tbuckley/cabot-search huggingface dataset:
Abstract 417: Chromosomal instability leads to durable tumor suppression upon macrophage-checkpoint disruption, with induction of anti-tumor IgG
Authors: Dennis E. Discher
Journal: Cancer Research (2024)

Abstract Solid tumors generally exhibit chromosome copy number variation caused by chromosomal instability (CIN) in mitosis, and the resulting aneuploidy associates with poor prognosis in various cancer types and poor Tcell checkpoint blockade response in melanoma. In such contexts, however, macrophages and the SIRPa-CD47 checkpoint are understudied. Here, CIN is induced pharmacologically in poorly immunogenic B16F10 mouse melanoma cells, generating micronuclei plus diverse aneuploidy and skewing macrophages towards an anti-cancer phenotype based on markers and short-term tumor studies. Mice bearing CIN-afflicted tumors with wild-type CD47 levels survive only slightly longer compared to chromosomally stable controls, but long-term survival can be maximized when anti-tumor IgG opsonization is combined with adoptive transfer of macrophages with SIRPa blockade or with CD47 knockout of the B16F10. Multi-epitope, de novo anti-cancer IgG in survivors promote phagocytosis of CD47 knockout B16F10 cells by macrophages and suppress tumoroids in vitro and growth of tumors in vivo. An unexpected benefit of pairing CIN with maximal macrophage anti-cancer activity is thus an anti-cancer vaccination-like response that can lead to durable cures and potentiate cell-mediated acquired immunity. Citation Format: Dennis E. Discher. Chromosomal instability leads to durable tumor suppression upon macrophage-checkpoint disruption, with induction of anti-tumor IgG [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 417.
Abstract 2325: NUWA-ms: A network-based method to infer quantification of missing proteins using multi-cohort proteomics profiles
Authors: Lihua Cao, Yuhao Xie, Jiale Chen, Man Wang, Tingting Zhao, Heli Yang, Yang Du, Yang Yang, Zhaode Bu, Jiafu Ji, Jianmin Wu
Journal: Cancer Research (2024)

Abstract Although mass spectrometry is powerful for proteomic quantification, the inherent issue of missing values remains a significant challenge. We found a prevalent lack of quantification of valuable proteins (e.g., immune cell markers and drug targets) in published datasets, limiting the functional utilities of quantitative proteomic profiles. This was exemplified by the substantial lack of quantification of immune cell marker, which impede the dissection of tissue-infiltrating immune cells by deconvolution analysis of cancer proteomic profiles. Thus, we introduce a network-based method NUWA-ms for robust abundance inference of missing proteins using multi-cohort proteomic profiles. By evaluating 561 tumors with paired proteomic and transcriptomic profiles, a significant improvement of deconvolution performance was shown with the aid of NUWA-ms. This was further validated by the comparison between scRNA-seq and proteomic analyses of a same gastric cancer tumor tissue. NUWA-ms applications to cancer proteomic profiles facilitated the inference of CD8+ T cell markers and effector proteins, enabling the associations of CD8+ T cell infiltration with MSI status in colorectal cancer and anti-PD-1 therapy response in melanoma. These findings demonstrated the utilities of NUWA-ms in depicting infiltrating lymphocytes in the tumor microenvironment using proteomic profiles. Furthermore, based on the proteomic profiles of six patient-derived tumor organoids (PDOs), NUWA-ms application helped identifying PDOs sensitive to a targeted therapeutic agent including the ones neglected by the raw MS quantification, and aided in revealing the resistant mechanism. Together, NUWA-ms could enable a robust inference of protein abundance, to help identifying protein biomarkers and therapeutic targets for cancer and other complex diseases. Citation Format: Lihua Cao, Yuhao Xie, Jiale Chen, Man Wang, Tingting Zhao, Heli Yang, Yang Du, Yang Yang, Zhaode Bu, Jiafu Ji, Jianmin Wu. NUWA-ms: A network-based method to infer quantification of missing proteins using multi-cohort proteomics 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 2325.
Abstract 3093: Combining lab automation with data analysis automation to enable high-throughput screening of patient-derived organoids
Authors: Abraham Lin, Maxim Le Compte, Tyler Gilcrest, Edgar Cardenas De La Hoz, Geert Roeyen, Jeroen Hendriks, Filip Lardon, Christophe Deben
Journal: Cancer Research (2024)

