tbuckley/cabot-search huggingface dataset:
Abstract P29: GSTT2 AND THE RESPONSE TO BCG IMMUNOTHERAPY
Authors: Mugdha Patwardhan, Kane Toh, Edmund Chiong, Ratha Mahendran
Journal: Cancer Research (2024)

Abstract Whilst M. bovis Bacillus Calmette-Guérin (BCG) therapy remains the gold-standard for treatment of high-risk non-muscle invasive bladder cancer (BC), 30-40% of patients fail therapy, resulting in disease recurrence and progression. A better understanding of the underlying mechanisms of BCG therapy can aid in revealing key response pathways, which may lead to the discovery of new targets, and in turn new approaches to treat BC. The glutathione-S-transferase theta 2 (GSTT2) gene is a member of the GST family. Loss of GSTT2 expression has been associated with modulation of intracellular ROS and BCG survival in BC cell lines. Retrospective analysis of BC patients revealed that patients with the GSTT2B deletion responded better to fewer instillations of BCG. To understand these responses, wild-type (WT) and GSTT2-knockout (KO) mice were implanted with MB49-PSA BC cells, in subcutaneous and orthotopic settings. Once tumors were established, the mice were treated with four weekly BCG instillations, after which the subcutaneous tumors and bladders were harvested for downstream analysis. Single-cell RNA sequencing of whole-bladders was used to identify specific cell clusters within the bladder, and to analyze differential gene expression. Hmga2, Ahnak and Peak1 were found to be differentially expressed in bladders from WT and GSTT2-KO mice. These genes are known to be involved in pro- and anti-tumorigenic pathways such as epithelial-mesenchymal transition and inflammation. Additionally, quantitative real-time PCR analysis in the subcutaneous and orthotopic tumors revealed differences in the expression of immune-related genes, especially markers of immune exhaustion such as PD-L1 and CTLA-4. Flow cytometry analysis of subcutaneous tumors also revealed differences in T-cell infiltration. Thus, loss of GSTT2 may influence the response to BCG therapy, through modulating downstream signaling pathways and immune responses. Elucidating such pathways can lead to a better understanding of the mechanism of BCG and its role as a therapy for BC. Citation Format: Mugdha Patwardhan, Kane Toh, Edmund Chiong, Ratha Mahendran. GSTT2 AND THE RESPONSE TO BCG IMMUNOTHERAPY [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P29.
Abstract P15: Aberrant Non-canonical NF-κB Signalling Reprograms the Epigenome Landscape to Drive Oncogenic Transcriptomes in Multiple Myeloma
Authors: Daniel A. Ang, Jean-Michel Carter, Kamalakshi Deka, Joel H.L. Tan, Jianbiao Zhou, Qingfeng Chen, Wee Joo Chng, Nathan Harmston, Yinghui Li
Journal: Cancer Research (2024)

Abstract Activation of the NF-κB pathway is recognized to be necessary for the survival and progression of haematological cancers including Multiple Myeloma (MM). In particular, recurrent genetic lesions resulting in the chronic induction of non-canonical NF-κB (ncNF-κB) signalling have been exclusively linked to MM. Such mutations among patients are associated with significant proliferative and metastatic advantages and have been causally linked to treatment resistance. How the constitutive activity of ncNF-κB transcription factors can support such adaptations in this common haematological malignancy has been a fundamental question in cancer. In this study, we captured the epigenomic landscape of patient-derived MM cell lines harbouring recurrent NF-κB activating mutations through perturbation of nfkb2/p52 and integrated these cis-regulatory changes with MM patient epigenome data. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a novel p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression. Citation Format: Daniel A. Ang, Jean-Michel Carter, Kamalakshi Deka, Joel H.L. Tan, Jianbiao Zhou, Qingfeng Chen, Wee Joo Chng, Nathan Harmston, Yinghui Li. Aberrant Non-canonical NF-κB Signalling Reprograms the Epigenome Landscape to Drive Oncogenic Transcriptomes in Multiple Myeloma [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P15.
