tbuckley/cabot-search huggingface dataset:
Abstract 2112: Identification of biomarkers associated with sensitivity to a novel PCNA inhibitor (AOH1996) by CRISPRi screening
Authors: Long Gu, Ming li, Chun-Wei Chen, Robert J. Hickey, Linda H. Malkas
Journal: Cancer Research (2024)

Abstract Proliferating cell nuclear antigen (PCNA) plays an essential role in regulating DNA synthesis and repair and is essential for cancer cell growth and survival. We discovered a cancer-associated isoform of PCNA (caPCNA), which is ubiquitously and highly expressed in a broad range of cancer cells and tumor tissues but is not significantly expressed in non-malignant cells. Further studies of this novel caPCNA isoform as an anti-cancer drug target led to the identification of a cancer distinct region of PCNA which is partly delineated by the L126-Y133 peptide sequence and the discovery of a small molecule (AOH1996), which binds to this cancer distinct region as shown by crystallization studies. By targeting caPCNA, AOH1996 selectively kills cancer cells by interfering with the resolution of transcription-replication conflicts (TRC). Importantly, it causes no discernable toxicity at 6 times of its effective dose in mice. AOH1996 is currently in a phase 1 clinical trial for adult solid tumors at City of Hope (IND 138273). To identify genes that may be used as biomarkers for patient selection or potential targets for combination therapies, we screened a CRISPR interference (CRISPRi) library, which targets genes that are involved in cell signaling and cell cycle regulation. After culturing transduced cells in the presence of DMSO or 250 nM AOH1996 (corresponding to IC20) in triplicates for 14 generations, we measured the relative abundance of each guide RNA (gRNA) construct. Significant changes in the abundance of the gRNA constructs in AOH1996-treated cells relative to that in DMSO-treated cells were determined by the MAGeCK method. The target genes of the depleted or enriched gRNAs are predominantly involved in DNA repair, cell cycle regulation, and transcription regulation, which is consistent with the action mechanism of AOH1996. We validated the effect of these genes on sensitivity to AOH1996 and identified a panel of target proteins whose up or down-regulation is associated with sensitivity to AOH1996. Some of these proteins are targets of known chemotherapeutic drugs, which may be used in combination with AOH1996 in the clinic. Citation Format: Long Gu, Ming li, Chun-Wei Chen, Robert J. Hickey, Linda H. Malkas. Identification of biomarkers associated with sensitivity to a novel PCNA inhibitor (AOH1996) by CRISPRi screening [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 2112.
Abstract 6096: Targeting premalignant lung cancer to intercept progression to invasive disease
Authors: Mitchell Martin, Yongfeng He, Bhavneet Bhinder, Liron Yoffe, Sijin Luo Zhong, Arshdeep Singh, Olivier Elemento, Shaoyi Jiang, Nasser Altorki, Vivek Mittal
Journal: Cancer Research (2024)

Abstract Increased implementation of low dose CT-guided screens in the clinic has led to the identification of premalignant lung nodules (ground glass opacity, GGO) which progress to invasive adenocarcinoma1,2. Using integrated genomic analysis of a cohort of &amp;gt;300 patients with premalignant lesions, we constructed the first high-resolution landscape of composition, lineage/functional states, developmental trajectories, and multicellular crosstalk networks, which revealed potential targets for therapeutic intervention. We uncovered that early lesions exhibit marked immune-suppressive phenotypes characterized by increased T lymphocyte exhaustion to cytotoxic scores, decrease in NKT cells, elevated Tregs, increased myeloid suppressor activity, accumulation of immunosuppressive myeloid cells activation of unfolded protein response (UPR) sensor IRE1α that activates the multitasking transcription factor XBP1 known to drive malignant progression. Targeting IRE1α endoribouclease with a small molecule drug limited disease progression with marked immunomodulation in our newly developed Kras and EGFR driven mouse models, which mirror progression of human precursor lesions to invasive disease. As an immunoprevention approach, we have generated LNP-mRNA vaccines targeting top two shared neoantigens in premalignant lesions, which have shown marked immunogenicity and efficacy in early disease. Our work provides the molecular foundation for precision oncology strategies to intercept transition of preinvasive to invasive adenocarcinoma. 1. Altorki, N.K., et al. Nat Rev Cancer, 2019. 2. Altorki, N.K., et al. Cell Rep, 2022. Citation Format: Mitchell Martin, Yongfeng He, Bhavneet Bhinder, Liron Yoffe, Sijin Luo Zhong, Arshdeep Singh, Olivier Elemento, Shaoyi Jiang, Nasser Altorki, Vivek Mittal. Targeting premalignant lung cancer to intercept progression to invasive disease [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 6096.
Abstract 5421: Characterizing functional cell migration states with highly multiplexed immunofluorescence imaging
Authors: William Dee Leineweber, Alice Finkelstein, Emma Lundberg
Journal: Cancer Research (2024)

