tbuckley/cabot-search huggingface dataset:
Abstract 1344: Improvement of the anti-tumor activity of NK cells and the efficacy of anti-CD20 monoclonal antibodies in the therapy of B cell-derived malignancies
Authors: Abdessamad Zerrouqi, Aleksandra Zdanowicz, Anna Torun, Andrzej Ciechanowicz, Bhaskar Pradhan, Grzegorz Rymkiewicz, Dimitar Efremov, Beata Pyrzynska
Journal: Cancer Research (2024)

Abstract Resistance of tumor cells to immunotherapy with monoclonal antibodies (mAbs) often relies on the reduced level of the antigen targeted by the particular mAb. We have therefore screened for the compounds able to upregulate selected antigens on the surface of lymphoma/leukemia cells, to minimize the possibility of resistance acquired by the tumor cells. We have found that members of a specific class of antibiotics, known as cation carriers, namely salinomycin (SAL), monensin (MON), narasin, and nigericin exhibit great CD20 antigen-upregulating abilities. A variety of Burkitt’s lymphoma and diffuse large B-cell lymphoma (DLBCL) cell lines as well as patients-derived primary malignant cells, such as DLBCL and chronic lymphocytic leukemia (CLL) cells exhibited upregulation of surface CD20 upon the treatment with SAL and MON at concentrations as low as 250nM and 50 nM, respectively. As a consequence, these compounds appeared to be beneficial for the therapy of lymphoma/leukemia with anti-CD20 mAbs, both in vitro and in animal models.Moreover, the proteomics analysis revealed that besides CD20, cation carriers upregulated a number of different proteins on the surface of tumor cells, including proteins implicated in the interaction with immune cells. These included ICAM1, HLA-A/B/C, CD155, CD80, CD86 and ULBP2/5/6. Particularly important appears to be the upregulation of antigens interacting with the activating receptors on NK cells, helping them to overcome the inhibitory signals and stimulate the lysis of tumor cells. Thus, the results of proteomics analysis explained why SAL- or MON-pretreated tumor cells were efficiently eliminated by NK cells, even in the absence of therapeutic mAb. In light of our discoveries, it seems reasonable to consider the cation carriers as promising drug candidates for the improvement of NK cell anti-tumor activity and potential treatment of B-cell non-Hodgkin lymphoma patients, in combination with anti-CD20 mAbs.Funding: National Science Centre (NCN, Poland), grants 2019/35/B/NZ5/01445 and 2020/39/B/NZ6/03513. Citation Format: Abdessamad Zerrouqi, Aleksandra Zdanowicz, Anna Torun, Andrzej Ciechanowicz, Bhaskar Pradhan, Grzegorz Rymkiewicz, Dimitar Efremov, Beata Pyrzynska. Improvement of the anti-tumor activity of NK cells and the efficacy of anti-CD20 monoclonal antibodies in the therapy of B cell-derived malignancies [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 1344.
