tbuckley/cabot-search huggingface dataset:
Abstract 213: NEK1-mediated phosphorylation of YAP1 is key to prostate cancer progression
Authors: Damilola M. Olatunde, Ishita Ghosh, Arrigo De Benedetti
Journal: Cancer Research (2024)

Abstract The key to preventing metastatic castration-resistant prostate cancer (mCRPC) progression is understanding how androgen-sensitive (AS) PCa cells progress to independence and modify accordingly their transcriptional repertoire. We recently identified a novel axis of the Hippo pathway characterized by the sequential kinase cascade induced by androgen deprivation, AR−&amp;gt;mTOR&amp;gt;TLK1B&amp;gt;NEK1&amp;gt;pYAP1-Y407, leading to CRPC adaptation. Phosphorylation of YAP1-Y407 increases upon androgen deprivation therapy (ADT), correlated with increased NEK1 activity, and this is suppressed in a YAP-Y407F mutant. Overexpression of wt-GFP-YAP but not the Y407F SDM resulted in dramatic morphologic changes. In fact, LNCaP expressing wt-YAP were AI whereas the Y407F mutant were AS, and LNCaP expressing wt-GFP-YAP underwent EMT transformation. This, largely reflecting transcriptional differences in both AR-dependent genes (FKBP5, PSA) and some involved in EMT (ZEB1, TWIST, E-CAD); all of which could be effectively reversed with J54-mediated inhibition of TLK1&amp;gt;NEK!&amp;gt;YAP signaling. We found that J54, a pharmacological inhibitor of the TLK1&amp;gt;NEK1&amp;gt;YAP1 nexus led to degradation of YAP1, suggesting that the Y407 phosphorylation is critical for transcriptional activation and stabilization of YAP. Specifically, Nek1-mediated phosphorylation of YAP-Y407 increases its productive interaction with transcriptional activators like TEAD or AR, resulting in its nuclear retention and stabilization. This was later demonstrated by coIP of TEAD4 or the AR with GFP-YAP antiserum, as well as via LUC expression transfections using ARE and Hippo reporter plasmids in LNCaP expressing wt-GFP-YAP or Y407F proteins, as well as by ChIP for key AR-responsive gene promoters. Further, in NEK1 haploinsufficient TRAMP mice we determined reduced YAP1 expression, a key transcriptional activator of CRPC progression, and, if castrated at 12 weeks, the mice failed to show to overt prostate carcinomas, even while displaying reduced E-Cadherin (E-Cad) expression in hyperplastic ductules. Finally, IHC examination of prostate cancer biopsies revealed that pYAP1-Y407 nuclear signal is low in samples of low-grade cancer but elevated in high GS specimens. Citation Format: Damilola M. Olatunde, Ishita Ghosh, Arrigo De Benedetti. NEK1-mediated phosphorylation of YAP1 is key to prostate cancer progression [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 213.
Abstract 3973: Cancer B cell blueprint reveals dysfunctional extra-follicular dominance with therapeutic opportunity
Authors: Jiaqiang Ma, Yingcheng Wu, Lifeng Ma, Xupeng Yang, Tiancheng Zhang, Guoji Guo, Jia Fan, Xiaoming Zhang, Qiang Gao
Journal: Cancer Research (2024)

Abstract B cells are essential components of humoral immunity but harbor multifaceted functions across cancers. To decode tumor-infiltrating B cells, we generated the B cell blueprint encompassing single-cell transcriptome, BCR repertoire, and chromatin accessibility data across 20 cancer types (483 samples, 266 patients). Strikingly, B cells harbored extraordinary heterogeneity and composed of 15 subsets, which were grouped into two independent developmental paths (extra-follicular [EF] versus germinal-center [GC]) exhibiting organ preference. Of note, colon adenocarcinoma and hepatocellular carcinoma are the two representative types of cancer enriched for GC and EF pathways, respectively. We affirm that EF-dominant cancers correlate with dysregulated immune responses and worse clinical outcomes. We then identify the dynamic metabolic-epigenetic-signaling networks in fine-tuning tumor-infiltrating B cell differentiation and managing the balance between the EF and GC pathways. Atypical memory (AtM) B cells, the primary progenitors of EF-derived ASCs, exhibit an exhausted and bystander phenotype and develop independently of the GC pathway. We find that the AtM B cells reside in the center of immature TLSs and spatially relocate to the periphery during TLS maturation. Finally, we mechanistically link these findings to specific transcription factors and epigenomic regulations. We demonstrate that the glutamine-derived metabolite α-ketoglutarate (αKG) could increase the expression of AtM B cell associated transcription factors Tbet and BATF and promote their differentiation, accompanied by the activation of mammalian target of rapamycin complex 1 (mTORC1) signaling. Consequently, AtM B cells acquire an immunoregulatory function that dampens anti-tumor T cell responses and fosters an immunosuppressive microenvironment. Citation Format: Jiaqiang Ma, Yingcheng Wu, Lifeng Ma, Xupeng Yang, Tiancheng Zhang, Guoji Guo, Jia Fan, Xiaoming Zhang, Qiang Gao. Cancer B cell blueprint reveals dysfunctional extra-follicular dominance with therapeutic opportunity [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 3973.
Abstract 693: The effect of butyrophilin 1A1 blockade in combination with radiation treatment in tumor models
Authors: Nan Li, Chen Braun, Young-Seung Kim, Andrew Park, Stephen S Yoo, Steven H. Lin
Journal: Cancer Research (2024)

