tbuckley/cabot-search huggingface dataset:
Abstract 2770: A novel MIRO2/MYO9B/RhoA signaling axis controls tumor cell invasion and metastasis
Authors: Dillon P. Boulton, Connor J. Hughes, Valentina Vaira, Ajita Jindal, Masoom Raza, Stephen Connor Purdy, Shilpa Sant, Heide L. Ford, M. Cecilia Caino
Journal: Cancer Research (2024)

Abstract Metastasis of cancer cells to vital organs remains the leading cause of cancer related deaths, emphasizing a strong need for actionable targets in advanced stage cancer. To address this, we study novel dysregulated mitochondrial signaling mechanisms that cells utilize to metastasize. Here, we focus on how outer mitochondrial membrane protein—Mitochondrial Rho GTPase 2 (MIRO2)—promotes tumor cell invasion and metastasis. Our previous work identified higher MIRO2 mRNA expression in cancer vs. normal patient samples in a multitude of cancer types, which correlated with worse patient outcomes. Furthermore, we demonstrated that MIRO2 was critical for prostate cancer cell growth and survival in vitro and in vivo. However, it remains unknown if MIRO2 only affects primary tumor growth or if this protein is important throughout tumor progression. Using siRNA mediated knockdown (KD) of MIRO2 we find MIRO2 KD ubiquitously reduces tumor cell invasion in breast, melanoma, pancreatic, and prostate cancer cells. Utilizing metastatic prostate and breast cancer models, we demonstrate that mice injected with MIRO2 shRNA cells have significantly lower metastatic burden compared to mice injected with control shRNA cells. To determine the mechanism that MIRO2 controls invasion and metastasis, we looked at which of the top protein-binding partners for MIRO2 may regulate tumor cell invasion. Of our top hits, we found that depletion of atypical myosin IXB (MYO9B) by siRNA most significantly reduced tumor cell invasion and phenocopied MIRO2 depletion. MYO9B has a well-defined role in controlling cell motility via inactivation of RhoA. Excitingly, we have found 1) MIRO2 KD results in increased active RhoA, phenocopying MYO9B KD, 2) dual ablation of MIRO2 and RhoA fully rescues tumor cell invasion, and 3) MIRO2 is required for MYO9B driven invasion. Taken together, we propose a novel signaling mechanism by which MIRO2 broadly promotes invasion and metastasis through MYO9B dependent inactivation of RhoA. Citation Format: Dillon P. Boulton, Connor J. Hughes, Valentina Vaira, Ajita Jindal, Masoom Raza, Stephen Connor Purdy, Shilpa Sant, Heide L. Ford, M. Cecilia Caino. A novel MIRO2/MYO9B/RhoA signaling axis controls tumor cell invasion and metastasis [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 2770.
Abstract 6666: Leveraging an obligate anaerobic salmonella strain for targeted cargo delivery in the tumor microenvironment to restore immunotherapy sensitivity
Authors: Yige He, Jiandong Huang
Journal: Cancer Research (2024)

Abstract Tumor immunotherapy is often hindered by unresponsive cold tumor microenvironments (TME). Although Salmonella-based immunotherapy has shown potential in overcoming these cold immune environments, safety concerns remain. Our study introduces a genetically reprogrammed Salmonella typhimurium strain (OASL) with a dual safety lock to enhance safety and modify immunosuppressive TME, sensitizing tumors to immunotherapies. We propose using OASL to alter the cold TME and locally release therapeutic cargos such as PDL1 nanobodies and tumor-specific neoantigen peptides identified through bioinformatic algorithms, activating immune cells within the tumor while minimizing side effects. We selected YB1, an obligate anaerobic Salmonella strain that thrives in hypoxic environments, as our base strain and incorporated a self-lysis genetic circuit for controlled bacterial growth and cargo release upon reaching a specific population density within the tumor core. We assembled and evaluated the self-lysis gene circuit in vitro, documenting the event using an optical density (OD) reader and confirming OASL's ability to express genetic cargos through western blot analysis. We then investigated OASL's therapeutic effect in vivo and characterized TME changes using flow cytometry and immunohistochemistry staining. Our results indicate that OASL undergoes lysis and releases cargos upon reaching a specific population density in vitro. Additionally, OASL-delivered neoantigen peptides elicited a tumor-specific immune response in vivo. OASL also demonstrated the capacity to modify the TME and restore sensitivity to PDL1 in previously unresponsive tumors, enhancing therapeutic effects. Citation Format: Yige He, Jiandong Huang. Leveraging an obligate anaerobic salmonella strain for targeted cargo delivery in the tumor microenvironment to restore immunotherapy sensitivity [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 6666.
Abstract 6276: In vitro neuroendocrine differentiation of BPH-1 cells under beta-adrenergic stimulation
Authors: Natascha Pigat, Laura N. Garrido, Coline Lefevre, Manon Baures, Vincent Goffin, Anne-Sophie Armand, Thierry Capiod
Journal: Cancer Research (2024)

