tbuckley/cabot-search huggingface dataset:
Abstract 4452: The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle
Authors: Ambroise Manceau, Koen M. Galenkamp, Cheska M. Galapate, Cosimo Commisso
Journal: Cancer Research (2024)

Abstract As an integral aspect of the metabolic reprogramming that occurs in cancer, oncogenic KRAS mutations drive the stimulation of macropinocytosis, a type of endocytosis that mediates nonselective fluid-phase uptake. Using KRAS-driven models of pancreatic ductal adenocarcinoma (PDAC), we were the first to demonstrate that macropinocytosis functions in tumor cells as a nutrient acquisition pathway. Macropinocytosis triggers the internalization of extracellular proteins via discrete endocytic vesicles called macropinosomes. The incoming protein cargo is targeted for lysosome-dependent degradation, causing the intracellular release of amino acids. These protein-derived amino acids support metabolic fitness by contributing to the intracellular amino acid pools, as well as to the biosynthesis of central carbon metabolites. In this way, macropinocytosis represents a novel amino acid supply route that tumor cells use to survive the nutrient-poor conditions of the tumor microenvironment. While the tenets of the signal transduction events that drive macropinocytosis in cancer have emerged, a detailed picture of the macropinosome itself is not yet available. With the aid of nanotechnology, we have developed a methodology to isolate a pure fraction of macropinosomes from PDAC cells. Using a large-scale proteomic approach, we have been able to generate a list of proteins that reside in macropinosomes. The specificity of this approach was confirmed through the identification and validation of proteins known to specifically localize to these organelles in different contexts, such as Rab5 or SDC1. Thanks to this innovative method, we have demonstrated the involvement of two calcium channels, ATP2B1 and ATP2B4, in the formation of macropinosomes. By elucidating the molecular anatomy of KRAS-driven macropinosomes, we will gain further insight into the regulation and function of macropinocytosis in cancer. Moreover, having a clearer picture of the macropinosome will make us better positioned to exploit this pathway therapeutically and deliver breakthroughs to patients. Citation Format: Ambroise Manceau, Koen M. Galenkamp, Cheska M. Galapate, Cosimo Commisso. The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle [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 4452.
Abstract 3146: HRA00130-C004, a novel anti-DLL3 ADC with bystander effect, high DAR and favorable safety profiles
Authors: Qingqing Yao, Changding Xue, Zhibin Xu, Lingfeng You, Zhendong Xue, Yuchang Mao, Sophie Lin, Jun Feng, Zhe Zhang, Xin Ye, Min Hu, Feng He
Journal: Cancer Research (2024)

Abstract Small Cell Lung Cancer (SCLC) is a highly aggressive neuroendocrine tumor, accounting for ~15% of all new lung cancer cases1. It is estimated that there are 250,000 new SCLC cases and at least 200,000 deaths globally each year2. SCLC exhibits high recurrence after first-line treatment, poor response to subsequent therapies, and rare survival3. Lacking of recommended treatments for prolonging survival remains a problem over decades4. DLL3 is an inhibitory ligand of the Notch receptor. It binds to its Notch receptor through a cis-interaction, thus, mediates inhibition of Notch pathway to facilitate neuroendocrine tumorigenesis5. DLL3 is highly upregulated and aberrantly expressed on the cell surface in SCLC and other high-grade neuroendocrine tumors with limited expression in normal tissues6.Here we presented a DLL3-directed ADC, HRA00130-C004, which features a differentiated topoisomerase I inhibitor payload DXh conjugated via a cleavable linker to a humanized IgG1 antibody. HRA00130-C004 strongly inhibited the proliferation of cell lines with different DLL3 expression. In the bystander killing assays, HRA00130-C004 was able to kill both DMS53 cells (DLL3 over-expressed) and U-2OS (DLL3-negative) cells when they are co-cultured. The in vivo treatment of HRA00130-C004 resulted in a dramatic and sustained inhibition of tumor growth in H1184 (DLL3 high) and DMS53 (DLL3 low) xenograft models. No obvious weight loss was observed during the experiment. Furthermore, HRA00130-C004 demonstrated a favorable PK profile and satisfactory molecular integrity in rats with 3mg/kg dosing and cynomolgus monkeys with 10 mg/kg dosing. The exposure of total antibody and intact ADC was consistent. Moreover, HRA00130-C004 was well tolerated in rats and cynomolgus monkeys with no related adverse findings, which indicated its favorable safety profiles. In summary, taking advantage of Hengrui’s DXh platform, HRA00130-C004 has demonstrated great potency and good safety profiles. These data support the future clinical development of HRA00130-C004. 1.CA Cancer J. Clin., 2018, 68, 7; 2.J. Natl. Compr. Cancer Netw. 2018, 16, 1171; 3.Mol. Ther. Oncolytics, 2021, 20, 470; 4.Journal of Cancer, 2022, 13, 2945; 5.Cellular Oncology, 2019, 42, 261; 6.Journal of Hematology and Oncology 2019, 12, 61; Citation Format: Qingqing Yao, Changding Xue, Zhibin Xu, Lingfeng You, Zhendong Xue, Yuchang Mao, Sophie Lin, Jun Feng, Zhe Zhang, Xin Ye, Min Hu, Feng He. HRA00130-C004, a novel anti-DLL3 ADC with bystander effect, high DAR and favorable safety profiles [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 3146.