Abstract Expression of radiation-induced immune escape molecules, including PD-L1, contributes to the efficacy of cancer immunotherapy. We used an unbiased in vivo gene knockdown screen in naïve T-cells and introduced them into irradiated host tumors to identify novel immunosuppressive genes activated during radiation. From the screen, we found that butyrophilin 1A1 (BTN1A1) knockdown causes T-cell expansion in irradiated tumors. This points to the potential immune checkpoint role of BTN1A1. We validated that BTN1A1 expression is inducible in activated T-cells and that blocking BTN1A1 contributes to T-cell activation. We tested an anti-mouse BTN1A1 antibody (STC109) in mouse colon tumor models (CT26 tumors), we observed partial anti-tumor efficacy using single agent STC109, which was enhanced by the combination of STC109 with radiation. We also got similar result in in mouse lung tumor models (LLC tumors) using anti-mouse BTN1A1 antibody, and the combination treatment showed an improved suppression of tumor growth and lung metastasis compared to single agent. Moreover, our data shown that knockout of BTN1A1 in 4T1 tumor models shown dramatic defect of tumor growth, and the BTN1A1 ko tumors are more sensitive to radiotherapy. These findings indicate the role of BTN1A1 in tumor immune response from radiation stress, and that anti-BTN1A1 has strong potential to enhance efficacy of radiotherapy for cancer treatment. Citation Format: Nan Li, Chen Braun, Young-Seung Kim, Andrew Park, Stephen S Yoo, Steven H. Lin. The effect of butyrophilin 1A1 blockade in combination with radiation treatment in tumor models [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 693.
Abstract 2521: New predictive markers for dasatinib responsiveness in triple-negative breast cancer: A biomarker discovery study
Authors: Daniel Ortega-Álvarez, David Tebar, Marta Casado, Elena Castillo, Cristina Guardia, David Olivares-Osuna, Eva Musulén, Elisabetta Mereu, Ginés Luengo, Eva M. Galán-Moya, Veronica Rodilla
Journal: Cancer Research (2024)

Abstract Triple negative breast cancer is the most heterogeneous and aggressive type of breast tumor type and is characterized by the lack of expression of clinical biomarkers (ER, PR, and HER2) and targeted therapies. In this regard, different clinical trials have failed, unable to stratify these patients to find an effective response to specific therapy. This study aimed to identify biomarkers exclusively expressed in the basal mammary compartment that can help us to subclassify the triple-negative breast cancer subtype. Based on computational analysis from single-cell RNA sequencing data, we have identified a list of basal identity-associated genes (BC-markers). Subsequent histological validation confirmed the expression pattern of these markers in a cohort of 50 samples, which has allowed us to stratify triple-negative breast cancer patients into BC-TNBC and luminal-like subtypes. Importantly, the expression of these markers correlated with poorer prognosis in TNBC patients. Functional analysis revealed that TAGLN played a significant role in cell proliferation and migration, potentially impacting tumor aggressiveness. Moreover, the expression of these BC-markers is associated with a mesenchymal phenotype which corresponds to the previously described Lehmannn’s mesenchymal-like signature. In this study, TAGLN appeared to influence dasatinib sensitivity, suggesting its potential as a predictive biomarker for dasatinib response in TNBC patients. Citation Format: Daniel Ortega-Álvarez, David Tebar, Marta Casado, Elena Castillo, Cristina Guardia, David Olivares-Osuna, Eva Musulén, Elisabetta Mereu, Ginés Luengo, Eva M. Galán-Moya, Veronica Rodilla. New predictive markers for dasatinib responsiveness in triple-negative breast cancer: A biomarker discovery study [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 2521.
Abstract 3563: Multi-modal mutational signatures elucidate the comprehensive consequences of mutational processes
Authors: Christopher D. Steele, Ludmil Alexandrov, Azhar Khandekar
Journal: Cancer Research (2024)