Abstract 4775: Unveiling caveolin-1's crucial role in breast cancer progression and metastasis: A molecular perspective
Authors: Rizwana Begum, Shilpa Thota, Dhirendra Pratap Singh, Naveen Chintala, Abhishek Pandit, Biplov Sapkota, Joseph Francis
Journal: Cancer Research (2024)

Abstract Background: Breast cancer, particularly its metastatic form, constitutes a significant portion of oncological mortality. Caveolin-1 (Cav-1), a caveolae structural protein, has been implicated in cellular processes such as proliferation, apoptosis, autophagy, and cellular motility (aberrant in breast cancer). With its dual role as a tumor suppressor and promoter, Cav-1's function in breast cancer pathophysiology requires elucidation for potential therapeutic targeting. Methods: We utilized a syngeneic mouse model to engineer Cav-1 deficient 4T1 murine mammary carcinoma cells which mirror the characteristics of stage IV breast cancer to investigate Cav-1's role in tumor growth and metastasis. We assessed cellular proliferation and lung metastasis, compared with wild-type controls, and performed molecular analyses to evaluate epithelial and mesenchymal marker expression, stemness-related markers, and autophagy-related gene expression. Results: Cav-1 ablation corresponded with a marked decrease in tumor proliferation and lung metastasis, indicating a suppressive role in tumor progression. Molecular characterization revealed downregulated epithelial markers (E-cadherin, β-catenin), transcription factors (TWIST1/2), and stem cell markers (NANOG, OCT4, SOX2, c-MYC, SALL4), with concurrent upregulation of the mesenchymal marker vimentin. Enhanced expression of autophagy-related genes (Beclin-1, ATG5, ATG16) was also observed, suggesting a disruption in autophagic pathways. Conclusion: Our findings underscore the critical role of Cav-1 in breast cancer progression, specifically its function in suppressing metastasis and modulating cellular phenotypes. Targeting Cav-1 could represent a novel therapeutic strategy to mitigate breast cancer growth and dissemination. Further research is warranted to explore the therapeutic potential of modulating Cav-1 in breast cancer treatment. Citation Format: Rizwana Begum, Shilpa Thota, Dhirendra Pratap Singh, Naveen Chintala, Abhishek Pandit, Biplov Sapkota, Joseph Francis. Unveiling caveolin-1's crucial role in breast cancer progression and metastasis: A molecular perspective [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 4775.
Abstract 4910: AI predicts drug response from the genomic features of cells and the kinase activity changes induced by compounds
Authors: Rens Janssens, Kimberly Rizzolo, Erin Artin, Joel Wagner, Markus Riester, Joshua Korn, Jisoo Park
Journal: Cancer Research (2024)

Abstract Human protein kinases are playing an important role in various biological activities including tumorigenesis and cancer progression, and for this reason, many kinase inhibitors have been developed as promising targeted therapies for cancer. To date, there are 72 FDA-approved treatments targeting about two dozen different protein kinases; 3 of them were approved in 2022. However, there are still critical challenges that can be addressed to improve the robustness and selectivity of the kinase inhibitors such as drug resistance, toxicity and compromised efficacy. To gain a deeper understanding of the biological mechanisms underlying the resistance to kinase inhibitors, we hereby design and train an artificial intelligence (AI) model that predicts in-vitro cell response to various kinase inhibition from the integration of the genomic features of cancer cell lines and the biochemical profiles of kinase activities. The inner-working of an optimized model provides important insights on the relevant kinase activities for the cell response. A major challenge for training such a model is that the training data for biochemical kinase activity is very sparse; the kinase panels are not consistent across different sources and each dataset contains many missing values. To address this, we train a secondary AI model to predict all the missing values for the kinase activity in our training data using the combination of the compound chemical structure and the kinase structure. The secondary model is independently validated to ensure the quality of the training data for the drug response prediction model. An investigation of the secondary model’s inner mechanism sheds light on the kinase binding sites and which chemical substructures are important for its inhibition. The model accurately predicts the cell response to different CDK inhibition. A focused analysis of the model characterizes off-target effects of the CDK inhibitors which may be linked to the drug resistance mechanisms, suggesting ways to improve the inhibitors or potential targets for combination therapies. Citation Format: Rens Janssens, Kimberly Rizzolo, Erin Artin, Joel Wagner, Markus Riester, Joshua Korn, Jisoo Park. AI predicts drug response from the genomic features of cells and the kinase activity changes induced by compounds [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 4910.
