tbuckley/cabot-search huggingface dataset:
Abstract 1093: Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma
Authors: Taryn Shaw, Kay Nakazawa, Purushottam Tiwari, Eryn Nelson, Jeffrey Formen, Christian Wolf, Jeffrey Toretsky, Aykut Üren
Journal: Cancer Research (2024)

Abstract Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. It is commonly divided into subtypes based on histopathological appearance. The oncogenic fusion proteins PAX3::FOXO1 or PAX7::FOXO1 are present in the alveolar subtype of RMS (ARMS). These chimeric proteins are formed by reciprocal chromosomal translocations and consist of an N-terminal portion of the PAX3 or PAX7 transcription factor fused to a C-terminal portion of the FOXO1 transcription factor. These fusion proteins have been shown to drive malignant transformation in ARMS, and patients with fusion-positive ARMS have a worse prognosis than patients with fusion-negative ARMS and embryonal RMS. We recently reported that piperacetazine, a phenothiazine derivative and first-generation antipsychotic, is capable of binding to and inhibiting the transcriptional activity of PAX3::FOXO1, reducing the expression of PAX3::FOXO1 target genes, and inhibiting the ability of fusion-positive RMS cells to grow in soft agar. We hypothesize that other phenothiazine derivatives may have stronger binding affinity for PAX3::FOXO1 and greater ability to reduce tumor growth in vivo. We employed a structure-activity relationship campaign to develop new phenothiazine derivatives that may be more potent inhibitors of PAX3::FOXO1 than piperacetazine. We synthesized and tested 10 new compounds, in addition to 9 existing FDA-approved phenothiazine derivatives, for their ability to bind to PAX3::FOXO1 and inhibit its transcriptional activity and target gene expression as well as inhibiting the growth of fusion-positive RMS cells in 3D culture. Seven derivatives inhibited PAX3::FOXO1 reporter activity better than piperacetazine, nine of them performed worse, and three of them showed comparable activity to piperacetazine. We demonstrated that piperacetazine does not alter PAX3::FOXO1 levels, subcellular localization, binding to a PAX3::FOXO1 target DNA sequence, or phosphorylation at Ser256 in the FOXO1 portion of the fusion protein. We therefore hypothesize that piperacetazine may be disrupting interactions between PAX3::FOXO1 and its partner proteins. We are employing a proximity-based biotinylation method to identify proteins that are competed away from PAX3::FOXO1 by piperacetazine. Our data suggest that it is possible to target PAX3::FOXO1 protein using small molecules that can directly bind to it and inhibit its activity in fusion-positive RMS cells. Citation Format: Taryn Shaw, Kay Nakazawa, Purushottam Tiwari, Eryn Nelson, Jeffrey Formen, Christian Wolf, Jeffrey Toretsky, Aykut Üren. Small molecule inhibitors of the PAX3::FOXO1 fusion protein in rhabdomyosarcoma [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 1093.
Abstract 4546: Pegargiminase and melphalan as a novel drug combination strategy for uveal melanoma
Authors: Iuliia Pavlyk, Josephine Carpentier, Emilia Appolonia Szlosarek, Pui Ying Chan, John S. Bomalaski, Peter Wojciech Szlosarek
Journal: Cancer Research (2024)

