tbuckley/cabot-search huggingface dataset:
Abstract 3366: FoRx-06-428 is a novel PARG inhibitor with potent anti-tumor efficacy in preclinical cancer models
Authors: Olivier Querolle, Ulrich Lücking, Luca Iacovino, Alena Freudenmann, Giacomo Rossetti, Marina Gysin, Serena Bologna, Vasilis Dionellis, Marta Malattia, Alessandro Potenza, Nicolas Bocquet, Irena Konstantinova, Andreas Goutopoulos, Sotirios Sotiriou, Thanos Halazonetis, Tarig Bashir, Frank Zenke
Journal: Cancer Research (2024)

Abstract The formation of poly(ADP-ribose) (PAR) chains from NAD+ precursors by PARP enzymes is a characteristic posttranslational modification during DNA damage repair. PAR chains function as docking platforms for DNA repair proteins that are required to resolve DNA lesions. Equally important is the subsequent removal of PAR chains from protein substrates to conclude the repair process and restore genomic integrity. Poly(ADP-ribose) glycohydrolase (PARG) is the key enzyme in this process and has recently garnered significant attention as a novel cancer target. FoRx-06-428 is a novel, orally bioavailable and highly potent, low molecular weight PARG inhibitor. It binds to the catalytic domain of human PARG with high affinity, as evidenced by surface plasmon resonance (SPR), and displays potent inhibition of enzymatic activity. FoRx-06-428 shows selective reduction of viability in a panel of cancer cell lines highlighting therapeutic potential in multiple cancer indications. Pharmacological inhibition of PARG leads to accumulation of PAR chains and is indicative of target engagement, accompanied by modulation of DNA damage response markers, such as phosphorylation of replication protein A (pRPA) and phosphorylation of H2AX (γH2AX). Compelling anti-tumor efficacy as single agent was observed in several xenograft models (breast and gastric cancer) with excellent tolerability. Dose-dependent accumulation of PAR chains was demonstrated in vivo and constitutes a tractable target engagement biomarker for clinical exploration. Sensitivity to PARG inhibition is partly driven by distinct genomic instabilities, such as defects in homologous recombination (HR) repair, however the activity of PARG inhibitors is also influenced by aberrations in other cancer-relevant pathways. This report represents the first disclosure of the pharmacological characterization of FoRx-06-428 and highlights the value of PARG inhibition as a novel targeted approach to treat DNA repair-deficient cancers. Citation Format: Olivier Querolle, Ulrich Lücking, Luca Iacovino, Alena Freudenmann, Giacomo Rossetti, Marina Gysin, Serena Bologna, Vasilis Dionellis, Marta Malattia, Alessandro Potenza, Nicolas Bocquet, Irena Konstantinova, Andreas Goutopoulos, Sotirios Sotiriou, Thanos Halazonetis, Tarig Bashir, Frank Zenke. FoRx-06-428 is a novel PARG inhibitor with potent anti-tumor efficacy in preclinical cancer 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 3366.
Abstract 4046: Orally active PD-L1 inhibitor MAX-10181 in combination with temozolomide effectively prolonged survival in GBM animal model study
Authors: Yuguang Wang, Zhenhua Feng, Qiang Zhao, Wu Zhang, Yiwei Jiang, Yingqi Huang, Chenxing Qi, Cheng Zhang
Journal: Cancer Research (2024)

