tbuckley/cabot-search huggingface dataset:
Abstract 439: Tackling oxidative phosphorylation of glioblastoma stem cells through the specific impairment of transmembrane chloride intracellular channel 1
Authors: Francesca Cianci, Ivan Verduci, Riccardo Cazzoli, Saverio Minucci, Michele Mazzanti
Journal: Cancer Research (2024)

Abstract Solid cancer cells show higher energy and biomolecules requirements compared with healthy cells, making the targeting of cancer metabolic dysfunctions an appealing therapeutic approach. Tackling the tumor metabolism is a daunting task, due to the ability of cancer cells to re-organize their metabolism switching between glycolysis and oxidative phosphorylation. Cancer metabolic plasticity and re-programming is partially supported by altered ionic channels expression and activity. Our laboratory has described the chronic presence transmembrane form of Chloride Intracellular Channel 1 (tmCLIC1) as a marker of malignancy in tumor cells and a possible therapeutic target since it is mainly absent in healthy cells. CLIC1 is described as a metamorphic protein able to shuttle between the cytoplasmic form to a transmembrane conformation. In the present investigation, we show that tmCLIC1 acts as a privileged metformin target in glioblastoma stem-like cells. Metformin is the first-line drug for type 2 diabetes and has been proposed as an antineoplastic drug, but no direct evidence of its’ membrane permeability nor of a specific membrane receptor in cancer cells has been found yet. Here we demonstrate that metformin impairs tmCLIC1 activity by direct and specific binding coordinated by arginine 29. This residue mutation prevents metformin from tmCLIC1 binding and abolishes the drug's effect on glioblastoma cells in 2D and 3D models and its actions on mitochondrial respiration. In vivo experiments in zebrafish embryos and mice orthotopically engrafted with glioblastoma cells and treated with metformin have shown that metformin binding to tmCLIC1 is crucial for its anti-neoplastic effect. Citation Format: Francesca Cianci, Ivan Verduci, Riccardo Cazzoli, Saverio Minucci, Michele Mazzanti. Tackling oxidative phosphorylation of glioblastoma stem cells through the specific impairment of transmembrane chloride intracellular channel 1 [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 439.
Abstract 5372: KITENIN leads immunosuppression in the glioblastoma microenvironment via CCL20
Authors: Eun-Jeong Ahn, Nah Ihm Kim, Sung Sun Kim, Jae-Hyuk Lee, Joon Haeng Rhee, Kyung-Keun Kim, Hangun Kim, Kyung-Hwa Lee, Kyung-Sub Moon
Journal: Cancer Research (2024)

Abstract Background: Glioblastoma (GBM) is characterized by an immunosuppressive tumor microenvironment (TME), limiting the effectiveness of existing treatments. The author investigated the role of KAI1 COOH-terminal interacting tetraspanin (KITENIN) in mediating this immunosuppression, focusing on its effect on cytokine secretion and tumor-infiltrating lymphocyte (TIL) profiles in the TME. Materials and Methods: Using cytokine array and Luminex multiplex assays, the author evaluated cytokine secretion in KITENIN-modulated GL261 cells. The author further isolated TILs from an orthotopic mouse model implanted with these cells and induced in vitro differentiation of myeloid cells. The effect of neutralizing antibody for target cytokine, was assessed in vivo, and clinical relevance was investigated using GBM patient data from our cohort and TCGA. Results: Employing cytokine array and Luminex multiplex assays, we found increased level of CC chemokine ligand 20 (CCL20) within KITENIN-overexpressed (KIT-HA) GL261 cell supernatants. Immunohistochemical analyses using GBM samples confirmed that both KITENIN and CCL20 expressions co-directionally increased and this was associated with decreased survival by TCGA analysis. Myeloid-derived suppressor cells (MDSCs), macrophages, and CD4+Foxp3+ regulatory T cells (Tregs) were observed to be higher in brain tumor implanted with KIT-HA GL261. Furthermore, KIT-HA GL261 conditioned medium expanded CD45+CD11b+Gr1-Ly6c+ monocytic MDSCs (M-MDSCs), an effect that was abrogated by CCL20 downregulation. In vivo neutralization of CCL20 resulted in reduced tumor volume, prolonged survival, and decreased M-MDSCs, thus affirming the role of CCL20 in mediating immunosuppression. Conclusion: These findings underscore the KITENIN-CCL20 axis as a promising target for alleviating the immunosuppressive TME in GBM, potentially unlocking new avenues for GBM immunotherapy. Citation Format: Eun-Jeong Ahn, Nah Ihm Kim, Sung Sun Kim, Jae-Hyuk Lee, Joon Haeng Rhee, Kyung-Keun Kim, Hangun Kim, Kyung-Hwa Lee, Kyung-Sub Moon. KITENIN leads immunosuppression in the glioblastoma microenvironment via CCL20 [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 5372.
Abstract 3344: Widespread <i>BRCA1/2</i>-independent homologous recombination defects are caused by alterations in RNA binding proteins
Authors: Babita Kaundal, Daniel J. McGrail, Yang Li, Roger S. Smith, Bin Feng, Hui Dai, Limei Hu, Briana Dennehey, Sharad Awasthi, Marc L. Mendillo, Anil K. Sood, Gordon B. Mills, Shiaw-Yih Lin, S. Stephen Yi, Nidhi Sahni
Journal: Cancer Research (2024)