Abstract 378: PHD3 dependent stabilization of β3-adrenoceptor induces HIF-1αactivation in Ewing sarcoma
Authors: Amada Pasha, Laura Zocca, Francesco Carrozzo, Cristina Banella, Rachele Amato, Annalisa Tondo, Claudio Favre, Maura Calvani
Journal: Cancer Research (2024)

Abstract Hypoxia is a condition of oxygen deficiency which occurs in most growing solid tumors and stimulates a cascade of cell signals through a family of transcription factors named as hypoxia inducible factors (HIFs) that transactivate several regulatory genes involved in tumor proliferation. β3-adrenoceptors (β3-ARs) are involved in several hypoxic scenarios and in pathological conditions where hypoxia leads to important steps for cancer progression. Studies showed that β-AR blockade of mice suppressed hypoxia induction of renal HIF-1α accumulation, erythropoietin production, and erythropoiesis in vivo. In this work we assumed that through PHD3 activity, β3-AR mediates hypoxia sensing needed for HIF-1α stabilization, thus we investigated a putative correlation between β3-AR/HIF-1α and PHD3. Data showed a similar outcome of β3-ARs and HIF-1α at short time of hypoxia, and that β3-AR antagonist, SR59230A reduced HIF-1α protein expression under hypoxia. β3-AR silencing under hypoxia revealed an evident reduction of HIF-1α protein expression that confirmed the β3-AR modulation of HIF-1α expression. SR59230A treatment strongly reduced the HIF-1α target genes as GLUT1, HK-2 and HIF-1α expression at long time treatment confirming the β3-AR modulation of HIF-1α transcriptional activity. Conversely, the HIF-1α-transcriptional inhibitor Topotecan did not affect β3-AR expression confirming that β3-AR mediates HIF-1α activation. Immunofluorescence and nuclear-cytoplasmic fragmentation showed that β3-AR co-localized with the nucleus under hypoxia, more than normoxia, and presence of both β3-AR and HIF-1α in the nucleus. Co-immunoprecipitation of β3-AR/HIF-1α revealed that under hypoxia, HIF-1α dissociates from β3-AR binding, but this process was abrogated by SR59230A. HIF-1α, released under hypoxia from the link with β3-AR, can play its transcriptional activity in the nucleus, while the binding with β3-AR blocks its transcriptional activity. Moreover, the β3-AR upregulation under hypoxia occurs trough an early inhibition of PHD3 activity that did not influence HIF-1α expression. Hypoxic PHD2 inhibition results after PHD3 leading to HIF-1α upregulation. Moreover, the blockade β3-AR by SR59230A, inhibited HIF-1α upregulation by increasing PHD2 activity. Citation Format: Amada Pasha, Laura Zocca, Francesco Carrozzo, Cristina Banella, Rachele Amato, Annalisa Tondo, Claudio Favre, Maura Calvani. PHD3 dependent stabilization of β3-adrenoceptor induces HIF-1αactivation in Ewing sarcoma [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 378.
Abstract 3454: Cell-free DNA methylation and fragmentomic signatures identify tissue damage and predict cancer risk
Authors: Nicholas Cheng, Kimberly Skead, Tom Oullette, Scott Bratman, Daniel De Carvalho, David Soave, Philip Awadalla
Journal: Cancer Research (2024)

Abstract Cell-free DNA (cfDNA) epigenetic and fragmentomic profiling has emerged as prominent non-invasive approaches for early cancer detection and subtyping. However, owing to difficulties in observing the early development of human malignancies, most cancer biomarker and evolution studies to date have primarily examined biologics following a diagnosis. Utilizing cfDNA as a screening tool for early disease detection requires assessment of blood plasma samples collected from asymptomatic individuals prior to the diagnosis of cancers. Here, we leverage the Ontario Health Study (OHS), a prospective longitudinal population cohort, to assess cfDNA profiles in blood plasma collected from participants that developed breast (n=476), prostate (n=342) and pancreatic (n=32) cancers throughout the study follow up time between 2009 and 2019. We performed cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) on baseline plasma samples from incident cancer cases up to eight years prior to diagnosis, in addition to matched controls (n=404) with no history of cancer through follow-up. Genome-wide plasma cfDNA differential methylation analysis revealed significantly hypermethylated regions, particularly among CpG island and shore regions, were predictive of early breast cancers, and overlapped hypermethylated regions in solid cancer tissues relative to adjacent normal tissues and peripheral blood leukocytes. Using a repeated cross-validation strategy we found that as few as 200 hypermethylated regions can identify individuals with breast cancer in blood up to seven years prior to diagnosis among discovery set samples (AUC=0.725) and are highly generalizable to samples processed in separate batches (AUC = 0.650). Remarkably, integrating biomarker hypermethylated regions with fragmentomic features including fragment length and 5’ tetranucleotide motif proportions further increased accuracy for detecting individuals with early prostate cancers (AUC=0.804). In addition, we observed shared genome-wide cfDNA methylome changes associated with aging and heavy alcohol consumption in cfDNA. We identified increased shedding of tissue-specific methylation markers from liver and pancreatic tissue among individuals consuming more than three drinks a week relative to non-drinkers, reflective of potential signatures of tissue damage. Citation Format: Nicholas Cheng, Kimberly Skead, Tom Oullette, Scott Bratman, Daniel De Carvalho, David Soave, Philip Awadalla. Cell-free DNA methylation and fragmentomic signatures identify tissue damage and predict cancer risk [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 3454.