Abstract Treatment of glioblastoma (GBM) with PD-1/PD-L1 immuno therapy is highly challenging due to the limited brain blood barrier (BBB) penetration of the marketed antibody drugs. During the past several years, we have successfully developed orally active, BBB penetrating, small molecule PD-L1 inhibitor MAX-10181 which is in the phase II clinical development. To demonstrate the utility of PD-1/L1 immuno therapy for the treatment of GBM, we completed the study of MAX-10181 in combination with Temozolomide (TMZ) in GL-261 animal model study. In this study, the combination of MAX-10181 with TMZ effectively prolonged the survival by 50% in comparison with TMZ single therapy. Details of this study will be reported in this meeting. Citation Format: Yuguang Wang, Zhenhua Feng, Qiang Zhao, Wu Zhang, Yiwei Jiang, Yingqi Huang, Chenxing Qi, Cheng Zhang. Orally active PD-L1 inhibitor MAX-10181 in combination with temozolomide effectively prolonged survival in GBM animal model study [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 4046.
Abstract 2898: Development of the lipid kinase PIKfyve PROTAC degrader against neuroendocrine prostate cancer
Authors: Yuanyuan Qiao, Chungen Li, Yang Zheng, Xia Jiang, Sarah Nicole Yee, Caleb Cheng, Yi Bao, Yuping Zhang, Yuzhuo Wang, Zhen Wang, Ke Ding, Arul Chinnaiyan
Journal: Cancer Research (2024)

Abstract Therapies targeting the androgen receptor (AR) as the main driver of prostate cancer (PCa) can lead to various mechanisms of resistance and promote progression to castration-resistant PCa (CRPC), which has a median survival of only 13-23 months. Amongst recurrent CRPC, 17%-30% of patients develop neuroendocrine prostate cancer (NEPC), which is a PCa subtype characterized by a unique histology. NEPC exhibits a loss of AR signaling during neuroendocrine transdifferentiation which results in resistance to AR-targeted therapies and gain of cell characteristics resembling poorly differentiated neuroendocrine tumors. Despite advances in the understanding of NEPC development, treatment options remain limited, with platinum-based chemotherapy as the first-line treatment for both de novo and treatment-induced NEPC. However, response to first-line chemotherapy in NEPC is short, with a median survival of only seven months. The poor prognosis of NEPC is attributed in part to late diagnosis and a lack of effective therapeutic agents. Our previous work demonstrated that NEPC and AR-negative PCa exhibit higher dependency on the lipid kinase PIKfyve than AR-positive CRPC. Thus, development of PIKfyve inhibitory therapies targeting the emergent vulnerabilities of NEPC or AR-negative forms of PCa is a promising approach. Using a proteolysis targeting chimera (PROTAC) technology, we designed a class of PIKfyve specific degrader. The in vitro degradation efficiency were determined by immunoblotting, and DC50s (degradation concentration at 50%) were calculated for top candidates. Pharmacokinetic and pharmacodynamic were evaluated for in vivo study. In summary, we have developed a class of PIKfyve specific degrader using the E3 ligase von Hippel-Lindau (VHL) as a ligand via a diverse set of linkers. Mechanistic studies revealed that it induced PIKfyve degradation in a VHL- and proteasome-dependent manner. Citation Format: Yuanyuan Qiao, Chungen Li, Yang Zheng, Xia Jiang, Sarah Nicole Yee, Caleb Cheng, Yi Bao, Yuping Zhang, Yuzhuo Wang, Zhen Wang, Ke Ding, Arul Chinnaiyan. Development of the lipid kinase PIKfyve PROTAC degrader against neuroendocrine prostate 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 2898.
Abstract 350: Targeting prohibitins by fluorizoline leads to the activation of ISR and apoptosis through DELE1 and HRI by an impairment of the mitochondrial protein import machinery
Authors: Ismael Sánchez-Vera, Nekane Maritorena-Hualde, Max-Hinderk Schuler, Ana M- Cosialls, Rodolfo Lavilla, Gabriel Pons, Lucas T Jae, Daniel Iglesias-Serret, Joan Gil
Journal: Cancer Research (2024)

