bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3042: Unraveling the mechanism of YAP toxicity in neuroendocrine solid tumors: Insights from Merkel cell carcinoma
Authors: Bahar Furkan , Frost Thomas C. , Ananthapadmanabhan Varsha , Schnabel Julia L. , Thakuria Manisha , DeCaprio James A. 
Published: March 2024

Abstract
The Hippo pathway, a pivotal regulator orchestrating organ size and tissue growth, has emerged as a central player in cancer biology. The downstream transcription factor YAP within this pathway has been implicated in diverse oncogenic processes. YAP activation contributes to drug resistance, metastasis, and poor clinical outcomes in many solid tumors. Conversely, YAP exhibits growth-suppressive effects in neuroendocrine (NE) solid cancers, a paradox that remains poorly understood. Analysis of RNAseq data from the Cancer Cell Line Encyclopedia (CCLE) revealed a distinct classification of tumors into YAP1-expressing (YAPon) and non-expressing (YAPoff) subgroups, with hematopoietic malignancies and NE solid tumors featured prominently in the latter. Merkel cell carcinoma (MCC) is a rare, high-grade, NE carcinoma of the skin with two distinct etiologies. Virus-positive MCC contains integrated Merkel cell polyomavirus that expresses the viral T antigens and virus-negative MCC caused by sunlight exposure and extensive UV damage. Bulk RNAseq performed with more than 60 MCC tumors revealed that YAP expression displayed an inverse correlation with an NE gene expression signature. To gain insight into why YAP expression is so low in MCC, we generated MCC cell lines with inducible expression of YAP. Expression of YAP led to growth arrest and cell death. We performed a genome-wide CRISPR-Cas9 screen to identify genes that when lost enable MCC cells to tolerate YAP expression. Functional enrichment analysis of the positively selected genes uncovered a variety of signaling pathways. Intriguingly, the CRISPR screen revealed a positive enrichment of non-canonical BAF complex members, including BRD9 and SMARCD1. To validate this finding, we treated MKL-1 cells with a BRD9 inhibitor, observing a substantial reduction in YAP toxicity. These findings open avenues for the development of targeted therapeutic strategies for high grade NE cancers, addressing a critical gap in our understanding of YAP biology in the context of MCC and beyond.
Citation Format: Furkan Bahar, Thomas C. Frost, Varsha Ananthapadmanabhan, Julia L. Schnabel, Manisha Thakuria, James A. DeCaprio. Unraveling the mechanism of YAP toxicity in neuroendocrine solid tumors: Insights from Merkel cell carcinoma [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 3042.
Abstract 3057: The TARZN complex binds to de novo enhancer mutations and promotes oncogenic expression in T-ALL
Authors: Anuar Nurkaiyisah Zaal , Goh Chai Yeen , Chua Boon Haow , Tan Shi Hao , Costa Joana R. , Mansour Marc R. , Sanda Takaomi , Kappei Dennis 
Published: March 2024

Abstract
TAL1 is overexpressed in 40-60% of T-cell acute lymphoblastic leukaemia (T-ALL) cases and forms an oncogenic core regulatory circuit (CRC) with other transcription factors such as LMO1, LMO2 and GATA3. In 5% of T-ALL cases an insertion of a consensus GT dinucleotide is observed upstream of the TAL1 gene, termed the “Mutation of TAL1 enhancer” (MuTE), driving TAL1 overexpression. Using an in vitro reconstitution DNA pull-down assay combined with quantitative mass spectrometry, we identified nine candidate proteins that preferentially bound to the MuTE sequence compared to the WT sequence. Among the candidates, we demonstrate by reciprocal immunoprecipitation experiments coupled to quantitative mass spectrometry that the RNA methyltransferase TARBP1 and the zinc finger proteins ZBTB2, ZBTB25 and ZNF639 formed a complex that we term TARZN. Interestingly, the TARZN complex also bound to de novo super enhancer sites upstream of the LMO1 and LMO2 genes in T-ALL cells, indicating a putative common mechanism between these different non-coding driver mutations. Furthermore, knock-down of all TARZN members resulted in lower TAL1 protein expression in MuTE-positive but not in MuTE-negative T-ALL cells. Overall, these data suggest that the TARZN complex cooperatively promotes oncogenic expression in T-ALL.