Abstract Summary: Defects in homologous recombination DNA repair (HRD) both predispose to cancer development and produce therapeutic vulnerabilities, making it critical to define the spectrum of genetic events that cause HRD. However, we found that mutations in BRCA1/2 and other canonical HR genes only identified 10-20% of tumors that display genomic evidence of HRD. Using a networks-based approach, we discovered that over half of putative genes causing HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA binding protein (RBP)-encoding genes. These putative drivers of HRD were experimentally validated, cross-validated in an independent cohort, and enriched in cancer-associated GWAS loci. Mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD, with implications for basic biology, genetic screening, and therapy stratification. Citation Format: Babita Kaundal, Daniel J. McGrail, Yang Li, Roger S. Smith, Bin Feng, Hui Dai, Limei Hu, Briana Dennehey, Sharad Awasthi, Marc L. Mendillo, Anil K. Sood, Gordon B. Mills, Shiaw-Yih Lin, S. Stephen Yi, Nidhi Sahni. Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA binding proteins [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 3344.
Abstract 454: microRNAs role in innate immunosenescence during anti-PD1 immunotherapy
Authors: Zhouting Zhu, Tariq M. Rana
Journal: Cancer Research (2024)

Abstract Checkpoint inhibitors have achieved durable responses and long-lasting immunologic memory in cancer patients. However, the initial and acquired resistance remains an unsolved problem. It’s urgent to learn the molecular mechanisms causing resistance. microRNAs (miRNAs) are short transcripts that regulate many pathophysiological processes. Here, we investigated the miRNAs expression changes after GVAX combined with monoclonal PD-1 antibody treatment in the murine melanoma B16F10 tumors and identified microRNAs down-regulated in responsive tumors. Deletion of this family member in three different syngeneic mouse tumors did not affect their in vitro nor in vivo proliferation but sensitized anti-PD1 immunotherapy. The miRNA deletion with anti-PD1 therapy increased total CD45+ leukocyte infiltration with all types of hematopoietic cells except macrophages. Both tumor bulk RNA sequencing and single-cell RNA sequencing revealed activated innate sensing genes especially for pathogen recognition and phagosome formation. Importantly, we found specific miRNA-deletion effects rely on tumor resident macrophage, IFN-γ release in the tumor microenvironment (TME) and the miRNA regulating machinery protein Argonaut2 (Ago2). Notably, the miRNA expression status of melanoma patients correlates with the survival and innate immune sensing gene expression. Our results suggest that this family of miRNAs participate in initial resistance by escaping innate immunosurveillance. Deletion of the miRNA may turn immune “cold” tumors to “hot” tumors, providing potential therapeutic targets to overcome resistance in melanoma, colorectal, triple-negative breast cancer and possibly other cancers. Citation Format: Zhouting Zhu, Tariq M. Rana. microRNAs role in innate immunosenescence during anti-PD1 immunotherapy [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 454.
Abstract 4076: Interleukin-18 engineered for resistance to IL-18 binding protein (IL-18BP) and half-life extension to enhance its therapeutic potential
Authors: Jean Chamoun, Clifford DiLea, Kristiana Dreaden, Pinar Gurel, Joshua Heiber, Robert G. Newman, Su-Ping Pearson, Chunhua Wang, Yanchun Zhao, Mark Whitmore
Journal: Cancer Research (2024)

