tbuckley/cabot-search huggingface dataset:
Abstract 1532: Improved reproducibility in multiplex immunofluorescence analysis of the tumor microenvironment using a novel quenching solution
Authors: Matt Levin, Jack Heath, April Schrank-Hacker, Shelby Dunn, Minh-Chau Vu, Imane Hamza, David Schwartz
Journal: Cancer Research (2024)

Abstract Formalin-fixed, paraffin-embedded (FFPE) tissues are commonly used in histopathology because the fixed tissues are stable and easy to store. In the context of immunofluorescence detection, however, endogenous autofluorescence of FFPE tissues can significantly reduce or mask immunofluorescent signals. The autofluorescence of FFPE tissues is caused by a variety of factors, including the presence of endogenous fluorophores, tissue fixation, and processing. While there are several methods that can be used to quench autofluorescence in FFPE tissues, chemical quenchers, which absorb or scatter light, are most frequently used for multiplex IF. Examples of chemical quenchers commonly used in manual multiplex staining include Sudan Black B and TrueBlack; however, these are not chemically compatible for use on automated platforms such as the Leica Biosystems BOND RX. Due to the need for increased throughput and decreased hands-on time, automation has risen in popularity versus manual staining, leading to a need for a versatile quenching solution compatible with automation. Here we demonstrate that NovaPlex Quenching Solution (NPQS), a novel proprietary quenching agent, reduces the background caused by autofluorescence and enhances the signal of the Cell IDx UltraPlex multiplex immunofluorescent (mxIF) assay across tissue types. Qualitative studies showed a decrease in autofluorescent signal in FFPE mouse spleen stained with antibodies against B220/Foxp3/CD3e, suggesting the utility of NPQS in mouse models of cancer and immunity. Similarly, nonspecific background was decreased across FFPE human tissue types, including lung adenocarcinoma stained for CD8/Foxp3/CD3e/CD4 and tonsil stained for CD8/Foxp3/PD-1/CD4. Further statistical studies in FFPE human tonsil tissue stained with CD8/Foxp3/PD-1/CD4 showed there was no significant decrease in dye intensity across all four markers and channels, resulting in a significant increase in signal-to-noise ratio for both CD8 at 490nm and PD-1 at 650nm (p&amp;lt;0.05). These experiments using Cell IDx/LBS UltraPlex mxIF technology demonstrate an effective method to improve the signal-to-noise ratios of fluorophores without reducing signal intensity from any of the target proteins in these parallel multiplex immunofluorescent assays. Citation Format: Matt Levin, Jack Heath, April Schrank-Hacker, Shelby Dunn, Minh-Chau Vu, Imane Hamza, David Schwartz. Improved reproducibility in multiplex immunofluorescence analysis of the tumor microenvironment using a novel quenching solution [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 1532.
Abstract 5811: Ultralong CDR3 engineered interleukin-15 antibody fusion for T and NK cell expansion
Authors: Ruiqi Huang, Duncan McGregor, Vaughn Smider
Journal: Cancer Research (2024)

Abstract Interleukin (IL)-15 is a promising immunotherapeutic cytokine for cancer treatment because it can stimulate the proliferation and cytotoxicity of CD8+ T lymphocytes and nature killer (NK) cells, similar to the action of IL-2, which has been used to treat metastatic melanoma and renal cancer. IL-15 may have improved pharmacologic properties over IL-2 because it doesn’t cause vascular leak syndrome or stimulate regulatory T cells. However, IL-15 is difficult to express as a stable soluble protein and has a short half-life in vitro and in vivo. To solve the problem, we designed an IL-15 ultralong CDR3 humanized bovine antibody fusion. Bovine ultralong CDR3 antibodies have a unique “stalk and knob” structure in which two antiparallel β-strands support a disulfide bonded knob protruding out of the antibody surface and forms a mini antigen binding domain. By replacing the knob domain with IL-15, we have created a chimeric CDR3-IL-15 IgG which functions as IL-15 in vitro and in vivo but can be easily produced in mammalian cells with increased