Citation Format: Nurkaiyisah Zaal Anuar, Chai Yeen Goh, Boon Haow Chua, Shi Hao Tan, Joana R. Costa, Marc R. Mansour, Takaomi Sanda, Dennis Kappei. The TARZN complex binds to de novo enhancer mutations and promotes oncogenic expression in T-ALL [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 3057.
Abstract 3070: CDK12 is a novel therapeutic target in glioblastoma
Authors: Mun Jeong-Yeon , Shu Chang , Gao Qiuqiang , Westhoff Mike-Andrew , Karpel-Massler Georg , Siegelin Markus D. 
Published: March 2024

Abstract
Glioblastoma (GBM), the most common primary brain tumor in adults carries a highly unfavorable prognosis of only one to two years despite treatment with the standard of care, involving surgery, temozolomide and radiation. Patient-derived xenograft (PDX) GBM cultures were assessed for their susceptibility to loss of CDK12 function, which was either mediated genetically (shRNA) or by the novel inhibitor, SR-4835. GBM metabolism was measured by utilizing extracellular flux analysis as well as LC/MS based carbon tracing analyses. In vivo efficacy was determined by orthotopic GBM models in mice. Based on Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and shRNA library screens in multiple GBM cell cultures we identified CDK12 as essential for the growth of GBM. Consistently, loss of function of CDK12 (genetically and pharmacologically) led to a reduction of growth of GBM patient-derived xenograft (PDX) lines in vitro. Notably, SR-4835 reduced GBM growth in the low nanomolar range and synergistically enhanced the potency of temozolomide. Extracellular flux analysis and metabolite screening analyses, including carbon tracing (U13C-Glucose, U13C-Glutamine) suggested that loss of function of CDK12 elicited a substantial inhibition of cellular respiration, causing energy deprivation with subsequent cell death with apoptotic features. On the molecular level, loss of function of CDK12 increased ATF4 along with pro-apoptotic Noxa, whereas anti-apoptotic Mcl-1 decreased. In turn, adenoviral mediated ectopic expression of Mcl-1 inhibited cell death mediated by loss of function of CDK12 in GBM cells. In an orthotopic murine PDX model of GBM animals receiving treatment with SR-4835 had a significantly longer overall survival without induction of toxicity as compared to mice treated with vehicle. In summary, these findings suggest that CDK12 is a novel treatment target for GBM and that CDK12 is an important driver of energy metabolism in GBM to partially mediate apoptotic resistance. Moreover, SR-4835 enhanced the potency of temozolomide in GBM models. Therefore, the novel CDK12 inhibitor, SR-4835 should be tested in a clinical trial in patients suffering from GBM.
Citation Format: Jeong-Yeon Mun, Chang Shu, Qiuqiang Gao, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D. Siegelin. CDK12 is a novel therapeutic target 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 3070.
