tbuckley/cabot-search huggingface dataset:
Abstract 6906: Engineered bacteria launch and control an oncolytic virus
Authors: Jonathan Pabon, Zakary Singer, Hsinyen Huang, Charles Rice, Tal Danino
Journal: Cancer Research (2024)

Abstract The ability of bacteria and viruses to selectively replicate in tumors has led to synthetic engineering of new microbial therapies. In our system, Salmonella has been programmed to produce Senecavirus A (SVA)-RNA and launch an SVA infection in bacterially-infected cancer cells. Utilizing time-lapse microscopy, we visualize S. typhimurium invasions into cancer cells and their subsequent delivery of multiple picornaviral species. S.-typhimurium-viral-RNA launch in vitro identified a small-cell-lung cancer cell line, H446, as a promising candidate for S.-typhimurium-SVA launch. This viral RNA-carrying Salmonella strain confers complete tumor regression in vivo. Finally, we integrate into this strain a protease-dependent mechanism to confer SVA-infection spatial localization. This work, to the best of our knowledge, is the first instance of bacteria delivering full-length viral RNAs for therapeutic oncolytic purposes. Citation Format: Jonathan Pabon, Zakary Singer, Hsinyen Huang, Charles Rice, Tal Danino. Engineered bacteria launch and control an oncolytic virus [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 6906.
Abstract 3823: Clinical outcomes of uveal melanoma patients in the emergency department
Authors: Alice A. Beneke, Kamil Taneja, Lauren Ladehoff, Kevin Root, Eric Toloza
Journal: Cancer Research (2024)

Abstract Purpose: Uveal melanoma is a rare ocular malignancy that has not been well characterized at a large scale. Specifically, uveal melanoma diagnosis and outcomes in the emergency department (ED) has not been characterized. Methods: The Nationwide Emergency Department Sample was queried from the last quarter of 2015 to 2019 to identify patients with a primary diagnosis of uveal melanoma. Multivariable logistic regression, with patient- and hospital-level characteristics as covariates, was used to identify factors associated with increased risk of inpatient admission. Results: From the last quarter of 2015 to 2019, there were 1,274 ED encounters with a primary diagnosis of uveal melanoma. Most patients were less than 11 years old (43.4%), male (51.1%), or a Medicaid beneficiary (37.8%), and most belonged to a family in the lowest income quartile (32.0%). The median age of these patients was 35 years (IQR: 2-64). Most patients presented to hospitals in the South (53.9%), with a Trauma Level I designation (51.4%), and most to a metropolitan teaching hospital (89.1%). The most common ED outcomes were same-day discharge (61.6%) and admission to the inpatient setting (31.2%). Patients presenting to Trauma Level I hospitals were most likely to be admitted (odds ratio [OR]=2.21; p=0.031). The factors that were most significantly associated with decreased odds of inpatient admission were: patients who were not charged for services (often due to charity) (OR=0.13; p=0.040), Medicaid beneficiaries (OR=0.27; p=0.031), and private insurance beneficiaries (OR=0.34; p=0.047). Among the admitted patients, patients can be discharged to home with self-care (76.2%) or with home-health care (14.9%) or can be transferred to an intermediate-care facility (8.1%). The mean hospital length of stay was 5.7±0.6 days. In-hospital mortality rate for admitted patients was very low (0.8%). Conclusion: Uveal melanoma patient outcomes are closely related to insurance status, indicating socioeconomic factors as a modulator of patient outcomes. Citation Format: Alice A. Beneke, Kamil Taneja, Lauren Ladehoff, Kevin Root, Eric Toloza. Clinical outcomes of uveal melanoma patients in the emergency department [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 3823.