stability. Thus, the CDR3 can stabilize IL-15 in the absence of its high affinity receptor α (Rα) chain. Furthermore, as IL-15 utilizes Rα for increased trans signaling to the receptor β and γ subunits, one variant candidate (CDR3-IL-15_Rα) was produced by co-expressing Rα sushi domain with the chimeric IgG. Both constructs have been demonstrated to be highly active in stimulating proliferation of NK cells and CD8+ T cells in vitro as well as in stimulating proliferation of NK cells and CD8+ T cells in rats and non-human primates (NHP). Although the CDR3-IL-15_Rα exhibited higher in vitro signaling activity than CDR3-IL-15, both were equally potent in stimulating the proliferation of NK cells and CD4+ and CD8+ T cells in NHP without any immunogenicity detected. Moreover, in vivo studies in NHP indicated that CDR3-IL-15 acted faster than CDR3-IL-15_Rα in stimulating the proliferation of these lymphocytes. CDR3-IL-15 is the first thermodynamically stabilized variant of IL-15 produced in the absence of its Rα chain, is highly active in vivo, and has multiple potential cancer applications as an T and NK cell stimulating agent. Citation Format: Ruiqi Huang, Duncan McGregor, Vaughn Smider. Ultralong CDR3 engineered interleukin-15 antibody fusion for T and NK cell expansion [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 5811.
Abstract 4411: Enhancing scalability and consistency in clinical multiomics via an optimized fixed cell ATAC-seq method​
Authors: Dafne Alves Winders, Riley Graham, Xiangying Mao, Ilaria De Vito, Andrea O'Hara, Laure Turner, Haythem Latif
Journal: Cancer Research (2024)

Abstract ATAC-seq has an emerging role in decoding mechanisms of gene regulation, offering valuable insights into pathology and treatment response in disease models. However, clinical adoption of ATAC-seq methods has been limited by logistical hurdles, including time-sensitive processing of fresh samples and compromised viability of cryopreserved cells. These constraints, compounded by changes in open chromatin regions (OCRs) following cryopreservation, introduce unintended bias and pose significant obstacles for the translational impact of ATAC-seq experiments. ​ Here, we introduce an optimized fixed-cell ATAC-seq approach to overcome these limitations and unlock new sample types for ATAC-seq analyses. Our solution improves and simplifies the workflow from sample collection to clinical deliverable. This method enables ATAC-seq investigation of a diverse range of samples and facilitates the execution of complex experimental designs, including time course studies and high throughput screening.​To demonstrate the effectiveness of this method, we compared our optimized fixed-cell method with traditional ATAC-seq preparations in both fresh and cryopreserved GM12878 cells in parallel. Human GM12878 cell line was obtained from Coriell Institute for Medical Research5. Remarkably, we observed consistent genome-wide patterns of OCR enrichment at key regulatory elements across the three sample preparation methods. We observed consistent OCR enrichment across the promoter region of known highly-expressed B-cell genes including CD48 and LCP1, underscoring this assay’s ability to detect chromatin changes at key genes in human disease models. ​ To investigate the potential for multiomic analysis using this method, we prepared RNA-seq libraries from fixed-cell samples in parallel to ATAC-seq. We observed significantly elevated gene expression related to B-cell function and B-cell diseases, demonstrating our method’s compatibility with RNA-seq data collection and integration. This optimized fixed-cell ATAC-seq approach offers enhanced scalability and consistency over conventional methods and presents new opportunities for the multiomic analysis of chromatin and transcriptional activity genome-wide from a single sample in both clinical and research settings. Citation Format: Dafne Alves Winders, Riley Graham, Xiangying Mao, Ilaria De Vito, Andrea O'Hara, Laure Turner, Haythem Latif. Enhancing scalability and consistency in clinical multiomics via an optimized fixed cell ATAC-seq method​ [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 4411.