Abstract Recent studies have shown that adrenergic fibers from the sympathetic nervous system (SNS), acting through stromal β2-adrenergic receptors, play an important role in the initial phases of cancer development by promoting tumor cell survival. Recent epidemiological data suggest that β-blocker intake is associated with improved survival of prostate cancer patients. Hypertension and high blood pressure have been suggested to increase prostate cancer development suggesting that the use of β-blockers in these patients could also reduce prostate cancer risk. β-adrenoceptors signal through the cAMP/PKA pathway that is known to promote neuroendocrine differentiation (NED) in LNCaP prostate cancer cell line. While neuroendocrine (NE) cells expressing synaptophysin (SYN) represent a minor cell population in the epithelial compartment of normal prostate glands, the population of NE-like cells, exhibiting NE phenotypes and expressing NE markers, is increased in, and correlates with, cancer progression, androgen-independent state and poor prognosis. Expression of the routine tissue biomarker of prostate cancer AMACR in NE-like cells discriminates them from NE cells. Our aim was to investigate whether NED could also be associated with benign prostatic hyperplasia (BPH) as recent studies showed that an increase in neuroendocrine cell density occurred before development of BPH in hypertensive rats. Our results showed that a 10-day treatment with 100µM IBMX (blocking cAMP degradation) and 10µM forskolin (FSK, adenylate cyclase activator) to trigger sustained activation of the cAMP/PKA pathway led to an increase in SYN and AMACR expression in BPH-1 cells (qPCR and WB). Similar results were observed by combining the effect of the β-adrenoceptor agonist isoproterenol (1µM) and FSK. The same treatments reduced BPH-1 cell proliferation rates by 40% and 60%, respectively, as expected for NED. Effects on AMACR and SYN expression and cell proliferation were fully reversed by the β-blocker carvedilol (5µM). This data suggests that β-adrenoceptors could be linked to the development of NE-like cells in BPH, a non-lethal disease affecting the transition zone (TZ). As 20% of the prostate cancer occur in this TZ, this observation may need further investigation. Citation Format: Natascha Pigat, Laura N. Garrido, Coline Lefevre, Manon Baures, Vincent Goffin, Anne-Sophie Armand, Thierry Capiod. In vitro neuroendocrine differentiation of BPH-1 cells under beta-adrenergic stimulation [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 6276.
Abstract 740: CNTN4 as a novel target for solid cancer with antibody-drug conjugate
Authors: Mi Young Cha, Hyunuk Kim, Seungmin Byun, Youngeun Ha, Kitae Park, Hyunkyung Yu, Bu-Nam Jeon, Mira Kim, Soojung Moon, Kyung Mi Park, Hansoo Park
Journal: Cancer Research (2024)

Abstract As a novel immune checkpoint, we previously confirmed that contactin 4 (CNTN4) regulates T cell activity negatively by binding to amyloid precursor protein (APP) on T cells. CNTN4 is highly expressed in various types of tumors, including gallbladder, pancreas, stomach, endometrium, liver, prostate, bladder cancer, melanoma, and other tumors, with positive rates over 70% through immunohistochemistry analysis in contrast to low-level expression in normal tissues. Based on the tumor-specific expression profile of CNTN4, we evaluated the potential of CNTN4 as a novel target for antibody-drug conjugate (ADC). First, the internalization of the anti-CNTN4 antibody in the IND submission stage, GENA-104A16, into CNTN4-positive cancer cells was confirmed. For investigation of the potential of targeting CNTN4 using ADC, clinically validated various linker-payloads (MMAE, MMAF, SN-38, and exatecan derivate) were conjugated to GENA-104A16 using thiol maleimide conjugation with average drug-to-antibody ratio (DAR) in the range of 4.0 to 4.8. After preparing ADCs, we confirmed the binding affinity for CNTN4 was maintained as high even after the payload conjugation through an ELISA. In vitro studies have demonstrated the highly cytotoxic effect of MMAF conjugate among the conjugates of GENA-104A16 on CNTN4-positive cancer cells compared to negative cancer cells. And there was no cytotoxic effect on normal cells. Furthermore, treating MMAF conjugate of GENA-104A16 showed promising efficacy in the Pan02 pancreatic orthotopic mouse model and the patient-derived xenograft model. These results suggest that CNTN4 could be a highly potential ADC target that could expand the options for cancer treatment strategies. Citation Format: Mi Young Cha, Hyunuk Kim, Seungmin Byun, Youngeun Ha, Kitae Park, Hyunkyung Yu, Bu-Nam Jeon, Mira Kim, Soojung Moon, Kyung Mi Park, Hansoo Park. CNTN4 as a novel target for solid cancer with antibody-drug conjugate [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 740.
Abstract 3862: Identification, profiling and clonotypic tracking of tumor-reactive T cells derived from bronchoalveolar lavage in lung cancer patients
Authors: Heeju Ryu, Wei Sun, Michelle A. Wurscher, Viswam S. Nair, Evan W. Newell
Journal: Cancer Research (2024)