Abstract Uveal melanoma (UM) is a hard-to-treat arginine auxotrophic cancer with approximately 50% of patients succumbing to metastases predominantly to the liver with a median overall survival of 19-22 months and a 5 year survival of around 10%. Novel drug strategies are urgently needed beyond the currently available immunotherapies that provide durable disease control in a small subset of patients. Arginine deprivation with pegylated arginine deiminase (ADI-PEG20; pegargiminase) is a novel anti-metabolite therapy which demonstrated activity in early phase trials in patients with UM, and more recently, increased survival in patients with the aggressive arginine-dependent cancer, non-epithelioid mesothelioma in the global phase 3 trial, ATOMIC-Meso. Here, we investigated the preclinical rationale for combining pegargiminase with melphalan, a drug which is delivered directly to the liver using an FDA-approved device from Delcath for patients with hepatic-centric UM disease. Two of four uveal melanoma cell lines were negative for expression of the rate-limiting enzyme for arginine production, argininosuccinate synthetase 1 (ASS1) and were submitted for drug evaluation accordingly. ADI-PEG20 treatment of ASS1-deficient cell lines 91.2 and MP41 demonstrated sensitivity to ADI-PEG20 (500ng/ml) compared to MP38 and MP46 ASS1-proficient cell lines. Moreover, the combination of ADI-PEG20 and melphalan (0.77µM) had at least an additive effect on ASS1 negative cell lines in 2D assay (92.1 p-value 0.0061; MP41 p-value is 0.0053). UM cell line proliferation was decreased by 50% in the combination group compared to ADI-PEG20 alone by 6 days of culture. Experiments to assess cytotoxicity and cell death analysis are ongoing. This drug combination therapy has the potential to improve outcomes in patients with uveal melanoma. Based on the good tolerability and safety of both drugs in patients, a clinical trial of pegargiminase with melphalan is planned for 2024 (ATOMIC-UM). Citation Format: Iuliia Pavlyk, Josephine Carpentier, Emilia Appolonia Szlosarek, Pui Ying Chan, John S. Bomalaski, Peter Wojciech Szlosarek. Pegargiminase and melphalan as a novel drug combination strategy for uveal melanoma [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 4546.
Abstract 1685: Investigating PAX8 interactions in ovarian cancer
Authors: Kostianna Sereti, Anna Russo, Ryan Raisner, Karen Gascoigne
Journal: Cancer Research (2024)

Abstract Ovarian cancer is the most lethal gynecological cancer and there is a critical unmet need to develop novel therapies. The transcription factor, PAX8, is upregulated in ~80% of renal, ovarian, endometrial and thyroid tumors and its overexpression correlates with higher risk of death and recurrence. PAX8 represents a promising target because of its high specificity and low expected toxicity, but how it promotes tumorigenesis remains elusive. Using proximity labeling followed by mass spectrometry, we identified a list of PAX8 binding partners and have further confirmed these interactions at the genomic level through ChIP-seq and ATAC-seq. Our findings reveal novel PAX8 interactions and a potential therapeutic approach for ovarian cancer treatment. Citation Format: Kostianna Sereti, Anna Russo, Ryan Raisner, Karen Gascoigne. Investigating PAX8 interactions in 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 1685.
Abstract 1673: KRAS dependency, a gene editing approach
Authors: Christophe Marcireau, Fréderic Lacroix, Dietmar Hoffmann, May Cindhuchao, Loreley Calvet, Yvette Ruffin, Laurent Debussche
Journal: Cancer Research (2024)

Abstract The RAS family genes encode small GTP-binding cytoplasmic proteins that are important signaling molecules. They regulate cell growth, survival and differentiation by coupling receptor activation to downstream effector pathways. Activating mutations of oncogenic RAS pathway genes are frequently detected in human cancers. The role of KRAS in tumor formation is not questionable. It’s implication in tumor maintenance is less well validated. The KRAS dependency is a key question to answer before to develop KRAS inhibitor. Targeted genome editing using CRISPR/Cas9 is a relatively new, revolutionary technology allowing for efficient and directed alterations of the genome. CRISPR is a genome-editing platform that makes use of the bacterially-derived endonuclease Cas9 to introduce DNA double-strand breaks at precise locations in the genome using complementary guide RNAs. These double strand breaks can be repaired by homologous recombination DNA repair mechanisms thank to a donor DNA template. By this way mutations can be introduced at desired loci, DNA fragment can be deleted or introduce at the desired location. We aimed at investigating the KRAS dependence and we applied the CRISPR-Cas9 technology to engineer isogenic cancer cells harboring a “conditional KRAS gene knockout" by exchanging the KRAS endogenous promoter. This promoter replacement approach can be used also to validate new targets. Citation Format: Christophe Marcireau, Fréderic Lacroix, Dietmar Hoffmann, May Cindhuchao, Loreley Calvet, Yvette Ruffin, Laurent Debussche. KRAS dependency, a gene editing approach [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 1673.
Abstract 4572: Ginsenoside Rh3 increases the susceptibility of regorafenib-mediated cancer cell death by inhibiting the JAK/STAT3 signaling pathway in hepatocellular carcinoma
Authors: Youngsic Jeon, Hyukjoon Kwon, Young Nyun Park, Dong-Young Woo, Taejung Kim, Jungyeob Ham, Young-Joo Kim
Journal: Cancer Research (2024)