Abstract P45: REDUCED IMMUNOGENICITY DRIVES SUPERIORITY OF THE NANOLUCIFERASE (NLUC) REPORTER IN AN IMMUNOCOMPETENT GL261 MOUSE GLIOMA MODEL
Authors: Carla Bianca Luena Victorio, Wisna Novera, Arun Ganasarajah, Joanne Ong, Peter Li, Sven Hans Petersen, Rasha Msallam, Ann-Marie Chacko
Journal: Cancer Research (2024)

Abstract Bioluminescence imaging (BLI) with luciferase-based reporters is a robust approach for monitoring tumour growth and treatment response in preclinical in vivo cancer models. Luciferases are considered foreign molecules that could elicit immune responses when introduced in immunocompetent live animal models [1, 2]. The immunogenicity of luciferases and other transgenic imaging reporters, though often overlooked, was recently discussed in relation to mouse cancer models [3-5]. Herein, we investigated the immunogenicity of two luciferase reporters: (1) red-shifted firefly luciferase (RFLuc, 61 kDa) and (2) deep-sea shrimp nanoluciferase (nLuc, 19 kDa) in an orthotopic brain tumour model using GL261 mouse glioma cells in a syngeneic C57BL/6J mouse. We evaluated their suitability for monitoring of brain tumour growth kinetics by BLI. Mice were implanted with 2 × 104 either GL261, GL261-NLuc or GL261-RFLuc cells in the right cerebrum using a stereotaxic device. GL261-RFLuc tumours could only be detected by BLI for 2 weeks, and the mice did not die of disease (median overall survival; mOS &amp;gt; 35 days). In contrast, GL261-nLuc cells formed lethal brain tumours that grew in volume as determined by BLI. GL261-NLuc implanted mice exhibited mOS comparable to mice implanted with GL261 cells (24.5 days vs. 23 days). These observations indicated that nLuc is not significantly immunogenic in mouse brains and did not cause rejection of the tumour cells as observed with RFluc. Cytokine expression profiles and immune cell profiles of the tumour-bearing brain hemispheres were comparable between tumours from GL261 and GL261-NLuc. In contrast, GL261-RFLuc tumours exhibited elevated CD8+ T cells, particularly effector (CD62L¯CD44+) and granzyme B-expressing (GZB+) CD8+ T cells. GL261-nLuc formed stable glioma tumors comparable to the original GL261 mouse model and is a suitable in vivo preclinical model for evaluating experimental therapeutic interventions against gliomas, when paired with Promega’s proprietary fluoro-furimazine substrate. Funding: This research was supported by Singapore’s Health and Biomedical Sciences (HBMS) Industry Alignment Fund Pre-Positioning (IAF-PP) grant H18/01/a0/018 (to AMC) administered by A*STAR and Singapore-MIT Alliance for Research and Technology (SMART) Innovation Grant (ING-000913 BIO) (to AMC). Citation Format: Carla Bianca Luena Victorio, Wisna Novera, Arun Ganasarajah, Joanne Ong, Peter Li, Sven Hans Petersen, Rasha Msallam, Ann-Marie Chacko. REDUCED IMMUNOGENICITY DRIVES SUPERIORITY OF THE NANOLUCIFERASE (NLUC) REPORTER IN AN IMMUNOCOMPETENT GL261 MOUSE GLIOMA MODEL [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P45.
Abstract P52: Combination of 5-fluorouracil and Menadione Exerts Synergistic Effect on Colorectal Cancer Cells by Targeting Wnt/β-catenin Signaling Pathway
Authors: Vidya P Warrier, Sankaran Venkatachalam, Sakthivel Ramasamy, M Michael Gromiha, Devarajan Karunagaran
Journal: Cancer Research (2024)

Abstract Colorectal cancer is the third most common type of cancer and the second most in terms of mortality rate worldwide. 5-fluorouracil (5-FU), the fluoropyrimidine drug, that interferes with DNA replication and repair processes, is the first-line-of-treatment against colorectal cancer. However, cells gain resistance over time and relapses occur upon continuous 5-FU therapy. Interestingly, 5-FU promotes stemness in colorectal cancer via Wnt signaling pathway which is critical for its progression. Studies have pointed out the possibility of using a Wnt signaling inhibitor along with 5-FU as a better strategy to overcome the poor outcomes of current 5-FU based therapies. We have previously shown that menadione (vitamin K3) suppresses Wnt signaling pathway in colorectal cancer cells. In the present study, we attempted to evaluate if the combination of menadione and 5-FU can exert a synergistic effect in the human colorectal cancer cell lines HCT116 and SW620. Analysis of the cell viability assay results using CompuSyn software confirmed that the combination indeed acts synergistically. The combination efficiently downregulated the expression of the Wnt signal transducer protein, β-catenin, and the expression of other proteins in the pathway such as phospho-GSK3β in the cell lines HCT116 and SW620. Docking of the individual drugs and their combination on β-catenin using Autodock Vina showed that 5-FU and menadione in combination bind to key protein-protein interaction (PPI) sites of β-catenin whereby they may inhibit β-catenin-TCF interaction or activate the β-catenin destruction complex. Taken together, our data possibly explains that the synergistic action of 5-FU and menadione in colorectal cancer cells may be due to the simultaneous binding of the two drugs to multiple PPI sites thereby blocking the activity of β-catenin. Citation Format: Vidya P Warrier, Sankaran Venkatachalam, Sakthivel Ramasamy, M Michael Gromiha, Devarajan Karunagaran. Combination of 5-fluorouracil and Menadione Exerts Synergistic Effect on Colorectal Cancer Cells by Targeting Wnt/β-catenin Signaling Pathway [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P52.