Abstract 4447: ZC3H18: A novel regulator of NAD+ metabolism in high-grade serous ovarian cancer
Authors: Benjamin Wilson, Natalie Wilson, Xianfeng Chen, Shuwen Zhang, Chen Wang, Larry M. Karnitz, Scott H. Kaufmann, Arun Kanakkanthara
Journal: Cancer Research (2024)

Abstract ZC3H18 is a multifunctional regulator of gene expression that is lost in a subset of high-grade serous ovarian cancers (HGSOC). Our prior studies have established that the loss of ZC3H18 diminishes BRCA1 levels, leading to the disruption of homologous recombination DNA repair (HR) and heightened sensitivity of HGSOC cells to PARP inhibitors. Here we show an additional facet to ZC3H18's impact, showing that its loss also induces a reprogramming of energy metabolism in HGSOC. Our findings demonstrate that the depletion of ZC3H18 results in reduced mRNA and protein levels of the NAD+-biosynthetic enzyme, NMNAT1, in HGSOC cells. Mechanistic studies uncovered that ZC3H18 occupies the NMNAT1 promoter, facilitating NMNAT1 transcription by recruiting CDK12 onto the promoter. Consistent with this mechanism, loss of ZC3H18 led to a reduction in CDK12 levels on the NMNAT1 promoter, diminishing NMNAT1 abundance and subsequently causing a decline in cellular NAD levels. These observations unveil a previously unknown role for ZC3H18 in HGSOC, shedding light on its involvement in the regulation of energy metabolism. Importantly, our findings provide valuable insights into potential therapeutic pathways that leverage the metabolic changes linked to ZC3H18 deficiency. Citation Format: Benjamin Wilson, Natalie Wilson, Xianfeng Chen, Shuwen Zhang, Chen Wang, Larry M. Karnitz, Scott H. Kaufmann, Arun Kanakkanthara. ZC3H18: A novel regulator of NAD+ metabolism in high-grade serous 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 4447.
Abstract 3873: Understanding spatial organization of cellular plasticity in pancreatic ductal adenocarcinoma
Authors: Izabella Zamora, Milan Parikh, Bidish K. Patel, Lynn Bi, Doron Haviv, Jingyi Cao, Carina Shiau, Martin Hemberg, William L. Hwang, Nir Hacohen, David T. Ting, Arnav Mehta
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is notorious for poor survival rates, underscoring the urgency of understanding factors that drive tumor progression. A key player in this process is epithelial-mesenchymal transition (EMT), known for its role in enhancing cancer cell adaptability, resistance to treatment, and metastasis. Our study focuses on EMT within PDAC, using single-cell spatial transcriptomics to explore how the tumor microenvironment influences changes in cellular states. We introduce a novel method involving Gaussian mixture models (GMM) to categorize EMT stages in single-cell data and utilize deep learning for label transfer of these tumor cell states, including intermediate cell states, onto spatial transcriptomic data with limited gene panels and sparse count profiles. We find strong spatial autocorrelation of classical cells and a dispersion of basal cells alongside other cells at intermediate stages of the EMT spectrum. By leveraging the spatial proximity of clonally related cells, we confirm that cells transition along the EMT spectrum in a gradient and infer transition rates. We next leverage density gradients of tumor cells in different states to identify distinct neighborhoods with varying EMT subtype composition. We observe significant variations in cell density among different EMT states. A focus on cancer-associated fibroblasts (CAFs) and macrophages reveals differences in these cells across density contours. We also examine differential ligand-receptor interactions across cell state gradients to better understand the cellular interactions that drive EMT transitions and alter the tumor environment. By leveraging spatial transcriptomics, this research aims to provide new biological insights into PDAC intratumoral heterogeneity, potentially leading to the identification of novel therapeutic targets to disrupt treatment resistance. Citation Format: Izabella Zamora, Milan Parikh, Bidish K. Patel, Lynn Bi, Doron Haviv, Jingyi Cao, Carina Shiau, Martin Hemberg, William L. Hwang, Nir Hacohen, David T. Ting, Arnav Mehta. Understanding spatial organization of cellular plasticity in pancreatic ductal adenocarcinoma [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 3873.