Abstract Interleukin-18 (IL-18) possesses a unique combination of innate and acquired immune functions with high potential to be transformative in cancer immunotherapy of solid tumors. In clinical studies, recombinant wild-type IL-18 was limited by rapid upregulation of IL-18 binding protein (IL-18BP), which serves as a negative feedback checkpoint of the IL-18 pathway. As its name implies, IL-18BP tightly binds to IL-18, thereby blocking its ability to activate the IL-18 receptor. We have focused our protein engineering efforts to obtain variants of IL-18 that are resistant to IL-18BP suppression while retaining IL-18 biological activity. To further capitalize on the immunological effects of IL-18, the IL-18BP resistant variants were fused to half-life extension protein scaffolds for enhanced in vivo exposure. Rational protein design and combinatorial approaches were used to generate a pool of IL-18 variants that were screened for potency and resistance to IL-18BP. Several IL-18 variants showed undetectable binding to IL-18BP (up to 1 mM IL-18BP) and displayed a spectrum of potencies relative to recombinant wild-type IL-18. Importantly, these variants retained their full biological activity in the presence of super-physiological levels of IL-18BP, as tested with in vitro cell-based IFN-γ release assays. In vivo pharmacokinetic studies in mice compared several IL-18BP resistant variants fused to a half-life extension scaffold with a non-half-life enhanced IL-18BP resistant variant. The half-lives for the fusion proteins ranged from 15 - 30h, while the non-fused variant showed a half-live of 0.6h. Furthermore, the IL-18 variants displayed a more durable, Th1 immune response compared to a non-half-life enhanced variant. Thus, IL-18 variants with strong resistance to IL-18BP that are fused to a half-life extension protein scaffold displayed enhanced pharmacokinetic and pharmacodynamic properties in preclinical mouse models. These protein engineering modifications will enable us to select an appropriate development candidate with enhanced pharmaceutical properties to achieve the full therapeutic potential of IL-18 to assess in patients with cancer. Citation Format: Jean Chamoun, Clifford DiLea, Kristiana Dreaden, Pinar Gurel, Joshua Heiber, Robert G. Newman, Su-Ping Pearson, Chunhua Wang, Yanchun Zhao, Mark Whitmore. Interleukin-18 engineered for resistance to IL-18 binding protein (IL-18BP) and half-life extension to enhance its therapeutic potential [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 4076.
Abstract 5362: Targeting IRE1α alleviates the immunosuppressive tumor microenvironment in prostate cancer
Authors: Bilal Unal, Omer Faruk Kuzu, Yang Jin, Daniel Camilo Hurtado, Marieke Lydia Kuijjer, Mads Daugaard, Htoo Zarni Oo, John B. Patterson, Fahri Saatcioglu
Journal: Cancer Research (2024)