Abstract Immunotherapeutic strategies for disinhibiting T cell responses have revolutionized lung cancer treatment. However, the identification of tumor-reactive T cells and the acquisition of adequate tissue for molecular and immune profiling remains a challenge that hinders our ability to adequately characterize the mechanisms of immunotherapy response versus resistance. To address this gap, we are investigating the use of bronchoalveolar lavage (BAL) as an alternative to blood or tumor biopsy samples to identify tumor reactive T cells. We collected cells from a prospective bronchoscopic biorepository of patients undergoing lung cancer evaluation that were subjected to bilateral BAL, phlebotomy, and tissue sampling. We then employed flow cytometry and single-cell multi-omic analyses to identify, characterize and clonotypically track tumor-reactive T cells obtained from BAL, blood and tumor samples from lung cancer patients. Analysis of BAL samples revealed a significant enrichment of terminally exhausted CD8+CD39+CD103+ T cells in BAL from tumor-bearing lungs compared to non-tumor bearing lung BAL and blood PBMCs in 14 patients. We then used single-cell sequencing-based multi-omics to deeply profile bilateral BAL cells, blood PBMCs and tumor tissues from 5 of these patients. By tracking T cell receptor (TCR) sequences across patient-matched samples, we found BAL derived T cell clonotypes that expressed markers of terminal exhaustion, such as CD39 and CXCL13 in the tumor, which strongly implicates them as being tumor reactive and relatively abundant in BAL. Further validation through functional assays is being used to confirm the tumor reactivity of these clones. These data demonstrate the feasibility of capturing tumor-specific T cells during bronchoscopy, providing promising opportunities for patient outcome characterization and exploration of novel therapies. This relatively non-invasive and practical test during routine bronchoscopy offers a cost-effective and safe alternative to identifying tumor-reactive T cells from surgical specimens or biopsies. Citation Format: Heeju Ryu, Wei Sun, Michelle A. Wurscher, Viswam S. Nair, Evan W. Newell. Identification, profiling and clonotypic tracking of tumor-reactive T cells derived from bronchoalveolar lavage in lung cancer patients [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 3862.
Abstract 5607: A highly efficient donor system for CRISPR knock-in editing
Authors: Lipeng Wu, Dezhong Yin, Hua Su, Justin Fellows, Mao Fu, Julian Heller, Brian Park, Alex Juminaga
Journal: Cancer Research (2024)