Abstract Cancer cell migration is a necessary step in the metastatic cascade, but there are heterogeneous cellular mechanisms to achieve this behavior. This study leveraged live-cell tracking and end-point spatial proteomics to better characterize what underlying molecular states drive migration heterogeneity. U2OS osteosarcoma stably expressing the FUCCI cell cycle reporter system were tracked for 20 hours on a Leica DMI8 widefield microscope. Immediately after, cells were fixed and prepared for highly-multiplexed immunofluorescence imaging on a Canopy CellScape instrument. Initial results from these experiments demonstrate that transferring the sample between these two systems is feasible and results in minimal loss of cells despite the multiple staining cycles. Unlike standard marker panels intended to differentiate between cell types, the initial panel used in this study includes markers that differentiate between migration modes. Even within one cell line, unsupervised clustering identified cell clusters for vimentin high/E-cadherin low and E-cadherin high/vimentin low, indicated an epithelial to mesenchymal transition (EMT) axis in the dataset. Furthermore, the spatial relationships between the cell neighborhoods show largely heterogeneous distributions of cell states, with clusters of more homogeneous cell states arising in more densely-packed regions of the coverslip. Further analysis of how single cell trajectories correlate to these cell states, as well as how cell cycle dynamics impact both migration and molecular cell states are in progress. Results from these analyses will shed new light on the “go vs. grow” hypothesis by directly testing how cell speed, persistence, and overall invasion correspond to cell cycle stage and progression. Furthermore, the high-resolution detail from the multiplexed imaging will allow for subcellular profiling of dynamic proteins, such as beta catenin, and directly link it to a larger protein and migration state. Overall, this experimental approach represents an important bridging between functional measurements and end-point omics technologies that will be crucial to gain actional insights amid the boom in multiomics. Citation Format: William Dee Leineweber, Alice Finkelstein, Emma Lundberg. Characterizing functional cell migration states with highly multiplexed immunofluorescence imaging [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 5421.
Abstract 5640: Unlocking the therapeutic potential of SF3B1 inhibitors for bladder cancer treatment
Authors: Rod Carlo Columbres, Arup Chakraborty, Andrea Apolo, Rouf Banday
Journal: Cancer Research (2024)