Abstract Unfolded protein response (UPR) is a central stress response pathway in normal cells that is hijacked by tumor cells for their survival. However, how activation of UPR in cancer cells shapes the tumor microenvironment (TME) remain largely unexplored. Here, we investigated the role of IRE1α-XBP1s pathway on modulation of TME dynamics in prostate cancer (PCa). We found that IRE1α is increased in PCa patients and genetic or pharmacological inhibition of IRE1α signaling in the immunocompetent syngeneic mouse PCa model dramatically reduced tumor growth. Multiomics analysis of tumor samples upon IRE1α deletion in cancer cells showed significantly potentiated interferon (IFN) response and activation of immune system related pathways in the TME. Single-cell RNA sequencing (scRNA-seq) analysis revealed that the abundance of immunosuppressive cells, such as tumor-associated macrophages (TAMs) and T regulatory cells were markedly reduced in the IRE1α deficient tumors. Analysis of differentially expressed genes in the annotated cell types in the TME demonstrated that expression signatures associated with IFN responses were significantly enriched in TAMs, cancer cells, and dendritic cells. In addition, a novel scRNA-seq derived TAM gene signature is strongly associated with poor PCa survival. Furthermore, IRE1α inhibition by the small molecule MKC8866 (ORIN1001) that is in clinical trials significantly enhanced anti-PD-1 checkpoint inhibitor therapy in mice. Our findings indicate that IRE1α not only promotes cancer cell growth and survival, but it also strongly inhibits anti-tumor immunity in the PCa TME. Citation Format: Bilal Unal, Omer Faruk Kuzu, Yang Jin, Daniel Camilo Hurtado, Marieke Lydia Kuijjer, Mads Daugaard, Htoo Zarni Oo, John B. Patterson, Fahri Saatcioglu. Targeting IRE1α alleviates the immunosuppressive tumor microenvironment in 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 5362.
Abstract 3681: Transcribed ultraconserved regions are associated with survival in multiple tumor types
Authors: Ana Carolina Rodrigues, Douglas Adamoski, Daniela F. Gradia, Jaqueline Carvalho de Oliveira
Journal: Cancer Research (2024)

Abstract Ultraconserved regions (UCRs), encompassing 481 genomic segments identical across humans, mice, and rats, and conserved in other species, are distributed across all human chromosomes except 21 and Y. Over 90% of these regions, termed transcribed ultraconserved regions (T-UCRs) are expressed in at least one human tissue. Although extensively studied in the context of cancer since their discovery, the prognostic significance of T-UCRs in a pan-cancer context has not been explored. For this, TCGA data extracted from the TANRIC platform was utilized, differential expression and survival analysis was performed on different tumor types. Our analysis revealed that approximately 300 UCRs were expressed in the majority of the 20 tumor tissues. Additionally, it was noted that all examined tumor tissues expressed a higher number of UCRs compared to their non-tumor counterparts. Through t-distributed stochastic neighbor embedding (t-SNE) analysis, UCR expression patterns could distinguish primary tumor origins and types. Regarding the prognostic value, we identified 100 (20,8%) T-UCRs associated with disease-specific survival (DSS) and 102 (21.2%) T-UCRs associated with progression-free interval (PFI). Those T-UCRs are particularly important in the survival outcomes of kidney renal clear cell carcinoma (KIRC) and low-grade gliomas (LGC). In addition, we verified that uc.44, uc.48, uc.135, uc.144, uc.153, uc.217, uc.255, uc.256, uc.344, uc.357, uc.390, uc.427 and uc.436 were associated with survival of more than one tumor. Particularly, uc.135 high expression was associated with poor prognosis in Kidney Renal Papillary Cell Carcinoma (KIRP) and LGC, and good prognosis in KIRC. Uc.135 are mapped on MECOM gene, coding an oncoprotein acting as transcriptional regulator and involved in apoptosis, proliferation, and cell differentiation. Our findings suggest that analysis of T-UCRs expression have the potential to be used as predictive biomarkers and can help in studying the mechanisms and specific roles of the highlighted T-UCRs in cancer. Citation Format: Ana Carolina Rodrigues, Douglas Adamoski, Daniela F. Gradia, Jaqueline Carvalho de Oliveira. Transcribed ultraconserved regions are associated with survival in multiple tumor types [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 3681.
The Eμ-Ret mouse is a novel model of hyperdiploid B-cell acute lymphoblastic leukemia
Authors: Ali Farrokhi, Tanmaya Atre, Jenna Rever, Mario Fidanza, Wendy Duey, Samuel Salitra, Junia Myung, Meiyun Guo, Sumin Jo, Anuli Uzozie, Fatemeh Baharvand, Nina Rolf, Franziska Auer, Julia Hauer, Stephan A. Grupp, Patrice Eydoux, Philipp F. Lange, Alix E. Seif, Christopher A. Maxwell, Gregor S. D. Reid
Journal: Leukemia (2024)

