tbuckley/cabot-search huggingface dataset:
Abstract LB096: Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma
Authors: Kristyna Tomasova, Karolina Seborova, Michal Kroupa, Josef Horak, Ludmila Vodickova, Lukas Rob, Martin Hruda, Marcela Mrhalova, Alena Bartakova, Jiri Bouda, Thomas Fleischer, Vessela Kristensen, Pavel Vodicka, Radka Vaclavikova
Journal: Cancer Research (2024)

Abstract Impaired telomere length (TL) maintenance in ovarian tissue may play a pivotal role in epithelial ovarian carcinoma (OvC) onset. TL in either target or surrogate tissue (blood) is currently being investigated as a predictor in anti-OvC therapy or as a biomarker of the disease progression, respectively. There is presently an urgent need for an appropriate approach to chemotherapy response prediction. We performed a monochrome multiplex qPCR measurement of TL in peripheral blood and tumor tissues of 209 OvC patients. Methylation status and gene expression of shelterin complex and telomerase catalytic subunit (hTERT) were determined within tumor tissues by High-Throughput DNA methylation profiling and RNA sequencing (RNA-Seq) analysis, respectively. The patients sensitive to cancer treatment (n=46) had shorter telomeres in peripheral blood cells compared to those treatment-resistant (n=93; P=0.037). Cancer tissue TL lower than the median predisposed to better overall survival (P=0.002). Gene expression of TPP1, which recruits telomerase to telomeres, was positively associated with TL in tumor tissue (P=0.026). TL measured in peripheral blood cells could serve as a marker of platinum therapy response in OvC patients. Additionally, TL determined in tumor tissue provides information on OvC patients' overall survival. The study was financed by the project NPO (LX22NPO05102), the Czech Health Research Council (NU21-03-00145), and the Czech Science Foundation (21-27902S). Citation Format: Kristyna Tomasova, Karolina Seborova, Michal Kroupa, Josef Horak, Ludmila Vodickova, Lukas Rob, Martin Hruda, Marcela Mrhalova, Alena Bartakova, Jiri Bouda, Thomas Fleischer, Vessela Kristensen, Pavel Vodicka, Radka Vaclavikova. Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB096.
Abstract LB033: Identification of small molecule Pan-TEAD inhibitors disrupting YAP-TEAD protein-protein interaction and targeting gastric cancer cells
Authors: Ramesh Kumar, Joel Toh, Joanne Thian, Noorul Farzana Mohideen, Jialin Sun, Sayan Chakraborty, Jayantha Gunaratne, Wanjin Hong
Journal: Cancer Research (2024)

Abstract Because of the Hippo pathway’s unique ability to restrict TAZ/YAP-TEAD in promoting regeneration, any abnormality of its core components, may promote the migration, invasion, and malignancy of cancer cells. Aberrant overexpression of YAP/TAZ-TEAD promotes tumorigenesis and is therefore considered oncogenes in many solid tumors. Drug resistance is a major factor undermining the efficacy of cancer drugs. As YAP/TAZ-TEAD complex plays a role in intrinsic and acquired resistance to various chemotherapeutic and targeted therapy drugs, there is increasing interest in combining a TEAD inhibitor with various cancer therapies. Since elevated YAP/TAZ-TEAD activity has been implicated in multiple cancer types at various stages of cancer progression and cancer types, Drugging the TEAD hydrophobic pocket, which was discovered in 2015, remains as an attractive and proven strategy to modulate the activity. Despite the progresses, only 3 small molecule TEAD inhibitors are currently being tested in Phase I clinical trials which includes: VT3989b NCT04665206 from Vivacare, IK-930b NCT05228015 from Ikena Oncology and IAG-933, NCT0485737 from the Novartis Oncology. As such, there is a need to uncover alternative TEAD inhibitors for cancer therapeutics. We report novel small molecule inhibitors that form a covalent complex with the conserved cysteine of the TEAD palmitoylation site. Compounds inhibited TEAD transcriptional target genes in cancer cells. Cellular proliferation and colony forming assay data strongly displayed cellular sensitivity in Hippo signaling altered cancer cell lines. TEAD1 dependency of gastric cancer cell lines enhance cellular sensitivity in response to small molecule inhibitors. Transcriptional profiling and RNA seq data indicate that the covalent inhibitors specifically downregulate down-stream transcriptional target genes. With our exciting key data, we are exploring multiple other oncology targets to use our Pan-TEAD inhibitors either as a monotherapy or combination therapy. We expect to complete our Technology Disclosure on additional targets before the meeting and to add exciting data for the Cancer drug development community. Citation Format: Ramesh Kumar, Joel Toh, Joanne Thian, Noorul Farzana Mohideen, Jialin Sun, Sayan Chakraborty, Jayantha Gunaratne, Wanjin Hong. Identification of small molecule Pan-TEAD inhibitors disrupting YAP-TEAD protein-protein interaction and targeting gastric cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB033.
