tbuckley/cabot-search huggingface dataset:
Interferon-α stimulates DExH-box helicase 58 to prevent hepatocyte ferroptosis
Authors: Kai-Wei Jia, Ren-Qi Yao, Yi-Wen Fan, Ding-Ji Zhang, Ye Zhou, Min-Jun Wang, Li-Yuan Zhang, Yue Dong, Zhi-Xuan Li, Su-Yuan Wang, Mu Wang, Yun-Hui Li, Lu-Xin Zhang, Ting Lei, Liang-Chen Gui, Shan Lu, Ying-Yun Yang, Si-Xian Wang, Yi-Zhi Yu, Yong-Ming Yao, Jin Hou
Journal: Military Medical Research (2024)

Liver ischemia/reperfusion (I/R) injury is usually caused by hepatic inflow occlusion during liver surgery, and is frequently observed during war wounds and trauma. Hepatocyte ferroptosis plays a critical role in liver I/R injury, however, it remains unclear whether this process is controlled or regulated by members of the DEAD/DExH-box helicase (DDX/DHX) family. The expression of DDX/DHX family members during liver I/R injury was screened using transcriptome analysis. Hepatocyte-specific Dhx58 knockout mice were constructed, and a partial liver I/R operation was performed. Single-cell RNA sequencing (scRNA-seq) in the liver post I/R suggested enhanced ferroptosis by Dhx58hep-/-. The mRNAs and proteins associated with DExH-box helicase 58 (DHX58) were screened using RNA immunoprecipitation-sequencing (RIP-seq) and IP-mass spectrometry (IP-MS). Excessive production of reactive oxygen species (ROS) decreased the expression of the IFN-stimulated gene Dhx58 in hepatocytes and promoted hepatic ferroptosis, while treatment using IFN-α increased DHX58 expression and prevented ferroptosis during liver I/R injury. Mechanistically, DHX58 with RNA-binding activity constitutively associates with the mRNA of glutathione peroxidase 4 (GPX4), a central ferroptosis suppressor, and recruits the m6A reader YT521-B homology domain containing 2 (YTHDC2) to promote the translation of Gpx4 mRNA in an m6A-dependent manner, thus enhancing GPX4 protein levels and preventing hepatic ferroptosis. This study provides mechanistic evidence that IFN-α stimulates DHX58 to promote the translation of m6A-modified Gpx4 mRNA, suggesting the potential clinical application of IFN-α in the prevention of hepatic ferroptosis during liver I/R injury.
Abstract LT06: Understanding the Role of Mutant <i>TP53</i> in Lung Cancer Using Novel Genetically Engineered Mouse Models
Authors: Tianwei Chen, Elizabeth Lieschke, Leanne Scott, Danielle Boyd, Kate Sutherland, Andreas Strasser, Gemma Kelly
Journal: Cancer Research (2024)

Abstract The tumour suppressor gene TP53 (Trp53 in mouse) is mutated in ~50% of human cancers and this is associated with poor therapeutic responses. Mutant TP53 protein was reported to promote tumour development in three ways: (1) loss of function (LOF) effects which abrogate normal TP53-mediated cellular processes; (2) dominant negative effects (DNE); and (3) gain of function effects (GOF) whereby mutant TP53 proteins bind to and modulate the functions of proteins that are not impacted by wildtype TP53. Despite extensive research efforts, the relative contributions of the LOF, DNE and GOF effects of mutant TP53 in cancer are largely unknown. This project aims to understand the relative importance of these three effects of TP53 mutant proteins in the initiation and sustained expansion of lung adenocarcinoma (LUAD). We will do this by using novel LUAD mouse models with switchable Trp53 status to trigger tumorigenesis through expression of mutant Trp53 and then conversion of mutant Trp53 either back to wildtype Trp53 or into a Trp53 knock-out state when desired. In vitro and in vivo studies were performed to investigate the immediate and long-term effects of different Trp53 status on tumour growth. Our data thus far show that conversion of mutant Trp53 back to wildtype Trp53 induced cellular senescence and cell cycle arrest in LUAD cells in vitro and substantially delayed tumour progression in vivo, which improved the overall survival of mice. In contrast, conversion of mutant Trp53 into a Trp53 knock-out state did not impair the sustained growth of these tumour cells either in vitro or in vivo. This suggest that the LOF but not GOF of mutant TRP53 is critical to sustain the expansion of lung cancer. These findings have important implications for the design of novel therapeutic approaches for cancers expressing mutant TP53. Citation Format: Tianwei Chen, Elizabeth Lieschke, Leanne Scott, Danielle Boyd, Kate Sutherland, Andreas Strasser, Gemma Kelly. Understanding the Role of Mutant TP53 in Lung Cancer Using Novel Genetically Engineered Mouse Models [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr LT06.
Abstract P37: Establishment of Gastric Organoids Biobank and Its Usage
Authors: Takeshi Hagihara, Kie Kyon Huang, Raghav Sundar, Tomoyuki Uchihara, Clara Shi Ya Ng, Su Ting Tay, Angie Lay Keng Tan, Jimmy Bok Yan So, Patrick Tan
Journal: Cancer Research (2024)