Abstract Ginsenosides, bioactive compounds derived from Panax ginseng, exhibit diverse pharmacological effects, including anti-cancer properties. Regorafenib, a potent multi-kinase inhibitor, is employed as a second-line therapy for advanced hepatocellular carcinoma (HCC). However, the modest survival benefits observed in treated patients may be attributed to drug resistance. In this study, we screened a panel of 40 ginsenosides for their activity in combination with regorafenib in HCC cell lines and investigated their underlying cellular mechanisms. Synergistic effects were evaluated using the WST-8 assay, and optimal drug concentrations were determined through synergy scoring. A phospho-kinase assay was conducted to elucidate the mechanism of action, and in vivo experiments validated our findings. Ginsenoside Rh3 emerged as a promising candidate, enhancing the sensitivity of HCC cells to regorafenib-induced anticancer effects by promoting apoptosis. The phospho-kinase array revealed that the combined treatment's apoptotic effect was associated with the inhibition of signal transducer and activator of transcription 3 (STAT3) activation through the Janus kinase pathway. In vivo results demonstrated the combination treatment's inhibitory effects on tumor growth. Our study proposes a novel treatment strategy, highlighting the potential efficacy of combining regorafenib and ginsenoside Rh3 for HCC treatment. Citation Format: Youngsic Jeon, Hyukjoon Kwon, Young Nyun Park, Dong-Young Woo, Taejung Kim, Jungyeob Ham, Young-Joo Kim. Ginsenoside Rh3 increases the susceptibility of regorafenib-mediated cancer cell death by inhibiting the JAK/STAT3 signaling pathway in hepatocellular carcinoma [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 4572.
Abstract 6879: Development of a rapid multiplex immunohistochemistry for characterizing tumor-immune microenvironment
Authors: Alisa Kimura, Takahiro Tsujikawa, Hiroki Morimoto, Junichi Mitsuda, Sumiyo Saburi, Shigeyuki Mukudai, Hikaru Nagao, Nana Sakurai, Nanako Murakami, Aya Miyagawa-Hayashino, Hiroshi Ogi, Saya Shibata, Eiichi Konishi, Kyoko Itoh, Shigeru Hirano
Journal: Cancer Research (2024)

