bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3047: Interrogating TEAD protein interactions in cancer
Authors: Guarnaccia Alissa , Lill Jennie , Dey Anwesha 
Published: March 2024

Abstract
The Hippo signaling pathway is a major regulator of cellular growth and is frequently deregulated in cancer. The main effectors of the Hippo pathway are the TEAD transcription factors which function by interacting with other co-effector proteins to modulate transcriptional outputs. Notably YAP and TAZ interact with TEAD to mediate oncogenic transcriptional programs, and blocking interaction of TEAD with YAP and TAZ is a sought-after mechanism for small molecule TEAD inhibitors. However, the interaction network of TEAD extends well beyond YAP and TAZ to a variety of additional cofactors, including chromatin remodelers, epigenetic factors, and other transcriptional regulators. Thus, the impact of inhibiting TEAD could extend to unanticipated protein interactions and cellular functions. The purpose of this study is to investigate, define, and interrogate TEAD interaction networks, providing foundational knowledge for interrogating TEAD biological functions and pharmacological effects. We are employing mass spectrometry-based technologies combined with chemical and genetic tools and biochemistry to interrogate TEAD protein interaction networks. We have performed affinity purification coupled with mass spectrometry for TEAD and have identified dozens of significant interacting proteins. TEAD interactions include expected proteins, such as known Hippo pathway members, as well as unexpected protein interactions, such as DNA damage response proteins. Cellular assays probing these DNA damage protein interactions implicate TEAD as a crucial factor for efficient DNA repair mechanisms and maintaining genomic stability. These results raise questions towards a combinatorial effect for TEAD inhibitors and DNA damaging chemotherapeutic agents. Altogether, these ongoing proteomic studies are providing insights into TEAD interaction networks, leading to a deeper understanding of TEAD biology, and providing foundational knowledge that can inform the development of TEAD inhibitors as effective cancer therapies.
Citation Format: Alissa Guarnaccia, Jennie Lill, Anwesha Dey. Interrogating TEAD protein interactions in 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 3047.
Abstract 3071: Differential susceptibility of breast cancer cells to mitochondrial dysfunction induced by Wnt inhibitors
Authors: Kam Yoonseok , Winer Lisa , Rogers George W. , Romero Natalia 
Published: March 2024

Abstract
Advances in research have shown that cancer cells have distinctive bioenergetic alterations to meet their energy requirements. It has been established that certain cancers are significantly reliant on mitochondrial respiration, suggesting that modulation of mitochondrial function may have therapeutic value. The Wnt signaling pathway is a potential therapeutic target of cancer, including breast and colorectal cancers. Recent findings suggest that bi-directional crosstalk between Wnt signaling and mitochondrial function plays a crucial role in tumorigenesis, as well as differentiation and self-renewal of stem cells. In this study, 71 agents known to alter Wnt signaling were screened for effects on mitochondrial function in BT474 and Hs578T breast cancer cell lines, which have highly oxidative and highly glycolytic bioenergetic phenotypes, respectively. This screen was performed using the Agilent Seahorse XF Mito Tox assay, which enables sensitive detection and characterization of mitochondrial modulators via a standardized, quantitative parameter, the Mito Tox Index (MTI). The MTI facilitates the comparison of drug efficacy by detecting modes of mitochondrial toxicity, inhibition, and uncoupling. The MTI-based screening of the Wnt modulators identified one inhibitor and two uncouplers as potent agents inducing mitochondrial dysfunction for both BT474 and Hs578T. Despite their distinctive bioenergetic phenotypes, MTI-based dose-response assays revealed no significant differences in the efficacy of these modulators between BT474 and Hs578T cell types. In contrast, significant differential effects on ATP production rates were detected, showing cellular energy depletion induced by these agents. Using the Agilent Seahorse XF Real-Time ATP Rate assay, BT474 cells showed significant metabolic energy crisis in the presence of all 3 compounds, whereas Hs578T cells maintained stable total ATP production. This differential impact on ATP production rate corresponds directly to differences in cell viability, with BT474 showing higher susceptibility to these compounds. These results suggest that the anti-cancer efficacy of mitochondrial modulators can be different depending on the metabolic phenotype of the target cell and should be considered in therapeutic design.
Citation Format: Yoonseok Kam, Lisa Winer, George W. Rogers, Natalia Romero. Differential susceptibility of breast cancer cells to mitochondrial dysfunction induced by Wnt inhibitors [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 3071.
Abstract 3084: Aldob regulates fructose metabolism to confer ferroptosis and immune response in colorectal cancer harboring microsatellite instability
Authors: Chang Yu-Chan , Chen Chi-Long 
Published: March 2024