Abstract 1656: ISM6331, a novel and potent pan-TEAD inhibitor, exhibits strong anti-tumor activity in preclinical models of Hippo pathway-dysregulated cancers
Authors: Qi Li, Jainfei Wan, Jinxin Liu, Jing Shang, Jiaojiao Yu, Wei Zhu, Celia X.-J. Chen, Junwen Qiao, Ling Wang, Man Zhang, Xiao Ding, Supriya Bavadekar, Sujata Rao, Feng Ren, Alex Zhavoronkov
Journal: Cancer Research (2024)

Abstract The Hippo-YAP/TAZ-TEAD signaling pathway plays critical roles in tumorigenesis and tumor progression. Genetic alterations of Hippo pathway regulators, such as NF2 or LATS1/2, have been shown to induce YAP/TAZ-TEAD transcriptional activity, promoting initiation and progression of many solid tumors. In addition, many studies have shown that YAP/TAZ-TEAD activation mediates resistance to multiple targeted therapies, particularly EGFR-KRas-MAPK pathway inhibitors. The TEAD family of transcription factors (TEAD1/2/3/4) share structural similarity and have overlapping functions in tumor development and TEAD auto-palmitoylation is critical for its interaction with YAP/TAZ and its transcriptional function. Therefore, blocking TEAD palmitoylation and allosterically disrupting YAP/TAZ-TEAD-mediated transcriptional regulation, is emerging as a promising approach for the treatment of tumors with Hippo pathway dysregulation. In this work, ISM6331, a novel and potent TEAD inhibitor with excellent inhibition against TEAD1/2/3/4 was identified leveraging an AI generative model. ISM6331 reversibly binds to the TEAD palmitoylation site and significantly suppresses TEAD transcriptional activity. ISM6331 potently and selectively inhibited the growth of many Hippo pathway-dysregulated tumor cells and dose-dependently suppressed the expression of TEAD target genes in vitro. In NF2-deficient or LATS1/2-mutant in vivo mesothelioma models, ISM6331 exhibited promising anti-tumor efficacy as monotherapy in a dose-dependent manner from 3 to 30mg/kg. ISM6331 also showed synergism with EGFR or KRasG12C inhibitors in inhibiting tumor cell growth and overcame drug resistance in in vitro and in vivo models. In addition, ISM6331 showed excellent pharmacokinetic properties in multiple preclinical species and was well-tolerated in GLP-toxicity studies. In summary, ISM6331 has promising potential to treat Hippo pathway-dysregulated tumors as monotherapy as well as in combination with targeted therapies. Citation Format: Qi Li, Jainfei Wan, Jinxin Liu, Jing Shang, Jiaojiao Yu, Wei Zhu, Celia X.-J. Chen, Junwen Qiao, Ling Wang, Man Zhang, Xiao Ding, Supriya Bavadekar, Sujata Rao, Feng Ren, Alex Zhavoronkov. ISM6331, a novel and potent pan-TEAD inhibitor, exhibits strong anti-tumor activity in preclinical models of Hippo pathway-dysregulated cancers [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 1656.
Abstract 7406: Visualization and analysis of cancer genomics data using UCSC Xena
Authors: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler
Journal: Cancer Research (2024)

Abstract UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Private data are kept on the researcher's computer and are never uploaded to our public servers. We support Mac, Windows, and Linux. Questions Xena can help you answer:* Is overexpression of this gene associated with lower/higher survival?* What genes are differentially expressed between these two groups of samples?* What is the relationship between mutation, copy number, expression, etc for this gene? Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, GDC, PCAWG, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data: SNPs, INDELs, copy number variation, gene expression, ATAC-seq, DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotype information, subtype classifications and biomarkers. All of our data is available for download via python or R APIs, or using our URL links. Our signature Visual Spreadsheet view shows multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. We also have dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, differential gene expression analysis, GSEA, charts, statistical analyses, genomic signatures, and the ability to generate URLs to live views. New features include: * Genome-wide differential gene expression analysis * GSEA analysis * Select samples directly from the screen for filtering and creating subgroups * Loading of Microsoft Excel files Our beta prototype site for visualizing single-cell data delivers million-cell-scale multi-omics data for interactive visualization in a web browser. Contact us for access to our beta prototype site. If you use us please cite our publication in Nature Biotechnology: https://www.nature.com/articles/s41587-020-0546-8 Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. Visualization and analysis of cancer genomics data using UCSC Xena [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 7406.