Abstract Intratumoral immune profiles have been related to prognosis and therapeutic efficacy; this could result in personalized treatment based on biomarkers. Although techniques for multifactorial evaluation of different tumor-immune microenvironments have been established, their practical implementation in clinical settings still requires further improvement, where the time required for testing needs to be reduced and the technology needs to be clinically validated. To develop a multiplex, quantitative, and rapid tissue evaluation method based on clinically established standard immunohistochemistry (IHC), we attempted to develop 6-marker rapid multiplex IHC based on our previously reported 14-marker multiplex IHC via the reduction of the number of labels and speeding up the staining procedure (Tsujikawa et al. Cell Reports, 2017). First, we confirmed whether immunological features that were found to be associated with prognosis in 14-marker multiplex IHC analyses could be identified with fewer labels. Quantitative results by selected six markers exhibited significant correlation with those by 14 markers in terms of immune classifications based on the balance of lymphoid and myeloid cells. Next, we developed a rapid staining protocol by optimizing the reaction temperature, chromogen, and washing time, allowing the completion of 6-marker analysis in 5 hours and 49 minutes as opposed to several days required for the conventional multiplex IHC. By using six markers, validation in benign tonsil tissue and head and neck cancer tissue exhibited significant correlation between rapid and standard multiplex IHC in terms of staining intensities, densities of T cells, macrophages, lymphoid/myeloid immune cells ratios, and spatial profiles of intratumoral immune infiltrates. This method may enable a quantitative assessment of tumor-immune microenvironment on a clinically feasible time scale, which promote the development of tissue biomarker-guided therapeutic strategies. Citation Format: Alisa Kimura, Takahiro Tsujikawa, Hiroki Morimoto, Junichi Mitsuda, Sumiyo Saburi, Shigeyuki Mukudai, Hikaru Nagao, Nana Sakurai, Nanako Murakami, Aya Miyagawa-Hayashino, Hiroshi Ogi, Saya Shibata, Eiichi Konishi, Kyoko Itoh, Shigeru Hirano. Development of a rapid multiplex immunohistochemistry for characterizing tumor-immune microenvironment [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 6879.
Abstract 1824: Hexadecanoic acid mediated cell cycle arrest involving inhibition of cell migration
Authors: Sasha-gay A. Wright, William Aiken, Helen Asemota, Kimberly Foster, Rupika Delgoda
Journal: Cancer Research (2024)

Abstract The Caribbean region accounts for the highest incidence and mortality rates of prostate cancer in the world. This warrants the need for targeted therapy as currently the most prevalent and effective option include chemotherapeutic drugs. Previous studies showed that an enriched sample extracted from the Jamaican Round Leaf yellow yam exhibited antiproliferative effects on DU145 prostate cancer cells. Based on the results obtained, this present study aims at exploring the underlying mechanism of action as well as the antimetastatic activities that the yam derived hexadecanoic acid may exhibit. Flow cytometry analysis was used to assess cell cycle arrest exhibited by hexadecanoic acid on the hormone insensitive DU145 prostate cancer cells. The western blot analysis was then utilized to determine the effects of the hexadecanoic acid enriched sample on cyclins in the cells. Transwell migration assays were then used to evaluate cell metastatic capabilities. Hexadecanoic acid enriched sample induced G1 S cell cycle arrest in the hormone insensitive prostate cancer cell line. Western blot assays also indicated that cell death was possibly induced through the cell cycle regulatory protein, cyclin D1 as its expression was downregulated in the treatment groups. Additionally, the observed metastatic inhibition of prostate cancer cells due to the action of the hexadecanoic acid in the wound healing assay may be attributed to a mechanism involving cyclin D1 as studies have indicated that abnormal Ccnd1 Cdk4 expression promotes tumor growth and metastasis. These results are substantial as it indicates a mechanistic pathway through which hexadecanoic acid is able to cause antiproliferative effects through a cell cycle arrest of hormone insensitive prostate cancer cell lines. Citation Format: Sasha-gay A. Wright, William Aiken, Helen Asemota, Kimberly Foster, Rupika Delgoda. Hexadecanoic acid mediated cell cycle arrest involving inhibition of cell migration [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 1824.
Abstract 6872: A spatio-temporal approach to mapping the dynamics of cutaneous squamous cell carcinoma progression and immunotherapy response: A journey through TiME
Authors: Niyati Jhaveri, Bassem Ben Cheikh, Dmytro Klymyshyn, Ning Ma, Aditya Pratapa, James Monkman, Nadine Nelson, Arutha Kulasinghe
Journal: Cancer Research (2024)