Abstract Gastric cancer is highly heterogeneous. To analyze their biology, patient-derived organoids (PDOs) are useful because they maintain intra-tumor heterogeneity (ITH) as well as inter-patient heterogeneity. Recently, four groups reported the establishment of gastric PDOs. However, it is still not easy because of the need to overcome a common problem: “contamination” of the culture with “non-cancer cell”-derived organoids from the specimen. These non-cancer organoids often overgrow and became dominant. Furthermore, PDOs have another limitation. They contain only epithelial cells and no other types of cells, making it difficult to study the tumor microenvironment (TME). Since October 2021, we have been working on establishing our own gastric PDO biobank. 63 gastric PDOs have been successfully established from 24 patients. Cancer organoids are enriched by manual selection under a microscopy. Our biobank contains 35 gastric cancer PDOs, 16 of which were confirmed as cancer using WES and WTS. Profiling for the remaining PDOs is ongoing. 12 fibroblasts and 26 cancer associated fibroblasts (CAFs) have also been successfully established. To overcome the difficulties of TME research with PDOs, co-culture platform for PDOs and fibroblasts has been established. This co-culture platform can provide new insights into the functions of CAFs, one of the major components of TME. In this poster, I will describe the progress of our gastric PDO biobank establishment and the prospects for my projects using it. Citation Format: Takeshi Hagihara, Kie Kyon Huang, Raghav Sundar, Tomoyuki Uchihara, Clara Shi Ya Ng, Su Ting Tay, Angie Lay Keng Tan, Jimmy Bok Yan So, Patrick Tan. Establishment of Gastric Organoids Biobank and Its Usage [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P37.
Abstract P53: Inhibition of STING/Galectin-9 Axis Sensitize Anthracyclines Treatment And Induce Anti-tumor Immunity
Authors: Xian Sun, Wei-Jan Wang, Jilu Lang, Riyao Yang, Wan-Jou Shen, Linlin Sun, Mien-Chie Hung
Journal: Cancer Research (2024)

Abstract Anthracyclines, are a class of conventional and routinely used firstline chemotherapy drugs to treat breast cancer. Immunogenic cell death (ICD) is characterized by the exposure of danger signals that promote dendritic cell maturation and antigen presentation and is often associated with the induction of cancer cell-intrinsic IFN-I signaling pathway. In addition, among multiple chemotherapeutic drugs such as doxorubicin (Dox) is well-known to promote tumor immunogenicity by interfering with DNA synthesis. Galectin-9 (Gal-9), as a member of β-galactoside-binding protein family, has been demonstrated to induce T cell death and promote immunosuppression in the tumor microenvironment. In addition, it has been shown that some interferon (IFN) and interleukin (IL) factors can induce Gal-9 expression. However, the mechanism cross-talk between anthracyclines and Gal-9 immunecheckpoint inhibitor remains unknown. Here we show that doxorubicin induces PD-L1 expression in human breast cancer cell lines and animal models. Mechanistically, doxorubicin promoted IFNβ expression, which in turn enhanced doxorubicin-induced Gal-9. Furthermore, we discovered that doxorubicin induces tumor Gal-9 via STING upregulation. The combination of doxorubicin and anti-Gal-9 therapy compared with each agent alone significantly increased the therapeutic efficacy in vivo. Clinically, a higher Gal-9 and p-STING level in the tumor region of after-treatment anthracyclines as compared to before treatment is indicated in breast cancer tumor tissue. Taken together, our study demonstrates crosstalk between anthracyclines-induced ICD and tumor-associated immunosuppression and provides a novel therapeutic strategy by combining anthracyclines and Gal-9 antibody in breast cancer. Citation Format: Xian Sun, Wei-Jan Wang, Jilu Lang, Riyao Yang, Wan-Jou Shen, Linlin Sun, Mien-Chie Hung. Inhibition of STING/Galectin-9 Axis Sensitize Anthracyclines Treatment And Induce Anti-tumor Immunity [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P53.
Abstract P09: AN EX-VIVO COMBINATION DRUG SENSITIVITY PLATFORM FOR PREDICTING SENSITIVITY TO FLT3 INHIBITOR-BASED COMBINATION IN ACUTE MYELOID LEUKEMIA
Authors: Noor Rashidha Bte Meera Sahib, Jen Wei Ying, Melissa Ooi, Yen Lin Chee, None Jayalakshmi, Jameelah Bte Sheik Mohamed, Masturah Rashid, Edward KH Chow
Journal: Cancer Research (2024)

