bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 252: A single-tube approach for detection of circulating tumor DNA using customized panels
Authors: Meltzer Robert , Kaur Jessalyn , Kintsurashvili Ekaterina , D'Amato Christopher , Godfrey Tony 
Published: April 2023

Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker for cancer. Applications of ctDNA analysis include screening, diagnosis, treatment selection, minimal residual disease (MRD) detection and recurrence monitoring. While some applications are best served by tumor-agnostic panels covering large regions of the genome, such large panels are not universally appropriate due to limitations in sensitivity, user-friendliness, turn-around time (TAT), and sequencing cost. One application where customized, tumor-informed panels can be preferable is detection of MRD and cancer recurrence, and multiple studies have shown that ctDNA can detect residual/recurrent disease several months earlier than routine clinical imaging. This application requires high sensitivity and in most cases will involve repeat testing of longitudinal samples collected over several months or years. In this scenario, the ideal assay characteristics include tumor-informed, personalized assay panels, with a simple, rapid workflow, and with minimal cost per assay. We have developed the Fluent LBx assay to meet these requirements. Fluent LBx analysis can be performed on-site in any appropriately equipped research or clinical laboratory, avoiding the extra cost and delay associated with external testing. Fluent LBx is a variation on SiMSen-Seq (PMID 27060140) that uses modified target and adapter primer sequences to facilitate barcoding and uniform amplification of multiple targets in a single-tube library construction protocol. Library preparation can be completed in under 1.5 hours with approximately 20 minutes of hands-on time. Using this approach, target DNA molecules are first barcoded and then amplified with indexed adaptors compatible with Illumina sequencers, in a single PCR reaction. After clean-up and sequencing, barcode information is used to compile reads from individual DNA molecules and minimize base calling errors introduced during PCR and sequencing. Here we present data demonstrating uniformity, sensitivity and specificity of Fluent LBx assays using LGC SeraCare quality control standards. Additionally, we present longitudinal clinical demonstration of residual disease detection from ctDNA collected from multiple head and neck and gastrointestinal cancer patients through longitudinal monitoring post therapeutic intervention. The Fluent LBx workflow allows rapid, inexpensive, patient-specific monitoring of MRD and recurrence in multiple cancer indications.
Citation Format: Robert Meltzer, Jessalyn Kaur, Ekaterina Kintsurashvili, Christopher D'Amato, Tony Godfrey. A single-tube approach for detection of circulating tumor DNA using customized panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 252.
Abstract 2525: Analyzing the role of MDMX for regulating cell death in prostate cancer cells
Authors: Alsarrani Ahmed , Natarajan Umamaheswari , Alsubhi Samia , Alzahrani Amal , Rathinavelu Appu 
Published: April 2023

Abstract
Prostate cancer (PCa) is the most prominent cancer type and the second leading cause of cancer death among men in the USA. The five-year survival rate for localized PCa is 98% but drops to 31% when PCa spreads to different parts of the body. Various treatment strategies that can induce cell death through different mechanisms are used while treating cancers. In recent years, necroptosis has been established as one of the effective mechanisms of inducing cell death in cancers. Necroptosis can be identified as a regulated form of cell death that can occur independently of executioner caspases. Despite numerous studies on the effects of necroptosis in cancer, it’s role on PCa has not been fully elucidated. In this study, we have evaluated the role of MDMX, a proto-oncogene involved in the negative regulation of p53, in causing cell death through p53-independent mechanisms. We have observed that inhibition of MDMX decreased the cell viability of LNCaP cells in response to 20 µM of NSC (NSC-207895), a MDMX specific inhibitor treatment, in a concentration-dependent manner. MDMX inhibition appears to induce necroptosis in LNCaP prostate cancer cells by elevating the expression of receptor-interacting protein kinase 1 (RIP1), which is a key element of the necroptotic pathway. In general, the necroptosis pathway can trigger two opposing mechanisms in cancer where it can promote tumor migration and metastasis on one hand and can also act as a defensive mechanism on the other hand when apoptosis is disrupted. To further assess the effect of MDMX on cell migration, the LNCaP cells were treated with 20 µM of NSC, which effectively blocked the cancer cell migration for up to 48 h, which was confirmed using the scratch assay. Interestingly, NSC treatment also reduced the expression of Vascular Endothelial Growth Factor A (VEGFA), which is one of the main markers for angiogenesis. Our results show that the p53-independent mechanisms that are activated following MDMX inhibition can regulate both cancer cell migration and angiogenesis. MDMX also seemed to be involved in regulating PCa cell survival through necroptosis. The outcomes of our experiments provide additional knowledge and strategies for making an accurate prognosis and choosing the most suitable therapeutic strategies for offering effective treatments for MDMX-positive PCa. (This research was supported by the Royal Dames of Cancer Research Inc. Ft. Lauderdale, Florida)
Citation Format: Ahmed Alsarrani, Umamaheswari Natarajan, Samia Alsubhi, Amal Alzahrani, Appu Rathinavelu. Analyzing the role of MDMX for regulating cell death in prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2525.
Abstract 2527: Investigation of doxorubicin interference in flow cytometry measurements of apoptosis and necrosis
Authors: Nicoletto Rachel E. , Wilkes Richard , Ofner Clyde M. 
Published: April 2023

