tbuckley/cabot-search huggingface dataset:
Abstract 663: Irreversible covalent azetidine-based small molecule inhibitors of Stat3 activity block growth of human pancreatic tumors
Authors: Yue Chen, Ning Zhai, Peibin Yue, Christine Brotherton-Pleiss, Wenzhen Fu, Kayo Nakamura, Weiliang Chen, Marcus Tius, Francisco Lopez-Tapia, James Turkson
Journal: Cancer Research (2024)

Abstract The incidence and death rates for pancreatic adenocarcinoma in the US have been increasing by about 1% per year and the death rate has increased by approximately 0.2% yearly. The five-year survival rate has remained below 10% for many years. With surgery, radiation, and chemotherapy being the main treatment options to extend survival or for symptom relief, there is an urgent unmet need for effective new treatment options. Signal Transducer and Activator of Transcription (Stat) 3, one of the Stat family members, is aberrantly activated in human pancreatic and many other cancers. Aberrantly-active Stat3 promotes abnormal tumor-cell intrinsic and extrinsic mechanisms, including dysregulation of gene expression and mitochondria energy metabolism in the tumor cells, and suppression of immune cell functions in the tumor microenvironment. Stat3 is therefore an important target for therapeutic development. Herein we present two small molecules, H182 and H333, which are covalent inhibitors of Stat3 and that potently block Stat3 DNA-binding activity in vitro, with IC50 0.66-0.98 µM. H182 and its structural analog, H333 bind Stat3 via irreversible covalent interactions with key cysteine residues in the Stat3 DNA-binding domain to induce a time-dependent inhibition of Stat3 activity. Both compounds inhibit intracellular constitutive Stat3 tyrosine phosphorylation and induce loss of viable cells and apoptosis in vitro of human pancreatic Panc-1 and Mia-Paca2 cells. H333 is 13-fold more specific and H182 is 4-fold more specific against tumor cells over normal cells. Furthermore, MiaPaca-2 cells treated with H182 and analyzed by Seahorse showed dramatically decreased mitochondria respiration. Notably, xenograft models of MiaPaca2 treated with H182 or H333 via i.p. every other day for 27 days showed dramatic growth inhibition. Collectively, our results identify H182 and H333 as therapeutically-viable small molecules with unique irreversible mechanism of Stat3 inhibition which accounts for their strong antitumor effects against human pancreatic tumor xenografts. Citation Format: Yue Chen, Ning Zhai, Peibin Yue, Christine Brotherton-Pleiss, Wenzhen Fu, Kayo Nakamura, Weiliang Chen, Marcus Tius, Francisco Lopez-Tapia, James Turkson. Irreversible covalent azetidine-based small molecule inhibitors of Stat3 activity block growth of human pancreatic tumors [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 663.
Abstract 441: Bioluminescent dehydrogenase assays: A novel approach for metabolic profiling and inhibitor screening in cancer biology
Authors: Kim Haupt, Natasha Karassina, Anthony Lauer, Kayla Sylvester, Jolanta Vidugiriene
Journal: Cancer Research (2024)

Abstract Dehydrogenases play a pivotal role in cellular metabolism, acting as gatekeepers in key metabolic pathways. Their activity reflects the metabolic state of the cell, which is particularly relevant in the context of cancer and the immune response, where metabolic reprogramming is a hallmark of tumor progression and differentiation stages. Here, we present the development and application of novel bioluminescent dehydrogenase assays for direct measurement of metabolic activity in cell lysates. Our assays are highly sensitive, requiring as few as 100-500 cells, and have been successfully miniaturized to a 384-well plate format conducive to high-throughput screening. This technological advance allows for the precise monitoring of dehydrogenase activity across the pentose phosphate pathway, glycolysis, and the mitochondrial tricarboxylic acid (TCA) cycle. We demonstrate how shifts in dehydrogenase activity can serve as indicators of the metabolic status of cells, and their modulation during differentiation. Moreover, our bioluminescent assays provide a rapid screening platform for pathway-specific metabolic inhibitors, with potential applications in identifying new therapeutic targets within cancer metabolism. Our data reveal a dynamic landscape of metabolic activity during T cell maturation, underscoring the potential of dehydrogenase activity profiling in cancer immunobiology and the development of targeted cancer therapies. Citation Format: Kim Haupt, Natasha Karassina, Anthony Lauer, Kayla Sylvester, Jolanta Vidugiriene. Bioluminescent dehydrogenase assays: A novel approach for metabolic profiling and inhibitor screening in cancer biology [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 441.
Abstract 2213: Vaping, smoking and lung cancer: A case-control study
Authors: Marisa A. Bittoni, David Carbone, Randall Harris
Journal: Cancer Research (2024)