Abstract Prohibitins are ubiquitously expressed within the cell, but they are mainly located at the inner mitochondrial membrane. These proteins are closely associated with tumour progression, invasion, and apoptotic resistance, being overexpressed in various primary tumours such as lymphoma and endometrial cancer. Notably, we have developed a novel synthetic molecule, fluorizoline, which induces apoptosis by selectively targeting PHBs in different cancer cell lines and primary samples from various haematological neoplasias. We have previously described that fluorizoline-induced apoptosis is mediated through the activation of the pro-apoptotic branch of the integrated stress response (ISR) pathway in HeLa and HAP1 cells, concretely, by the ATF4-CHOP-NOXA axis. In a recent study, we identified compensatory mechanisms for four ISR-related kinases. Importantly, HRI emerged as the primary kinase responsible for activating this pathway and promoting apoptosis, suggesting that mitochondrial stress could lead to this activation of the ISR.Here, we investigate the OMA1-DELE1-HRI molecular pathway responsible for sensing mitochondrial stress and activating the ISR cancer cell lines. Firstly, we demonstrate that fluorizoline treatment triggers the cleavage of large DELE1 (L-DELE1) to its cleaved form (S-DELE1) through western blot analysis, and its subsequent sorting to the cytosol as confirmed by confocal analysis. Using DELE1 KO lines generated by CRISPR/Cas9 technology, we demonstrate that DELE1 is involved in the activation of the ISR and apoptosis induced by fluorizoline. However, although we cannot rule out OMA1 involvement, fluorizoline-induced ISR activation does not strongly depend on OMA1. Interestingly, our data suggests that targeting PHBs, either by fluorizoline or by their downregulation, could result in mitochondrial protein import machinery impairment. This impairment may potentially be the cause of DELE1 accumulation in the cytosol, leading to the subsequent activation of the ISR by HRI upon fluorizoline treatment. Citation Format: Ismael Sánchez-Vera, Nekane Maritorena-Hualde, Max-Hinderk Schuler, Ana M- Cosialls, Rodolfo Lavilla, Gabriel Pons, Lucas T Jae, Daniel Iglesias-Serret, Joan Gil. Targeting prohibitins by fluorizoline leads to the activation of ISR and apoptosis through DELE1 and HRI by an impairment of the mitochondrial protein import machinery [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 350.
Abstract 2785: Beyond the role of transcobalamin 1 (TCN1) as a vitamin B12-binding protein in hepatocellular carcinoma
Authors: Gregory Kenneth Muliawan, Carmen Oi Ning Leung, Terence Kin Wah Lee
Journal: Cancer Research (2024)

Abstract Hepatocellular carcinoma (HCC) is a common form of primary liver cancer and is associated with poor prognosis. Although sorafenib and lenvatinib have shown promising results in HCC treatment, their clinical benefits for patients have been limited owing to drug resistance and tumor relapse. This may be associated with the presence of tumor-initiating cells (T-ICs), which require further investigation to identify the key pathways or molecules involved in their regulation. Through in vitro enrichment of liver T-IC populations via a series of sphere passages under treatment with chemotherapeutic drugs, subsequent bulk RNA sequencing analysis identified a vitamin B-12 binding protein, transcobalamin 1 (TCN1), as the most upregulated molecule in such enriched T-IC populations. This result was consistent with the enrichment profiles of the stem cell signature in TCN1High HCC samples in the clinical dataset. TCN1 is a secretory protein expressed at high levels in salivary glands and glandular cells; however, its function beyond its native role as a vitamin B12-binding protein in the regulation of T-ICs is unclear. Using lentiviral shRNA overexpression and knockdown approaches, we identified a critical role for TCN1 in regulating the properties of T-ICs, including self-renewal, invasiveness, tumorigenicity, and drug resistance, through in vitro and in vivo assays. Clinically, we also observed a substantial increase in TCN1 mRNA signatures in HCC samples, which was associated with poor prognosis of HCC patients. By analyzing the TCGA-LIHC dataset with confirmation by immunoprecipitation, we report, for the first time, that TCN1 directly interacts with integrin subunit alpha 3 (ITGA3), thereby regulating the Notch signaling pathway. Furthermore, ELISA results revealed the presence of the secretory form of TCN1 in HCC cells, which exerts a T-IC-enhancing effect on HCC cells via autocrine regulation. In conclusion, our study provides novel insights into how TCN1 functions in HCC via a non-canonical mechanism, which goes beyond its conventional role as a vitamin B12-binding protein and uncovers a potential novel therapeutic target for HCC. Citation Format: Gregory Kenneth Muliawan, Carmen Oi Ning Leung, Terence Kin Wah Lee. Beyond the role of transcobalamin 1 (TCN1) as a vitamin B12-binding protein in hepatocellular 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 2785.
Abstract 3479: Evaluation of subclonal deconvolution pipelines using reference cell-lines and patient plasma samples
Authors: Xiaoxi Dong, Yong Huang, Tom Zhang, Shidong Jia, Pan Du
Journal: Cancer Research (2024)