Abstract
Microsatellite instability (MSI) is a genetic alteration that occurs during cancer progression, specifically in colorectal cancer. Objective evidence demonstrates that colorectal cancer patients with MSI have better survival rates than those without MSI. Moreover, patients with both dMMR and MSI respond equally well to immunotherapy. We evaluated the MSI status of colorectal cancer specimens and identified an activation of aldolase B (ALDOB), the primary regulator of fructose metabolism, in the MSI group. Our analysis of the cancer cell panel revealed that the expression level of ALDOB in MSI+ cells (HCT116 and LoVo) was significantly higher than that in the microsatellite stable (MSS) group (SW480 and HT29). We also discovered a significant negative correlation between ALDOB and numerous dMMR-related genes, such as MLH1 and MSH2. We investigated how fructose concentration and pathway activation affected MSI occurrence. Our results demonstrated that abnormal fructose metabolism leaded to SLC7A11-mediated ferroptosis. SLC7A11 functioned as the active subunit and generated glutathione, GPX4, and lipid epoxides in response to transported cystine. This may explain the better clinical outcomes observed in colorectal patients with MSI. On the other hand, we also observed that ALDOB could increase certain immune ratios, such as CD4+ T cells and B cells. This aligns with the implementation of immunotherapy in the MSI community, which has been proven to yield positive effects. Consistent results were still being shown. Our study revealed significant increases in various chemokines and cytokines in media conditioned with fructose. It was interesting to note that fructose resulted in more significant changes than glucose. Based on the gathered evidence, it could be posited that ALDOB plays a crucial role as a promoter of fructose metabolism, leading to the induction of ferroptosis and immune responses in MSI colorectal cancer. The findings shed new light on known consequences and provide new avenues of information.
Citation Format: Yu-Chan Chang, Chi-Long Chen. Aldob regulates fructose metabolism to confer ferroptosis and immune response in colorectal cancer harboring microsatellite instability [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 3084.
Abstract 3098: CETSA for navigating your chemistry and exploring the biology of protein degraders
Authors: Brehmer Victoria , Lundgren Stina , Friman Tomas , Amadio Daniele , Chernobrovkin Alexey , Molina Daniel Martinez 
Published: March 2024

Abstract
Protein degradation is a non-classical modality with the potential to tackle therapeutically interesting proteins, previously deemed undruggable. In this area, CETSA is a powerful technology for identifying new binders, assessing target engagement, and investigating the mechanism of action of the degraders in the intact cell environment - without the need to modify your compound, the proteins or the cellular environment.  CETSA can provide insights into the binding of the degrader to both the E3 ligase and the protein of interest (POI), as well as follow the downstream cellular and molecular effects. Here we will exemplify how CETSA can be applied in various stages of drug discovery to provide biologically relevant data to guide the design and optimization of new degraders. For example, CETSA can provide valuable information of the cell permeability and the in-cell performance of the degrader, which is important for understanding how the degrader enters cells and reaches its target proteins. By combining data from CETSA with data from degradation readout, in our case quantitative proteomics, it is possible to correlate cellular target engagement potencies with degradation efficiency and importantly, also identify any drug:protein binding that does not result in degradation By using the proteome-wide CETSA Explore format, the selectivity of the degrader and the downstream protein consequences of the elimination of the target protein could be studied.
Citation Format: Victoria Brehmer, Stina Lundgren, Tomas Friman, Daniele Amadio, Alexey Chernobrovkin, Daniel Martinez Molina. CETSA for navigating your chemistry and exploring the biology of protein degraders  [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 3098.
Abstract 3155: Metabolic stress induces an intrinsic inflammatory CAF phenotype that regulates stromal architecture in pancreatic cancer
Authors: Zhang Yijuan , Maganti Swetha , Hope Jennifer , Lin Li , Galapate Cheska Marie , Carrette Florent , Bradley Linda , Commisso Cosimo 
Published: March 2024