Abstract The development of mutational signatures defined individually in the contexts of single/double base substitutions, insertions and deletions, structural variants and copy number variation have led to improved understanding of cancer mutagenesis and potential for improved patient stratification. We hypothesized that combining these contexts into a multi-modal mutational signature framework may improve the accuracy of assigning mutational processes to samples, and provide a holistic view of the full repertoire of mutations conferred from such processes. In order to develop multi-modal signatures, bespoke feature engineering was required for each mutational modality to enhance signal, in addition to individual modality matrix normalization so that the data could be harmonized and analyzed as a whole. These methods, and subsequent signature extraction were developed on 2,438 whole genome sequenced cancers from 21 distinct cancer types from the PCAWG consortium for which all modalities of data were available, incorporating a 348 channel signature definition. Deployment of these methods identified multi-modal signatures that encompass multiple mutation types known to associate with specific processes, for example SBS, indel and rearrangement channels defining a signature of homologous recombination deficiency. In contrast, some signatures remain defined by a single mutational modality, highlighting the distinction between broadly mutational processes, and more focused mutation processes. Multi-modal signatures show promise in increasing accuracy for difficult to assign signatures, such as those for homologous recombination deficiency, and therefore in improving patient stratification for life-saving treatment. Citation Format: Christopher D. Steele, Ludmil Alexandrov, Azhar Khandekar. Multi-modal mutational signatures elucidate the comprehensive consequences of mutational processes [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 3563.
Abstract 3600: Reversal of iNKT cell dysfunction in cholangiocarcinoma
Authors: Khin Su Su Htwe, Kitipong Soontrapa, Siwanon Jirawatnotai, Sunisa Prasopporn, Pimkanya More-Krong, Somponnat Sampattavanich, Adisak Wongkajornsilp
Journal: Cancer Research (2024)

Abstract Invariant natural killer T (iNKT) cells are CD1d-restricted unconventional T cells possessing innate and adaptive immunity with high anti-tumor activities. Yet, the effectiveness of iNKT cell therapy in clinical trials is limited due to iNKT cell dysfunction after exposure to the tumor microenvironment. Aggressive cholangiocarcinoma (CCA) cell lines were used to study iNKT cell reactivity. These CCA cell lines lacked CD1d molecules and responded poorly to iNKT cells. The iNKT cells became dysfunctional after the exposure to CCA by 48 h. In this study, we overcame iNKT cell dysfunction by searching for a small molecule to prevent or reverse the gene sets regulating iNKT cell dysfunction, thus prolonging anti-tumor activity. It was found that P53 and estrogen early response pathway gene sets were enriched in dysfunctional iNKT cells which were reversed by vorinostat, an HDAC inhibitor. Anti-CCA activity of iNKT cells was regained with a subtherapeutic dose of vorinostat as protection. Interestingly, vorinostat could not totally recover the anti-tumor effect of iNKT cells that have already developed into the dysfunctional stage. Significant tumor size reduction was seen in the humanized mouse model after iNKT cell adoptive therapy was given in combination with vorinostat compared to monotherapy with either iNKT cell or vorinostat alone. This study demonstrated that inhibiting the gene sets regulating iNKT cell dysfunction by vorinostat could prevent iNKT cell dysfunction, and prolong its anti-tumor activities. This combination could be a novel treatment option for CD1d-negative CCA patients resistant to standard chemotherapy. Citation Format: Khin Su Su Htwe, Kitipong Soontrapa, Siwanon Jirawatnotai, Sunisa Prasopporn, Pimkanya More-Krong, Somponnat Sampattavanich, Adisak Wongkajornsilp. Reversal of iNKT cell dysfunction in cholangiocarcinoma [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 3600.
Abstract 2513: MAGE-A3, MAGE-A4, and PD-L1 protein show co-expression in colon, lung and bladder cancer
Authors: Rachel Gonzalez, YiChen Guo, Jina Yom, Bailey Gilmore, Eden Zewdu, Xi-Andy Han, Dehe Kong, Tianli Qu, Qi Ren, Xiaomin Hu, Ranran Zhang, Zhaohui Wu, Alex Strom, Xuan Liu, Wei Fu
Journal: Cancer Research (2024)