Abstract Background: Intratumor heterogeneity plays a pivotal role in treatment resistance, emphasizing the need for a comprehensive understanding of tumor clonal architecture. While various methods exist for extracting this information from bulk tumor sequencing data, few studies have evaluated the entire workflow, from sample processing to subclone calls. Methods: To address this gap, we utilized cell lines with known copy number changes and somatic mutations, constructing 12 ground truth sample sets with varying cellular proportions and tumor purities. These cell lines underwent NGS pipeline using PredicineWES+ with increased sequencing depth across ~600 cancer-related genes. Subclonal analysis workflows, including FACETS, PyClone, and ECLIPSE, were implemented to to assess variant assignment and cellular fractions. The subclone analysis was extended to 91 plasma samples from cancer patients. Results: Our findings indicate that subclonal decomposition effectively segregates mutations from distinct cell lines. Notably, analyzing multiple samples with different proportions of the same subclones outperformed deconvolution from single mixture samples. In plasma samples from cancer patients, nearly one-third exhibited subclonal clinically actionable variants. Conclusions: The established subclonal deconvolution pipeline enhances biomarker analysis from assays utilizing WES with boosted sequencing depth for selected genes. Citation Format: Xiaoxi Dong, Yong Huang, Tom Zhang, Shidong Jia, Pan Du. Evaluation of subclonal deconvolution pipelines using reference cell-lines and patient plasma samples [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 3479.
Abstract 2449: Case report: DETECT-A participants with pre-malignant conditions
Authors: Omair A. Choudhry, Angana Kharge, Seema P. Rego, Paul Z. Elias, Adam H. Buchanan, Anne Marie Lennon, Nickolas Papadopoulos, Frank Diehl, Tomasz M. Beer
Journal: Cancer Research (2024)

Abstract Background: Blood based tests for multi-cancer early detection (MCED) are being developed to facilitate the earlier detection of various cancer types. The Detecting cancers Earlier Through Elective mutation-based blood Collection and Testing (DETECT-A) study evaluated the CancerSEEK MCED test, an early version of the Exact Sciences MCED test in development, in 9,911 women, age 65-75, without previous history of cancer (Lennon et al., Science 2020). The degree to which MCED testing will facilitate detection of precancerous conditions or incidental findings is unclear. Here we focus on DETECT-A participants who had pre-cancerous conditions diagnosed during a diagnostic work-up for a positive CancerSEEK MCED test. Methods: In a post-hoc analysis, we report on the detection of precancerous conditions consequent to CancerSEEK MCED testing and follow-up. Electronic health records were reviewed for diagnostic procedures performed, details of premalignant and cancer diagnoses, and vital status. Results: In three individuals, mutations in PIK3CA, TP53, or KRAS genes led to a positive CancerSEEK MCED test result. The prescribed imaging protocol using 2-deoxy-2[fluorine-18] fluoro-D-glucose positron emission tomography-computed tomography (18-FDG PET-CT), revealed a 10.3 × 9.8 × 7.8(cm) ovarian mucinous cystadenoma, a 0.8 cm appendiceal mucinous neoplasm, and 3 colonic polyps displaying high-grade dysplasia. All three participants were diagnosed with clinically significant pre-cancerous lesions, subsequently underwent surgical treatment, and remain alive and cancer-free as of February 2023 (Table 1). Conclusion: The diagnostic evaluation of a positive MCED test may occasionally reveal clinically significant pre-cancerous conditions amenable to interventions. The frequency of such findings and their clinical impact warrants further study. Citation Format: Omair A. Choudhry, Angana Kharge, Seema P. Rego, Paul Z. Elias, Adam H. Buchanan, Anne Marie Lennon, Nickolas Papadopoulos, Frank Diehl, Tomasz M. Beer. Case report: DETECT-A participants with pre-malignant conditions [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 2449.
Abstract 6916: InnoPanelTMand InnoPediaTM: resources of engineered cell lines and xenografts for drug discovery
Authors: Siyu Li, Chang Liu, Na Wang, Yuqing Hu, Jinying Ning, Feng Hao
Journal: Cancer Research (2024)