Abstract 3073: ACTL6a drives metabolic reprogramming and chemoresistance in head and neck squamous cell carcinoma
Authors: Monavarian Mehri , Finegersh Andrey 
Published: March 2024

Abstract
Actin like protein 6A (ACTL6a), a subunit of the SWI/SNF chromatin remodeling complex, is amplified in a third of all squamous cell carcinomas including head and neck (HNSCC) cancers. Recent studies implicate ACTL6a as an oncogenic driver that potentiates SWI/SNF-related chromatin remodeling; however, the underlying mechanisms in HNSCC progression yet to be elucidated. Using the HNSCC cell lines FaDu, SCC90, and SCC2, ACTL6a knockdown (siACTL6a) led to a significant reduction in cell proliferation compared to control when measured by sulforhodamine B but not resazurin, suggesting up-regulation of oxidative phosphorylation with siACTL6a. We used RNA-seq datasets of siACTL6a in FaDu cells and found that there was a significant up-regulation of components of complex I and IV of the electron transport chain compared to control. Gene set enrichment analysis also demonstrated a significant up-regulation in glycolysis in ACTL6a amplified tumors within the HNSCC TCGA dataset. Since metabolism is a key driver of chemotherapy resistance, we studied effects of ACTL6a expression on cisplatin-mediated cytotoxicity. Compared to control, siACTL6A of the HNSCC cell lines FaDu and SCC2 had significantly decreased IC50 to cisplatin, indicating ACTL6a mediates toxicity. We also observed significantly decreased migration in a transwell migration assay in siACTL6A FaDu and SCC2 cells compared to control. We are studying the effects of shRNA directed against ACTL6a using a syngenic in vivo tumor model with a mouse oral cavity (MOC2) cell line that grows in C57BL/6J mice. Subcutaneous injection of MOC2 cells demonstrated significantly decreased tumor growth in shACTL6a cells compared to control. We are performing additional studies to identify specific mechanisms of ACTL6a mediated metabolic reprogramming in tumor cells. In conclusion, ACTL6A amplification is common in HNSCC and facilitates metabolic reprogramming, which drives tumor proliferation, cell migration, and drug resistance.
Citation Format: Mehri Monavarian, Andrey Finegersh. ACTL6a drives metabolic reprogramming and chemoresistance in head and neck squamous cell carcinoma [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 3073.
Abstract 3081: Targeting lipid kinases to enhance autophagy inhibition for the treatment of pancreatic cancer
Authors: Schechter Elyse G. , DeLiberty Jonathan M. , Stalnecker Clint A. , Bryant Kirsten L. 
Published: March 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized as the most KRAS-addicted cancer type, with KRAS mutations found in &gt;95% of cases. Mutant KRAS relies on dysregulated metabolism to support growth. One dysregulated pathway upregulated in PDAC is autophagy, a lysosome-mediated process that degrades proteins and organelles to supply macromolecules for growth. Our lab and others have shown that inhibition of KRAS or the mitogen activated protein kinase (MAPK) components, MEK or ERK, further increases PDAC dependency on autophagy as a resistance mechanism. Cotreatment with ERK MAPK inhibitors and the autophagy inhibitor chloroquine (CQ) decreased autophagic flux, inhibited proliferation, and induced apoptosis in PDAC cells. CQ is the only FDA-approved autophagy inhibitor, and it demonstrates low potency in vivo, motivating our studies to identify strategies to improve autophagy inhibition in PDAC. We utilized a CRISPR-Cas9 loss-of-function screen to identify sensitizers to CQ in PDAC and identified 25 autophagy-related targets.
We hypothesize that targeting the autophagy pathway at multiple nodes will increase the efficacy of CQ treatment in PDAC. To validate hits identified in the CRISPR-Cas9 screen, I designed an siRNA array that contained three distinct oligos for each target. I quantified changes in proliferation in a panel of four PDAC cell lines after siRNA-mediated suppression of the target genes following 3- or 6-day time points.
I hypothesized that targets identified to be non-essential on their own would allow for potential synthetic lethality with CQ. To test this, I performed a 3-day knockdown followed by 3-day exposure to a dose response of CQ. I found that suppression of lipid kinases PIP4K2A, PIP4K2C, or PIK3C3 shift the dose response to CQ in a panel of PDAC lines. This indicates that loss of those targets sensitizes PDAC cells to CQ treatment. Furthermore, we found that pharmacological inhibition of VPS34, the lipid kinase encoded by PIK3C3 by the ATP-competitive inhibitor SAR-405 synergizes with CQ.
My future studies will be focused on validating other targets identified in the loss-of-function CRISPR-Cas9 screen. I will measure changes in autophagic flux and apoptosis due to the loss of validated targets. The long-term goal of this project is to enhance the translatability of autophagy inhibition for patient care through identifying combinational approaches to improve CQ response in PDAC.
Citation Format: Elyse G. Schechter, Jonathan M. DeLiberty, Clint A. Stalnecker, Kirsten L. Bryant. Targeting lipid kinases to enhance autophagy inhibition for the treatment of pancreatic 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 3081.
