outcomes [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 4273.
Abstract 2298: Optimization of high-volume cell free DNA extraction and end-to-end automation for TSO 500 ctDNA library prep
Authors: Nripesh Prasad, Rachel Rock, Rebecca Beatty, Melanie Robinson, Dineen Wildman, Michael Sykes, Boris Umylny, Thomas Halsey
Journal: Cancer Research (2024)

Abstract Liquid biopsy such as plasma, has emerged as one of the most valuable sample types for profiling circulating tumor DNA (ctDNA) for screening, response to treatment, and monitoring relapse in oncology patients. Due to the diffuse nature of ctDNA however, both extraction and library preparation must be optimized for the efficient downstream next-generation sequencing (NGS) application. We initially addressed the optimization of quality and quantity of cfDNA recovery from healthy and various oncology patients by evaluating QIAsymphony DSP Circulating DNA Kit and Apostle MiniMax cfDNA isolation kits. Overall, the cfDNA yields from Apostle MiniMax kit were approximately 12X higher. We then optimized high-volume automated cfDNA extraction from 1ml, 3ml and 6ml plasma samples using the Biomek i7 for Apostle MiniMax kit. Colorectal, Gastric and Ovarian cancer gave the highest yield of cfDNA whereas, Esophageal, Lung and Kidney cancers were the lowest cfDNA yielding samples. We then analyzed ctDNA from plasma from healthy donors, colorectal, kidney, Breast, and endometrial cancer patients along with Oncospan and Seraseq ctDNA mutation mix (5-0.5% AF) to evaluate the mutation detection efficacy, repeatability, and reproducibility by targeted NGS using TSO 500ctDNA assay ay 10ng, 20ng, and 30ng inputs. For library preparation batches of 48 samples were prepared using a fully automated processes for the library prep, Hybridization capture and post capture enrichment on the Beckman i5 robot. Libraries were sequenced on NovaSeq 6000 at 600M Paired-end depth. This method demonstrates an overall concordance of inter-run and intra-run accuracy of variant detection to be 90% demonstrating that this method run as described produces highly repeatable and reproducible variant detection to sub-1% allele frequencies. The inter-run, lot-to-lot, and operator-to-operator variability was ≥99%. Down-sample analysis demonstrated high levels of assay performance with sample inputs of 30 ng with ≥96% sample passing Illumina cut-off metrics at 150M PE read depth as compared to Illumina recommended 420M PE reads. Taken together, we provide a high-volume automated solution for cfDNA extraction from plasma samples, additionally these data demonstrate a robust, reproducible, and highly accurate targeted DNA sequencing method that can be used for low allele frequency variant detection in cfDNA. Citation Format: Nripesh Prasad, Rachel Rock, Rebecca Beatty, Melanie Robinson, Dineen Wildman, Michael Sykes, Boris Umylny, Thomas Halsey. Optimization of high-volume cell free DNA extraction and end-to-end automation for TSO 500 ctDNA library prep [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 2298.
Abstract 2990: Differential micro-RNA expression in circulating exosomes of pancreatic ductal adenocarcinoma patients
Authors: Rupinder Kaur, Sandeep Bhoriwal, Promod Kumar Gautam
Journal: Cancer Research (2024)