Abstract RNA splicing dysregulation is a hallmark of cancer, occurring in multiple solid and hematological malignancies. Splicing factor 3 subunit B1 (SF3B1), a key component of the U2 small nuclear ribonucleoprotein (snRNP) complex that regulates RNA splicing, is frequently altered in a variety of cancer types, including non-muscle-invasive and muscle-invasive bladder cancer, where the E902K mutation is common. In this study, we investigated the therapeutic potential of the SF3B1 inhibitor, pladienolide B, in bladder cancer using in vitro models. We used a recombinant plasmid containing the SF3B1E902K mutation and established an UMUC3E902K mutant urothelial cell line. Both UMUC3WT and UMUC3E902K cells were treated with pladienolide B alone or in combination with cisplatin to evaluate differences in cell viability. Flow cytometry using annexin V staining and propidium iodide exclusion was utilized to assess the cell death mechanism. RNAseq was performed after RNA extraction from UMUC3WT, UMUC3E902K, RT4, and HT1376 bladder cancer cell lines were treated with pladienolide alone or combined with cisplatin. We determined that the IC50 for pladienolide B is 5nM for UMUC3 cells observed 72 hours post-treatment. Treatment with pladienolide B halted the cell cycle and caused cell death by apoptosis for both UMUC3WT and UMUC3E902K cell lines. We also observed that UMUC3E902K cells were significantly more sensitive to pladienolide B compared to UMUC3WT cells (p≤0.05). Furthermore, there was a synergistic effect observed after co-treatment with low-dose pladienolide B (2 nM) and cisplatin (3 µM) for both UMUC3WT and UMUC3E902K cell lines, with UMUC3E902K cells showing greater sensitivity to combination treatment. Our results provide insights into the potential use of splicing inhibitors, alone or in combination with chemotherapy, for treating bladder cancer, specifically for tumors that bear driver mutations in splicing factors. Currently, we are evaluating the mechanism by which SF3B1 mutations make cells sensitive to pladienolide B in vitro and in vivo, with the goal of identifying specific mRNA splicing vulnerabilities that can be targeted by anti-sense or splice-switching oligonucleotides to achieve anti-tumor outcomes. Additional differential splicing patterns and preliminary in vivo results will be presented. Citation Format: Rod Carlo Columbres, Arup Chakraborty, Andrea Apolo, Rouf Banday. Unlocking the therapeutic potential of SF3B1 inhibitors for bladder cancer treatment [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 5640.
Abstract 3881: Discovery of highly potent, selective and efficacious STAT3 PROTAC degraders capable of achieving long-lasting tumor regression
Authors: Haibin Zhou, Dimin Wu, Longchuan Bai, Ranjan K. Acharyya, Hoda Metwally, Donna McEachern, Bo Wen, Duxin Sun, Shaomeng Wang
Journal: Cancer Research (2024)

Abstract STAT3 (signal transducer and activator of transcription 3) is a transcription factor and a promising therapeutic targets for cancer and other human diseases. We have previously reported the discovery of SD-36 and SD-91 as potent, selective and highly efficacious STAT3 degraders. In the present study, we report the discovery and extensive evaluation of new, highly potent, selective and efficacious new STAT3 degraders. In direct comparison, these compounds are &amp;gt;50-times more potent than SD-36 in inducing STAT3 degradation in cells and demonstrates &amp;gt;500-fold degradation selectivity over other STAT members. Proteomic analysis showed that our best lead compound (UM-STAT3-1218) only reduces the levels of STAT3 protein in cells over other &amp;gt;6,700 proteins. (UM-STAT3-1218) achieves low nanomolar IC50 values in leukemia and lymphoma cancer cell lines with activated STAT3. A single intravenous dose of (UM-STAT3-1218) at 3 mg/kg reduces the STAT3 protein for &amp;gt;4 days in xenograft tumor and native tissues, without reducing another other STAT members. Impressively, a single dose of (UM-STAT3-1218) at 3 mg/kg achieves complete and long-lasting tumor regression in multiple xenograft tumor models without any signs of toxicity. Taken together, (UM-STAT3-1218) is a highly promising STAT3 degrader for the treatment of the treatment of human cancers and other human diseases in which STAT3 plays a key role. Citation Format: Haibin Zhou, Dimin Wu, Longchuan Bai, Ranjan K. Acharyya, Hoda Metwally, Donna McEachern, Bo Wen, Duxin Sun, Shaomeng Wang. Discovery of highly potent, selective and efficacious STAT3 PROTAC degraders capable of achieving long-lasting tumor regression [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 3881.
Abstract 5401: Vasculogenic mimicry: A three-step progress to form lumen-containing and fluid-conducting tubular structures <i>in vitro</i>
Authors: Gareth I. Owen, Nicolle Santander, Gabriel Mingo, Pamela Gonzalez, Valentina George, Nicole Babbitt, Alejandra Espinioza, Isidora Vega, Cristobal Canales, Carolina Ibañez, Roger Gejman, Juan Carlos Roa, Francisco Nualart, Andrea Ravasio, Cristina Bertocchi
Journal: Cancer Research (2024)

