tbuckley/cabot-search huggingface dataset:
Abstract 372: Cell polarity proteins as novel regulators of macropinocytosis in pancreatic cancer
Authors: Guillem Lambies Barjau, Szu-Wei Lee, Cosimo Commisso
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is considered one of the deadliest cancers. This is likely because it is detected at a very late stage and the therapeutic approaches that have been used for its treatment have proven to be quite ineffective. Therefore, new therapeutic strategies are needed for a better prognosis in patients suffering of pancreatic cancer. PDAC cells often rewire their metabolism to survive and progress. This metabolic rewiring permits the acquisition of nutrients by the cells when these are exposed to a poor nutrient microenvironment. One of the most used processes in nutrient stress conditions is the “cell-drinking” pathway macropinocytosis, an endocytic pathway that cancer cells exploit to support cancer metabolism in such unfavorable conditions. Macropinocytosis inhibition has shown to suppress PDAC growth in mice and thus, it has become a promising therapeutic target for PDAC treatment. Here, we describe that atypical Protein Kinase C (aPKC) isoforms Protein Kinase C zeta (PKCζ) and Protein Kinase C iota (PKCι) regulate PDAC macropinocytosis in the context of glutamine stress. Genetic depletion and pharmacological inhibition of aPKC impair macropinocytosis promotion in PDAC cells exposed to a glutamine-deprived environment and in cells treated with DON, a glutamine analog that blocks glutamine metabolism. In epithelial cells, aPKCs are known to regulate the establishment of cell polarity in association with the scaffold proteins Par3 and Par6, constituting the cell polarity complex, which controls the function of different targets such as Par1 kinases. Loss of Par3, Par6 and Par-1a affects glutamine stress associated macropinocytosis in a similar extent than aPKC depletion, presenting a novel role of the cell polarity protein network in the modulation of macropinocytic uptake. Citation Format: Guillem Lambies Barjau, Szu-Wei Lee, Cosimo Commisso. Cell polarity proteins as novel regulators of macropinocytosis in pancreatic 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 372.
Abstract 1642: NuMA exclusive post-translational modification in epithelial cancer cells is a novel target for cell eradication
Authors: Malka Cohen-Armon
Journal: Cancer Research (2024)

Abstract The post-translational modification of proteins implicated in mitosis in healthy and in cancer epithelial cells was measured by 2-D gels analysis. The post-translational modifications of NuMA in a variety of human epithelial cancer cells was prevented by treatment with a small phenanthridine, PJ34, while not impaired in similarly treated healthy epithelial cells. NuMA in the cancer cells was phosphorylated by pim1 kinase, and was polyADP-ribosylated by Tankyrase1. These post-translational modifications are inhibited by PJ34. Tankyrase1 is not expressed in healthy epithelial cells, and pim1 kinase was hardly expressed in these cells. Preventing the post-translational modification of NuMA in the epithelial cancer cells also suppressed the protein binding capacity of NuMA. NuMA clustering in the mitotic spindle poles, which stabilizes the mitotic spindle, and is required for the alignment of chromosomes in the spindle mid-zone was impaired. In epithelial cancer cells treated with PJ34, the mitotic spindle poles were distorted, extra-centrosomes were not clustered in multi-centrosomal cancer cells, and chromosomes were dispersed. Chromosomes dispersion violated mitosis termination. Mitosis arrested in the anaphase led to mitotic catastrophe cell death. PJ34 treated epithelial cancer cells were eradicated during 72-96 hours, regardless of their mutations, while treated healthy epithelial cells were not affected, and continued to proliferate. Citation Format: Malka Cohen-Armon. NuMA exclusive post-translational modification in epithelial cancer cells is a novel target for cell eradication [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 1642.