Abstract PD-L1 programmed death ligand 1/CD274 has been shown to be an excellent immune therapy target for many tumors. Currently, studies have shown PD-L1in combination with other immune therapy targets can improve patient outcomes generating the need for new targets. One candidate is the cancer testis antigen Melanoma Antigen Gene Family (MAGE-A) because these genes have limited expression in normal tissues and high expression in cancer. Clinical trials have already begun targeting MAGE-A3 and MAGE-A4 proteins in multiple tumor types. Protein assessment of individual MAGE-A family members has been challenging due to sequence homology as high as ninety-five percent between members. Previously, with the use of CytoSections two highly specific antibodies for immunohistochemistry to MAGE-A3 (clone OTI1H1) and MAGE-A4 (clone OTI2C1) were found. In this study, the MAGE-A3 and MAGE-A4 antibodies were screened with PD-L1 on colon, lung, and bladder cancers. Results show detection of both MAGE-A3 and MAGE-A4 in 25% of colon; 30% of lung; and 20% of bladder cancers. More than 70% of the lung and bladder cancers were positive for MAGE-A4 but only six of twenty-four colon cancers were positive for MAGE-A4. The results show 60 percent of the positive for MAGEA3 or MAGEA4 in colon, lung, and bladder cancers were also positive for PD-L1. This study suggests that MAGE-A3 and MAGE-A4 have tumor specific expression patterns and a potential to be a co-immunotherapy target with PD-L1. Citation Format: Rachel Gonzalez, YiChen Guo, Jina Yom, Bailey Gilmore, Eden Zewdu, Xi-Andy Han, Dehe Kong, Tianli Qu, Qi Ren, Xiaomin Hu, Ranran Zhang, Zhaohui Wu, Alex Strom, Xuan Liu, Wei Fu. MAGE-A3, MAGE-A4, and PD-L1 protein show co-expression in colon, lung and bladder 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 2513.
Abstract 2126: Efficacy and underlying mechanisms of surufatinib in non-small cell lung cancer treatment
Authors: Yanfang Zheng, Binjie Shan, Meng Wang, Xiaoran Wu, Rui Cai, Feiyu Niu, Yan Yuan, Lu Liu, Xiongjie Zhu
Journal: Cancer Research (2024)

Abstract Background: The prevalence and fatality of lung cancer, especially non-small cell lung cancer (NSCLC), highlight the urgency for efficacious therapies. Surufatinib, an inhibitor of tyrosine kinases like VEGF receptors (VEGFR) 1, 2, and 3, Fibroblast growth factor receptor 1 (FGFR1), and CSF-1R, shows potential in augmenting chemotherapy efficacy and reducing adverse effects. Preliminary clinical studies (NCT04922658) have indicated survival benefits for NSCLC patients treated with surufatinib. This investigation seeks to delineate the therapeutic efficacy of surufatinib, correlating clinical benefits with mechanistic insights. Methods: To elucidate mechanisms, proliferation assays (CCK8), migration (scratch assay), and apoptosis (flow cytometry) were conducted in A549 and H1299 cell lines. Angiogenesis and macrophage polarization were examined via vascular junction points and mRNA expression profiling. In nude mice, subcutaneous tumors were induced and treated with the study drugs, with tumor growth and angiogenic markers assessed. Results: In vitro, surufatinib potently inhibited angiogenesis and exerted a dose-dependent suppression of proliferation and colony formation in lung cancer A549 and PC9 cell lines. It also enhanced apoptosis and cell migration. Additionally, surufatinib shifted macrophage polarization towards an M1 phenotype while diminishing M2 macrophages, thereby, contributing to a more robust anti-tumor immune milieu. In vivo studies corroborated these findings, with surufatinib and vinorelbine combination therapy significantly curtailing tumor growth and reducing CD31 expression in tumor tissues, highlighting its potential for substantial therapeutic gains in NSCLC management. Conclusion: Surufatinib achieved notable antitumor effect consistent with clinical findings in NSCLC, effectively inhibiting cellular proliferation and migration, attenuating angiogenesis, and enhancing apoptosis. Significantly, it also modulated macrophage polarization to favor an M1/M2 balance, thus activating the immune response. Therapeutic strategies with surufatinib have underscored augmented antineoplastic efficacy, meriting additional clinical investigations. Citation Format: Yanfang Zheng, Binjie Shan, Meng Wang, Xiaoran Wu, Rui Cai, Feiyu Niu, Yan Yuan, Lu Liu, Xiongjie Zhu. Efficacy and underlying mechanisms of surufatinib in non-small cell lung 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 2126.
Abstract 3599: Recombinant chimeric antibody-based gamma-delta TCR targeting GPC3 induces potent antitumor response against hepatocellular carcinoma
Authors: Dan Li, Tianyuzhou Liang, Zhijian Duan, Hongbing Zhang, Cheng Liu, Mitchell Ho
Journal: Cancer Research (2024)