Abstract Pancreatic ductal Adenocarcinoma (PDAC) is a highly lethal solid tumor with 5-year survival rate of 5-8%. Extracellular vesicles like exosomes circulating in the blood are crucial mediators of intracellular communication, immunomodulation and tumor progression. The microRNAs being the major cargo of exosomes, are the primary carriers of intracellular information. The role of exosomal-miRNA (exoMIR’s) in regulating the pathogenesis of tumors is well-established in oncology but its potential is still unexplored. To the best of our knowledge no study has yet explored the contrasting exoMIR expression in cancer patients before and after their surgery. In this study, differential exoMIR’s profile of three pancreatic ductal adenocarcinoma patients at three stages: pre-surgery, post-surgery, and follow-up was established using small RNA sequencing on the Illumina platform. In blood samples taken before and after surgery total of 181, 201 and 201 microRNAs were dysregulated in circulating exosomes of three different patients viz. P_1, P_9 &amp; P_11 (Patient identifiers) respectively. Out of the total dysregulated microRNAs in post-op samples 76 were upregulated and 105 downregulated in P_1, 95 upregulated and 106 downregulated in P_9 &amp; 69 upregulated and 132 downregulated in P_11 as compared to their Pre surgery samples. Further, when exoMIR’s of post-op samples were compared to that of follow-up samples after 6 months of surgery their expression profile changed notably such that a total of 184, 157 &amp; 190 microRNAs dysregulated in follow-up of P_1, P_9 and P_11 respectively. Out of the total dysregulated microRNAs in follow up samples 93 were upregulated and 91 downregulated in P_1, 69 upregulated and 88 downregulated in P_9 &amp; 96 upregulated and 94 downregulated in P_11 as compared to their post-op samples. On Venn diagram analysis 27 microRNAs were found to be commonly dysregulated in all 3 patients before surgery and 22 common micro RNAs were again dysregulated even after 6 months of surgery. Bioinformatic analysis of these differentially expressed miRNAs and their respective protein targets revealed that their role in oncogenic molecular pathways is very prominent, thus highlighting their potential use in cancer therapeutics, diagnostics as well as prognosis. Citation Format: Rupinder Kaur, Sandeep Bhoriwal, Promod Kumar Gautam. Differential micro-RNA expression in circulating exosomes of pancreatic ductal adenocarcinoma patients [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 2990.
Abstract 4297: Interrogating metabolic heterogeneity and cooperation in lung cancer collective cell invasion
Authors: Isaac E. Robinson, Veronika Matsuk, Mala Shanmugam, Janna K. Mouw, Adam I. Marcus
Journal: Cancer Research (2024)

Abstract Tumor heterogeneity contributes to tumor progression and a variable response to treatment. We have previously shown that tumor heterogeneity - including metabolic, transcriptional and mutational - underlies non-small cell lung cancer (NSCLC) collective invasion. Using stable subpopulations derived with our Spatiotemporal Cellular and Genomic Analysis (SaGA) technique, we found that two distinct subpopulations of the H1299 NSCLC line cooperate during collective tumor invasion in vitro; while H1299 pack leaders are heavily dependent on oxidative phosphorylation, H1299 pack followers are more reliant on glycolysis. To further dissect how intratumoral heterogeneity enables cancer progression to metastasis, we incorporate high resolution imaging, stable fluorescent labeling, gene editing, and in vitro tumor invasion models to interrogate mechanisms of metabolic cooperation between heterogeneous NSCLC subpopulations. We hypothesize that cooperation and communication between these distinct metabolic subpopulation drives metastatic tumor progression. To determine mechanisms of metabolic cooperativity between subpopulations, we stably transduced our subpopulations to fluorescently label either the mitochondria (through TOM20 labeling) or a key enzyme in glycolysis (through glucose 6-phosphate isomerase GPI labeling), cultured labeled subpopulations with unlabeled subpopulations, and observed metabolic changes and exchange via time-lapse, fluorescence microscopy and flow cytometry in 2D culture conditions. Next steps include visualizing the metabolic cooperation that occurs in conditions mimicking the tumor microenvironment (i.e., 3D invasion assays) using super-resolution microscopy. Taken together, we have developed a method of temporally visualizing metabolic exchange with high spatial resolution between NSCLC subpopulations to investigate the underlying mechanisms enabling successful cell invasion in a variety of tumor microenvironments. Thus far, we have discovered multiple broad mechanisms of exchange including tunneling nanotubes and extracellular vesicles, both of which are inducible with certain stressors common to the tumor microenvironment. Citation Format: Isaac E. Robinson, Veronika Matsuk, Mala Shanmugam, Janna K. Mouw, Adam I. Marcus. Interrogating metabolic heterogeneity and cooperation in lung cancer collective cell invasion [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 4297.
Abstract 3640: RAB26 accelerates endometrial cancer cell progression by regulating the Hedgehog signaling pathway
Authors: Chao Gao, Yanyan Liu, Yanyan Han, Fengxia Xue, Yingmei Wang
Journal: Cancer Research (2024)