Abstract P58: Utilizing Cancer Vulnerabilities and Dependencies to Explore Cancer Biomarkers by Triangulating Large-Scale Gene Knockout and Drug Response Data
Authors: Shen Yong Yeo, Wai Yee Wong, None Jesslyn, Tan Boon Toh, Valerie Shiwen Yang, Xing Yi Woo
Journal: Cancer Research (2024)

Abstract The identification of biomarkers of therapeutic response for different cancers presents significant challenges owing to the heterogeneity of these diseases. Whole-genome CRISPR gene knockout screening (DepMap) and large-scale drug dosing (e.g. PRISM, and Sanger GDSC) performed across large panels of cancer cell lines reveal a whole spectrum of cancer vulnerabilities and dependencies that can be used to identify potential biomarkers and perturbed pathways in subtypes of cancers. In this study, we identified tumor type-specific dependent genes with CRISPR screening data. Functional relationships among genes were systematically examined by clustering genes with pronounced dependencies based on established biological pathways and conducting a co-dependency analysis. We found that both tumor type and subtype-specific analysis allowed the classification of cell lines based on gene dependency. Next, we correlated gene dependency of the selected dependent genes with normalised drug sensitivity scores (AUC) to triangulate potential biomarkers of drug response. We first applied this method to several tumor types which are well-characterised by known cancer drivers, and successfully identified known biomarkers and targeted pathways. However, we also identified previously unknown gene-drug relationships which will be further explored. Subsequent analysis of rarer cancers, including soft tissue sarcoma, yielded promising gene targets. This analysis pipeline can be used extensively to mine DepMap data using any subset of cell lines of interest for biomarker discovery. Citation Format: Shen Yong Yeo, Wai Yee Wong, Jesslyn, Tan Boon Toh, Valerie Shiwen Yang, Xing Yi Woo. Utilizing Cancer Vulnerabilities and Dependencies to Explore Cancer Biomarkers by Triangulating Large-Scale Gene Knockout and Drug Response Data [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P58.
Abstract LT07: Signalling Inhibition by Ponatinib Disrupts Productive Alternative Lengthening of Telomeres (ALT)
Authors: Frances Kusuma, Aishvaryaa Prabhu, Galen Tieo, Syed Moiz Ahmad, Pushkar Dakle, Wai Khang Yong, Elina Pathak, Vikas Madan, Yan Yi Jiang, Wai Leong Tam, Dennis Kappei, Peter Dröge, H. Phillip Koeffler, Maya Jeitany
Journal: Cancer Research (2024)

Abstract Enabling replicative immortality is one prominent feature of cancer cells. To that end, cancer cells activate means to elongate their telomeres. While 85% of cancers re-express telomerase, around 15% of all cancers rely on the ALT (Alternative Lengthening of Telomeres) mechanism. Despite its frequency, no clinically approved ALT-targeted therapy exists to date. By performing anti-cancer compound library screen on isogenic cell lines and using extrachromosomal telomeric C-circles, as a bona fide marker of ALT activity, we identified a receptor tyrosine kinase inhibitor, ponatinib, that deregulates ALT mechanisms, induces telomeric dysfunction, reduced ALT- associated telomere synthesis, and targets, in vivo, ALT-positive cells. By scrutinizing the mode of action of ponatinib on ALT, we identified an ABL1-JNK-JUN signalling circuit to be inhibited by ponatinib and to have a role in suppressing extrachromosomal telomeric C-circle formation. Furthermore, transcriptome and interactome analyses of JUN suggested a role of JUN in DNA damage repair pathways, independently of its capacity as a transcription factor. These results were corroborated by new synergistic drug interactions between ponatinib and either DNA synthesis or repair inhibitors such as triciribine and KU-60019, respectively. Overall, we identified a novel signalling pathway impacting ALT which can be targeted by a clinically approved kinase inhibitor. Citation Format: Frances Kusuma, Aishvaryaa Prabhu, Galen Tieo, Syed Moiz Ahmad, Pushkar Dakle, Wai Khang Yong, Elina Pathak, Vikas Madan, Yan Yi Jiang, Wai Leong Tam, Dennis Kappei, Peter Dröge, H. Phillip Koeffler, Maya Jeitany. Signalling Inhibition by Ponatinib Disrupts Productive Alternative Lengthening of Telomeres (ALT) [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr LT07.