Abstract 6633: Tracking cell-cell interactions using intercellular barcode transfer
Authors: Neil Q. Tay, Tiffany Juan, Joseph J. Muldoon, Justin Eyquem, Michael T. McManus
Journal: Cancer Research (2024)

Abstract Cell-cell interaction is one of the fundamental biological mechanisms by which cells communicate and is a key modality by which cancer cells interact with other cells in their microenvironment. Current methods, such as enzymatic labeling and proximity-based tagging, allow the experimental tracking of these interactions but are not compatible with sequencing-based readouts, which are essential for high-throughput analyses. We have developed a highly scalable intercellular barcode transfer technology that bridges this gap. Our novel “Relay” technology offers a scalable solution to monitor cell-cell interactions with unprecedented single-cell resolution, seamlessly integrating with existing high-throughput and sequencing platforms. Relay employs RNA barcodes to mark and track cell interaction events, providing definitive quantitative data on cell interaction partners. We used Relay to track interactions between cancer cells and T cells, capturing both potent antigen-specific engagements and subtler contacts involved in antigen sampling. Additionally, by integrating CRISPR libraries with Relay, we pioneered a novel approach for pooled CRISPR screens, focusing on intercellular interactions across different cell types. In this context, the cell harboring genetic perturbation may differ from the cell under analysis. To demonstrate this, we are conducting genome-wide perturbations in cancer cells and interrogating cancer cell factors that affect antigen sampling and trogocytosis by T cells and macrophages. Beyond its application in CRISPR screening, Relay can also be used with single-cell RNA sequencing to directly track and measure immune-cancer and immune-immune cell interactions at the single cell level. We applied single-cell Relay to a dendritic cell-T cell system to link dendritic cell signatures to T cell signatures based on direct cell contact and regulatory signaling. The design of Relay as a highly modular system extends its utility beyond cancer research, making it broadly applicable across various biological models and systems where cell-cell communication is a fundamental property in complex multicellular settings. This tool promises to accelerate the transition from theoretical understanding to practical exploration of cell-cell interactions, with profound implications for immunology, oncology, and beyond. Citation Format: Neil Q. Tay, Tiffany Juan, Joseph J. Muldoon, Justin Eyquem, Michael T. McManus. Tracking cell-cell interactions using intercellular barcode transfer [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 6633.
Abstract 7422: Enabling biomarkers of chromosomal instability for tumor only targeted gene panel sequencing
Authors: David Gómez-Sánchez, Joe Sneath Thompson, Barbara Hernando, Diego García-López, Hector de Galard, Abhipsa Roy, Amy Cullen, Laura Madrid, José Teles, Ania Piskorz, Jason Yip, Alice Cádiz, Maria Escobar-Rey, Roberto Moreno-Vellisca, Nuria Carrizo, Eva Álvarez, Miguel Quintela-Fandino, Mariano Barbacid, Javier Ramos-Paradas, Juan Manuel Coya, Irene Ferrer, Jon Zugazagoitia, Luis Paz-Ares, Geoff Macintyre
Journal: Cancer Research (2024)

Abstract Capture-based targeted sequencing is routinely used for small variant detection in cancer clinical care. Alongside targeted DNA, off-target DNA is also sequenced. These off-target reads are distributed across the genome, allowing for a whole genome copy number profile to be derived without the need for a SNP backbone. Here we present CopyRight, a method that generates robust genome-wide copy number profiles, which can be used for downstream chromosomal instability (CIN) quantification, overcoming various sources of technical noise with a novel approach that only requires a single tumor sample. We analyzed a variety of capture-based NGS protocols using our novel computational method, including the TruSight Oncology 500 (TSO500) panel, and compared them to the current gold standard for genome-wide copy number profiling from FFPE tissues: shallow whole genome sequencing (sWGS). Comparable results were obtained from targeted sequencing depending on sample purity, preservation method, and read depth. Additionally, benchmarks of CopyRight against other computational algorithms show an improvement in performance without the need for a matched normal tissue, the usual drawback for other methods in the cancer field. CIN signatures are a new set of emerging biomarkers that reflect the diversity of defective pathways that have operated in a tumor, which require robust genome-wide copy number profiles. These CIN signatures can be used to predict response to cytotoxic agents and targeted therapies and could ultimately help guide therapy selection in patients. As most clinical sequencing workflows rely on targeted sequencing, CopyRight can be included in current clinical assays, enabling CIN biomarker quantification with no extra technical or experimental requirements. Citation Format: David Gómez-Sánchez, Joe Sneath Thompson, Barbara Hernando, Diego García-López, Hector de Galard, Abhipsa Roy, Amy Cullen, Laura Madrid, José Teles, Ania Piskorz, Jason Yip, Alice Cádiz, Maria Escobar-Rey, Roberto Moreno-Vellisca, Nuria Carrizo, Eva Álvarez, Miguel Quintela-Fandino, Mariano Barbacid, Javier Ramos-Paradas, Juan Manuel Coya, Irene Ferrer, Jon Zugazagoitia, Luis Paz-Ares, Geoff Macintyre. Enabling biomarkers of chromosomal instability for tumor only targeted gene panel sequencing [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 7422.