Abstract 2979: Pancreatic cancer cells upregulate LPAR4 in response to isolation stress to create a fibronectin-rich extracellular matrix niche and promote tumor initiation
Authors: Chengsheng Wu, Taha Rakhshandehroo, Hiromi I. Wettersten, Alejandro Campos, Tami Von Schalscha, Shashi Jain, Ziqi Yu, Jiali Tan, Evangeline Mose, Betzaira G. Childers, Andrew M. Lowy, Sara M. Weis, David A. Cheresh
Journal: Cancer Research (2024)

Abstract Tumor initiation is an inefficient process in which tumor cells must develop cell-autonomous mechanisms to survive harsh microenvironments, establish colonies, and thereby overcome “isolation stress.” We report that pancreatic cancer cells transiently upregulate lysophosphatidic acid receptor 4 (LPAR4), a G-protein coupled receptor, in response to microenvironmental stress or chemotherapy, which promotes stress tolerance, drug resistance, and tumor initiation. Even without exogenous LPA, LPAR4 drives the expression of a subset of extracellular matrix (ECM) genes via an AKT/CREB axis, including fibronectin and versican, which are established drivers of cancer stemness. The upregulation of fibronectin is indispensable for LPAR4-induced tumor initiation in vivo and anchorage-independent growth in vitro. Furthermore, the ligation of this fibronectin-containing ECM created by LPAR4-positive cells via integrins α5β1 or αvβ3 can transfer cancer stemness and stress tolerance to LPAR4-negative cells by activating Yes-associated protein 1 (YAP). Our findings reveal that in response to isolation stress, pancreatic tumor cells that upregulate LPAR4 can autonomously generate a fibronectin-enriched ECM niche and thereby initiate tumor formation. Citation Format: Chengsheng Wu, Taha Rakhshandehroo, Hiromi I. Wettersten, Alejandro Campos, Tami Von Schalscha, Shashi Jain, Ziqi Yu, Jiali Tan, Evangeline Mose, Betzaira G. Childers, Andrew M. Lowy, Sara M. Weis, David A. Cheresh. Pancreatic cancer cells upregulate LPAR4 in response to isolation stress to create a fibronectin-rich extracellular matrix niche and promote tumor initiation [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 2979.