Abstract LB267: Disrupting cytoplasmic proton motive force induces ferroptotic cell death in colorectal cancer: A novel anti-cancer mechanism
Authors: Shreyas R. Gaikwad, Mohamed A. Eltokhy, Morgan Moore, Keerthi Kailath, Sanjay K. Srivastava
Journal: Cancer Research (2024)

Abstract Introduction: Chemotherapeutic resistance and tumor recurrence remain the leading causes of poor prognosis in colorectal cancer (CRC). Herein, we evaluated the anti-cancer effect of a novel repurposed drug HLN* in CRC. Methods: The changes in membrane potential were studied using DiSC(3) fluorescence by confocal microscopy. Cytotoxic activity of compound was studied using Sulphorhodamine-B (SRB) assay. Changes in mitochondrial membrane potential were studied using JC-1 dye. ROS accumulation was analyzed using DCFDA fluorescence using FACS analysis. Ferrorange assay was used to check the ferrous ion influx within the cell. Western blot was used to identify mode of cell death enacted. Results: Our results show that HLN treatment reduced the survival of human and murine CRC cells (CT26, HCT116, Colo 205 and MC38) with IC50 ranging 1-4 µM. HLN further inhibited proton motive force (PMF) by sequentially depolarizing and hyperpolarizing the cell membrane, as examined by cellular membrane potential using DiSC(3) dye by confocal microscopy. Disruption of the PMF leads to changes in various cellular signaling cascades including ROS production and mitochondrial membrane potential (MMP) changes. The MMP was significantly reduced by HLN treatment in CRC cells. Furthermore, we also observed an increase in ROS production by HLN. Pretreatment with N-acetyl cysteine (NAC), an antioxidant, blocked the effects of HLN. Interestingly, ferroptotic cell death markers GPX4, GPX1, SLC7A11/xCT, NRF2 and KEAP1 were significantly inhibited by HLN treatment in CRC cells as observed by western blotting. Ferroptotic induction was then confirmed using ferrorange assay wherein we observed a concentration dependent increase in ferrorange intensity indicating an increase in Fe+2. Overall, HLN dissipates ΔpH by modulating iron influx leading to ferroptotic cell death through ROS. Conclusion: Taken together, our results demonstrate the anti-cancer activity of a novel repurposed drug HLN and its unique mechanism of action. Our results provide a promise for developing this drug as a potential treatment option for CRC, through a novel anti-cancer mechanism. * Due to Intellectual property issued, the name of the drug is not provided Citation Format: Shreyas R. Gaikwad, Mohamed A. Eltokhy, Morgan Moore, Keerthi Kailath, Sanjay K. Srivastava. Disrupting cytoplasmic proton motive force induces ferroptotic cell death in colorectal cancer: A novel anti-cancer mechanism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB267.