Abstract The presence of supernumerary chromosomes is the only abnormality shared by all patients diagnosed with high-hyperdiploid B cell acute lymphoblastic leukemia (HD-ALL). Despite being the most frequently diagnosed pediatric leukemia, the lack of clonal molecular lesions and complete absence of appropriate experimental models have impeded the elucidation of HD-ALL leukemogenesis. Here, we report that for 23 leukemia samples isolated from moribund Eμ-Ret mice, all were characterized by non-random chromosomal gains, involving combinations of trisomy 9, 12, 14, 15, and 17. With a median gain of three chromosomes, leukemia emerged after a prolonged latency from a preleukemic B cell precursor cell population displaying more diverse aneuploidy. Transition from preleukemia to overt disease in Eμ-Ret mice is associated with acquisition of heterogeneous genomic abnormalities affecting the expression of genes implicated in pediatric B-ALL. The development of abnormal centrosomes in parallel with aneuploidy renders both preleukemic and leukemic cells sensitive to inhibitors of centrosome clustering, enabling targeted in vivo depletion of leukemia-propagating cells. This study reveals the Eμ-Ret mouse to be a novel tool for investigating HD-ALL leukemogenesis, including supervision and selection of preleukemic aneuploid clones by the immune system and identification of vulnerabilities that could be targeted to prevent relapse.
Abstract 5599: Role of HOX gene expression in differentiation of colon cancer stem cells
Authors: Brian T. Osmond, Caroline O. Facey, Lynn O. Opdenaker, Chi Zhang, Bruce M. Boman
Journal: Cancer Research (2024)

Abstract HOX genes encode a highly conserved set of transcription factors critical for stem cell (SC) function and embryonic development. Several HOX genes have also been implicated in a myriad of cancers, including colorectal cancer (CRC). However, how HOX genes play a role in SC regulation and contributes to cancer development is unclear. HOX expression is regulated by WNT, FGF, and retinoic acid (RA) signaling - pathways which also become dysregulated in cancer. Goal: To determine how regulation of HOX genes specifies differentiation of colonic SCs into specialized cell lineages and how dysregulation of HOX genes contributes to CRC development. Hypotheses: i) Each of the different cell types within human colonic epithelium has a distinct HOX gene expression signature; ii) All-trans retinoic acid (ATRA) induced differentiation of CRC cells changes HOX expression that correlates with specific HOX expression signatures in normal colon and CRC cells. Results: Immunostaining shows that specific HOX proteins (e.g., HOXA9 &amp; HOXC9) are selectively expressed in ALDH-positive SCs and expression of these HOX genes is increased in CRC tissues compared to normal epithelium. Bioinformatics analysis predicted that these HOX genes (plus HOXA4, HOXA10, HOXC8) are regulated by RA signaling. Accordingly, we studied how ATRA influences HOX expression in CRC cells (HT29 &amp; SW480). We found ATRA treatment: 1) Decreases proliferation and increases neuroendocrine cell (NEC) differentiation; and 2). Leads to specific changes in HOX gene expression patterns. Using NanoString profiling, we also discovered that LGR5+ SCs, ALDH+ SCs and GLP2R+ NECs have unique HOX signatures. By defining how these HOX gene expression changes in response to ATRA treatment in comparison to the HOX gene signatures of different colonic cell lineages will help us understand the role that HOX genes play in SC differentiation and how dysregulation of HOX gene expression contributes to CRC development. Citation Format: Brian T. Osmond, Caroline O. Facey, Lynn O. Opdenaker, Chi Zhang, Bruce M. Boman. Role of HOX gene expression in differentiation of colon cancer stem 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 5599.