Abstract Introduction: Vasculogenic mimicry (VM) is a clinical phenomenon by which cancer cells can form vessel-like structures in an endothelial-free (CD31-) fashion. VM presence in tumors correlates to poor patient prognosis. In our laboratory we have established an in vitro model where cancer cells from either cell lines or primary culture form lumen-lined and fluid-conducting tubular structures when grown on laminin-rich Matrigel over a four-day period. Given the duration of formation and the complexity of these structures, we hypothesize that VM in vitro is a multistep process, where each stage requires spatio-temporal organization of adhesive proteins, stemness and EMT (suggesting the need for epithelial to mesenchymal transition) signaling. Methods: Using our in vitro models, we analyzed by siRNA, immunostaining and live cell imaging with Airyscan the distinct phases and the corresponding spatio-temporal organization of selected proteins. Results: We show that VM in vitro has three distinct phases that are characterized by (1) alignment and migration, (2) contraction, proliferation and bridge formation, and (3) tubular structure closure and lumen formation. These steps require spatio-temporal distribution of ZEB1 and E-cadherin (suggesting gain and loss of epithelial to mesenchymal transition), the presence of Integrin β1 and laminin 111, and the distinct localization of Laminin and CD44. Conclusion: A better characterization of VM may lead to the identification of a clinically useful marker to predict poor patient prognosis and shed light on a druggable pathway to treat this subgroup of aggressive cancer. Citation Format: Gareth I. Owen, Nicolle Santander, Gabriel Mingo, Pamela Gonzalez, Valentina George, Nicole Babbitt, Alejandra Espinioza, Isidora Vega, Cristobal Canales, Carolina Ibañez, Roger Gejman, Juan Carlos Roa, Francisco Nualart, Andrea Ravasio, Cristina Bertocchi. Vasculogenic mimicry: A three-step progress to form lumen-containing and fluid-conducting tubular structures in vitro [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 5401.
Abstract 4190: Patient-derived xenograft (PDX) models with differential HER2 expression for preclinical evaluation of HER2-targeted therapies
Authors: Xiaoliu Yang, Shiying Guo, Huiyi Wang, Xu Su, Jing Zhao, Xiang Gao, Cunxiang Ju
Journal: Cancer Research (2024)

Abstract Human epidermal growth factor receptor 2 (HER2) is a critical therapeutic target in gastric cancer. However, the varying expression levels of HER2 in patients present a significant challenge in selecting the appropriate HER2-targeted therapies. Patient-derived xenograft (PDX) models offer a valuable tool to address this clinical concern. We established a panel of PDX models derived from gastric cancer patients, each representing a distinct range of HER2 expression levels. These models were subsequently treated with HER2-targeted drugs, including Trastuzumab (Herceptin), Margetuximab, and Enhertu. Our results demonstrated differential drug responses corresponding to the varying HER2 expression levels in the PDX samples. Trastuzumab, Margetuximab, and Enhertu exhibited distinct efficacies across the HER2 expression spectrum. This underscores the significance of selecting the right therapeutic approach based on the HER2 status of individual patient. Our collection of PDX models with differential HER2 expression levels provides a robust platform for preclinical evaluation of HER2-targeted therapies. This approach not only addresses the clinical challenge of HER2 heterogeneity but also facilitates a more personalized and effective treatment strategy for gastric cancer patients. Citation Format: Xiaoliu Yang, Shiying Guo, Huiyi Wang, Xu Su, Jing Zhao, Xiang Gao, Cunxiang Ju. Patient-derived xenograft (PDX) models with differential HER2 expression for preclinical evaluation of HER2-targeted therapies [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 4190.
Abstract 5643: Targeted RNA-seq of dried blood microsamples for convenient RNA biomarker monitoring
Authors: Lester Kobzik, Tianbing Liu, Mikhail Makhanov, Dongfang Hu, Khadija Ghias, Paul Diehl, Alex Chenchik
Journal: Cancer Research (2024)