Abstract 6655: Oncolytic adenovirus dually expressing interferon beta and membrane-stable CD40 ligand increases polyfunctional CD8+T cells associated with antitumor activity
Authors: Mark J. Cantwell, Andreas N. Saltos, Hong Zheng, Dana Foresman, Amer A. Beg
Journal: Cancer Research (2024)

Abstract MEM-288 is a dual-transgene armed oncolytic adenovirus in phase 1 clinical development as a standalone agent and in combination with immune checkpoint inhibitors (ICI). It encodes two potent immune agonists: IFNβ and a recombinant membrane-stable chimeric form of CD40L (MEM40). We previously demonstrated this agonist combination is better than either agonist individually to activate conventional dendritic cells type 1 (cDC1) crucial for CD8+ T cell cross-priming, and to increase tumor-antigen reactive CD8+ T cells. Furthermore, first-in-human Phase 1 clinical trial (NCT05076760) results of MEM-288 for advanced non-small cell lung cancer (NSCLC) and other solid tumors showed MEM-288 tumor shrinkage was associated with systemic antitumor T cell immunity as demonstrated by cytokine, T cell clonotype, and tumor neoantigen analysis. Here, we investigated the precise nature of the localized and systemic T cell response induced by MEM40 + IFNβ in preclinical tumor models. Single-cell RNA sequencing of tumor infiltrating T lymphocytes (TILs) revealed that MEM40 + IFNβ elicited a strong increase in T cells expressing Granzyme B and PRF1, key effector cytokines and cytotoxicity mediators. We tracked the CD8+ T cell response in CD45.1 C57BL/6 mice implanted with syngeneic B16 tumor expressing the model antigen OVA. Interestingly, intratumoral treatment with adenovirus encoding MEM40 + IFNβ did not cause an appreciable increase in absolute numbers of antigen-reactive CD8+ T cells, despite tumor growth inhibition. However, MEM40 + IFNβ compared to control unarmed adenovirus induced a significant (p &amp;lt; 0.005) 5-fold increase in polyfunctional IFNγ+TNFα+PRF1+ and IFNγ+TNFα+Granzyme B+ CD8+ T cells. Polyfunctional CD8+ T cells have the capacity to simultaneously produce effector cytokines and cytotoxicity mediators and are known to be strongly associated with antitumor T cell activity. The robust polyfunctional CD8+ T cell response in these studies is consistent with T cell-driven antitumor activity found in both our preclinical tumor experiments and our clinical studies in advanced NSCLC patients responding to MEM-288. Overall, our findings suggest MEM40 + IFNβ generates a strong polyfunctional CD8+ T cell response in the TME that warrants continued evaluation to understand the pleiotropic mechanisms of this cancer immunotherapy. Citation Format: Mark J. Cantwell, Andreas N. Saltos, Hong Zheng, Dana Foresman, Amer A. Beg. Oncolytic adenovirus dually expressing interferon beta and membrane-stable CD40 ligand increases polyfunctional CD8+T cells associated with antitumor activity [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 6655.