Abstract P23: Mitochondrial Delivery of Functional Nucleic Acids for Targeting of Mitochondrial Dysfunction
Authors: Jinglin Ruan, Volker Patzel
Journal: Cancer Research (2024)

Abstract Mitochondria is the main power supply for cellular activity and a key player for the regulation of cellular metabolism, and they contain their own DNA. Critical proteins for mitochondrial functions are not only encoded by nuclear DNA (nDNA) but also by mitochondrial DNA (mtDNA). Abnormalities in mitochondrial functions could lead to diseases including neurodegeneration, diabetes, and cancer progression. The ability for a non-coding RNA (β2.7) of human cytomegalovirus (CMV) to localize to the host mitochondria revealed its potential to be used as a tool for mitochondria gene targeting. Using computational methods, our lab identified four thermodynamically conserved structural subdomains (D1 to D4) within the β2.7 RNA. While all four domains exhibited mitochondrial uptake potential, sub-domain D3 exhibited the highest absolute mitochondrial targeting activity and sub-domain D2 the highest activity per nucleotide. Further modifications on different sub-domain alignments found that maximum uptake efficiency was achieved by tandem repeats of 4 copies of D3 domains followed by 4 copies of D2 domains (abbreviated as D3 × 4_D2 × 4). Delivery of a GFP-coding mRNA or antisense RNA targeting mitochondrial genes mt-ATP6 and mt-ATP8 both confirmed its ability to co-deliver functional RNA into mitochondria. To cleave and destroy mutated mitochondrial genomes for future gene therapeutic applications, we explore mitochondrial delivery of the CRISPR-Cas9 system. The mRNAs coding for the wild-type Cas9 as well as more specific Cas9 variants were fused to the mitochondrial delivery vector (D3 × 4_D2 × 4). Latest RT-qPCR on mitochondrial RNA showed delivery of Cas9 mRNA into mitochondria of HepG2 cells. Currently, we investigate co-delivery of single-guide RNA and quantify Cas9 expression in mitochondria. In an alternative approach we deliver sequences coding for functional mitochondrial protein. Examples are the mRNAs coding for mitochondrial proteins mt-ND1, -ND4 or -ND6 which are frequently mutated is patients with Leber’s hereditary optic neuropathy (LHON). Citation Format: Jinglin Ruan, Volker Patzel. Mitochondrial Delivery of Functional Nucleic Acids for Targeting of Mitochondrial Dysfunction [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P23.