Abstract
Macropinocytosis is a critical amino acid supply pathway that fuels the metabolism of tumor cells and cancer-associated fibroblasts (CAFs) in pancreatic ductal adenocarcinoma (PDAC). PDAC tumors are deficient in glutamine, a critical amino acid that tumor cells and CAFs use to sustain their cellular fitness. We have previously shown that both PDAC cells and CAFs stimulate macropinocytosis as an adaptive response to glutamine depletion. How these linked metabolic mechanisms might co-operate to control stromal architecture remains elusive. In this study, we employed glutamine starvation and 5-(N-ethyl-N-isopropyl)-amiloride (EIPA), a selective inhibitor of macropinocytosis, to investigate how metabolic stress impacts the tumor microenvironment. We find that concomitant suppression of glutamine metabolism and macropinocytosis synergizes to drive an intrinsic inflammatory CAF phenotype that requires metabolic stress-induced ERK/MAPK signaling. Utilizing immunocompetent syngeneic mouse models of PDAC, we find that blocking macropinocytosis in these glutamine-depleted tumors diminishes tumor growth and reorganizes the tumor stroma by decreasing collagen deposition, increasing vasculature expansion and enhancing the infiltration of both CD8+ and CD4+ T cells. Alterations in the stromal landscape under these conditions are linked to the enhancement of CAFs that display an inflammatory signature while simultaneously suppressing more myofibroblastic identities within the tumor. Interestingly, we find that these effects on the tumor microenvironment can be harnessed to improve therapeutic responses. We determine that combining macropinocytosis inhibition with immune checkpoint blockade reduces PDAC tumor burden and significantly inhibits metastasis. We also find that macropinocytosis inhibition enhances drug delivery, thereby improving the efficacy of gemcitabine chemotherapy. Our findings demonstrate that intratumoral metabolic stress plays a critical part in preserving and modulating the tumor stroma.
Citation Format: Yijuan Zhang, Swetha Maganti, Jennifer Hope, Li Lin, Cheska Marie Galapate, Florent Carrette, Linda Bradley, Cosimo Commisso. Metabolic stress induces an intrinsic inflammatory CAF phenotype that regulates stromal architecture in 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 3155.
Abstract 3160: PufA promotes proliferation, migration and tumorigenesis through NF-kB pathway in cholangiocarcinoma
Authors: Chen Chiao-Ping , Yeh Chun-Nan , Pan Yi-Ru , Hsiao Yu-Tien , Lo Chih-Hong , Lin Chia-Hsien , Wu Chiao-En 
Published: March 2024