Abstract 3087: The m6A methyltransferase RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism
Authors: Park Su Hwan , Park Yun-Yong , Lee Jong-Ho 
Published: March 2024

Abstract
N6-adenosine methylation (m6A) is critical for controlling cancer cell growth and tumorigenesis. However, the function and detailed mechanism of how m6A methyltransferases modulate m6A levels on specific targets remains unknown. In the current study, we identified significantly elevated levels of RBM15, an m6A writer, in basal-like breast cancer (BC) patients compared to non-basal like BC and linked it to worse clinical outcome. Gene expression profiling uncovered correlations between RBM15 and serine and glycine metabolism genes including PHGDH, PSAT1, PSPH, and SHMT2. RBM15 influences overall m6A levels and, specifically, m6A of serine and glycine metabolism genes via direct binding to target RNA. Further RBM15 effects on cell growth were largely dependent on serine and glycine metabolism. Thus, RBM15 coordinates cancer cell growth through altered serine and glycine metabolism suggesting RBM15 as a new therapeutic target in BC.
Citation Format: Su Hwan Park, Yun-Yong Park, Jong-Ho Lee. The m6A methyltransferase RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism [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 3087.
Abstract 3104: A NanoBRET target engagement assay for querying domain selectivity at full-length polymerase theta in live cells
Authors: Edenson Steven , Slater Michael , Corona Cesear , Beck Michael , Vasta James , Teske Kelly , Michaud Ani , Robers Matthew 
Published: March 2024

Abstract
In HR-deficient cells, Polymerase Theta (Pol-theta) serves to repair double strand breaks and has emerged as a therapeutic target in HR-deficient cancers. Encoded by the POLQ gene, Pol-theta is a large (290 Kda) protein with two distinct functional domains (polymerase, helicase), separated by an unstructured region. Each domain of Pol-theta has proven vulnerable to small molecule inhibitors, with a number of molecules undergoing clinical evaluation. Unlike the helicase domain, target engagement at the polymerase domain requires cooperativity with DNA fragments. Here we describe a novel NanoBRET Target Engagement assay that enables domain-specific analysis of small molecule occupancy in live cells. To observe the high affinity-state of small molecule inhibitors to the polymerase domain, we have developed a cell-permeable pol domain NanoBRET probe, along with a novel work flow to introduce small DNA fragments into live cells. Together these components form a nucleoprotein complex with full length polymerase theta. This assay method can be used to quantify and rank-order engagement to the polymerase domain in live cells. To enable domain-selectivity analysis, we have developed a second NanoBRET probe directed to the helicase domain. Together these two NanoBRET probes allow for the mechanism of action studies at Pol-theta in living cells.
Citation Format: Steven Edenson, Michael Slater, Cesear Corona, Michael Beck, James Vasta, Kelly Teske, Ani Michaud, Matthew Robers. A NanoBRET target engagement assay for querying domain selectivity at full-length polymerase theta in live 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 3104.