Abstract
Background: Doxorubicin (DOX) is frequently used for investigations of breast cancer using flow cytometry with fluorescent stains for apoptosis and necrosis. DOX interference, however, can occur with these fluorescent measurements which is not reported in many published reports. The objectives of this study were to identify such interference and to assess its extent.
Methods: MDA-MB-231 and MCF-7 cells were incubated for 24 h with 0.1, 1, and 10 µM DOX. Cells were then stained for apoptosis and necrosis using two commercial assay kits. Fluorescence was measured with FL1 (apoptosis), FL2 (primary for DOX), and FL3 (necrosis) detectors in cells with DOX alone, with DOX plus stains, and in control cells without DOX. Measurements were repeated two to five times using replicates and trials. Statistics were evaluated by t-tests.
Results: Overall, DOX fluorescence interference increased with concentration in both cell lines. After DOX incubation, cells stained with caspase 3/7 and SYTOX showed fluorescence in the FL1 detector indicating caspase 3/7 activation in apoptosis. But the DOX component of fluorescence with this detector ranged from 11 to 95%. Dox fluorescence in the FL3 detector for SYTOX measurements indicating necrosis ranged from 26 to 96% of total fluorescence. Cells stained with Annexin V (with the FITC label) and propidium iodide (PI) showed fluorescence in the FL1 detector for Annexin V indicating apoptosis. However, the DOX component of fluorescence ranged from 11 to 25%. DOX fluorescence in the FL3 detector for PI indicating necrosis ranged from 87 to 106%.
Conclusions: Without correction for DOX interference, and even at low concentrations, substantial errors can occur for apoptosis and necrosis measurements using flow cytometry with these stains in breast cancer cells. At high DOX concentrations, the interference can erroneously indicate an extensive presence of these cell death processes. Corrections for DOX interference include background subtraction and flow cytometer compensation.
Acknowledgments: The authors gratefully acknowledge financial support from the Agnes Varis Trust for Women in Science (REN), the Milton Lev Memorial Faculty Research Fund (CMO) as well as Saint Joseph’s University support for student research. The authors also thank Bin Chen, PhD, and Richard Howley for assistance with flow cytometry.
Citation Format: Rachel E. Nicoletto, Richard Wilkes, Clyde M. Ofner. Investigation of doxorubicin interference in flow cytometry measurements of apoptosis and necrosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2527.
Abstract 2529: Necrosome translocates to lysosome to induce lysosome membrane permeabilization and subsequent necroptotic cell death
Authors: Mammadova Jamila , Fatirkhorani Rojin , Liu Shuzhen , Chen Ken , Wang Zhigao 
Published: April 2023

Abstract
Introduction: Necroptosis is a cellular process known to be downregulated by cancer cells, and its molecular steps have been described in the literature. Mixed-lineage kinase domain like (MLKL) protein is the most terminal effector of necroptosis. Necroptosis has previously been shown to be activated by the formation of necrosome complex consisting of receptor interacting serine/threonine kinase 1 (RIPK1)-RIPK3-MLKL. MLKL is activated by RIPK3 via phosphorylation, forming phospho-MLKL (P-MLKL), leading to MLKL polymerization and cell necroptosis via lysosome membrane permeabilization (LMP) and plasma membrane rupture. We propose that the necrosome locates onto the lysosome, leading to MLKL-activation induced LMP before cell membrane rupture.
Objectives: Our objective is to show that necrosome formation occurs on lysosomal membrane, which then leads to the formation of P-MLKL, and, subsequently, necroptosis via LMP and plasma membrane rupture.
Methods: HT-29 cells with hemagglutinin (HA) tagged lysosomal transmembrane protein were induced to undergo necroptosis with the treatment of TNF (T), Smac-mimetic (S) and Z-VAD-FMK (Z) (abbreviated as T/S/Z). Lysosomes were extracted first by cell rupture via homogenization and then immunoprecipitation using anti-HA magnetic beads.
Results: Our results suggest that LMP precedes plasma membrane permeability and that MLKL activation takes place on lysosomal membrane. Western blotting demonstrated that lysosomal cathepsin proteases, including CTSA, CTSB, CTSC, CTSD and CTSK, were released into cytosol during necroptosis, confirming lysosomal damage. Furthermore, P-RIPK1, P-RIPK3, P-MLKL and MLKL tetramer were found to be specifically associated with purified lysosomes upon necroptosis induction.
Conclusions: MLKL activation on lysosomal membrane and LMP constitute an important step of necroptosis. [J.M. and R.F. contributed equally to this work.]
Citation Format: Jamila Mammadova, Rojin Fatirkhorani, Shuzhen Liu, Ken Chen, Zhigao Wang. Necrosome translocates to lysosome to induce lysosome membrane permeabilization and subsequent necroptotic cell death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2529.
Abstract 2545: NNMT is a novel effector of EGFR driven glioblastoma malignancy
Authors: Ma Lianping , Li Ming 
Published: April 2023