Abstract 5298: BSI-093, a best-in-class anti-BTN3A monoclonal antibody for cancer immunotherapy by activation of Vg9Vd2 T cells
Authors: Wenwen Dai, Jun Li, Jinyu Liu, Hongyan Li, Xiaodong F. Liu, Shukai Xia, Qun Lyu, Hugh M. Davis, Mingjiu Chen, Zeyu Peng
Journal: Cancer Research (2024)

Abstract Background: Gamma delta T (γδ T) cells are potent anti-cancer effectors with the potential to target tumors broadly, independent of patient-specific neoantigens or human leukocyte antigen background. Among tumor-infiltrating lymphocytes, the presence of γδ T cells is the most favorable prognostic marker for overall survival of patients with various solid and hematologic tumors. Vγ9Vδ2 T cells are the predominant γδ T cells in peripheral circulation. Butyrophilin 3A (BTN3A) members, widely expressed in tumors, have emerged as novel molecules modulating the function of Vγ9Vδ2 T cells. Targeting BTN3A for activation of Vγ9Vδ2 T cells provides an alternative strategy for cancer immunotherapy. Experimental procedures: BALB/c mice were immunized with recombinant BTN3A1-ECD-Fc. The Biosion proprietary H3 (High-throughput, High-content and High-efficiency) antibody discovery platform was used to identify an anti-BTN3A monoclonal antibody lead candidate - BSI-093. The target binding specificity, binding activity, and affinity of BSI-093 were evaluated by protein-based ELISA, cell-based FACS and Biacore-based SPR. Ex vivo assays were used to evaluate the cellular bioactivity of BSI-093 on activating Vγ9Vδ2 T cells for killing activity of various tumor cells. B-NDG mice bearing Jurkat-GFP-Luc tumors were used to evaluate the tumor inhibitory activity of the anti-BTN3A antibody. Summary: BSI-093 is a humanized monoclonal antibody with the following critical properties: (1) binds to all BTN3A members (BTN3A1, BTN3A2 and BTN3A3) with high affinity; (2) has potentially longer half-life and silenced Fc-effector function by Fc-engineering; (3) exhibits cross-reactivity to rhesus BTN3A members; (4) demonstrates strong activity on activating Vγ9Vδ2 T cells to kill a variety of natural cancer cells in ex vivo assays; and (5) shows significant anti-tumor efficacy in a CDX model. Conclusion: BSI-093 demonstrates potential best-in-class biophysical properties and functional characteristics, supporting the initiation of development activities including manufacturing and IND-enabling studies. Citation Format: Wenwen Dai, Jun Li, Jinyu Liu, Hongyan Li, Xiaodong F. Liu, Shukai Xia, Qun Lyu, Hugh M. Davis, Mingjiu Chen, Zeyu Peng. BSI-093, a best-in-class anti-BTN3A monoclonal antibody for cancer immunotherapy by activation of Vg9Vd2 T cells [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 5298.
Abstract 289: Temporal and spatial dynamics of glial cells apolipoprotein E expression in astrocytoma microenvironment
Authors: Ting-Yi Chien, Chi-Shiun Chiang
Journal: Cancer Research (2024)

Abstract Introduction: Brain tumors have proven challenging to treat due to the complex and sensitive architecture of the brain. Previous research has shown that GBM cells depend highly on cholesterol uptake, and apolipoprotein E (APOE) is required to transport cholesterol among tissues or cells. APOE is primarily synthesized by astrocytes and has been extensively studied in neurodegenerative diseases. While extensively studied in neurodegenerative diseases, limited studies are focusing on their roles in brain tumor development. Here, we analyzed the temporal and spatial expression of APOE during brain tumor progression in a murine astrocytoma tumor model. Material and method: ALTS1C1 astrocytoma cells were intracranially injected into the mouse brain. The animal was sacrificed, and the left hemisphere, right hemisphere, and tumor tissue were collected for flow cytometry analysis. CD45, CD11b, and GFAP were used to recognize macrophages, microglia, and astrocytes. CD68, TMEM119, and GFAP were used for tissue immunostaining to label macrophages, microglia, and astrocytes, respectively. Results and Discussion: Flow cytometry analysis revealed