Abstract FMS-like tyrosine kinase-3 (FLT3) mutations are often linked with poor prognosis in Acute myeloid leukemia (AML). Despite increasing availability of targeted therapy, such as FLT3 inhibitors (FLT3i), remission is often short-term and followed by relapse and drug resistance. With varying response rates to standard treatments, the need to understand the molecular mechanisms driving drug resistance and accurately predict responses to treatment is crucial. Here, we present the ability of Quadratic phenotypic optimization platform (QPOP), in accurately identifying potential responders to possible combination therapies in AML. AML cell lines and AML patient samples were treated with a set panel of drugs including FLT3i. QPOP drug combination scores and ranking were derived from cell viability response following treatment. 40 patients were recruited for the study, of which 20 patients were evaluated for their clinical concordance. RNA sequencing and molecular analysis was further conducted to determine the accuracy of QPOP predicted response and to determine mechanism of resistance to FLT3i. QPOP predicted response was concordant to patient treatment outcome with 80% sensitivity and specificity. QPOP analysis on AML cell lines accurately identified responders to FLT3i including the differential response between a FLT3- ITD isogenic parental and FLT3i resistant cell line. Serial QPOP analysis in a FLT3 mutant patient sample indicated a decrease in FLT3i sensitivity concordant with an increasing FLT3 allelic burden and the development of resistance. The development of resistance to FLT3i based combinations was correlated to an increase in phosphorylated AKT expression. Activation of AKT is associated with the upregulation of Forkhead box M1 (FoxM1) in the resistant cell line. Co-treatment with an AKT inhibitor restored sensitivity to FLT3i treatment in the resistant cells. We demonstrate that QPOP analysis accurately predicts sensitivity to drug-combinations and can be used as a tool to identify sensitivity to FLT3i-based combination therapy in AML. Citation Format: Noor Rashidha Bte Meera Sahib, Jen Wei Ying, Melissa Ooi, Yen Lin Chee, Jayalakshmi, Jameelah Bte Sheik Mohamed, Masturah Rashid, Edward KH Chow. AN EX-VIVO COMBINATION DRUG SENSITIVITY PLATFORM FOR PREDICTING SENSITIVITY TO FLT3 INHIBITOR-BASED COMBINATION IN ACUTE MYELOID LEUKEMIA [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P09.
Abstract P41: <i>Ex vivo</i> Drug Testing Identifies a Novel Drug Pair in Targeting STS
Authors: Sharon Pei Yi Chan, Wai Yee Wong, Nur Nadiah Ismail, Baiwen Luo, Benjamin Jieming Chen, Brandon Xuan Ming Phua, Xing Yi Woo, Tan Boon Toh, Edward Kai-Hua Chow, Valerie Shiwen Yang
Journal: Cancer Research (2024)