Abstract Introduction: Nicotine exposure through the use of electronic delivery systems (vaping) has been found to elevate the risk of certain conditions of the lungs, e.g., vaping associated lung injury. However, the potential impact of vaping on lung cancer risk remains largely unexplored. We, therefore, examined the association of vaping and cigarette smoking with lung cancer risk in a case-control study conducted at The Ohio State University in Columbus, Ohio. Methods: Medical records examined from the James Cancer Hospital and Solove Research Institute revealed 4,975 cases with newly diagnosed, pathologically confirmed lung cancer during 2013-2021. These cases were compared to 27,294 controls without cancer that were group-matched on a 5:1 ratio to cases by age, gender, race and year of ascertainment. Descriptive statistics were calculated, and logistic regression analyses were performed to assess the associations between vaping, smoking and lung cancer. Results: The lung cancer cases in this study were 55% male, 88% white, with mean age at diagnosis of 62 years. The adjusted odds ratio (OR) for individuals who reported vaping and smoking was OR=21.1 (95% CI=17.1, 26.1) versus OR=6.3 (95% CI=5.8, 6.8) for smoking only. Estimates for gender and histologic cell type of lung cancer, e.g., pulmonary adenocarcinoma, squamous cell carcinoma and small cell carcinoma, were consistently over threefold higher for vaping and smoking compared to smoking only (p&amp;lt;0.001), and the vaping effect persisted even after adjustment for comorbidities, COPD and cardiovascular disease. Conclusion: Adjusted estimates of odds ratios (OR) revealed over threefold higher risk of lung cancer among individuals who had vaped and smoked compared to individuals who only smoked. Our results suggest that the addition of vaping to smoking greatly accelerates the risk of developing lung cancer. Future studies are needed to further confirm these results. Citation Format: Marisa A. Bittoni, David Carbone, Randall Harris. Vaping, smoking and lung cancer: A case-control 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 2213.
Abstract 4464: Ferredoxin 1 is essential for embryonic development and lipid homeostasis
Authors: Jin Zhang, Sharkur Mohibi, Xinbin Chen, Vivian Perng, Yanhong Zhang
Journal: Cancer Research (2024)

Abstract Mammalian ferredoxin 1 and 2 (FDX1/2) belong to an evolutionary conserved family of iron-sulfur cluster containing proteins and act as electron shutters between ferredoxin reductase (FDXR) and numerous proteins involved in critical biological pathways. FDX1 is involved in biogenesis of steroids and bile acids, Vitamin A/D metabolism, and lipoylation of tricarboxylic acid (TCA) cycle enzymes. FDX1 has been extensively characterized biochemically but its role in physiology and lipid metabolism has not been explored. In this study, we generated Fdx1-deficient mice and showed that knockout of both alleles of the Fdx1 gene led to embryonic lethality. We also showed that like Fdxr+/− mice, Fdx1+/− mice had a shorter life span and were prone to steatohepatitis. However, unlike Fdxr+/− mice, Fdx1+/− mice were not prone to spontaneous tumors. Additionally, we showed that FDX1 deficiency led to lipid droplet accumulation possibly via the ABCA1-SREBP1/2 pathway. Specifically, untargeted lipidomic analysis showed that FDX1 deficiency led to alterations in several classes of lipids, including cholesterol, triacylglycerides, acylcarnitines, ceramides, phospholipids and lysophospholipids. Taken together, our data indicate that FDX1 is essential for mammalian embryonic development and lipid homeostasis at both cellular and organismal levels. Citation Format: Jin Zhang, Sharkur Mohibi, Xinbin Chen, Vivian Perng, Yanhong Zhang. Ferredoxin 1 is essential for embryonic development and lipid homeostasis [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 4464.
Abstract 1205: Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
Authors: Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael
Journal: Cancer Research (2024)

Abstract Tumors evolve through the acquisition of somatic mutations over time and across space. While the temporal aspects of tumor evolution can be inferred by applying phylogenetic techniques to bulk or single-cell DNA sequencing data, the spatial aspects of tumor evolution remain understudied. Spatially resolved transcriptomics (SRT) measures gene expression at thousands of spatial locations in a tumor, but does not directly measure genetic aberrations. Thus, SRT data has not yet been fully utilized for tumor evolution studies. We introduce CalicoST, an algorithm that simultaneously infers allele-specific copy number aberrations (CNAs) and derives a phylogeographic model of tumor evolution from SRT data. By modeling CNA-induced perturbations in both gene expression and allele frequencies, CalicoST identifies important types of CNAs - including copy-neutral loss of heterozygosity (CNLOH) and mirrored subclonal CNAs - that are invisible to total copy number analysis. On SRT data from nine patients from the Human Tumor Atlas Network (HTAN), CalicoST achieves an average accuracy of 86%, approximately 21% higher than existing methods. On two of these patients with multiple adjacent slices, CalicoST reconstructs a tumor phylogeography that describes the spread of cancerous clones in three-dimensional space. CalicoST analysis of multiple SRT slices from a cancerous prostate organ reveals five spatially coherent clones, with mirrored subclonal CNAs distinguishing clones on the two sides of the prostate, and a bifurcating phylogeography in both genetic and physical space that suggests a polyclonal cancer. Citation Format: Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael. Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics [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 1205.
Abstract 6282: Novel androgen related gene network in prostate cancer cell model
Authors: Alex L. McDonald, Spencer Snow, Shuk-mei Ho, Yuet-kin Leung
Journal: Cancer Research (2024)