Abstract LB015: Differential expression of deubiquitinating enzymes and its related DNA damage response genes in neuroblastoma heterogeneity
Authors: Vaibhav Vaibhav, Fahika Nazeerulla, Tatjana Paunesku, Ekta Tripathi, Gayle Woloschak, Prashanthi Karyala, Rao V. Papineni
Journal: Cancer Research (2024)

Abstract SK-N-AS and SK-N-DZ are two cell lines of pediatric solid tumors neuroblastomas well characterized to evaluate heterogeneity between different neuroblastomas and are presumed as models for differences between different neuroblastoma. Using this model system, we recently evaluated if radiation could improve efficacy of radiation therapy and to follow these studies later with animal models to determine decrease of tumor burden. Differences between the N-type and S-type neuroblastoma cell lines SK-N-DZ and SK-N-AS, respectively were observed to be high and their responses to radiation stress were equally heterogeneous. Ubiquitin signaling plays a key role during the DNA damage response in protein recruitment and protein interactions. Deubiquitinating enzymes (DUBs) deconjugate ubiquitin from ubiquitylated substrate proteins to control their activity and stability and are shown to regulate various biological processes. DUBs may play a role in regulating the radiosensitivity of cancer cells by modulating DNA damage response and repair pathways. Determination of specific DUBs that are involved in regulating radiosensitivity in cancer cells will provide opportunity for drug targeting and visa-vis enhance the efficacy of radiation therapy in neuroblastoma cancer treatment. Here, using bioinformatic tools, the differentially regulated DUBs were identified. The relationship between DEGs-DUBs with the genes involved in various DNA repair pathways (NHEJ, HR and Fanconi anemia pathway; KEGG pathway database) are described. We identified 32 DEGs (14 upregulated and 18 downregulated) with these neuroblastoma cell lines. USP22 and USP41 DUBs and its differential expression in these cell lines denotes the importance of such analysis. Especially considering USP22 a potentially biomarker for predicting the outcome of patients with neuroblastoma. These DEG-DUBs were likewise correlated with 91 DNA damage response (DDR) genes belonging to three different pathways (NHEJ, HR and Fanconi anemia pathway). Out of which 44 of the DDR genes showed significant correlation with DEG-DUBs. Further studies are needed to determine the mechanisms underlying the complex relationship of these DUBs and to determine the critical DUBs for drug targeting and to enhance the efficacy of radiation therapy in cancer treatment. Citation Format: Vaibhav Vaibhav, Fahika Nazeerulla, Tatjana Paunesku, Ekta Tripathi, Gayle Woloschak, Prashanthi Karyala, Rao V. Papineni. Differential expression of deubiquitinating enzymes and its related DNA damage response genes in neuroblastoma heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB015.
Abstract LB297: Toll-like receptor 8 in tumor associated macrophages regulates miR-192-5p expression and drug resistance in neuroblastoma
Authors: Nicolo Toldo, Verena Martinez Rodriguez, Muller Fabbri
Journal: Cancer Research (2024)

Abstract MicroRNAs (miRs) are small non-coding RNAs (ncRNAs) with gene expression regulatory functions. MiRs are frequently dys-regulated in human cancers and orchestrate the biology of the disease, and its resistance to chemotherapy. Increasing evidence supports a role of the tumor microenvironment (TME) in promoting cancer growth and resistance to treatments. Tumor Associated Macrophages (TAMs) are a predominant cellular component of the TME of several types of cancers, including neuroblastoma (NB), the most frequent pediatric extra-cranial solid tumor. NB cells secrete miRs within small extracellular vesicles called exosomes, and these miR are shuttled to surrounding TAMs. Our lab was the first to show that cancer-derived exosomal miRs bind to Toll-like receptor 8 (TLR8) in TAMs, triggering an NF-κB-dependent production of TAM-derived miRs, that are then shuttled back to NB cells. Following up on that discovery, we identified a signature of miRs that are up/down-regulated in NB cells when co-cultured with TAMs expressing TLR8 or in which the TLR8 had been deleted with CRISPR/Cas9 engineering. We identified miR-192-5p as significantly down-regulated in NB cells when co-cultured with wild-type TAMs, however miR-192-5p expression was significantly increased in NB cells when co-cultured with TLR8-knock out TAMs, supporting a TLR8-mediated modulation of miR-192-5p in the NB TME. Additionally, we found that over-expression of miR-192-5p in NB cells increased sensitivity of NB cells to temozolomide and cisplatin, two commonly used drugs in the treatment of this malignancy. Overall, these findings support the use of TLR8 inhibitors to up-regulate miR-192-5p and increase sensitivity of NB cells to chemotherapy. Citation Format: Nicolo Toldo, Verena Martinez Rodriguez, Muller Fabbri. Toll-like receptor 8 in tumor associated macrophages regulates miR-192-5p expression and drug resistance in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB297.