Abstract Although patient-derived tumor organoids (PDOs) better-represent patient tumors compared to traditional in vitro cell cultures, limitations of PDO analysis remain a major hurdle for high-throughput screening (HTS) applications. In particular, current PDO analysis fall short in at least 1 of 2 major criteria: 1) accurate recapitulation of patient tumor or 2) scalability. To address this, we have developed an automation-compatible protocol to satisfy these 2 major criteria to facilitate the adoption of PDOs for HTS applications1. Our novel protocol leverages live-cell imaging techniques to capture the dynamic interactions and intricate complexities of PDOs, which allowed for more precise and comprehensive analysis. To further enhance the accuracy and efficiency of our approach, we developed a fully automated image and data analysis pipeline (Orbits). Using label-free detection of organoids from brightfield images, Orbits integrates growth-rate-based drug response metrics with drug synergy metrics to significantly improve the identification of synergistic drug interactions. Here, present the results of our HTS protocol on 10 distinct drug combination strategies, specifically focusing on the repurposed drug candidate Auranofin, a Thioredoxin reductase inhibitor. We screened on 10 PDOs sourced from healthy lung, non-small cell lung cancer, and pancreatic ductal adenocarcinoma. Not only were we able to distinguishing cytostatic from cytotoxic drug responses at a single-organoid level, we identified drug candidates that can synergistically enhanced the efficacy of Auranofin in a tumor selective manner. Our study presents a major step forward in the field of PDO-based drug discovery, offering a robust protocol for HTS and automated data analysis. The implementation of our method will accelerate the discovery of effective therapeutic strategies, ultimately translating to improved patient outcomes. 1 Le Compte, M., et al JoVE 190 (2022) Citation Format: Abraham Lin, Maxim Le Compte, Tyler Gilcrest, Edgar Cardenas De La Hoz, Geert Roeyen, Jeroen Hendriks, Filip Lardon, Christophe Deben. Combining lab automation with data analysis automation to enable high-throughput screening of patient-derived organoids [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 3093.
Abstract 3087: The m6A methyltransferase RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism
Authors: Su Hwan Park, Yun-Yong Park, Jong-Ho Lee
Journal: Cancer Research (2024)

Abstract N6-adenosine methylation (m6A) is critical for controlling cancer cell growth and tumorigenesis. However, the function and detailed mechanism of how m6A methyltransferases modulate m6A levels on specific targets remains unknown. In the current study, we identified significantly elevated levels of RBM15, an m6A writer, in basal-like breast cancer (BC) patients compared to non-basal like BC and linked it to worse clinical outcome. Gene expression profiling uncovered correlations between RBM15 and serine and glycine metabolism genes including PHGDH, PSAT1, PSPH, and SHMT2. RBM15 influences overall m6A levels and, specifically, m6A of serine and glycine metabolism genes via direct binding to target RNA. Further RBM15 effects on cell growth were largely dependent on serine and glycine metabolism. Thus, RBM15 coordinates cancer cell growth through altered serine and glycine metabolism suggesting RBM15 as a new therapeutic target in BC. Citation Format: Su Hwan Park, Yun-Yong Park, Jong-Ho Lee. The m6A methyltransferase RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism [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 3087.
Abstract 4177: High-throughput <i>in vivo</i> monitoring of splenomegaly and tumor burden in a murine breast cancer model
Authors: Craig McMannus, Tomek J. Czernuszewicz, Ryan C. Gessner, Jeffrey D. Peterson
Journal: Cancer Research (2024)