Abstract P70: HIGH-THROUGHPUT IMAGING-BASED PHENOTYPIC PROFILING OF IMMUNE CELLS FROM <i>BRCA2</i> VARIANT CARRIERS AND NON-CARRIERS
Authors: Guorui Zhong, Oscar Fu, Claresta Yeo, Siao Ting Chong, Sock Hoai Chan, Joanne Ngeow, Lit-Hsin Loo
Journal: Cancer Research (2024)

Abstract Mutated germline alleles in the DNA damage repair (DDR) genes BRCA1/2 are major risk factors for breast and ovarian cancers. Recent studies have found that BRCA1-mutant tumors tend to have higher abundance of immune cells within the tumor microenvironment, but much better response was observed from the BRCA2-mutant tumors when given immune-checkpoint inhibitors, suggesting possible functional and phenotypic effects of germline BRCA2 mutations on the immune cells. However, most existing studies focus on investigating the genomic instability and phenotypes of hereditary mutations in breast and ovarian cancer cells. Thus, the impact of these mutations on immune cells’ phenotypes and functions remains largely unknown. Here, we report a study of immune cells with and without BRCA2 mutations using High-throughput Imaging-based Phenotypic Profiling (HIPP), which can identify changes in cellular morphology and protein subcellular localization patterns that are not obvious from other traditional functional assays. We performed HIPP on immune cells from nine BRCA2 pathogenic variant carriers and eight non-carriers. Automatic quantification of ~200 phenotypic features from each single cell revealed that CD8+ T cells from BRCA2 variant carriers have distinct and quantifiable changes in their morphological features (such as cytoskeleton structures) and immunological features (such as Granzyme B expressions). Moreover, we found that BRCA2-mutant CD8+ T cells proliferate faster than normal CD8+ T cells. Our results suggest that BRCA2 mutations affect the functions and phenotypes of immune cells. Some of these phenotypic features and markers may be used to classify BRCA2 variants and predict the pathogenicity of variants of uncertain significance (VUS). Our study provides new insight into the immune phenotyping of cancer patients at individual level and may help to stratify patients, leading to the development of more effective therapeutic strategies. This method can potentially extend to other germline variants and overcome the challenge of VUS interpretation in clinical management. Citation Format: Guorui Zhong, Oscar Fu, Claresta Yeo, Siao Ting Chong, Sock Hoai Chan, Joanne Ngeow, Lit-Hsin Loo. HIGH-THROUGHPUT IMAGING-BASED PHENOTYPIC PROFILING OF IMMUNE CELLS FROM BRCA2 VARIANT CARRIERS AND NON-CARRIERS [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P70.
Abstract P46: Small Extracellular Vesicles from Therapy-induced Senescent TNBC Elicit Paracrine Anti-tumour Effects
Authors: Matius Robert, Rekha Jakhar, Bijin Veonice Au, Gracie Wee Ling Eng, Alvin Kunyao Gao, You Heng Chuah, Karishma Sachaphibulkij, Lina Hsiu Kim Lim, Derrick Sek Tong Ong, Elaine Hsuen Lim, Yoko Itahana, Koji Itahana, Jit Kong Cheong, John Edward Connolly, Karen Carmelina Crasta
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancers (TNBC), associated with poor prognosis and high tumour recurrence, are often treated with taxanes. However, cells may bypass treatment-induced cell death via mitotic slippage, resulting in multinucleated polyploid cells and therapy-induced senescence (TIS). TIS cancer cells represent a population of residual disease and may modulate therapy resistance and recurrence through secretion of the senescence-associated secretory phenotype (SASP). While SASP have been heavily linked with pro-tumorigenic behaviour mediated through soluble cytokines, small extracellular vesicles (sEVs) derived from TIS cancer cells represent an underappreciated aspect of the senescent tumour secretome, as its mechanistic role in mediating paracrine effects remains poorly understood. In this study, we uncovered an unexpected role for TIS-derived sEVs within the secretome, which conferred paracrine anti-tumour activity in recipient TNBC cancer cells, in contrast to SASP that support pro-tumorigenic behaviour. SEVs profiling through mass-spectrometry revealed that DKK1, a negative regulator of WNT signalling, is enriched in TIS-derived sEVs. Further investigation into the tumour microenvironment with animal models and neoadjuvant chemo-treated patient samples revealed STING-dependent immune response. Hence, our study suggests that sEVs should be considered as distinct SASP entities within the senescent tumour secretome and provide an additional basis for combinatorial use of senomorphics with taxanes to potentially modulate senescence-associated sEVs while suppressing pro-tumorigenic SASP factors. Citation Format: Matius Robert, Rekha Jakhar, Bijin Veonice Au, Gracie Wee Ling Eng, Alvin Kunyao Gao, You Heng Chuah, Karishma Sachaphibulkij, Lina Hsiu Kim Lim, Derrick Sek Tong Ong, Elaine Hsuen Lim, Yoko Itahana, Koji Itahana, Jit Kong Cheong, John Edward Connolly, Karen Carmelina Crasta. Small Extracellular Vesicles from Therapy-induced Senescent TNBC Elicit Paracrine Anti-tumour Effects [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P46.