Abstract As one of the most common gynecological malignant tumors, endometrial cancer (EC) is continuously being studied since its etiology is still not clear. RAB26, a member of the RAB family, has been shown to influence cell proliferation, metastasis and other malignant phenotypes in several cancers. However, whether and how RAB26 plays roles in EC remain unknown. Our previous study showed that RAB26 was related to the cell cycle-associated protein IK, which has been shown to contribute to carcinogenesis. Herein, we further explored the clinical significance and biological function of RAB26 in EC. Immunohistochemical staining of 615 endometrial tissue samples was conducted to explore whether RAB26 expression was related to the clinicopathological characteristics of EC. In vitro and in vivo experiments were used to evaluate the role of RAB26 in EC and investigate the underlying mechanism. RAB26 expression was higher in EC than in normal endometrium (NE), hyperplastic endometrium (HE) and atypical hyperplastic endometrium (AHE). High RAB26 expression was positively correlated with tumor histological grade (P=0.010), FIGO stage (P=0.042) and tumor size (P=0.003) in EC. RAB26 attenuation inhibited cell proliferation and metastasis but promoted cell apoptosis and caused G0/G1 arrest. After RAB26 attenuation, RNA sequencing data showed that the Hedgehog signaling (SHH) pathway was enriched. Further western blot results confirmed that the levels of SHH pathway proteins (SHH, PTCH1, smo and Gli1) decreased as RAB26 expression was attenuated. Moreover, an agonist of the SHH pathway, purmorphamine, blocked the inhibitory effect of RAB26 attenuation on EC progression. The results of an in vivo study also showed that RAB26 attenuation exerted a significant antitumor effect. Accordingly, RAB26 may act as an oncogenic protein to promote EC progression through the SHH pathway. RAB26 may be a potential target for the treatment of EC patients. Citation Format: Chao Gao, Yanyan Liu, Yanyan Han, Fengxia Xue, Yingmei Wang. RAB26 accelerates endometrial cancer cell progression by regulating the Hedgehog signaling pathway [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 3640.
Abstract 2641: Transcriptional reprogramming of Ewing tumors: gains and losses noted when utilizing immunocompetent in vivo models
Authors: Jessica D. Daley, Elina Mukherjee, A Carolina Tufino, Riyue Bao, Kelly M. Bailey
Journal: Cancer Research (2024)

Abstract Objective: Ewing sarcoma is an aggressive cancer most frequently diagnosed in adolescents and young adults. Currently, there is a limited understanding of the immunobiology of Ewing sarcoma, including limited pre-clinical studies of immunotherapeutic interventions. This, in part, is due to the historical lack of an immuno-competent murine model. Here, we utilize an immunocompetent, humanized mouse model to investigate the Ewing tumor immune microenvironment. Specifically, we sought to determine the transcriptional differences that occur when comparing human Ewing tumors established in a humanized backdrop versus those developed in an NSG (immuno-deficient) model. Methods: Human Ewing cell lines (A673, TC32, TC71) and PDX (PSaRC219) were injected orthotopically into humanized or NSG mice. After ~3 weeks, bulk RNA sequencing was performed on tumors utilizing an Illumina Next Generation Sequencer. Tumor single-cell suspensions underwent immunophenotyping by flow cytometry (CyTek Aurora) for the following human markers: CD45, CD3, CD4, CD8, CD56, CD14, CD16, etc.. Peripheral blood was collected, PBMCs isolated, and immunophenotyping was again performed to determine peripheral blood immune cell populations. Results: Ewing tumors established in humanized mice demonstrate infiltration of human CD45+ cells as well as immune cell sub-populations (CD3+, CD14+, CD56+ cells). Bulk RNA sequencing analysis utilizing unsupervised hierarchal clustering revealed that the transcriptional profile of Ewing tumors generated in humanized vs NSG mice cluster distinctly. Pathway analysis of differentially expressed genes (p &amp;lt;0.05) in Ewing tumors developed in humanized versus NSG mice demonstrates upregulation of pathways including extracellular matrix remodeling, collagen biosynthesis, and Wnt signaling. Notably, transcripts known to be specific to TGFBeta-dependent signaling in Ewing tumors are upregulated in the immune competent model, including TGFB1, FBLN5, and COLEC12. Conclusion: This work demonstrates the Ewing tumor transcriptional remodeling that occurs when tumors are developed in an immunocompetent in vivo backdrop. Upregulation of several pro-metastatic pathways were noted. Ongoing work focuses on testing drug response differences between Ewing tumors developed in humanized versus NSG backdrops and pursuing immunocompetent Ewing models as a component of preclinical agent testing. Citation Format: Jessica D. Daley, Elina Mukherjee, A Carolina Tufino, Riyue Bao, Kelly M. Bailey. Transcriptional reprogramming of Ewing tumors: gains and losses noted when utilizing immunocompetent in vivo models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2641.