upregulated APOE in tumor-infiltrating microglia, macrophages, and lymphocytes. GFAPhigh astrocytes displayed lower APOE levels than GFAPlow astrocytes. IHC analysis showed that CD68+ macrophages exhibited higher APOE expression at the tumor edge than normal tissue. On the contrary, GFAP+ astrocytes at the tumor edge displayed a lower APOE signal than the normal tissue. Previous studies have shown the participation of APOE in regulating immune response in various cancers. Further studies to analyze the dynamic change of APOE on the gene expression level with in situ hybridization and the quantification of cholesterol levels in the microenvironment may help uncover their roles in the glioma microenvironment. Conclusion: This study demonstrated that APOE was temporal and spatial differentially expressed in macrophages and astrocytes in the brain tumor microenvironment. Tumor-infiltrating cells showed an elevated APOE expression, while GFAP+ astrocytes expressed reduced APOE levels. Although the mechanism of these alterations remains unclear, this study provides a basis for future studies about the roles of APOE in the brain tumor microenvironment. Citation Format: Ting-Yi Chien, Chi-Shiun Chiang. Temporal and spatial dynamics of glial cells apolipoprotein E expression in astrocytoma 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 289.
Abstract 627: IL-6 signaling via JAK/STAT axis influences PIM1 expression in renal cell carcinoma
Authors: Kimberly S. Meza, Kimberly Seymour, Sheldon L. Holder
Journal: Cancer Research (2024)

Abstract Renal cell carcinoma (RCC) is a top ten malignancy in the U.S. Overexpression of the proviral integration site for moloney murine leukemia virus 1 (PIM1) kinase is associated with poor clinical outcomes in RCC patients. PIM1 is a constitutively active serine/threonine kinase promoting cell proliferation, apoptosis resistance, invasion, and migration. The mechanisms underlying PIM1 expression and its function in RCC are not fully delineated. IL-6 is a pleiotropic cytokine that activates the JAK/STAT signaling cascade. High serum IL-6 levels are associated with the poor prognosis of RCC patients and may contribute to RCC invasion and metastasis. STAT3/5 binds directly to the PIM1 promoter inducing PIM1 expression. An IL-6/STAT3/PIM1 axis exists in pancreatic and breast cancer. We previously reported that PIM1 is overexpressed in a panel of human RCC cell lines relative to normal and immortalized renal proximal tubule epithelial cells. We also identified that RCC cells secrete IL-6. Our prior studies suggest that differential expression of PIM1 may be linked to autocrine IL-6 signaling. We thus hypothesize that an IL-6/JAK/STAT pathway regulates the expression of PIM1 in RCC. To understand how IL-6 signaling through the JAK/STAT pathway may regulate PIM1 expression in RCC cells, we examined whether IL-6 blockade using anti-IL-6 antibody or tocilizumab, would modulate PIM1 expression. Similarly, we assessed whether ruxolitinib, and LLL12, a STAT3 inhibitor could regulate PIM1 expression. We then evaluated the effect of ruxolitinib treatment on cell viability. In RCC cell lines, IL-6 blockade through either anti-IL-6 antibody or tocilizumab was sufficient to decrease PIM1 protein levels. Treatment with ruxolitinib leads to a dose and time-dependent decrease in PIM1 levels. Incubation with a STAT3 inhibitor also resulted in decreased PIM1 levels in RCC cells. Treatment with ruxolitinib also appears to decrease cell viability in a dose-dependent manner. These results suggest that differential expression of PIM1 in RCC may be linked to autocrine IL-6 signaling via a JAK/STAT/PIM1 axis. Multiple FDA-approved agents are available that target this pathway. Further investigation is required to determine the efficacy of these agents in pre-clinical models and even clinical trials. Citation Format: Kimberly S. Meza, Kimberly Seymour, Sheldon L. Holder. IL-6 signaling via JAK/STAT axis influences PIM1 expression in renal cell 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 627.