Abstract 6650: Macrophage pro-inflammatory phenotype skewing by the application of tumor treating fields (TTFields)
Authors: Tal Kan, Yiftah Barsheshet, Boris Brant, Tharwat Haj Khalil, Tali Voloshin, Alexandra Volodin, Lilach Koren, Bella Koltun, Anat Klein-Goldberg, Efrat Zemer-Tov, Rom Paz, Adi Haber, Moshe Giladi, Uri Weinberg, Yoram Palti
Journal: Cancer Research (2024)

Abstract Introduction: Tumor Treating Fields (TTFields) are low intensity electric fields that disrupt cellular processes critical for cancer cell viability. TTFields have previously been shown to induce immunogenic cell death, promote dendritic cell maturation, and elicit a systemic anti-cancer immune response in preclinical models. The benefit of applying TTFields together with immune checkpoint inhibitors (ICI) was demonstrated in a phase 3 study in non-small cell lung carcinoma. In the current research, we investigated possible effects of TTFields on regulation of macrophage phenotype. Methods: Bone marrow-derived macrophages (BMDMs) were generated from the femurs and tibias of 5-8-week-old Balb\C mice. LPS+IFN-γ or IL-4 were applied to the BMDMs to induce polarization (M1 and M2, respectively). The BMDMs were then treated with TTFields (150 kHz, 24 h), and then examined by flow cytometry for surface expression of the macrophage biomarker F4/80 and the activation markers CD80, major histocompatibility complex class II (MHC II), inducible nitric oxide synthase (iNOS), CD206, and ARG-1. Cell supernatants were collected and analyzed by multiplexed secretion assay for secretion levels of CXCL1 (KC), IL-18, IL-23, IL-12p70, IL6, TNF-α, IL-12p40, TGF-β1, CCL22 (MDC), IL-10, IL-6, G-CSF, CCL17 (TARC), and IL-1β. Cell lysates were examined using a RhoA activation kit and Western blot to determine GEF-H1, c-Jun, and p65 phosphorylation levels. Results: BMDMs exposed to TTFields demonstrated elevated expression of the pro-inflammatory M1 markers CD80+ and MHC IIhigh, and decreased expression of the M2 markers CD206 and ARG-1. A pro-inflammatory secretion pattern was detected, with increased levels of CXCL1, IL-18, IL-23, IL-12p70, TNF-α, IL-12p40, CCL22, G-CSF, CCL17 and IL-1β. The treated cells further demonstrated RhoA activation and GEF-H1 phosphorylation, with subsequent activation of the transcription factors c-Jun and p65. Conclusions: This study reveals a novel immunomodulatory role for TTFields, promoting in vitro pro-inflammatory polarization of macrophage. Citation Format: Tal Kan, Yiftah Barsheshet, Boris Brant, Tharwat Haj Khalil, Tali Voloshin, Alexandra Volodin, Lilach Koren, Bella Koltun, Anat Klein-Goldberg, Efrat Zemer-Tov, Rom Paz, Adi Haber, Moshe Giladi, Uri Weinberg, Yoram Palti. Macrophage pro-inflammatory phenotype skewing by the application of tumor treating fields (TTFields) [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 6650.