Abstract CRISPR is a potent tool widely used for genome editing. While CRISPR knock-out, achieved through in-del mutations via cellular repair mechanisms, has proven remarkably effective, the knock-in system for exogenous fragment insertion encounters challenges due to limited specificity and efficiency. Two primary methods for exogenous fragment insertion, namely NHEJ (Non-Homologous End Joining) and HR (Homologous Recombination), exist. HR allows for the construction of DNA insertions with precise junctions but is comparatively less efficient than NHEJ. To address these limitations, our system focuses on enhancing the efficiency of HR-based genome editing. Primarily, we have optimized the Lenti All-in-one CRISPR system to augment the delivery and targeting efficiency of the Cas9-gRNA complex. The system has been successfully employed to knock out Glutamine Synthetase (GLUL) in HEK293T cells, exhibiting superior efficiency compared to commercially available tools. Secondly, we have implemented a pseudo-lenti system to amplify the entry capacity of donor DNA with homology arms into target cells. This technique has shown an improved HR effect in the experiment to tag a GFP at the C terminals of CDC25A. Lastly, we leverage proximity effects by fusing Cas9 with a capture protein that can grasp a bait sequence attached to the donor DNA, thereby facilitating its transfer to the target sites. Our system has demonstrated exceptional efficacy as a CRISPR knock-out platform and a powerful tool for DNA tagging functionality on target genes. Citation Format: Lipeng Wu, Dezhong Yin, Hua Su, Justin Fellows, Mao Fu, Julian Heller, Brian Park, Alex Juminaga. A highly efficient donor system for CRISPR knock-in editing [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 5607.
Abstract 666: ASTX295 engages p53-mediated apoptosis and an inflammatory response in patient derived mesothelioma explants
Authors: Dean Anthony Fennell, Joanna Dzialo, Jan Rogel, Daniel Faulkner, Nada Nusrat, Aleksandra Bzura, Kudzayi Kutywayo, Peter Wells-Jordan, Charlotte Poile, Andrea Biondo, Martin Sims, Apostolos Nakas, Jin-Li Luo, Min Zhang, Maria Ahn
Journal: Cancer Research (2024)

Abstract Mesothelioma is a universally lethal, rare cancer caused by asbestos that is lacking effective targeted treatments, particularly in the relapsed setting. P53 is predominantly wildtype (WT 83%) but is likely restrained by MDM2 particularly in the context of 9p21 deletion, a common, clonal somatic event affecting around half of all mesotheliomas that results in deletion of the MDM2 suppressor ARF. 9p21 deletion is also associated with a cold, immunosuppressed microenvironment. Unleashing p53WT by inhibiting its interaction with MDM2 has therapeutic potential in mesothelioma. To test this hypothesis, we employed live patient derived explants (PDEs) as a model that reflects the genomic inter-patient heterogeneity of mesotheliomas, and harbours an intact tumour microenvironment. Between August 2017 and April 2021 a total of 71 patients were consented prior to extended pleurectomy decortication, and PDEs were harvested at the time of surgery. PDEs were then cultured and treated with ASTX295, an inhibitor of p53-MDM2 interaction, using two concentrations (0.5 and 1 micromolar) and two timepoints (48 and 72 hours). PDEs passing quality control were subjected to spatial profiling using multiplex immunofluorescence microscopy. PDEs harbouring p53WT showed ASTX295-induced p21 (CDK1A) upregulation, which correlated with induction of apoptosis (p=0.04). PDE rank-order sensitivity was conserved across different doses and exposure-times. Transcriptome analysis confirmed ASTX295 induced p53 pathway activation in conjunction with a pro-inflammatory phenotype; both of which were absent in one PDE harbouring an inactivating p53 single nucleotide variant. Constitutive epithelial mesenchymal transition (EMT) was enriched in responding PDEs, as well as MDM2 inhibitor sensitive mesothelioma cell lines. 9p21 deletion (revealed by exome sequencing) was detected in both responding and non-responding PDEs. In summary, inhibition of MDM2-P53 interaction triggers robust p53 activation and a pro-inflammatory phenotype, which is potentiated in EMT enriched mesothelioma PDEs. ASTX295 is currently under clinical investigation (NCT03975387). Citation Format: Dean Anthony Fennell, Joanna Dzialo, Jan Rogel, Daniel Faulkner, Nada Nusrat, Aleksandra Bzura, Kudzayi Kutywayo, Peter Wells-Jordan, Charlotte Poile, Andrea Biondo, Martin Sims, Apostolos Nakas, Jin-Li Luo, Min Zhang, Maria Ahn. ASTX295 engages p53-mediated apoptosis and an inflammatory response in patient derived mesothelioma explants [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 666.
Abstract 4629: QClampTM Plex VEXAS syndrome UBA1 mutation detection assay: A noval XNA based assay to simultaneously detect eight UBA1 somatic mutations associated with VEXAS syndrome
Authors: Yunqing Ma
Journal: Cancer Research (2024)