Abstract Splenomegaly is a valuable parameter in mouse model cancer studies, as it can reflect the magnitude of cancer burden, hematopoietic activity, immune status, and can provide an indirect measure of cancer treatment efficacy. In liquid cancer models specifically (leukemia/lymphoma), spleen sizing is important as it is usually the only measure of in vivo tumor burden that can be assessed noninvasively without genetic labeling of tumor cells. Magnetic resonance imaging (MRI) and contrast-enhanced computed tomography (CT) are highly effective at evaluating spleen size in small animals. However, these techniques can impose limitations on large-cohort study designs due to high cost, long scan time, and ionizing radiation. Ultrasound is an alternative method with lower cost, high frame rate, and no ionization, but can suffer from poor inter-user variability, limited 2D field-of-view, and low throughput due to manual operation. In this work, we evaluated a novel 3D automated ultrasound scanner (Vega, Revvity, Inc.) for rapid assessment of splenomegaly in a murine cancer model. Female BALB/c mice (n=10) were implanted with 5e5 4T1 (ATCC) cells on the right flank. Mice were imaged at five timepoints over 25 days to track longitudinal progression of both spleen and tumor enlargement. Images were segmented manually in 3D using the “Slice Draw” and “Fill Between Slices” effects in SonoEQ v2.0.1 (Revvity, Inc.) to quantify tissue volume. After the final timepoint, mice were euthanized, and spleen weight was measured ex vivo. An additional cohort of age-matched mice without tumors (n=7) were imaged at the final timepoint to serve as controls. Imaging revealed a substantial enlargement of the spleen over time, from 30 ± 3 mm3 to 545 ± 105 mm3, representing an 18-fold increase. In the same time span, tumor volume grew to 1966 ± 87 mm3. Correlation analysis demonstrated good agreement between ultrasound volumes and ex vivo spleen weights (R² = 0.90). The results in this study demonstrate that noninvasive, nonlabelled quantification of murine spleen size with automated ultrasound is feasible, robust, and fast. The average time to acquire the spleen image for each mouse was less than 30 seconds. Future studies will apply this workflow in liquid cancer models, as well as explore using machine learning approaches to automatically segment spleen borders for faster data analysis. Citation Format: Craig McMannus, Tomek J. Czernuszewicz, Ryan C. Gessner, Jeffrey D. Peterson. High-throughput in vivo monitoring of splenomegaly and tumor burden in a murine breast cancer model [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 4177.
Abstract 1631: A homogeneous assay system for discernment of proliferative, antiproliferative, and cytotoxic effects in culture
Authors: Dan F. Lazar, Kevin R. Kupcho, Andrew L. Niles, James J. Cali
Journal: Cancer Research (2024)

Abstract We describe a novel homogeneous cell-based assay developed for the quantitative detection of Ki-67 protein, a recognized marker of cell proliferation, utilizing Lumit™ immunoassay technology. This luminescent assay has been effectively multiplexed with a fluorescent measure of cell death, employing a cell-impermeant fluorogenic DNA dye. This multiplex allows for the clear distinction between antiproliferative activity and overt cytotoxicity in cell culture models. Through varying lytic conditions, we demonstrated effective cell lysis and detection of nuclear Ki-67 protein. Specifically, Lumit™ Lysis Buffer II provided efficient recovery of Ki-67 protein without compromising assay performance, including the requisite binding of labeled antibodies to the target protein. This assay exhibited excellent signal-to-background (up to 40-fold) and signal linearity (R^2 = 0.99) in wildtype HeLa cells (~1000 to 80,000/well), while the signal in Ki-67 knockout HeLa cells was comparable to the no-cell background, indicating excellent specificity for Ki-67 protein. Due to the unavailability of recombinant full-length Ki-67 protein, two different recombinant Ki-67 protein fragments were used to corroborate assay sensitivity of &amp;lt;1 pM Ki-67 protein. The assay's suitability for human Ki-67 protein detection, not mouse, was observed through further cell-based testing. The proliferation/cytotoxicity assay multiplex was validated in both suspension and adherent cell lines, as well as primary cell culture, detecting antiproliferative and proliferative responses. CDK4/6 inhibitors are a class of antiproliferative agents of significant interest for their potential in treating cancer. In Jurkat cells, treatment with the CDK4/6 inhibitor palbociclib led to a dose-dependent reduction in Ki-67 protein expression with an EC50 of 88 nM, and total Ki-67 elimination at 2 μM compound concentration. Notably, there was no cytotoxicity detected at the tested doses and treatment duration (up to 48 h), but a significant reduction in viable cell number at maximal palbociclib concentrations, aligning with an antiproliferative mechanism. This work establishes a rapid, simple, luminescent assay for determining Ki-67 levels that can be paired with a fluorogenic readout of cell death, facilitating efficient and quantitative discernment of altered proliferation in mammalian cell culture using standard microplate readers. Citation Format: Dan F. Lazar, Kevin R. Kupcho, Andrew L. Niles, James J. Cali. A homogeneous assay system for discernment of proliferative, antiproliferative, and cytotoxic effects in culture [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 1631.
Abstract 2656: The selective IKZF2 molecular glue degrader, PVTX-405, counters Treg immune suppression,shows significant tumor growth delay as single agent and synergistic response with immune checkpoint therapies (ICTs)
Authors: Harshil D. Dhruv, Donna McEachern, Longchuan Bai, Xuqing Zhang, Zhixiang Chen, Rakesh Nagilla, Elham Behshad, Bomie Han, Peter Orth, Rohan Rej, Paul Kirchhoff, Niu Shin, Larry Jolivette, Corey Strickland, Zhihua Sui, Scott Priestley, Shaomeng Wang, Helai Mohammad
Journal: Cancer Research (2024)