Abstract 6547: Dysregulated FGFR3 signaling alters immune landscape in bladder cancer and presents therapeutic possibilities
Authors: Daniel R. Bergman, Erica Trujillo, Lie Li, Alexander T. Pearson, Randy Sweis, Trachette L. Jackson
Journal: Cancer Research (2024)

Abstract Bladder cancer is an increasingly prevalent global disease that continues to cause morbidity and mortality despite recent advances in treatment. Immune checkpoint inhibitors (ICI) and FGFR-targeted therapeutics have had limited success in bladder cancer when used as monotherapy. Emerging data suggests that the combination of these two therapies could lead to improved clinical outcomes. The optimal strategy for combining these agents remains uncertain. Mathematical models, and more specifically agent-based models (ABMs), have shown recent successes in uncovering the multiscale dynamics that shape the trajectory of cancer. They have enabled the optimization of treatment methods and identification of novel therapeutic strategies. To assess the combined effects of anti-PD-1 antibodies and anti-FGFR3 small molecule inhibitors (SMI) on tumor growth and the immune response, we built an ABM that captures key facets of tumor heterogeneity and CD8+ T cell compartments, their spatial interactions, and their response to therapeutic pressures. With our model, we quantify how tumor antigenicity and FGFR3 activating mutations impact disease trajectory and response to anti-PD-1 antibodies and anti-FGFR3 SMI. We find that even a small population of weakly antigenic tumor cells bearing an FGFR3 mutation can render the tumor resistant to combination therapy. However, highly antigenic tumors can overcome therapeutic resistance mediated by FGFR3 mutation. The optimal therapy depends on the strength of the FGFR3 signaling pathway. Under certain conditions, ICI alone is optimal; in others, ICI followed by anti-FGFR3 therapy is best. These results point to the need to quantify FGFR3 signaling and the fitness advantage conferred on bladder cancer cells harboring this mutation. Employing this ABM modeling approach may enable rationally designed treatment plans to improve clinical outcomes. Citation Format: Daniel R. Bergman, Erica Trujillo, Lie Li, Alexander T. Pearson, Randy Sweis, Trachette L. Jackson. Dysregulated FGFR3 signaling alters immune landscape in bladder cancer and presents therapeutic possibilities [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 6547.
Abstract 6965: Characterizing the proteome landscape of extracellular vesicles from prostate cancer cell lines by mass spectrometry
Authors: Megan L. Ludwig, Abderrahman Day, Hannah E. Bergom, Zoi Sychev, Alec Horrmann, Justin Hwang, Justin M. Drake
Journal: Cancer Research (2024)

Abstract Multiple subtypes of prostate cancer can emerge in advanced stages of disease, such as tumors that maintain androgen receptor features (AR+), those without AR but with neuroendocrine features (AR-/NE+), and those without AR or NE features (AR-/NE-). These latter subtypes are particularly aggressive and incredibly lethal. Extracellular vesicles (EVs) are small particles that are mediators of cell-cell communication and have been nominated as potential biomarkers of disease state. We hypothesized that the proteome of EVs contains information about their originating cell that can distinguish between prostate cancer subtypes. To address this, we isolated EVs from cell lines of differing subtypes – AR+ (LNCaP, LNCaP95, C4-2, 22RV1), AR-/NE+(NCI-H660, EF1, LASCPC-01), and AR-/NE- (PC3, DU145) – and prepared the EV proteome for quantitative, label-free mass spectrometry analysis. This identified 2,000+ proteins in the EVs for each cell line where EVs from similar subtypes clustered together. Interestingly, we also found that EVs contained enough protein information to utilize developed gene signatures for AR or NE activity. EVs isolated from AR-/NE+ cells contained known NE signature proteins such as SYP, CHGA, and UCHL1. EVs from the AR+ cell lines displayed &amp;gt;50% AR activity driven by PSA and STEAP1 proteins in addition to other significant distinguishing protein markers. This supports the potential for using the proteome of tumor-derived EVs to identify novel signature molecular markers besides those already known to the field for developing liquid-based biomarker assays. In addition, our work characterizes the EV surfaceome which is critical for enriching signals from tumor-derived EVs feasible for clinical diagnostics assay development. While PSMA has been a reliable marker for cells reliant on AR signaling, less is known about protein markers in the AR- subset. Our work highlights TROP2 as especially enriched in the EVs from AR-/NE- cell lines, supporting its relevance as a target in patients without treatment options. To evaluate disease outcomes, further clinical studies are needed to develop specific and sensitive tests based on the EV proteome derived from advanced prostate cancer patients. Citation Format: Megan L. Ludwig, Abderrahman Day, Hannah E. Bergom, Zoi Sychev, Alec Horrmann, Justin Hwang, Justin M. Drake. Characterizing the proteome landscape of extracellular vesicles from prostate cancer cell lines by mass spectrometry [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 6965.