Abstract VEXAS syndrome (acronym for Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) is a monogenic disease discovered in December 2020. It is an adult-onset systemic inflammatory disorder genetically characterized by somatic mutation of the UBA1 gene which encodes the ubiquitin like modifier activating enzyme 1. VEXAS patients have overlapping rheumatologic and hematologic manifestations, including increased risk for myelodysplastic syndrome (MDS). It is critically important to diagnose VEXAS syndrome, but UBA1 mutation test is still not commercially available. The three most frequent mutations of UBA1 gene are p.M41T(122T&amp;gt;C), p.M41V (c.121A&amp;gt;G), and p.M41L (c.121A&amp;gt;C) in codon 41 of exon 3. Other mutations including splice site mutations at exon 3 (c.118-2A&amp;gt;C, c.118-1G&amp;gt;C and c.118- 9_118-2del), p.S56F (c.167C&amp;gt;T) in codon 56 of exon 3, and p.S621C (c.1861A&amp;gt;T) in codon 621 of exon 16 have been reported. Based on XNA technology, we developed a QClampTM Plex platform to detect all the eight mutations in a single reaction with Luminex system. XNA technology enriches mutant target sequence in a PCR reaction by using synthetic DNA analog XNA (xenonucleic acid) to block wild type DNA. With spiking synthetic mutant DNA in GM24385 cell line DNA, we determined that this assay can detect mutations with a detection limit of variant allele frequency (VAF) for M41T at 0.1%, M41V at 0.1%, M41L at 0.25%, c.118-2A&amp;gt;C at 1%, c.118-1G&amp;gt;C at 1%, c.118- 9_118-2del at 1%, S56F at 0.25% and S621C at 1%, respectively, and specificity of 100% for all mutations. We tested saved DNA samples extracted from whole blood previously collected from suspected VEXAS patients and tested at the National Cancer Institute by Sanger sequencing, including 13 positive and 20 negative samples. Our assay detected all corresponding UBA1 mutations in the 13 positive patient samples, and did not detect UBA1 mutation in 18 of the 20 negative patient samples. Two of the 20 negative samples were also tested positive for UBA1 M41T and M41L on our assay, respectively, due to its significantly higher sensitivity than the Sanger sequencing platform, which has a detection limit of 15-20% VAF. Citation Format: Yunqing Ma. QClampTM Plex VEXAS syndrome UBA1 mutation detection assay: A noval XNA based assay to simultaneously detect eight UBA1 somatic mutations associated with VEXAS syndrome [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 4629.
Abstract 7385: Explainable AI model incorporating uncertainty estimation for enhanced MSI-H prediction and immunotherapy response in gastrointestinal cancer
Authors: Sunho Park, Minj Kim, Ji-Youn Sung, Jeong Hwan Park, Sung Hak Lee, Sam C. Wang, Jaeho Cheong, Tae Hyun Hwang
Journal: Cancer Research (2024)

Abstract Background: Microsatellite instability-high (MSI-H) tumors respond well to immune checkpoint blockade and oftentimes not to chemotherapeutics. Despite value of determining MSI status to guide therapy, many patients’ samples are not untested. Deep learning models may be able to predict MSI status by analyzing hematoxylin and eosin (H&amp;E) stained whole-slide images (WSIs). Validation of this tool will provide another tool to increase MSI testing. However, to be deployed into clinical routine care, prediction models need be externally validated in large and diverse patient cohorts. In addition, these models should provide uncertainty of prediction to help clinicians make informed decisions. Results: In this study, we introduce a novel Bayesian prediction model using whole-slide images (WSIs) and deep Gaussian processes (DGPs) in a weakly supervised learning context. Extensively tested on large datasets (n=3,146) from multiple centers, our model not only demonstrated superior performance but also showed that incorporating uncertainty into predictions significantly improves MSI prediction accuracy, achieving AUROC of &amp;gt;0.91 in colon cancer and &amp;gt;0.94 in gastric cancer. Additionally, an in-depth analysis within the gastric cancer cohort indicated a significant correlation between predicted MSI-H regions and immunotherapy response. Patients who responded to immune checkpoint inhibitors had a higher proportion of MSI-H regions (P-value &amp;lt; 0.05). This correlation was also observed in patients categorized as MSS but responsive to ICIs, highlighting the potential of our model to identify MSI-H patterns not detected through standard laboratory tests. This advancement could lead to more precise patient selection for ICI therapy, enhancing personalized treatment strategies in gastrointestinal cancer. Citation Format: Sunho Park, Minj Kim, Ji-Youn Sung, Jeong Hwan Park, Sung Hak Lee, Sam C. Wang, Jaeho Cheong, Tae Hyun Hwang. Explainable AI model incorporating uncertainty estimation for enhanced MSI-H prediction and immunotherapy response in gastrointestinal 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 7385.