Abstract Soft tissue sarcomas (STS) are a highly heterogeneous collection of tumors that arise from primitive mesenchymal cells. Due to a reliance on cytotoxic chemotherapy as standard of care, survival outcomes for advanced STS patients remain poor. While efforts to understand sarcomagenesis have revealed potential biomarkers, the diversity of STS subtypes and interpatient tumour heterogeneity has led to the lack of effective molecular targeted therapies available. Given the uniquely individualized nature of STS, we hypothesize that the application of an experimental-analytics method, Quadratic Phenotypic Optimization Platform (QPOP), towards primary STS patient samples can improve identification of patient-specific drug combinations. Across a total of 45 patient samples collected, QPOP identified a novel drug pair as most frequently top-ranked, outperforming standard of care ifosfamide and doxorubicin. Interestingly, analysis of QPOP ranking trends revealed this combination to be broadly effective, implying common targetable pathways independent of STS subtype. Single-drug and combination dose-response assays performed in a panel of established patient lines supported its synergistic interaction, accompanied by increased PARP and caspase-3 cleavage with immunoblotting, and increased apoptotic response with Annexin V assay. Mechanistically, this synergy results in cell cycle arrest and induction of programmed cell death pathways, as revealed by molecular profiling on representative patient and cell lines. We further showed that co-treatment synergistically repressed oncogenic MYC and activated the p27kip1 tumor suppressor. Finally, this combination was more effective at impairing tumor progression than single agents alone in an STS xenograft mouse model. Overall, work here provides preliminary clinical evidence for the prioritization of a novel drug pair in addressing STS beyond known clinicopathologic parameters. Citation Format: Sharon Pei Yi Chan, Wai Yee Wong, Nur Nadiah Ismail, Baiwen Luo, Benjamin Jieming Chen, Brandon Xuan Ming Phua, Xing Yi Woo, Tan Boon Toh, Edward Kai-Hua Chow, Valerie Shiwen Yang. Ex vivo Drug Testing Identifies a Novel Drug Pair in Targeting STS [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P41.
Abstract P30: MUTATIONAL SIGNATURE ASSIGNMENT HETEROGENEITY IS WIDESPREAD AND CAN BE ADDRESSED BY ENSEMBLE APPROACHES
Authors: Wu Jialun Andy, Akila Perera, Linganesan Kularatnarajah, Anna Korsakova, Jason James Pitt
Journal: Cancer Research (2024)

Abstract Single base substitution (SBS) mutational signatures have become standard practice in cancer genomics. In lieu of de novo signature extraction, reference signature assignment allows users to estimate the activities of pre-established SBS signatures within individual malignancies. Several tools have been developed for this purpose, each with differing methodologies. However, due to a lack of standardization, there may be inter-tool variability in signature assignment. We deeply characterized three assignment strategies and five SBS signature assignment tools. We observed that assignment strategy choice can significantly influence results and interpretations. Despite varying recommendations by tools, Refit performed best by reducing overfitting and maximizing reconstruction of the original mutational spectra. Even after uniform application of Refit, tools varied remarkably in signature assignments both qualitatively (Jaccard Index = 0.38 – 0.83) and quantitatively (Kendall tau-b = 0.18 – 0.76). This phenomenon was exacerbated for “flat” signatures such as the homologous-recombination repair deficiency (HRD) signature SBS3. An ensemble approach (EnsembleFit), which leverages output from all five tools, increased SBS3 assignment accuracy in BRCA1/2-deficient breast carcinomas. After generating synthetic mutational profiles for thousands of pan-cancer tumors, EnsembleFit reduced signature activity assignment error 15.9 – 24.7% on average using COSMIC and non-standard reference signature sets. We have also released the EnsembleFit web portal (https://www.ensemblefit.pittlabgenomics.com) for users to generate or download ensemble-based SBS signature assignments using any strategy and combination of tools. Overall, we show that signature assignment heterogeneity across tools and strategies is non-negligible and propose a viable, ensemble solution. Citation Format: Wu Jialun Andy, Akila Perera, Linganesan Kularatnarajah, Anna Korsakova, Jason James Pitt. MUTATIONAL SIGNATURE ASSIGNMENT HETEROGENEITY IS WIDESPREAD AND CAN BE ADDRESSED BY ENSEMBLE APPROACHES [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P30.
Abstract P20: Unveiling the Influence of Tumor Microenvironment and Spatial Heterogeneity on Temozolomide Resistance in Glioblastoma using an Advanced Human <i>in vitro</i> Model of the Blood-brain Barrier and Glioblastoma
Authors: Maxine SY Lam, Joey JY Aw, Damien Tan, Ragavi Vijayakumar, Hui Yi Grace Lim, Swathi Yada, Qing You Pang, Nick Barker, Carol Tang, Beng Ti Ang, Radoslaw M. Sobota, Andrea Pavesi
Journal: Cancer Research (2024)