Abstract Immunosuppressive regulatory T-cells (Tregs) are key modulators of tumor immune evasion and resistance to immune checkpoint therapies (ICTs). IKZF2 (Helios) is a transcription factor that is selectively expressed by Treg and has been shown to be essential for maintaining function and stability of Tregs in the face of inflammatory conditions that include autoimmune disease as well as cancer. Here we describe the discovery of PVTX-405, a potent and selective IKZF2 molecular glue degrader (DC50=6.3 nM). Our molecular glue degrader promotes a productive ternary complex with the E3 ubiquitin ligase substrate receptor cereblon (CRBN) to selectively degrade IKZF2 while sparing other CRBN neosubstrates (IKZF1/3, GSPT1, CK1a). PVTX-405 demonstrates rapid and selective degradation of IKZF2 in Jurkat cells in vitro, human PBMC derived Tregs ex vivo, and in cynomolgus monkeys in vivo. Degradation of IKZF2 in Jurkat cells leads to dose dependent increase in production of inflammatory cytokine IL-2. In ex vivo co-cultures of Tregs and effector T-cells, PVTX-405 reduces the suppressive activity of Tregs. To determine whether the relief of Treg suppressive activity observed in vitro and ex vivo can translate to anti-tumor activity in vivo we utilized CRBNI391V(humanized CRBN) mice. We developed a novel MC38 syngeneic tumor model to test both monotherapy and combination efficacy in an immune-competent setting. Once daily oral administration of PVTX-405 as single agent significantly delays the growth of MC38 tumors. Further, in vivo treatment of PVTX-405 in combination with ICTs, anti-PD1 or anti-LAG3, significantly increased animal survival and led to durable tumor regressions compared to ICTs alone. Together, these results demonstrate a strong synergy between ICTs and Treg destabilization through pharmacological degradation of IKZF2 and represent a promising combination strategy for treatment of cancer. Citation Format: Harshil D. Dhruv, Donna McEachern, Longchuan Bai, Xuqing Zhang, Zhixiang Chen, Rakesh Nagilla, Elham Behshad, Bomie Han, Peter Orth, Rohan Rej, Paul Kirchhoff, Niu Shin, Larry Jolivette, Corey Strickland, Zhihua Sui, Scott Priestley, Shaomeng Wang, Helai Mohammad. The selective IKZF2 molecular glue degrader, PVTX-405, counters Treg immune suppression,shows significant tumor growth delay as single agent and synergistic response with immune checkpoint therapies (ICTs) [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 2656.
Abstract 1097: CD73 contributes to the pathogenesis of fusion-negative rhabdomyosarcoma through the purinergic signaling pathway
Authors: Karla Gabriela Cano Hernandez, Akansha Shah, Victor Lopez, Vincent Tagliabracci, Kenian Chen, Lin Xu, Rhonda Bassel-Duby, Eric Olson, Ning Liu
Journal: Cancer Research (2024)