Abstract The Development of precision medicine relies on well-characterized experimental models that carry naive, induced, or engineered genomic and epigenetic features targetable by certain treatments. Patient-derived xenografts (PDX) and cell lines can serve as such in vivo and in vitro models by harboring abnormalities such as somatic and driver mutations, dysregulated gene expression and silencing, microsatellite instability, gene fusions, copy number amplification and loss of heterozygosity. In addition, cell lines can also be engineered to introduce sometimes rare-occurring abnormalities that the engineered cell line shares an identical genetic background with its parental cell line, thus providing a clearly contrasting pair to evaluate treatment specificity. With the advancement of disease research and drug discovery, existing cell lines can no longer meet the needs of various types of drug discovery. To evaluate drug efficacy more quickly and accurately, Kyinno has constructed and identified more than 4,000 engineered cell lines, including overexpressed cell lines constructed through transposon systems or lentivirus infection, gene-edited cell lines constructed through CRISPR-Cas9 technology, and reporter cell lines targeting multiple signaling pathways and membrane receptors. Besides, InnoPanelTM, a panel of over 1000 engineered cell lines was established and characterized to cover a wide range of heavily targeted genes such as CLDN18.1, CLDN18.2, LAG3, OX40, PD-L1, PD-L2, and TIM3. Cell line families were also developed for genes with multiple known driver mutations. All cell lines are annotated with background information, engineering details, functional characterization, and efficacy studies. Furthermore, we developed xenografts for several engineered cell lines and showed that the combination of cell lines and xenografts can accelerate drug development. Additionally, all of this information can be accessed in our free database, InnoPediaTM. The database also offers browsing, searching, and analytical capabilities for over 600 commonly used tumor cell lines and thousands of engineered cell lines with essential genomic and pharmacological data, cell line efficacy data for nearly 2000 common anti-tumor drugs, and comprehensive details for over 100 standard antibodies. Our engineered cell lines are now registered in the online cell line database Cellosaurus, which is available on the ExPASy server. Citation Format: Siyu Li, Chang Liu, Na Wang, Yuqing Hu, Jinying Ning, Feng Hao. InnoPanelTMand InnoPediaTM: resources of engineered cell lines and xenografts for drug discovery [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 6916.
Abstract 7257: Examining the promise of precision medicine in immuno-oncology: Vectors for targeted therapeutic delivery
Authors: Crystal Richardson, Prassanna Rao, Cassandra Koole, Michael J. Karney, Sumit Kumar
Journal: Cancer Research (2024)

Abstract At the forefront of therapeutic delivery is an array of vectors and targeting methods that hold immense promise for precision medicine. Vehicles such as viral vectors (AAV and lentivirus), lipid nanoparticles (LNPs) or liposomes, and peptide micelles each possess distinct and inherent properties, empowering researchers with tools to navigate the intricate challenges of specificity and efficiency in drug transport. Herein, we discuss and demonstrate design principles underpinning these vectors, elucidating their unique mechanisms for targeted delivery including:- A high-throughput viral packaging process to enable rapid downstream CRISPR or shRNA screening- Proprietary AAV plasmid synthesis and preparation techniques to maintain ITR integrity and improve gene delivery- Rapid synthesis, in vitro transcription, and novel sequencing of mRNA constructs for complete characterization of critical components such as the polyA tailBy synthesizing advancements in vector technologies, this poster serves as a roadmap for researchers and practitioners navigating the evolving landscape of targeted drug delivery in immuno-oncology. Citation Format: Crystal Richardson, Prassanna Rao, Cassandra Koole, Michael J. Karney, Sumit Kumar. Examining the promise of precision medicine in immuno-oncology: Vectors for targeted therapeutic delivery [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 7257.