Abstract Background: Cutaneous squamous cell carcinoma (cSCC), arising from proliferation of malignant epidermal keratinocytes, is the second most common non-melanoma skin cancer. cSCC accounts for 75% of all skin cancer related deaths excluding melanoma, and metastatic and immunotherapy-resistant cases pose an emerging global threat. Tumor development is a gradual process characterized by high mutational burden and an immunosuppressive tumor immune microenvironment (TiME); therefore, identifying the underlying changes across the spatial and temporal landscape of these tumors will be crucial to understanding the key cellular and molecular drivers of disease progression and response. Methods: In this longitudinal study, we used a single-cell, whole-slide approach to mapping key proteins of immune lineage, tissue architecture, cellular metabolism, and stress to study the spatial landscape of cSCC at baseline (pre-treatment) and multiple time points over the course of immunotherapy with the aim to develop a temporal atlas of the tumor. An ultra-high plex antibody panel encompassing over 50 major determinants in the tumor microenvironment was employed on the PhenoCycler®-Fusion spatial biology platform. Deep bioinformatic analyses was performed to identify cellular phenotypes, spatial neighborhoods, heterogenous functional states and cellular interactions by spatial proximity determinations. Results: Previous studies in our laboratory have identified unique phenotypes correlating with response and resistance to immunotherapies in pre-treatment cSCC biopsies. Our results expand on these findings with temporal data tracking the dynamic changes in the TiME over the course of immune checkpoint inhibitor therapy. Apart from differences in immune cell composition and spatial localization patterns, we also saw differences in macrophage polarization and expression of metabolic markers in the responder and non-responder cohorts. Conclusions: Overall, ultrahigh-plex spatio-temporal monitoring of cSCC revealed distinct signatures of response and resistance and identified key features in the TiME that reveal deeper insights into the pathobiology of the tumor. Our discovery-based approach identifies novel biomarkers for patient stratification and therapeutic modulation. Citation Format: Niyati Jhaveri, Bassem Ben Cheikh, Dmytro Klymyshyn, Ning Ma, Aditya Pratapa, James Monkman, Nadine Nelson, Arutha Kulasinghe. A spatio-temporal approach to mapping the dynamics of cutaneous squamous cell carcinoma progression and immunotherapy response: A journey through TiME [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 6872.
Abstract 4232: Exploring chemotherapy resistance in pancreatic cancer: Insights from a 3D organoid model
Authors: Hee Seung Lee
Journal: Cancer Research (2024)

Abstract Pancreatic cancer is marked by a dismal prognosis, with a 5-year survival rate at approximately 10%. A key contributor to its lethality is the development of chemotherapy resistance, followed by early metastasis. However, studies elucidating the mechanisms behind chemotherapy resistance in pancreatic cancer are limited. Previous research has relied on 2D cell line models, which present limitations, such as uniform cell types that fail to capture tumor heterogeneity and an inaccurate representation of clinical realities, wherein resistance often develops gradually rather than through continuous exposure to high drug concentrations. In this study, we developed a more sophisticated organoid model of chemotherapy resistance. Six organoids from three patients were matched to study chemotherapy resistance in a personalized context. Comprehensive whole-exome sequencing and transcriptomic analyses were performed, along with an examination of chemotherapy resistance protein expression and EMT-related markers. Notably, differential expression levels of CK19 and Vimentin were observed between samples. Our analysis also focused on the expression of the ATP-Binding Cassette Subfamily G Member 2 (ABCG2) gene in chemoresistant organoids. Western blot analysis indicated a significant increase in ABCG2 expression in these organoids compared to controls. According to the Moffitt RNA signature, the primary and corresponding chemoresistant organoids retained their molecular subtype classifications both before and after developing chemoresistance. Gene set enrichment analysis uncovered significant upregulation of pathways related to DNA repair and cell cycle regulation, particularly the G2M checkpoint, in chemoresistant organoids. Furthermore, gene ontology functional analysis suggested a notable overrepresentation of activities related to amino acid transmembrane transport and extracellular matrix constituents, underscoring their potential role in the chemoresistance phenotype. Citation Format: Hee Seung Lee. Exploring chemotherapy resistance in pancreatic cancer: Insights from a 3D organoid 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 4232.