Abstract Background and Significance: Hepatocellular carcinoma (HCC), a major type of primary liver cancer, is the third leading cause of cancer-related death worldwide. While Glypican-3 (GPC3) is highly upregulated in HCC, it is minimally expressed in normal tissues. The research in our laboratory has been focused on the development of GPC3 as an immunotherapeutic target for liver cancer. Despite many clinical trials, there has not been any approved therapy targeting GPC3 largely due to the combination of antigen heterogeneity, poor tumor penetration, and the inability to induce a durable, potent immune response in the tumor microenvironment (TME). Here, we made a recombinant chimeric antibody-based T cell receptors (named AbTCR) targeting GPC3 and explored its anti-tumor efficacy in xenograft mouse models. Methods: The AbTCR constructs were built by fusing an antigen recognition domain (hYP7 scFv or HN3 VH) specific for GPC3 to the gamma-delta TCR constant region along with a secondary T cell signaling activation motif. The NFAT-tdTomato reporter cell line was established and used to measure the AbTCR-triggered T cell signaling upon stimulation with tumor cells. Anti-tumor efficacy of AbTCR-T cells was determined via luciferase-based cell killing assay as well as multiple HCC xenograft mouse models. Results: The hYP7 GPC3 AbTCR-T cell not only enhances antigen-binding capacity and T cell activity, but also induces infiltration and expansion of T cells in the TME, thereby causing robust liver tumor regression in mice. Conclusion: Our data show that new hYP7-directed GPC3 AbTCR is a promising strategy for treating liver cancer. This work provides a rationale for the use of hYP7 GPC3 AbTCR in clinical studies for treating HCC and other GPC3-positive solid tumors. Citation Format: Dan Li, Tianyuzhou Liang, Zhijian Duan, Hongbing Zhang, Cheng Liu, Mitchell Ho. Recombinant chimeric antibody-based gamma-delta TCR targeting GPC3 induces potent antitumor response against 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 3599.
Abstract 357: Reducing reagent-resistant transferrin receptor 1 dimer is a specific marker for ferroptosis
Authors: Jianping He, Mackenzie Kelleher, Lucas Reynolds, Hannah Tanczos, Zhengrong Huang, Brett McLaughlin, Wesley Huang, Lauren Pope, Geraldine Veeckmans, Tom Vanden Berghe, Scott J. Dixon, Yatrik Shah, Zachary T. Schafer
Journal: Cancer Research (2024)

Abstract Ferroptosis is an iron-dependent cell death caused by the catastrophic accumulation of lipid peroxidation. Despite the burgeoning ferroptosis research, there remains a void for an intrinsic and comprehensive ferroptosis indicator. Here we reported a simple and cost-effective way to detect ferroptotic cell death using reducing reagent-resistant (RRR) transferrin receptor 1 (TfR1). The TfR1 RRR dimer strongly correlates with ferroptosis induced by various ferroptosis-inducing conditions and relies on lipid peroxidation, which is not observed in other types of cell death. Through iron-overloading and tumor xenograft mouse models, we validate the in vivo ferroptosis detection using this technique. Furthermore, we identify the presence of TfR1 RRR dimers in extracellular vesicles isolated from the plasma of mice with ferroptosis-related diseases. Since TfR1 is a ubiquitously expressed protein, the increase of TfR1 RRR dimer can be used as a specific and endogenous ferroptosis marker with potential clinical applications. Citation Format: Jianping He, Mackenzie Kelleher, Lucas Reynolds, Hannah Tanczos, Zhengrong Huang, Brett McLaughlin, Wesley Huang, Lauren Pope, Geraldine Veeckmans, Tom Vanden Berghe, Scott J. Dixon, Yatrik Shah, Zachary T. Schafer. Reducing reagent-resistant transferrin receptor 1 dimer is a specific marker for ferroptosis [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 357.