Abstract
Cholangiocarcinoma (CCA) exhibits a poor prognosis despite the recent advances in targeted therapy and immunotherapy. Therefore, exploring the novel mechanism of CCA tumorigenesis and identifying the effective targeted therapy is critical for advanced CCA to improve future treatment. A novel biogenesis factor of the 90S pre-ribosome named PufA, is higher expressed in tumors than normal tissue based on the TCGA databank implying the role of CCA tumorigenesis. Our results showed that PufA expression was significantly associated with larger tumor size, more lymph node metastasis, more tumor relapse, death, and unfavorable survivals in 205 patients with resectable CCA in Chang Gung Memorial Hospital. We demonstrated the inhibited effect of cell survival, migration ability, and the sphere-formation potential by silencing of PufA in CCA cell lines. Tumor growth is also suppressed in PufA knockdown xenograft mice. Mechanistic investigation showed that PufA was expression associated with nuclear factor kappa B p65 (RELA) activity and facilitated activity of the NF-κB transactivation. RELA, a transcription factor, is the principal regulator of the inflammatory response and is crucial for the homeostasis of the immune system and the expression of the immune checkpoint. Furthermore, decreased PufA levels also downregulated PD-L1 expression in CCA. Together, these findings suggested that the PufA-RELA axis could be a potential target for further application of targeted therapy in combination with immunotherapy.
Citation Format: Chiao-Ping Chen, Chun-Nan Yeh, Yi-Ru Pan, Yu-Tien Hsiao, Chih-Hong Lo, Chia-Hsien Lin, Chiao-En Wu. PufA promotes proliferation, migration and tumorigenesis through NF-kB pathway in cholangiocarcinoma [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 3160.
Abstract 3200: Assessing the utility of cell membrane lipid-extracted nanoliposomes (CLENs) as a targeted drug delivery system for pancreatic cancer
Authors: Alshammari Khaznah , Verdery Sergio , George Sujin , Campbell Robert B 
Published: March 2024

Abstract
Background: Pancreatic cancer is a challenging type of cancer to treat as evidenced by a 9% 5-year survival and a dismal rate of mortality. Nanoparticles represent a revolutionary treatment method, primarily due to characteristics including cellular absorption, boosting therapeutic effectiveness, and mitigating side effects through localized actions. For nanomedicine, optimizing liposome formulations is crucial for achieving the highest level of specificity in drug targeting. This study aims to evaluate cellular interaction of pancreatic cancer lipid-extract modified nanoliposomes when compared to unmodified varieties in vitro.
Method: Cell membrane lipid-extracted nanoliposomes (CLENs) were prepared via the thin film evaporation technique. The composition included various compositions and ratios of DOPC, DOTAP, Cholesterol, DPPE-PEG-5000, and lipid extracts derived from MS1-VEGF target cells. MS1-VEGF was the cellular model of pancreatic cancer used for this study. Cellular binding studies were performed using cellular suspension and adherent cell populations. Studies were performed in 48-well plates under different experimental conditions including alterations in time of incubation, and periods of cellular exposure to dual humidified and oscillation environments in the presence of lipid-extracted (LE) nanoliposomal preparations and conventional controls.
Results: The particle size for nanoliposomes employed for this study was approximately 115 ± 0.7 nm for control and 128 ± 2.7 nm for experimental (lipid extract-modified) nanoliposomes. Following cellular exposure to different lipid extract concentrations (typically 0 to 100 nmoles per ml of growth medium), the fluorescence values demonstrated increased cellular uptake with greater LE content for floating and adhered MS1-VEGF cell populations. With the floating cells, LE-modified nanoliposomes demonstrated significantly higher fluorescence intensity values compared to conventional nanoliposomes. Similarly, with MS1-VEGF adherent cells, LE-modified nanoliposomes targeted cells to a greater extent compared to unmodified controls.
Conclusions: The increased cellular uptake of CLENs designed for targeting pancreatic tumor cells (both floating and adherent cells) demonstrated an improvement over the use of conventional nanoliposomes under similar experimental conditions. Further research is needed to fully explore the potential use of CLENs for targeting and treatment of pancreatic cancer.
Citation Format: Khaznah Alshammari, Sergio Verdery, Sujin George, Robert B Campbell. Assessing the utility of cell membrane lipid-extracted nanoliposomes (CLENs) as a targeted drug delivery system for 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 3200.
Abstract 322: Ultraplex genome and exome sequencing of rare single cells
Authors: Andreou Ioanna , Rulli Samuel , Heitz Katja , Huebner Silke , Meerschiff Christin , Lader Eric 
Published: March 2024