Abstract LB002: Deactivation of ligand-receptor interactions enhancing lymphocyte infiltration drives melanoma resistance to immune checkpoint blockade
Authors: Sahil Sahni, Binbin Wang, Di Wu, Saugato Rahman Dhruba, Matthew Nagy, Sushant Patkar, Ingrid Ferreira, Kun Wang, Eytan Ruppin
Journal: Cancer Research (2024)

Abstract Immune checkpoint blockade (ICB) is a promising cancer therapy; however, resistance often develops. To learn more about ICB resistance mechanisms, we developed IRIS (Immunotherapy Resistance cell-cell Interaction Scanner), a machine learning model aimed at identifying candidate ligand-receptor interactions (LRI) that are likely to mediate ICB resistance in the tumor microenvironment (TME). We developed and applied IRIS to identify resistance-mediating cell-type-specific ligand-receptor interactions by analyzing deconvolved transcriptomics data of the five largest melanoma ICB therapy cohorts. This analysis identifies a set of specific ligand-receptor pairs that are deactivated as tumors develop resistance, which we refer to as resistance deactivated interactions (RDI). Quite strikingly, the activity of these RDIs in pre-treatment samples offers a markedly stronger predictive signal for ICB therapy response compared to those that are activated as tumors develop resistance. Their predictive accuracy surpasses the state-of-the-art published transcriptomics biomarker signatures across an array of melanoma ICB datasets. Many of these RDIs are involved in chemokine signaling. Indeed, we further validate on an independent large melanoma patient cohort that their activity is associated with CD8+ T cell infiltration and enriched in hot/brisk tumors. Taken together, this study presents a new strongly predictive ICB response biomarker signature, showing that following ICB treatment resistant tumors turn inhibit lymphocyte infiltration by deactivating specific key ligand-receptor interactions. Citation Format: Sahil Sahni, Binbin Wang, Di Wu, Saugato Rahman Dhruba, Matthew Nagy, Sushant Patkar, Ingrid Ferreira, Kun Wang, Eytan Ruppin. Deactivation of ligand-receptor interactions enhancing lymphocyte infiltration drives melanoma resistance to immune checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB002.
Abstract LB427: UBA1 blockade induces homologous recombination deficiency and is synthetic lethal with PARP inhibition
Authors: Sharad Awasthi, Daniel J. McGrail, S. Stephen Yi, Nidhi Sahni
Journal: Cancer Research (2024)

Abstract Therapeutic strategies targeting DNA damage have revolutionized cancer treatment, yet their efficacy often comes at the cost of substantial adverse effects. The emergence of poly-ADP-ribose polymerase (PARP) inhibition as a targeted approach to disrupt DNA repair in tumors deficient in homologous recombination (HR) has shown promise. However, the limited response of most cancers to PARP inhibitors has posed a significant challenge. This study employs a genome-wide CRISPR knockout functional genomics screen, revealing that depletion of ubiquitin-activating enzyme E1 (UBA1) enhances sensitivity to PARP inhibition in HR-proficient ovarian cancer cells. Validation across different ovarian and breast cancer cell lineages, utilizing cell line and organoid models, establishes that pharmacological inhibition of UBA1, a pivotal player in ubiquitination, sensitizes cells to PARP inhibition and other DNA damaging therapies. In vivo experiments combining PARP and UBA1 inhibition demonstrate not only tolerability but also significant extension of survival in patient-derived xenografts compared to individual therapies. Mechanistic studies uncover that UBA1 inhibition not only impedes HR repair, sensitizing cells to PARP inhibition, but also induces widespread increases in PARylation, subsequently targeted by PARP inhibition. These findings underscore the multifaceted pathways through which UBA1 inhibition potentiates the efficacy of PARP inhibition. The demonstrated tolerability and substantial therapeutic gains establish the combined approach as a promising strategy to maximize the benefits of PARP inhibition in cancer therapy. Citation Format: Sharad Awasthi, Daniel J. McGrail, S. Stephen Yi, Nidhi Sahni. UBA1 blockade induces homologous recombination deficiency and is synthetic lethal with PARP inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB427.