Abstract 4364: Molecular insight of non-canonical Gsk3β-Gli-AR axis: Therapeutic implications of truncated-Gli3 in castration-resistant prostate cancer
Authors: Jyoti Bala Kaushal, Pratima Raut, Sarathy Seshacharyulu, Zahraa W. Alsafwani, Gunjan Sharma, Abdullah M. Khan, Sushanta Halder, Satyanarayana Rachagani, Surinder K. Batra, Jawed A. Siddiqui
Journal: Cancer Research (2024)

Abstract The aberrant activation of the hedgehog (Hh) signaling pathway causes the progression of therapy-resistant castration-resistant prostate cancer (CRPC). In this study, we aimed to unravel the biological significance of Gli-family proteins and their functional involvement of Gsk3β-mediated regulatory mechanism(s) in CRPC. We have discovered a novel function of the truncated form of Gli (t-Gli3) in advancing CRPC. This was accomplished through in silico analysis, in vitro experiments, PCa patient clinical data, and in vivo PCa MYC overexpression mouse models. Our investigation into the Gli3 regulation, typically influenced by receptor-mediated ciliary localization, uncovered a Smo-independent mechanism. Surprisingly, despite the lack of a transactivation domain in t-Gli3, we found a specific requirement for an androgen receptor variant 7 (AR-V7) for its action, as evidenced by co-immunoprecipitation and chromatin immunoprecipitation assays. Mechanistically, Gsk3β activation leads to the t-Gli3 generation, and inhibition of Gsk3β supported the accumulation of full-length Gli3 through a non-canonical mechanism. Knockdown of Gsk3β (Gsk3β KD) reduces CRPC cell proliferation in 2-D and 3-D culture models, inhibiting key proliferative signaling pathways and inducing apoptosis via mitochondrial fragmentation. These findings were supported using an orthotropic PCa mouse model. RNA-seq analysis also showed upregulated phenotype enrichment of the apoptosis, P53, and glycolysis pathway genes in 22Rv1Gsk3β KD cells. Compared to scramble, a lower OCR/mitochondrial respiratory rate is evident in 22Rv1Gsk3β KD cells. Next, our exploration of potential therapies for PCa showed that individually targeting Smo or Gli1 is insufficient to inhibit cell viability. Interestingly, we uncovered that solely targeting Gli3 was sufficient to inhibit the growth of CRPC cells. In conclusion, our study provides the significance of Gli-family proteins and novel insights into the interplay of Gsk3β, t-Gli3, and AR, offering therapeutic implications in CRPC. Citation Format: Jyoti Bala Kaushal, Pratima Raut, Sarathy Seshacharyulu, Zahraa W. Alsafwani, Gunjan Sharma, Abdullah M. Khan, Sushanta Halder, Satyanarayana Rachagani, Surinder K. Batra, Jawed A. Siddiqui. Molecular insight of non-canonical Gsk3β-Gli-AR axis: Therapeutic implications of truncated-Gli3 in castration-resistant prostate 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 4364.