Abstract 7418: LongFuse: Detecting gene fusion transcripts from high throughput long-read single cell RNA sequencing data
Authors: Cheng-Kai Shiau, Yueying He, Hsiao-Yun Lin, Lina Lu, Xiao-Dong Lu, Jindan Yu, Ruli Gao
Journal: Cancer Research (2024)

Abstract Gene fusion resulted from genomic translocation plays important oncogenic roles including but not limited to gene activation and changing protein coding sequences. Historically, fusion gene analysis has been limited to bulk levels resulting in mixed oncogene activation models. Single cell Nanopore RNA sequencing (scNanoRNAseq) has the unique strength in detecting full-length chimeric transcripts in thousands of single cells in parallel. However, robust computational tools for detecting fusion genes in single cells from scNanoRNAseq data are missing. Here, we developed LongFuse, a fast and accurate tool, to detect fusion genes and their splicing isoforms in single cells from scNanoRNAseq data. LongFuse implements an XOR logic gate algorithm to speed up fusion candidate searching and stringent criteria to eliminate false discoveries due to trans-splicing events and randomly ligated chimeras. We applied LongFUSE onto scNanoRNAseq data of both human prostate cancer cell line, VCaP, and tumor tissues with known TMPRSS2-ERG fusion. Our results showed that both cancer cell line and prostate tumors harbored a mixture of fusion positive and fusion negative tumor cells. Gene expression analysis revealed transcriptional differences between fusion positive and negative cells including genes involved in cancer cell proliferation and invasion programs such as ELL2, ZBTB16, IGF1R, ANK3, MYPOP and PLPP1 genes. LongFUSE also calculates the splicing isoforms of fusion gene transcripts, allowing prediction of protein sequences of fusion gene transcripts. Taken together, our data demonstrated that LongFUSE is a robust computational tool for detecting gene fusions and their splicing isoforms at single cell level from scNanoRNAseq data. Citation Format: Cheng-Kai Shiau, Yueying He, Hsiao-Yun Lin, Lina Lu, Xiao-Dong Lu, Jindan Yu, Ruli Gao. LongFuse: Detecting gene fusion transcripts from high throughput long-read single cell RNA sequencing data [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 7418.