Abstract LB067: Tumor-reactive CD8 TIL with an exhausted phenotype can be expanded and regress human tumors
Authors: Andrew Weinberg, Brendan Curti, Ryan Montler, Colin Thalhofer, Elaine Ballinger, Jessica Cross, Eric Tran, Nelson Sanjuan, Matthew Taylor, Christopher Fountain, Roxanne Payne, James Cardia, Nicholas Morris
Journal: Cancer Research (2024)

Abstract Tumor-reactive human CD8 T cells are found predominantly in the tumor microenvironment with an exhausted phenotype (extremely high levels of CD39, PD-1, CTLA-4, and TIM-3). The tumor-reactive cells can be enriched from patients’ tumors by sorting CD8+ TIL that express both CD39 and CD103. Our unique expansion method allowed these phenotypically exhausted cells to grow from thousands into billions. After expansion the CD39 and CD103 Double Positive (DP) CD8 TIL can recognize/kill autologous tumor cells in vitro. We tested whether the CD8 DP TIL could recognize/kill autologous tumor in vivo using a xenograft model with immune-compromised mice that constitutively secrete human IL-2 (NOG-hIL-2). The CD8 DP TIL were able to persist long-term, traffic to the tumor site, recognize autologous tumor, and facilitate tumor regression. Human IL-2 was necessary for their long-term survival in the periphery and for tumor regression. These preclinical data were the basis for a human clinical trial design for the adoptive transfer of CD8 DP TIL (product termed, AGX148). We recently opened a Phase 1 clinical trial using the CD39/103 DP CD8 TIL in a first-in-human protocol for adults with solid tumors (NCT05902520). The trial design has three cohorts based on giving IL-2 for 2 weeks, 3 weeks, or 4 weeks after adoptive transfer with six patients/cohort (3 receiving DP TIL alone and 3 receiving DP TIL combined with PD-1 siRNA knockdown with the INTASYLTM compound PH-762). The first 3 patients have been treated and received 27, 40, and 8 billion DP TIL, respectively. All 3 patients had failed standard therapy prior to their enrollment, including checkpoint blockade. No serious adverse events were observed in the first three patients. Two of three patients had partial responses 29 days after treatment and the third patient had stable disease for &amp;gt;56 days. Blood draws and tumor biopsies were obtained prior to and after treatment and we are currently assessing the CD8 T cell repertoire (TCRseq) and phenotype from these patient samples. In conclusion, this is the first study showing that CD8 T cells with an exhausted phenotype isolated from human tumors can be expanded to billions and induce tumor regression in vivo. Citation Format: Andrew Weinberg, Brendan Curti, Ryan Montler, Colin Thalhofer, Elaine Ballinger, Jessica Cross, Eric Tran, Nelson Sanjuan, Matthew Taylor, Christopher Fountain, Roxanne Payne, James Cardia, Nicholas Morris. Tumor-reactive CD8 TIL with an exhausted phenotype can be expanded and regress human tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB067.