Abstract
Nicotinamide N-methyltransferase (NNMT) is a metabolic enzyme that catalyzes the conversion of methyl groups from S-adenosyl-L-methionine (SAM) to nicotinamide (NAM) to generate S-adenosine hyperblastoids (SAH) and 1-methylnicotinamide (MNA). Upregulation of NNMT has been observed in a variety of cancers, including glioblastoma. The mechanism by which NNMT is overexpressed in glioblastoma remains largely unknown. Epidermal growth factor receptor (EGFR) gene amplification or mutation is one of the most common genetic lesions in glioblastoma, and EGFRvIII is the most common mutant contributing to glioblastoma cell proliferation, invasion, therapeutic resistance, metastasis, and stemness. In this study, we show that activation of wild-type EGFR by EGF or the constitutively active mutant EGFRvIII promoted NNMT expression in established glioblastoma cell lines and glioblastoma stem-like cells via the p38 mitogen-activated protein kinase pathway. Furthermore, we identified STAT1 as a downstream transcription factor required for EGFR/EGFRvIII-induced NNMT upregulation. Knockdown of NNMT by RNA interference in glioblastoma cells significantly inhibited EGFRvIII-promoted glioblastoma cell invasion and proliferation in vitro. Targeting NNMT inhibited EGFRvIII-driven glioblastoma tumorigenicity and prolonged survival of tumor-bearing mice. Clinically, NNMT was highly expressed and positively correlated with EGFR expression in human glioblastoma tumors. Taken together, these findings establish NNMT as a previously unknown downstream target gene of EGFR/EGFRvIII expression and nominate it as a new potential therapeutic target for inhibiting EGFRvIII-driven glioblastoma.
Citation Format: Lianping Ma, Ming Li. NNMT is a novel effector of EGFR driven glioblastoma malignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2545.
Abstract 2551: CASC4 drives anoikis resistance in high grade serous ovarian cancer through recycling of EGFR
Authors: Bapat Jaidev , Brubaker Lindsay W. , Watson Zachary L. , Yamamoto Tomomi M. , Bitler Benjamin G. 
Published: April 2023

Abstract
Introduction: Ovarian cancer is the deadliest gynecological malignancy, and accounts for over 150,000 deaths per year worldwide. The high grade serous ovarian cancer (HGSOC) subtype accounts for almost 60% of ovarian cancers and is the deadliest. HGSOC originates in the fimbria of the fallopian tube and disseminates through the peritoneal cavity. Survival of tumor cells in the peritoneal fluid requires cells to resist anoikis (anchorage-independent apoptosis). CRISPR/Cas9 and transcriptomic screens identified the Golgi protein CASC4 (GOLM2, H63) as a “driver” of anoikis resistance. As CASC4 is highly uncharacterized in literature, we sought to determine how CASC4 confers anoikis resistance to HGSOC cells.
Methods: Mining of publicly available ovarian cancer datasets (TCGA) showed that CASC4 is associated with worse clinical outcomes, such as worse overall survival and increased resistance to platinum-based chemotherapies. For experiments, we used HGSOC cell lines PEO1, CaOV3, and OVCAR3 with shRNA-mediated CASC4 knockdowns (CASC4 KD), cultured in forced suspension.
Results: Culturing cells in suspension, to recapitulate the peritoneal fluid environment in vitro, showed that CASC4 KD hampers cell proliferation and colony formation ability, and increases apoptosis. Additionally, a Reverse Phase Protein Assay (RPPA) showed that CASC4 KD results in significant changes in proteins known to be localized to the cell surface or secreted, including decreased protein levels of the receptor tyrosine kinase (RTK) Epidermal Growth Factor Receptor (EGFR), an initiator of several oncogenic signaling pathways. A paralog of CASC4, GOLM1, is known to drive hepatocellular carcinoma through various mechanisms, such as the recycling of internalized RTKs, including EGFR. Indeed, our experiments showed that CASC4 KD in ovarian cancer cells leads to decreased EGFR levels and decreased EGFR recycling.
Conclusion: Knocking down CASC4 results in decreased survivability in suspension, decreased EGFR levels at the plasma membrane, and decreased recycling of EGFR. Further elucidating mechanisms of CASC4-dependent anoikis resistance could lead to the development of novel therapeutic approaches, such as inhibitory peptides, and may assist in developing newer biomarkers for predicting ovarian cancer malignancy.
Citation Format: Jaidev Bapat, Lindsay W. Brubaker, Zachary L. Watson, Tomomi M. Yamamoto, Benjamin G. Bitler. CASC4 drives anoikis resistance in high grade serous ovarian cancer through recycling of EGFR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2551.
Abstract 2553: Elucidation of the downstream signaling of PIK3CA genomic alterations in serous ovarian cancer
Authors: Zhang Shibo , Hong Hei Ip , Mak Victor CY , Zhou Yuan , Wang Panpan , Cheung Lydia Wai Ting 
Published: April 2023