Abstract 3857: Tumor-extrinsic BIRC3 promote sensitivity to checkpoint inhibition immunotherapy in breast cancer
Authors: Dejuan Yang, Jiazheng Sun, Guosheng Ren, Hongzhong Li
Journal: Cancer Research (2024)

Abstract Baculoviral IAP repeat containing 3 (BIRC3) protein play a critical role in breast cancer. Blocking BIRC3 cause apoptosis in tumor cells, but its correlation with tumor immunity remains elusive. TCGA databases were employed to examine the expression of BIRC3 in breast cancer. The correlation between BIRC3 expression and T cell infiltration and function was employed in breast cancer tissues (n=92) by immunohistochemistry. Birinapant, a selective BIRC3 inhibitor, was then used to investigate the effect of BIRC3 blockade on tumor immune microenvironment (TIME) landscape of breast cancer syngeneic mouse models by flow cytometry. Survival analysis suggested that the low expression of BIRC3 was associated with poor overall survival (OS). Additionally, we uncovered the close association between BIRC3 expression and the profiles of immune cells in breast cancer microenvironment based on the TCGA dataset. Interestingly, we found that BIRC3 expression was positively correlated with cytotoxic T lymphocyte infiltration and T-cell effector function by immunohistochemistry. The in vivo experiments suggested that blocking BIRC3 might convert ‘hot’ tumor into ‘cold’ tumor, which was characterized by a decreased of CD8+ T cell infiltration and inhibition of CD8+T cell function. Furthermore, we observed that BIRC3 blocking combined with immune checkpoint blockade therapy (ICT) greatly restrains immunotherapy efficacy of breast cancer model. Our study revealed a positively association between BIRC3 and anti-tumor immune landscape in breast cancer. Notably, we established a validated prognosis model based on BIRC3 and BIRC3 associated immunomodulators in breast cancer. Citation Format: Dejuan Yang, Jiazheng Sun, Guosheng Ren, Hongzhong Li. Tumor-extrinsic BIRC3 promote sensitivity to checkpoint inhibition immunotherapy in breast 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 3857.
Abstract 5807: Bicycle Toxin Conjugates®for the treatment of solid tumors
Authors: Stephen J. Walsh, Johanna Lahdenranta, Philip Huxley, Gemma Mudd, Gavin Bennett, Amy Brown, Katerine an Rietschoten, Liuhong Chen, Heather Scott, Gabriella Ivanova-Berndt, Katarzyna Dzionek, Mike Rigby, Olga Burenkova, Phil Jeffrey, Paul Beswick, Michael Skynner, Nicholas Keen
Journal: Cancer Research (2024)

Abstract Bicycle Therapeutics is developing a unique class of chemically synthesized medicines. Based on its proprietary bicycle peptide (Bicycle®) phage display platform, Bicycles are a unique class of highly constrained peptides, which have demonstrated utility in the targeted delivery of different classes of payloads (for example cytotoxic agents, radioisotopes, immune modulators) into tumors. Bicycles are currently being explored in the clinic as Bicycle Toxin Conjugates® (BTCs) for targeted delivery of cytotoxic payloads into tumors. BTCs consist of a bicyclic peptide that is conjugated to a cytotoxic payload via a cleavable linker, which allows payload release in the tumor microenvironment or within the tumor cell. BTCs were developed to address the shortcomings of antibody drug conjugates (ADCs) in several ways. First, the small size of BTCs (∼4 kDa) compared to large biologic entities such as monoclonal antibody (mAb)-based conjugates (∼150 kDa) allows rapid distribution to tissues and extensive tumor penetration, which enables rapid delivery of payload into the tumor. Second, the peptidic nature of BTCs results in relatively short, yet tunable, duration of systemic exposure and liver-sparing renal elimination. These properties limit the body’s exposure to payload and should therefore minimize damage to normal tissue. In this body of work, we used in vitro cytotoxicity and cell uptake assays and mouse and rat cell line derived xenograft models for 1) cytotoxicity and anti-tumor activity evaluation, and 2) Bicycle and toxin uptake and biodistribution evaluation. Here, we show that BTCs targeting a number of different tumor antigens can deliver toxins to tumor tissue producing durable responses in a range of preclinical in vivo models, spanning several solid tumor indications. Citation Format: Stephen J. Walsh, Johanna Lahdenranta, Philip Huxley, Gemma Mudd, Gavin Bennett, Amy Brown, Katerine an Rietschoten, Liuhong Chen, Heather Scott, Gabriella Ivanova-Berndt, Katarzyna Dzionek, Mike Rigby, Olga Burenkova, Phil Jeffrey, Paul Beswick, Michael Skynner, Nicholas Keen. Bicycle Toxin Conjugates®for the treatment of solid 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 5807.