Abstract 3143: The ADC payload PNU-159682 is highly active in a wide range of cancer indications by inducing DNA damage and cell death via a distinct mode of action
Authors: Kaiser Monika , Fiedler Ulrike , Gerlach Daniel , Kraut Norbert , Bammert Lukas 
Published: March 2024

Abstract
During the last decade antibody-drug-conjugates (ADCs) have become an important and validated treatment modality for cancer patients. Here, we introduce a unique next generation ADC platform based on Sortase-mediated antibody conjugation (SMAC-Technology) yielding in very homogenous and stable drug conjugates with limited systemic, but powerful anti-tumor activity. The highly potent payload used is a proprietary derivative of the Anthracycline PNU-159682. Our PNU-159682-based ADCs are known to not only induce DNA damage in the target cell, but importantly also trigger immunogenic cell death and thus, stimulating anti-tumor immunity offering untapped combination potential. ADCs based on the SMAC-Technology platform currently undergo clinical development. In this work, we present functional studies that were performed to further elucidate the mode of action (MoA) of the ADC payload PNU-159682 and to investigate any potential liabilities with respect to sensitivity, which could limit treatment options for cancer patients. Flow cytometry-based readouts verified that PNU-EDA, a derivative of PNU-159682, is a highly potent inducer of DNA damage, cell cycle arrest and cell death. Interestingly, PNU-EDA arrests cells and inhibits DNA synthesis in S-phase in contrast to other Anthracyclines such as Doxorubicin, which leads to a block in the G2/M-phase. High-throughput cell line panel sensitivity screens confirmed that the activity of PNU-EDA is broad and not restricted to specific cancer indications. Notably, a correlation between lower potency and increased ABCB1 (MDR1) expression levels was observed for PNU-EDA, but not for parental PNU-159682. More detailed mechanistic insights were obtained by performing a genome-wide CRISPR-Cas9 KO screen, which revealed a partial dependency of the PNU-EDA potency on the proficiency of the TC-NER DNA damage repair mechanism. This finding further highlights a distinct MoA of PNU-159682 compared to Doxorubicin or other DNA-targeting compounds such as Cisplatin. Overall, our screens and mechanistic studies verified that PNU-159682-based ADCs efficiently kill cancer cells via a particular MoA and thereby, offer highly promising therapeutic options to a diverse and large population of cancer patients.
Citation Format: Monika Kaiser, Ulrike Fiedler, Daniel Gerlach, Norbert Kraut, Lukas Bammert. The ADC payload PNU-159682 is highly active in a wide range of cancer indications by inducing DNA damage and cell death via a distinct mode of action [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 3143.
Abstract 3173: Impact of hypoxia on the integrated stress response activated by imipridones ONC201 and ONC206 in pediatric diffuse midline glioma cells
Authors: Roady Tyler J. , Stubbs Nolan , Chen Josephine , Xia Yutong , Uruchurtu Ashley Sanchez Sevilla , Tian Xiaobing , Zhou Lanlan , El-Deiry Wafik S. 
Published: March 2024

Abstract
Diffuse midline gliomas (DMGs) are highly aggressive, high-grade gliomas which typically arise in children and young adults. With currently approved treatments the median survival from time of diagnosis for pediatric DMG is 8-10 months with only 10% of children living to 2 years post diagnosis. Despite being only 15% of the cases it makes up 40% of the pediatric brain cancer deaths making it the leading cause of death for all pediatric glioma cases. Two recent clinical studies, NCT03416530 and NCT03134131, have shown the clinical efficacy of Dordaviprone (ONC201/TIC10) for the treatment of DMG; increasing median survival to 22 months in patients following radiation treatment prior to recurrence. Imipridone ONC206, a chemical derivative of ONC201, is under clinical development for treatment of pediatric and adult patients with primary brain tumors (NCT04732065 and NCT04541082). To further improve treatment, we must continue to study how the tumor microenvironment impacts the efficacy of imipridones. One crucial aspect of all brain cancers is hypoxia, so the IC50s of the SU-DIGP-25, SU-DIPG-XIII and SU-DIPGIV pediatric DMG cell lines treated with ONC201 or ONC206 were measured using the CellTiter-Glo assay under conditions of hypoxia and normoxia. Imipridones mediate apoptosis through the upregulation of the TRAIL death receptor DR5 and the activation of the integrated stress response (ISR), so western blots were used to show changes in the ISR protein expression in ONC201 treated DMG cells at multiple different degrees of hypoxia. To understand how hypoxia inducible factors (HIFs) play a role in resistance and susceptibility to ONC201 or ONC206, HIF-1a, HIF-2a, and HIF-3a were knocked down showing altered ISR protein expression after treating with the imipridones under hypoxic and normoxic conditions.
Citation Format: Tyler J. Roady, Nolan Stubbs, Josephine Chen, Yutong Xia, Ashley Sanchez Sevilla Uruchurtu, Xiaobing Tian, Lanlan Zhou, Wafik S. El-Deiry. Impact of hypoxia on the integrated stress response activated by imipridones ONC201 and ONC206 in pediatric diffuse midline glioma 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 3173.