Abstract
Single-cell genome analysis enables researchers to gain novel insights into tumor heterogeneity. Conducting single-cell genomic analysis using next-generation sequencing (NGS) methods has traditionally been challenging since the amount of genomic DNA present in a single cell is limited. PCR-based amplification methods normally have high error rates, low coverage uniformity, and extensive allelic drop-outs making interpretation of SNVs and CNVs challenging.Here we introduce a new whole-genome amplification method which utilizes an optimized isothermal DNA amplification reaction with a Hi-fidelity, error correcting polymerase and downstream library preparation protocol to allow pooling of amplified DNA. The key DNA amplification steps use multiple displacement amplification (MDA) technology to amplify gDNA directly from single cells, nuclei or previously isolated genomic DNA. During the MDA reaction, sample-barcodes are incorporated into the newly synthetized DNA, allowing the amplified DNA to be pooled and processed in to one ultraplex library. This method saves library preparation time, reduces DNA library costs and limits plastic consumable usage.Our current workflow allows 24 samples to be multiplexed in one library and 24 libraries to be produced for a total of 576 samples per sequencing flow cell. This method can be used to investigate chromosomal instability with low pass sequencing or SNV and CNV analysis following whole genome, exome-capture workflows.
Citation Format: Ioanna Andreou, Samuel Rulli, Katja Heitz, Silke Huebner, Christin Meerschiff, Eric Lader. Ultraplex genome and exome sequencing of rare single 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 322.
Abstract 3242: TNG917 is a clinical-grade, potent and selective inhibitor of EHMT1/2 for the treatment of immune cold tumors
Authors: Lu Alvin , Haines Brian , Lei Ji , Zhang Wenhai , Zhang Minjie , Whittington Douglas A. , Ferdinez Maria Lucia , Yu Yi , Meier Samuel R. , Choi Ashley , Bejnood Alborz , Bandi Madhavi , Lazarides Katherine , Pan Xuewen , Gu Lina , Tsai Alice W. , Sudsakorn Sirimas , Liang Colin , Come Jon , Williams Brett , Throner Scott , Vacca Joseph , Maxwell John P. , Anderson Jannik N. , Huang Alan , Min Chengyin , Chen Yingnan P. 
Published: March 2024

Abstract
CRISPR-based functional genomics screening can be designed to identify novel cancer cell intrinsic targets that increase tumor immunogenicity. Using a FACS-based CRISPR sorting screen for PD-L1 expression, we identified Euchromatic histone-lysine-N-methyltransferase 1 and 2 (EHMT1/2) as negative modulators of the interferon signaling pathways. EHMT1 and EHMT2 are histone methyltransferases that mono- and di-methylate lysine 9 of histone H3 to repress gene transcription of defined target genes. Gene knockout or pharmacological inhibition of EHMT1/2 in cancer cells resulted in de-repression of gene promoters, upregulation of interferon-stimulated genes (ISGs), and secretion of pro-inflammatory cytokines. Here, we present the preclinical characterization of TNG917 - an oral and highly selective EHMT1/2 inhibitor with low nanomolar cellular potency, and favorable pharmacodynamic and pharmacokinetic properties. In humanized and syngeneic mouse models, treatment with TNG917 in combination with anti-PD1 promoted a T-cell-infiltrated tumor microenvironment, led to significant anti-tumor activity, and resulted in survival benefit. In summary, our in vitro and in vivo studies provide a rationale for the clinical development path of TNG917, in combination with checkpoint inhibition, in patients with immune cold tumors.
Citation Format: Alvin Lu, Brian Haines, Ji Lei, Wenhai Zhang, Minjie Zhang, Douglas A. Whittington, Maria Lucia Ferdinez, Yi Yu, Samuel R. Meier, Ashley Choi, Alborz Bejnood, Madhavi Bandi, Katherine Lazarides, Xuewen Pan, Lina Gu, Alice W. Tsai, Sirimas Sudsakorn, Colin Liang, Jon Come, Brett Williams, Scott Throner, Joseph Vacca, John P. Maxwell, Jannik N. Anderson, Alan Huang, Chengyin Min, Yingnan P. Chen. TNG917 is a clinical-grade, potent and selective inhibitor of EHMT1/2 for the treatment of immune cold 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 3242.