Abstract 5859: PLK1 predicts aggressive behavior in CRC patients and its inhibition reverse chemoresistance in CRC cells
Authors: Divya Padmaja, Maha Al-Rasheed, Pratheesh Kumar Poyil, Abdul K. Siraj, Sandeep Kumar Parvathareddy, Wael Haqawi, Fouad Al-Dayel, Khawla S. Al-Kuraya
Journal: Cancer Research (2024)

Abstract Polo-like kinase 1 (PLK1) is a serine/threonine-protein kinase, that is involved in multiple stages of cell cycle progression in mammals. Dysregulation of PLK1 has been found in a variety of human cancers and was associated with poor prognoses in various cancers. However, its role in the pathogenesis of CRC from Middle Eastern ethnicity has not yet been explored. Therefore, we examined the expression of PLK1 protein in a large cohort of over 1000 Middle Eastern CRC cases by immunohistochemistry. Correlation with clinico-pathological parameters were performed. PLK1 overexpression was noted in 60.3% (693/1149) CRC cases and was significantly associated with larger tumor size (T3/T4 tumors), lymphnode metastasis, Stage III tumors, MSI-H status and p-ERK1/2 over-expression. Interestingly, on multivariate logistic regression analysis, we found that PLK1 was an independent predictor of lymphnode metastasis. However, no association was noted between PLK1 expression and clinical outcomes (DFS, RFS, OS, CSS). Our in vitro experimentation revealed that CRC cells expressing high levels of PLK1 exhibited resistance to 5-Fu treatment, whereas cells with low PLK1 expression demonstrated sensitivity to the treatment. To explore the role of PLK1 on chemoresistance, we inhibited PLK1 using specific inhibitor, volasertib and we showed that volasertib effectively reversed 5-Fu resistance in these cells. Furthermore, knockdown of PLK1 reduced the progression of epithelial-to-mesenchymal transition (EMT) and the stem cell-like properties in 5-Fu resistant cells, showing the role of PLK1 on inducing EMT and stemness in CRC. Interestingly, the forced expression of PLK1 triggered the activation of the CRAF-MEK-ERK-ZEB1 signaling cascade, whereas its inhibition led to the suppression of this cascade. In addition, we showed that silencing of ERK1/2 reversed the chemoresistance, EMT and stemness of PLK1 expressing CRC cell lines. Our findings underscore the significant role of PLK1 in conferring chemoresistance, and targeting PLK1 could represent a viable therapeutic approach for the treatment of patients with an aggressive subtype of CRC. Citation Format: Divya Padmaja, Maha Al-Rasheed, Pratheesh Kumar Poyil, Abdul K. Siraj, Sandeep Kumar Parvathareddy, Wael Haqawi, Fouad Al-Dayel, Khawla S. Al-Kuraya. PLK1 predicts aggressive behavior in CRC patients and its inhibition reverse chemoresistance in CRC 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 5859.
Abstract 6892: Murine <i>ex vivo</i> platform: A powerful tool for biomarker assessment and high throughput screening of translationally relevant <i>in vivo</i> tumor models for PD and efficacy studies
Authors: Sunitha Bachawal, Janet Leung, Remie Mandawe, Malia Garza, Kimberly ly, Ofir Stefanson, Jack Lohre, Diba Kamali, Ngan Doan, Benjamin King, Elliot Kim, Ganapathi Hegde, Xiaoyun Liao, Scot Liu, Jeong Kim, Amanda Mikels Vigdal, Anandaroop Mukhopadhyay
Journal: Cancer Research (2024)

Abstract Ex vivo model systems using tumor biopsies from patients are often utilized to develop predictive biomarkers. However, these readouts are often proximal and do not inform on downstream mechanisms (distal pharmacodynamics) and their relationship to anti-tumor efficacy. In vivo murine models represent a powerful tool to bridge this gap. However, selection of an appropriate translationally relevant murine model can often be a time-consuming process given that the complexity of the tumor microenvironment (TME). Additionally, in vivo models are generally not amenable to high throughput screening. Here, we demonstrate that ex vivo mouse tumor platforms can be used for rapid screening of treatment responsive and translationally relevant tumor models. These models can be used to interrogate the impact of a therapeutic on anti-tumor efficacy in a long-term in vivo study, thus allowing for the establishment of biomarker/response relationships in a rational and rapid manner. To operationalize this platform, ex vivo cultures of dissociated tumor cells (DTC) or tumor tissue slices (histoculture) were first optimized for maximum viability and/or preservation of tissue architecture. To allow for high throughput screening, feasibility of freezing DTCs or tumor chunks prior to sectioning was also explored. Finally, both ex vivo tumor cultures and in vivo tumors were treated with a Innate agonist as a proof of concept to demonstrate functional equivalency. In conclusion, this work provides a novel way of screening responsive, translationally relevant murine tumor models in a high throughput and cost-effective manner. These efforts have the potential benefits of saving time and animal usage, while also maximizing the probability of successfully evaluating a therapeutic’s benefit. Citation Format: Sunitha Bachawal, Janet Leung, Remie Mandawe, Malia Garza, Kimberly ly, Ofir Stefanson, Jack Lohre, Diba Kamali, Ngan Doan, Benjamin King, Elliot Kim, Ganapathi Hegde, Xiaoyun Liao, Scot Liu, Jeong Kim, Amanda Mikels Vigdal, Anandaroop Mukhopadhyay. Murine ex vivo platform: A powerful tool for biomarker assessment and high throughput screening of translationally relevant in vivo tumor models for PD and efficacy studies [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 6892.