Abstract
Genomic aberrations of PIK3CA, which encodes the catalytic subunit p110α of the class IA phosphatidylinositol 3-kinase (PI3K), is frequently observed in cancers. In ovarian cancer of the serous subtype (the most common histotype of the disease), PIK3CA amplification is dominant over single nucleotide mutations in multiple patient cohorts, suggesting the possibility that PIK3CA amplification is an alternative to PIK3CA “hot spot” mutation for serous ovarian tumorigenesis. However, whether PIK3CA amplification and mutation exert the same functional consequences on serous ovarian tumorigenesis remains uncertain. This study aims to explore and compare the functional roles between the two types of PIK3CA gene aberrations on tumorigenicity, cellular signaling, and therapeutic responses in serous ovarian cancer. We confirmed that both PIK3CA amplification and E545K mutation could induce multiple tumorigenic phenotypes in CRISPR/Cas9-mediated E545K knock-in or wild-type PIK3CA overexpressing serous ovarian cancer cell lines. Signaling pathway analyses showed that E545K knock-in cells, but not PIK3CA-overexpressing cells, had the MAPK signaling pathway activated and were sensitive to MAPK pathway inhibition. An induction of AKT phosphorylation and PDK1 phosphorylation was observed in both E545K knock-in cells and wild-type PIK3CA-overexpressing cells. Accordingly, these cells displayed higher sensitivity towards p110α or AKT inhibitors. Intriguingly, in line with previous report which demonstrated YAP as AKT substrate, the activation of AKT associated with an increase in YAP S127 phosphorylation in the knock-in or PIK3CA-overexpressing cells. AKT inhibition suppressed YAP phosphorylation. Corroborating with the role of S127 in nuclear exclusion of YAP, YAP accumulated in the cytoplasm of these cells, leading to reduced transcriptional activity of YAP. While the functional significance of YAP cytoplasmic accumulation is yet to be investigated, our results reveal the common and distinct downstream pathways between PIK3CA amplification and mutation. These findings may be applicable to p110α-targeting therapies in serous ovarian cancer.
Citation Format: Shibo Zhang, Hei Ip Hong, Victor CY Mak, Yuan Zhou, Panpan Wang, Lydia Wai Ting Cheung. Elucidation of the downstream signaling of PIK3CA genomic alterations in serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2553.
Abstract 2556: Phosphatase nanozyme combination with kinase inhibitor for decreasing prostate cancer cell viability
Authors: Myrzagaliyeva Arailym , Nazarbek Guldan , Myrzagali Sandugash , Amin Amr , Xie Yingqiu 
Published: April 2023

Abstract
Background: Phosphatase has been well studied in anti-cancer research. The dietary amino acid cysteine plays essential roles in protein structure by disulfide bonds, metal ion binding, detoxification, and many metabolic functions. Cysteine has been shown in inducing human bladder cancer cells apoptosis. However, the cysteine mediated nanoparticles enzyme (nanozyme) activity and their function, signaling pathways are yet unknown. We aim to test whether the cysteine mediated nanoparticles nanozyme activity of phosphatase could enhance targeting of kinases.
Methods: Fresh L-cysteine were applied for synthesis of less than 200 nm sized nanozyme. The phosphatase enzyme activity was measured using NBT/BCIP substrate. Scanning electron microscopy, transmission electron microscopy were used for nanoparticle analysis. Cell viability was measured by crystal violet staining of cells.
Results: L-cysteine at 0.1mg/mL combined with MET inhibitor (1µm or 5µm) showed the better effect of enhanced efficacy and decreased the viability of prostate cancer cells compared to inhibitor alone or cysteine. Combination did not affect the phosphatase activity of cysteine nanozyme.
Conclusion: L-cysteine may be applied to be combined with kinase inhibitors in drug delivery for increased efficacy.
Citation Format: Arailym Myrzagaliyeva, Guldan Nazarbek, Sandugash Myrzagali, Amr Amin, Yingqiu Xie. Phosphatase nanozyme combination with kinase inhibitor for decreasing prostate cancer cell viability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2556.