Abstract Rhabdomyosarcoma (RMS) is the most common type of soft tissue sarcoma in children and adolescents. Fusion-Negative RMS (FN-RMS) accounts for more than 80% of all RMS cases. The long-term event-free survival rate for patients with high grade FN-RMS is below 30%, highlighting the need for improved therapeutic strategies. CD73 is a 5’ ectonucleotidase that hydrolyzes AMP to adenosine and regulates the purinergic signaling pathway. We found that CD73 is elevated in FN-RMS tumors that express high levels of TWIST2. While high expression of CD73 contributes to the pathogenesis of multiple cancers, its role in FN-RMS has not been investigated. We found that CD73 knockdown decreased FN-RMS cell growth while upregulating the myogenic differentiation program. Moreover, mutation of the catalytic residues of CD73 rendered the protein enzymatically inactive and abolished its ability to stimulate FN-RMS growth. Overexpression of wildtype CD73, but not the catalytically inactive mutant, in CD73 knockdown FN-RMS cells, restored their growth capacity. Likewise, treatment with an adenosine receptor A2A-B agonist partially rescued FN-RMS cell proliferation and bypassed the CD73 knockdown defective growth phenotype. These results demonstrate that the catalytic activity of CD73 contributes to the pathogenic growth of FN-RMS through the activation of the purinergic signaling pathway. Therefore, targeting CD73 and the purinergic signaling pathway represents a potential therapeutic approach for FN-RMS patients. Citation Format: Karla Gabriela Cano Hernandez, Akansha Shah, Victor Lopez, Vincent Tagliabracci, Kenian Chen, Lin Xu, Rhonda Bassel-Duby, Eric Olson, Ning Liu. CD73 contributes to the pathogenesis of fusion-negative rhabdomyosarcoma through the purinergic signaling pathway [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 1097.
Abstract 2671: Sustained inhibition of CSF1R signaling effectively augments antitumor immune responses through inhibiting tumor-associated macrophages
Authors: Takahiko Sato, Daisuke Sugiyama, Yasuhiro Kojima, Satomi Hattori, Kazuki Sone, Tomohiro Ishikawa, Yuichi Ishikawa, Takuma Kato, Hitoshi Kiyoi, Hiroyoshi Nishikawa
Journal: Cancer Research (2024)

Abstract Tumor-associated macrophages (TAMs) are one of the key immunosuppressive components in the tumor microenvironment (TME) and contribute to tumor development, progression, and resistance to cancer immunotherapy. Several reagents targeting TAMs have been tested in preclinical and clinical studies, but they have had limited success. Here, we show that a novel reagent, FF-10101, exhibits a sustained inhibitory effect against colony stimulating factor 1 receptor by forming a covalent bond and reduces immunosuppressive TAMs in the TME, which leads to strong antitumor immunity. In preclinical animal models, FF-10101 treatment significantly reduced immunosuppressive TAMs and increased antitumor TAMs in the TME. In addition, tumor antigen-specific CD8+ T cells were increased; consequently, tumor growth was significantly inhibited. Moreover, combination treatment with an anti-PD-1 antibody and FF-10101 exhibited a far stronger antitumor effect than either treatment alone. In human cancer specimens, FF-10101 treatment reduced PD-L1 expression on TAMs, as observed in animal models. Thus, FF-10101 acts as an immunomodulatory agent that can reduce immunosuppressive TAMs and augment tumor antigen-specific T cell responses, thereby generating an immunostimulatory TME. We propose that FF-10101 is a potential candidate for successful combination cancer immunotherapy with immune checkpoint inhibitors, such as PD-1/PD-L1 blockade. Citation Format: Takahiko Sato, Daisuke Sugiyama, Yasuhiro Kojima, Satomi Hattori, Kazuki Sone, Tomohiro Ishikawa, Yuichi Ishikawa, Takuma Kato, Hitoshi Kiyoi, Hiroyoshi Nishikawa. Sustained inhibition of CSF1R signaling effectively augments antitumor immune responses through inhibiting tumor-associated macrophages [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 2671.