Abstract Prostate cancer stands as the foremost cause of cancer-related deaths among men in the United States, with the primary treatment being androgen receptor (AR) antagonists relying on current androgen signaling knowledge. Most of this knowledge is derived from next-generation sequencing experiments, but the oversight of splice variants and highly similar sequences in multiple loci can hinder a comprehensive understanding. In an effort to unveil the complete androgen receptor transcriptional program, we employed a novel sequencing analysis protocol. Using a R1881-LNCaP model, we identified 212 upregulated and 92 downregulated genes, of which a notable one-third (68 upregulated and 39 downregulated) had not been previously associated with androgen. Among these novel transcripts, 5.6% lacked splice variants, while 16.3% exhibited one or more splice variants, including 3.8% from seven unique gene families. Recognized androgen-regulated genes, such as ORM1, STEAP4, NPPC, ORM2, and KLK3, were validated as upregulated, while GRB10, FN1, PPFIA2, and PLA2G2A were confirmed as downregulated in this in-vitro model. Utilizing chromatin immunoprecipitation-sequencing (ChIP-seq) data, we found that 13% of the genes contained at least one androgen response element within 5 kb upstream or downstream. Further validation through real-time PCR confirmed the expression levels of 90% of the selected genes (18). Ingenuity Pathway Analysis revealed two major regulators (ESRRA and ARFGEF2) in causal networks likely interacting with the novel genes. Intriguingly, 57.1% of ESRRA-involved genes contained at least one ESRRA binding site in a ChIP-seq dataset. Although ESRRA is known to activate androgen biosynthesis in castration-resistant prostate cancer, its interaction with AR and co-regulation of androgen signaling remain unknown. Ongoing studies involve the characterization of these networks in prostate cancer cell lines, examining anchorage-independent capacity, invasion, migration, proliferation, and progression. Data collection and comparison will ascertain whether the signaling is driven by mutated AR, and the role of ARv7 will be elucidated through gene lockdown experiments. Citation Format: Alex L. McDonald, Spencer Snow, Shuk-mei Ho, Yuet-kin Leung. Novel androgen related gene network in prostate cancer cell model [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 6282.
Abstract 313: Benchmarking immune repertoire sequencing technologies
Authors: Shamoni Maheshwari, Carolyn Morrison, Sarah Taylor
Journal: Cancer Research (2024)

Abstract In the past decade, single cell gene expression technologies have transformed basic and translational research and are more frequently found in the toolbox of immunologists alongside the standard bulk B-cell receptor (BCR) sequencing and transcriptome profiling assays. While conventional bulk BCR assays capture the frequency of single chains, single-cell immune profiling reveals the frequency of paired heavy and light chains along with the cells transcriptional profile. Here we present the results of a single-blind benchmarking experiment conducted in collaboration with the U.S. Food and Drug Administration (FDA) that compares the performance of standard bulk DNA and RNA BCR repertoire sequencing assays, with the 10x Genomics Single Cell Immune Profiling solution. The FDA selected nine unambiguously monoclonal BCR-expressing cell lines to generate a reference mixture that was shared with each study participant, without revealing the input proportions. This reference cell line mixture was also diluted to 10% and 1% with B-cells sorted from peripheral blood mononuclear cells (PBMC) to further test the limits of clonotype detection. For each experiment, we targeted ~10,000 cells and in aggregate generated a paired gene expression and V(D)J dataset from ~100,000 cells. BCR clonotypes were detected in 78% of the captured cells across all samples profiled. Each of the 9 top unique clonotypes observed in our dataset corresponded to a cell line in the reference mixture, allowing us to decode the mixing percentages of each BCR-expression cell line. In addition, we were able to identify rare cell line clonotypes to as low as 0.01% in the dilution experiments. Furthermore, the multimodal nature of the single cell data also resolved the transcriptional profile of each cell line into its own cluster thus enabling independent verification of clonotype proportions. In summary, we have generated a resource for the immunology community to evaluate and compare data generated with different repertoire sequencing technologies. Citation Format: Shamoni Maheshwari, Carolyn Morrison, Sarah Taylor, BCR-SEQC consortium. Benchmarking immune repertoire sequencing technologies [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 313.
Abstract 3278: Analysis of the mechanism of resistance to selpercatinib in thyroid cancer cells with <i>RET/PTC1</i> fusion gene
Authors: Masatsugu Amitani, Ken-ichi Ito
Journal: Cancer Research (2024)