Abstract Microsampling lancet-induced blood drops enables frequent and comprehensive analysis of various metabolites, lipids, cytokines, and proteins. This approach holds promise for monitoring immunotherapy patients using RNA biomarkers, but a suitable method for processing RNA has been lacking. In this study, we employed a targeted RNA-sequencing protocol, the DriverMap™ EXP assay, to process 30 ul of dried blood. We compared the gene expression profile in traditionally collected blood samples with that of blood absorbed onto a Mitra® microsampling device containing an RNA-stabilization reagent. Following endotoxin incubation, RNA was extracted from stimulated and unstimulated blood samples. Targeted PCR amplification of 274 immune/inflammatory genes using the DriverMap targeted RNA-Seq protocol demonstrated robust detection and high correlation (r = 0.94) between the two methods in both unstimulated and endotoxin-stimulated blood. Moreover, differentially expressed genes (DEGs) identified in standard and microsampling methods exhibited substantial overlap with publicly available datasets from similar experiments. Furthermore, we compared whole blood extracted from Tempus™ blood RNA tubes to Mitra microsamples pre- and post-immunization with the Pneumovax® vaccine using the DriverMap EXP genome-wide 19K panel for targeted RNA-sequencing. We observed approximately 90% overlap in the top 10K genes between Tempus and Mitra microsamples. Notably, microsamples stored at 4ºC for over a year exhibited similar expression profiles to more recently drawn whole blood samples. Citation Format: Lester Kobzik, Tianbing Liu, Mikhail Makhanov, Dongfang Hu, Khadija Ghias, Paul Diehl, Alex Chenchik. Targeted RNA-seq of dried blood microsamples for convenient RNA biomarker monitoring [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 5643.
Abstract 4187: Transcriptome profiling and characterization of peritoneal metastasis ovarian cancer xenografts in humanized mice
Authors: Sung Wan Kang, Ji-young Lee, Ok-Ju Kang, Yong-Man Kim, Eun Kyung Choi, Shin-Wha Lee
Journal: Cancer Research (2024)

Abstract Background: Although immunotherapy has not yet been as successful in ovarian cancer (OC), it remains a potential therapeutic strategy. Preclinical models of OC are necessary to evaluate the efficacy of immuno-oncology (IO) drugs targeting human cancer and immune components but have been underutilized. Developing mouse models with a humanized (Hu) immune system can help understand the human immune response to IO drugs, including immune checkpoint inhibitors (ICIs), which have demonstrated limited effectiveness in OC patients. Methods: We established OC xenograft Hu-mouse models by intraperitoneally injecting luciferase-expressing SKOV-3 Luc and OVCAR-3 Luc OC cells into CD34+ Hu-mice. Tumor growth was monitored through bioluminescence imaging (BLI). We assessed the efficacy of PD-1 blockade with pembrolizumab in the SKOV-3 Luc Hu-mouse model. The immune profiles of the tumors were characterized using colorimetric immunostaining and flow cytometry. Additionally, we analyzed RNA-seq data to investigate the gene expression signature of pembrolizumab refractory tumors. Results: We confirmed tumor development in both OC cell lines within CD34+ Hu-mice. In these models, human lymphocyte and myeloid cell subsets were present in the tumors, draining lymph nodes, blood, and spleens. The SKOV-3 Luc tumor-bearing Hu-mice did not respond to pembrolizumab monotherapy. These tumors exhibited a high presence of tumor-infiltrating macrophages. Tumors in Hu-mice unresponsive to pembrolizumab showed a lower abundance of CD8+ T-cells, memory B cells, plasma cells, and a higher proportion of naïve M0 macrophages and mast cells compared to the PBS control. Furthermore, we identified 43 significantly enriched gene sets in these tumors. The differentially expressed genes (DEGs) were predominantly enriched in HDAC class I, RB1, KLF1/3, TCF21, MYD88, SMARCE1 target genes, and genes associated with epithelial-mesenchymal transition (EMT) and fibroblasts. Conclusion: Our xenograft Hu-mouse model of OC provides a valuable tool for investigating the efficacy of IO drugs. The insights gained from this model offer potential avenues to explore mechanisms of resistance to PD-1/PD-L1 blockade in OC. Citation Format: Sung Wan Kang, Ji-young Lee, Ok-Ju Kang, Yong-Man Kim, Eun Kyung Choi, Shin-Wha Lee. Transcriptome profiling and characterization of peritoneal metastasis ovarian cancer xenografts in humanized mice [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 4187.