Abstract 4350: Characterization of PUF60 splicing activity that is essential for the survival of triple negative breast cancer
Authors: Alexandra Tankka, Trent Gomberg, Cathy Zhou, Vivian Pham, Gene Yeo
Journal: Cancer Research (2024)

Abstract Alternative splicing driven by RNA-binding proteins (RBPs) plays a significant role in TNBC, however, pharmacological modulators of core spliceosomal proteins can disrupt early stages of spliceosome assembly and lead to toxic effects in normal tissues, limiting their utility as safe therapeutics. Here, we used in vivo CRISPR-Cas9 screening to evaluate RBP dependencies in TNBC and identified 17 splicing regulatory candidates that are essential in TNBC but dispensable for normal cell growth and survival. Within this cohort, the alternative splicing factor, PUF60, was the most significantly upregulated candidate in patient TNBC tumors. We found that depletion of PUF60 induced apoptosis in human TNBC cell lines and impeded xenografted tumor growth in vivo while upregulation of PUF60 expression increased TNBC cellular proliferation. Although PUF60 has been shown to also bind DNA and influence transcription, TNBC cells constructed with a previously characterized mutation (L140P) required for 3’ splice site recognition displayed significantly decreased cellular proliferation compared to cells containing wild type PUF60. Integrated eCLIP and KD RNA-sequencing revealed that PUF60 selectively regulates the splicing of mRNAs in TNBC that contribute to essential processes including DNA repair, replication and cell cycle progression. RNA-seq following L140P-mediated inhibition of 3’ ss recognition revealed a cohort of splicing events within genes enriched for similar processes following knockdown of endogenous PUF60 including cell cycle and histone modification. Altogether, our study highlights a critical role for PUF60-mediated splicing in the maintenance of genomic integrity in TNBC as well as the therapeutic potential of identifying and targeting splicing effector RBPs only responsible for TNBC survival. Citation Format: Alexandra Tankka, Trent Gomberg, Cathy Zhou, Vivian Pham, Gene Yeo. Characterization of PUF60 splicing activity that is essential for the survival of triple negative breast 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 4350.
Abstract 1203: Mushroom: a tool for identification of 3D cellular neighborhoods in multi-modal spatial datasets
Authors: Erik Storrs, Siqi Chen, Chia-Kuei Mo, Andrew Houston, Andrew Shinkle, Austin Southard-Smith, Faria Simin, Andre Targino, Xiang Li, Ateih Abedin, Reyka Jayasinghe, Alla Karpova, Jingxian Liu, John Herndon, David Fenyo, Feng Chen, Ryan Fields, Tao Ju, Ben Raphael, Li Ding
Journal: Cancer Research (2024)

Abstract A comprehensive understanding of the spatial localization of cellular processes is necessary to fully describe tissue biology. Numerous techniques exist to identify cellular neighborhoods in spatial datasets, however, these techniques are limited in that they either only capture two-dimensional phenomena - and can't describe the full, 3-dimensional tumor volume, or they are restricted to one spatial technology (i.e. IF, 10X Visium, Xenium, MERFISH, etc.). To address this, we developed Mushroom, a tool for identification of three-dimensional cellular neighborhoods in serial-sectioned multi-modal datasets. Mushroom’s methodology consists of two main steps: 1) registration of multi-modal technologies taken in serial sections (such as multiplex imaging, H&amp;E, or spatial transcriptomics), and 2) identification of 3-dimensional cellular neighborhoods comprising the tissue volume that has been serially sectioned. Keypoint registration is performed with BigWarp, after which the resulting dense displacement field (DDF) is used to register neighboring serial sections - including those from different data modalities. We then implement a neural network to identify three dimensional cellular neighborhoods. The network is a variational autoencoder (VAE) with a vision transformer (VIT) backbone that has been adapted to work with multiple spatial data modalities. Features extracted from the VIT backbone are then clustered to identify cellular neighborhoods unique to each input data type. With 3D neighborhoods in hand, biological questions not answerable in traditional 2D approaches can be investigated, such as z-dimensional changes in morphology and cellular interactions. Further, seamless characterization of cellular neighborhoods by simultaneous technologies at multiple levels of spatial and genomic resolution becomes possible. Citation Format: Erik Storrs, Siqi Chen, Chia-Kuei Mo, Andrew Houston, Andrew Shinkle, Austin Southard-Smith, Faria Simin, Andre Targino, Xiang Li, Ateih Abedin, Reyka Jayasinghe, Alla Karpova, Jingxian Liu, John Herndon, David Fenyo, Feng Chen, Ryan Fields, Tao Ju, Ben Raphael, Li Ding. Mushroom: a tool for identification of 3D cellular neighborhoods in multi-modal spatial datasets [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 1203.