Abstract Purpose: Precision oncology, in which molecularly targeted drugs are selected based on genetic mutations, has begun in thyroid cancer, and drugs targeting BRAF, RET, and NTRK are already in clinical use. However, as with previous therapeutic agents for malignant tumors, there have been cases of resistance to these drugs either initially or during treatment, and the mechanisms of drug resistance need to be elucidated. So far, little is known about the mechanisms of resistance to molecularly targeted drugs in thyroid cancer. To overcome resistance to the RET inhibitor, selpercatinib (SEL), and to consider next therapeutic strategies, we aimed to elucidate the mechanisms of resistance to SEL. Method: We used papillary carcinoma cell lines TPC-1 and CUTC48, which harbor the RET/PTC1 fusion gene. We established an SEL-resistant subline (TPC-1/SELR) in TPC-1 by long-term exposure to SEL. The growth inhibitory effect of drugs was analyzed using the WST assay. The alteration of intracellular signal transduction was analyzed by western blotting. Result: The 50% inhibitory concentration (IC50) for SEL in the parental TPC-1 was 3 nM, while growth inhibition in TPC-1/SELR did not reach 50% even at more than 100 nM of SEL. On the other hand, growth inhibition by SEL in CUTC48 did not reach 50% even at more than 100 nM of SEL. The sensitivity to SEL in CUTC48 was comparable to that in TPC-1/SELR, and CUTC48 showed an intrinsic resistance to SEL. TPC-1/SELR showed increased phosphorylation of EGFR, Erk, Akt, and mTOR compared to TPC-1. In CUTC48, phosphorylation of EGFR and Erk was not increased compared to that of TPC-1, while phosphorylation of Akt and mTOR was increased. We investigated the growth inhibitory effect of an mTOR inhibitor everolimus and found that TPC-1 (IC50: 1.3 nM), TPC-1/SELR (5 nM), and CUTC48 (9.4 nM) were all highly sensitive to everolimus. Discussion: Our results showed that Akt and mTOR phosphorylation were elevated in the SEL-resistant TPC-1/SELR and the SEL-intrinsic resistant CUTC48 in common, suggesting the involvement of activation of the Akt-mTOR pathway in SEL resistance in thyroid cancer. The inhibition of the Akt-mTOR pathway in parallel with RET may have therapeutic potential to overcome SEL resistance in thyroid cancer. Citation Format: Masatsugu Amitani, Ken-ichi Ito. Analysis of the mechanism of resistance to selpercatinib in thyroid cancer cells with RET/PTC1 fusion gene [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 3278.
Abstract 5612: MRE11 function in DNA damage response is regulated by SIRT2 deacetylation
Authors: Mark Essien, Fatmata Sesay, Hui Zhang, Andrew Jung, David Yu
Journal: Cancer Research (2024)

Abstract MRE11 is known to play a role in DNA damage repair through the MRE11-RAD50-NBS1 (MRN) complex and homologous recombination. However, the upstream signaling mechanisms regulating MRE11 in DNA repair are unclear. Here, we aimed to determine the extent to which MRE11 is regulated by deacetylation by the SIRT2 sirtuin deacetylase and tumor suppressor protein. We overexpressed MRE11 in HEK293T cells, induced DNA damage through radiation treatment, and performed a series of co-immunoprecipitation (co-IP) studies with and without ionizing radiation (IR). Additionally, we evaluated the acetylation of MRE11 with and without the presence of SIRT2. In a series of functional experiments, immunofluorescence staining assays were performed in U2OS-265 Fok1 cells with SIRT2 knockdown to determine the effect of on MRE11 recruitment to DNA damage sites. Co-IP studies and in vitro DNA pulldown assays were performed to determine the role of SIRT2 in impacting MRE11 interaction with RAD50 and NBS1 and binding to DNA damage. We also examined for IR-induced RPA70 foci formation and downstream ATM-dependent signaling. We found that SIRT2 interacts with and deacetylates MRE11. Furthermore, SIRT2 deacetylation facilitated MRE11 binding to DNA but not interaction with RAD50 and NBS1. Finally, SIRT2 deacetylation facilitated DNA end resection and ATM-dependent phosphorylation of KAP1. In conclusion, our results define a role for SIRT2 in directing MRE11 localization and binding to DNA to promote DNA end resection and ATM-dependent signaling through deacetylation. Citation Format: Mark Essien, Fatmata Sesay, Hui Zhang, Andrew Jung, David Yu. MRE11 function in DNA damage response is regulated by SIRT2 deacetylation [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 5612.