Abstract 5792: Rapid and efficient generation of panels of T cell engaging (TCE) multispecific antibodies via complementary technologies
Authors: Cory Ahonen, Nathan Sharkey, Melissa Durkin, Andrew Avery, Michael Battles, Beth Sharkey, Kyle Barlow, Arvind Sivasubramanian, Caitlin Stein, Bradley Lunde, Kevin Schutz, Bianka Prinz, Rob Pejchal, Paul Widboom, Eric Krauland
Journal: Cancer Research (2024)

Abstract A goal of immunotherapy is to induce an anti-tumor response that is potent and specific. However, there is increasing understanding that currently approved monospecific checkpoint inhibitors are not effective for all patients and/or indications. Thus, investigators are increasingly pursuing multispecific antibody treatments in an attempt to enhance clinical outcomes. These treatments may either take the form of mixtures (administered simultaneously or in series) of multiple monospecific antibodies, or as single entity, multispecific antibodies (‘multispecifics’). In the case of multispecifics, the large number of possible topologies and complexity of manufacture necessitate the development and application of a robust set of complementary technologies. We have developed an exemplary set of such technologies. Herein, we demonstrate the ability to direct desired antibody chain pairing (HC-HC and HC-LC), isolate and engineer single-domain antibodies, as well as generate large (&amp;gt;100) panels of multispecific antibodies with diverse topologies from a limited number of input molecules. These technologies can be leveraged in combination with our affinity and developability-optimized TCE αCD3 and αCD28 antibody panels to achieve desired potency without the need for additional discovery or engineering. Citation Format: Cory Ahonen, Nathan Sharkey, Melissa Durkin, Andrew Avery, Michael Battles, Beth Sharkey, Kyle Barlow, Arvind Sivasubramanian, Caitlin Stein, Bradley Lunde, Kevin Schutz, Bianka Prinz, Rob Pejchal, Paul Widboom, Eric Krauland. Rapid and efficient generation of panels of T cell engaging (TCE) multispecific antibodies via complementary technologies [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 5792.
Abstract 3875: Glioblastoma mutational profiles drive cancer cell signaling and immune evasion
Authors: Maryam Pourmaleki, Brian D. Greenstein, Caitlin J. Jones, Subhiksha Nandakumar, Daniel A. Navarrete, Smrutiben Mehta, Carl Campos, Travis J. Hollmann, Nicholas D. Socci, Tejus Bale, Sohrab P. Shah, Ingo K. Mellinghoff
Journal: Cancer Research (2024)

Abstract Glioblastoma multiforme (GBM) is the most common malignant brain tumor in adults with a median survival below two years. Characterization of GBM through gene expression profiling and DNA sequencing has identified disease subgroups and commonly altered genes and pathways, including alterations in the genes encoding neurofibromin-1 (NF1) and the epidermal growth factor receptor (EGFR). NF1 and EGFR are involved in receptor tyrosine kinase (RTK), RAS/MEK/ERK, and PI3K signaling, and together, are genetically altered in over 60% of adult GBMs. Interestingly, NF1 and EGFR alterations in GBM are almost always mutually exclusive. Here, we designed a multimodal approach integrating spatial proteomics, transcriptomics, and genomics to measure cell composition, immune cell function, cancer cell signaling, cellular spatial organization, gene expression, transcriptional subtypes, and genome alterations in 80 NF1 and EGFR altered human GBMs with extensively curated treatment and survival data. We quantified the spatial expression of 42 proteins in over 31 million single cells measuring RTK/RAS/PI3K and Rb signaling and features of the TME, including 23 cell types covering tumor cells, immune cells, and brain resident cells. In addition to tumor genotype labels, we classified each GBM tumor by its transcriptional subtype (i.e., mesenchymal, classical, or proneural). We identified genotype-phenotype associations in GBM including hyperactive RAS signaling cellular niches, a macrophage-rich TME, and an epithelial-mesenchymal signature in NF1 altered tumors and hyperactive RTK signaling and an immune desert TME in EGFR amplified tumors. Furthermore, we observed spatial heterogeneity in cancer cell signaling patterns suggestive of the presence of different tumor cell clones within different regions of each GBM tumor. Together, we identify several genotype-associated features of GBMs, reinforcing the value of integrating spatial multi-omic data for generation of genotype-driven therapeutic hypotheses, with implications for GBM genotype-based therapeutic stratification. Citation Format: Maryam Pourmaleki, Brian D. Greenstein, Caitlin J. Jones, Subhiksha Nandakumar, Daniel A. Navarrete, Smrutiben Mehta, Carl Campos, Travis J. Hollmann, Nicholas D. Socci, Tejus Bale, Sohrab P. Shah, Ingo K. Mellinghoff. Glioblastoma mutational profiles drive cancer cell signaling and immune evasion [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 3875.