Abstract Glioblastoma (GBM) is the most common primary malignant brain cancer in adults, with a dismal prognosis of 15 months. This is despite decades of research and improvements in surgery and radiotherapy. Temozolomide (TMZ) is the only first-in-line chemotherapeutic; however, resistance is frequent and multifactorial. While many molecular and genetic factors have been linked to TMZ resistance, the role of the solid tumor morphology and the tumor microenvironment (TME), particularly the blood-brain barrier (BBB), is unknown. Complex 3D in vitro models are able to recapitulate aspects of clinical disease such as the tumor microenvironment, such that research into the role of the TME and how it affects tumor biology and therapy resistance can be studied more easily and accurately. We have developed a complex 3D in vitro model for GBM and its surrounding BBB, that recapitulates important clinical features such as a dense tumor core with tumor cells that invade along the perivascular space; and a perfusable BBB with a physiological permeability with morphology that is altered in the presence of a tumor spheroid. We demonstrate that TMZ sensitivity decreases with increasing cancer cell spatial organization, and that the BBB can contribute to TMZ resistance. Proteomic analysis of cultured microtissues using low volume sample workflows revealed proteins linked to aggressive tumors and TMZ resistance. Notably, proteomic analysis revealed a potential role for cell cycle proteins in TMZ resistance. Preliminary data with tumor spheroids formed by patient derived GBM progenitor cells revealed a similar trend of an increase in proteins associated with tumor aggressiveness upon co-culture with a BBB. The data demonstrate the utility of combining complex physiological in vitro models and next generation mass spectrometry for interrogating the tumour microenvironment, tumor biology and accurate in vitro therapy validation. Citation Format: Maxine SY Lam, Joey JY Aw, Damien Tan, Ragavi Vijayakumar, Hui Yi Grace Lim, Swathi Yada, Qing You Pang, Nick Barker, Carol Tang, Beng Ti Ang, Radoslaw M. Sobota, Andrea Pavesi. Unveiling the Influence of Tumor Microenvironment and Spatial Heterogeneity on Temozolomide Resistance in Glioblastoma using an Advanced Human in vitro Model of the Blood-brain Barrier and Glioblastoma [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P20.
Abstract P07: Extracellular Vesicles Secreted from Daratumumab Resistant Cells Promote Resistance and Proliferation of Daratumumab Sensitive cells, possibly Through the Transfer of miRNA Cargo
Authors: Muhamad Irfan Bin Azaman, Wee Joo Chng, Sanjay de Mel, Nurulhuda Mustafa
Journal: Cancer Research (2024)

Abstract Daratumumab (dara) is an anti-CD38 monoclonal antibody used for Multiple Myeloma (MM) treatment, but responses are heterogeneous, and resistance is inevitable. We established three dara resistant (dara R) cell lines in Natural Killer T-cell Lymphoma (NKTL), T-cell acute lymphoblastic leukaemia (T-ALL) and MM via long-term exposure to increasing concentrations of dara. We have previously demonstrated that the exosome biogenesis pathway plays a significant role in the survival of dara R cell lines. Coculture of dara sensitive (dara S) cell lines with dara R cell lines separated by a cell-impermeable transwell insert promoted cell proliferation and reduced response to dara treatment in dara S cell lines thereby suggesting a potential role for extracellular vesicles (EVs) in mediating these responses. To assess the specific role of EVs, we isolated dara R EVs and added it to the culture of dara S cells. We observed that uptake of dara R EVs directly promote proliferation and reduced cytotoxic response to dara treatment in dara S cells. In this study, we seek to investigate the role of EVs secreted by dara R cells, in particular, that of EV-derived miRNAs. Exosomal miRNAs are known to play a role in regulating cellular pathways driving cancer cell resistance and survival. To evaluate the potential role of EV-derived miRNA cargo, we performed miRNA sequencing of EVs isolated from the plasma fraction of bone marrow samples obtained from MM patients. We found that the EVs from patients with a progression free survival (PFS) of less than 2 years after dara based therapy had an enrichment of mir-155 and mir-181a as compared to those with a PFS longer than 2 years. These data align with our findings in the cell lines and suggest that these miRNAs may be utilised as potential biomarkers for daratumumab resistance. Citation Format: Muhamad Irfan Bin Azaman, Wee Joo Chng, Sanjay de Mel, Nurulhuda Mustafa. Extracellular Vesicles Secreted from Daratumumab Resistant Cells Promote Resistance and Proliferation of Daratumumab Sensitive cells, possibly Through the Transfer of miRNA Cargo [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P07.