Abstract 6664: In situ vaccination with hyper-interferon sensitive influenza induces adaptive immune response and sensitizes murine non-small cell lung cancer to PD-1 blockade
Authors: Ramin Salehi-Rad, Yushen Du, Tianhao Zhang, Yuan Shi, Bin Liu, Sun Ren
Journal: Cancer Research (2024)

Abstract Despite recent advances in immunotherapy with immune checkpoint inhibitors (ICI), many patients with non-small cell lung cancer (NSCLC) fail to respond or develop resistance after an initial response. The exclusion of T cells from the tumor or the presence of a dysfunctional T cell compartment within the tumor microenvironment (TME) constitute two central hallmarks of resistance to ICI in patients with NSCLC. Seminal studies have identified that loss of LKB1 in KRAS-mutant NSCLC drives resistance to ICI, potentially by suppressing STING, thereby leading to dysregulation of the interferon (IFN) signaling. There is a pressing demand for the development of innovative immune therapies designed to bolster anti-tumor T cell responses to overcome resistance to ICI. In situ vaccination (ISV) with oncolytic viruses has emerged as a promising, antigen-agnostic strategy capable of conditioning the TME and amplifying anti-tumor T cell responses. We engineered a live attenuated viral vaccine, Hyper-Interferon Sensitive virus (HIS), by conducting a genome-wide functional screening and introducing eight interferon (IFN)-sensitive mutations in the influenza A genome. We utilized multiple syngeneic murine models of NSCLC with distinct driver mutations [KrasG12D/P53+/−/Lkb1−/− (KPL); KrasG12D/P53+/− (KP); and KrasG12D (K)] and varying tumor mutational burden to assess the safety and efficacy of intratumoral HIS virotherapy. Compared to wild-type (WT) influenza, HIS replication was attenuated, enhancing its potential as a safe option for cancer therapy. HIS ISV elicited robust yet transient type I IFN responses in murine NSCLCs, leading an influx of polyfunctional effector Th1 CD4 and cytotoxic CD8 T cells into the tumor. HIS ISV demonstrated enhanced anti-tumor efficacy compared to WT in multiple syngeneic murine models of NSCLC. This efficacy was dependent on host type 1 IFN responses and T lymphocytes. HIS ISV synergized with anti-PD-1 to eradicate immune resistant LKB-1 deficient NSCLC in a subset of mice, resulting in improved overall survival and enduring systemic tumor-specific immunity. These studies provide compelling evidence to support further clinical evaluation of HIS as a novel ‘off-the-shelf’ ISV strategy for patients with NSCLC refractory to ICI. Citation Format: Ramin Salehi-Rad, Yushen Du, Tianhao Zhang, Yuan Shi, Bin Liu, Sun Ren. In situ vaccination with hyper-interferon sensitive influenza induces adaptive immune response and sensitizes murine non-small cell lung cancer to PD-1 blockade [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 6664.
Abstract 664: GSC000190, a highly potent inhibitor of KIF18A, for tumors with chromosome instability
Authors: Peng Tu, Chen Zhang, Biao Lu, Yuanfeng Xia, Fanglong Yang
Journal: Cancer Research (2024)

Abstract Chromosome instability (CIN) and Genetic instability is a common feature of malignant tumor cells, which may contribute to tumor progression and lead to drug resistance and tumor metastasis. KIF18A, a member of the kinesin-8 family, is an ATP dependent plus end microtubule motor protein. Studies have found that genetic depletion of KIF18A greatly impacts the chromosome alignment, elongation of mitotic spindles, activation spindle assembly checkpoint of CIN+ tumor cell and leads to cell death, while have little impact towards the survival of normal cells, making KIF18A an attractive therapeutic target for targeting the vulnerability of CIN related tumors. Here we report the pharmacology characterization of a “best in class” potential KIF18A inhibitor for CIN+ tumors. In vitro, GSC000190 inhibited KIF18A ATPase activity with a single nM potency and has great potency inhibiting growth of a wide range of TP53 mutant/CIN+ tumor cells. In vivo, GSC000190, at approximately one tenth of systematic exposure comparing to that of AMG650, the leading clinical KIF18A inhibitor, causes tumor shrinkage in multiple CDX models including ovarian, colon and lung cancers. In an HGSOC PDX model which is resistant to platinum and olaparib, GSC000190 induced strong tumor regression both as single agent and through combination without significant body weight reduction. PD study confirms a more elevated mitotic phosphorylated histone 3 (PH3) staining in GSC000190 treated tumor tissues, correlating with a better in vivo efficacy than that of AMG650. GSC000190 has a favorable ADME profile in rodents, dogs and NHPs, as well as a much better safety profile. GSC000190 is now under IND-enabling study and P1 study is planned in the second quarter of 2024. Legal entity responsible for the study: The authors. Disclosure: All authors have declared no conflicts of interest. Citation Format: Peng Tu, Chen Zhang, Biao Lu, Yuanfeng Xia, Fanglong Yang. GSC000190, a highly potent inhibitor of KIF18A, for tumors with chromosome instability [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 664.