Abstract 5606: The role of KMT2C in the homologous recombination repair in epithelial ovarian cancer
Authors: Mirielle C. Ma, Z. Ping Lin, Elena S. Ratner
Journal: Cancer Research (2024)

Abstract Background: Epithelial ovarian cancer (EOC) with homologous recombination (HR) deficiency is susceptible to PARP inhibitor therapy due to synthetic lethality. Identification of the patient population for PARP inhibitor therapy is imperative to reduce recurrence of EOC and improve the survival outcomes of patients. Current biomarkers for PARP inhibitor therapy consist of an array of genes involved in the HR repair pathway in EOC, including BRCA1, BRCA2 and PALB2. Through TCGA analysis, we found that the lysine (K)-specific methyltransferase 2C (KMT2C) gene is mutated in 10.3% of all EOC patients and considerably enriched in BRCA1 mutated EOC patients. However, the role of KMT2C in HR repair and PARP inhibitor sensitivity of EOC remains largely undefined. Methods: BRCA2-mutated PEO1 and BRCA2-wild type PEO1-NR cells were transfected with KMT2C siRNA and assayed for KMT2C protein expression by western blotting. DR-GFP (HR) and EJ5-GFP (NHEJ)-SKOV3 cell lines were co-transfected with the ISceI-expressing plasmid pCBA-ISceI and KMT2C siRNA. GFP-positive cells were analyzed by flow cytometry. SKOV3 cells were transfected with KMT2C siRNA and the expression of BRCA2 and Rad51 mRNA was determined using quantitative RT-PCR analysis. Results: siRNA-mediated knockdown of KMT2C resulted in marked down-regulation of KMT2C protein in PEO1 and PEO1-NR cells. KMT2C knockdown caused a significant decrease in ISceI-induced HR activity in DR-GFP-SKOV3 cells (p &amp;lt; 0.05). In contrast, KMT2C knockdown had no effects on ISceI-induced NHEJ activity in EJ5-GFP-SKOV3 cells. As a control, Rad51 knockdown caused complete suppression of HR activity and had no effects on NHEJ activity. Furthermore, quantitative RT-PCR analysis of key HR genes showed that KMT2C knockdown resulted in a moderate but significant down-regulation of BRCA2 (p &amp;lt; 0.05) and Rad51 (p &amp;lt; 0.01) expression in SKOV3 cells. Conclusion: Our results suggest that KMT2C partakes in the HR repair pathway in EOC. However, the contribution of KMT2C to HR activity is not rate-limiting. Based on the known function of KMT2C in histone modification, we speculate that KMT2C serves to positively regulate the transcription of HR genes and therefore promote HR activity. Future investigation into the exact roles of KMT2C in HR repair, etiology of EOC, and diagnostic biomarkers for the PARP inhibitor sensitivity of EOC is warranted. Citation Format: Mirielle C. Ma, Z. Ping Lin, Elena S. Ratner. The role of KMT2C in the homologous recombination repair in epithelial ovarian 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 5606.