tbuckley/cabot-search huggingface dataset:
Abstract 3805: Intestinal microbiome with chemotherapy response and RAS mutation in patients with advanced or metastatic colorectal cancer: a pilot, exploratory study
Authors: Jwa Hoon Kim, Boyeon Kim, Soohyeon Lee
Journal: Cancer Research (2024)

Abstract Intestinal microbiomes interact with the tumor microenvironment, participating in inflammation and immune regulation, and are associated with the response to anticancer therapy. However, there has been limited research exploring the relationship between changes in the microbiome and treatment response in patients with metastatic colorectal cancer (mCRC) during chemotherapy and radiation therapy.This study included all 15 patients with mCRC treated with first-line systemic therapy between October 2021 and February 2023. We conducted 16S rRNA sequencing on baseline stool samples and investigated the association of intestinal microbiome with chemotherapy response and RAS mutation. The QIIME2 and R packages were used for analysis. As a results, Median age was 61 years (range, 35-73), and there were 8 patients with RAS-mutated mCRC. All patients were treated with first-line systemic therapy; FOLFOX (5-fluorouracil and oxaliplatin)-based (n=13) and FOLFIRI (5-fluorouracil and irinotecan)-based chemotherapy (n=2). Of them, 2 patients received short-course radiotherapy (ScRTx) to primary tumor before systemic chemotherapy, where pre- and post-ScRTx stool samples were collected. Among 15 patients, 9 patients (60%) achieved responses. Non-responders tend to exhibit higher alpha diversity (Chao1, Observed ASV) compared to responders. Firmicutes, Lactobacillus, Faecalibacterium, and the [Luminococcus]_gauvreauii_group were more prevalent in responders, whereas Bacteroidota, Prevotella, DTU089, Alistipes, Christensenellaceae_R-7_group, and Porphyromonas in non-responders. Despite no statistical significance, alpha diversity decreased in post-ScRTx compared to pre-ScRTx samples. Akkermansia, Prevotella, and Peptostreptococcus were more prevalent in the post-ScRTx compared to pre-ScRTx samples. Regarding the association of intestinal microbiome with RAS mutation, Bray curtis and weighted unifrac analyses revealed significant differences in beta diversity; higher incidence of Faecalibacterium, Lactobacillus, Prevotella, Anaerofilum, and UCG-005 in the RAS-wild type mCRC, while Bacteroides, Collinsella, Holdemanella, and Anaerostipes in RAS-mutated mCRC.This pilot study suggests the prognostic value of gut microbiomes and its association with RAS mutation in patients with mCRC treated with first line systemic therapy. A microbial functional study with immune cytokine change is planned to confirm these findings in future. Citation Format: Jwa Hoon Kim, Boyeon Kim, Soohyeon Lee. Intestinal microbiome with chemotherapy response and RAS mutation in patients with advanced or metastatic colorectal cancer: a pilot, exploratory 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 3805.
Abstract 7491: ctDNA liquid biopsy result among gynecologic cancer patients: Does it give additional information
Authors: Min Kyu Kim
Journal: Cancer Research (2024)

Abstract Objectives: There are many target molecules for precisional cancer therapy Precision diagnosis-based target treatment is believed to be better survival approach compared than conventional treatment. Predictive markers are variant and vast. This study evaluated the initial experience of ctDNA liquid biopsy as a precision tumor marker for gynecologic cancer patients? Methods: we retrospectively identified ovary/endometrial and cervical cancer patients who approved ctDNA test for various purpose. Two methods were used. Guardant 360 and Foundation One Liquid CDx. Results: There were 31 cases. Median age was 60(46-84). Half of cases were ovarian cancer(17/31 55%).Cervix and endometrial cancer are 12(39%) and 2(6%).We found about ten percentages of actional genetic mutation patients(3/31).Two BRCA1 mutation(each patients have variant allele frequency(VAF) percentages are 50.4,49.6).One high bTMB(blood tumor mutational burden)was 21.There was no mutation in 6/31(19 %). Conclusions: It seems additional supportive information may be acquired through well-established ctDNA liquid biopsy test among this population. Role of ctDNA liquid biopsy test for precision tumor marker should be investigated for future study. Keywords: Liquid biopsy; Precision medicine; Tumor marker Citation Format: Min Kyu Kim. ctDNA liquid biopsy result among gynecologic cancer patients: Does it give additional information [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 7491.
Abstract 7477: Isoxanthohumol inhibits LPS-induced inflammatory responses in macrophages
Authors: Tzu-Han Kao, Chia-yang Li
Journal: Cancer Research (2024)

Abstract Background: Pathogen infection, such as bacteria, viruses, and fungus, frequently leads to septicemia through a series of inflammatory responses that have very high fatality rates. And, servere inflammation may cause gene mutation which is beginning of cancer. Macrophages are a critical type of antigen-presenting cells that control both innate and adaptive immune responses. During pathogen infection, activated macrophages secret many proinflammatory mediators and cytokines, including nitric oxide (NO), TNF-α and IL-6 against pathogens; however, an overwhelming inflammatory response provokes abundant cells to undergo apoptosis. In the present study, we aimed to examine the anti-inflammatory effect of isoxanthohumol, a prenylflavonoid from hops and beer. Method: We used lipopolysaccharide (LPS) as a pathogenic stimulus to induce inflammatory responses by J774A.1 macrophages. MTT assay was used to detect cell viability. The secretion of NO was analyzed by Griess reagent assay, while the production of TNF-α, IL-6, IL-1β was measured by enzyme-linked immunosorbent assay (ELISA). The expression of iNOS, COX-2, and MAPKs was examined by Western blotting. The activity of NF-κB was analyzed by promotor reporter assay. The activation of NLRP3 inflammasome was examined by ELISA and immunofluorescence staining. In addition to that, we explored the secretion of cytokines, IL-1β, in THP-1 cell. Result: We found that isoxanthohumol significantly suppresses the secretion of NO and attenuates the production of TNF-α and IL-6 by LPS-induced macrophages. In addition, isoxanthohumol also inhibits the expression of iNOS and COX-2, suppresses the phosphorylation of JNK, and attenuates the activity of NF-κB by LPS-induced macrophages. Moreover, isoxanthohumol decreases the activation of NLRP3 inflammasome by reducing the production of IL-1β and repressing the ASC speck formation of NLRP3 inflammasome in LPS/ATP-induced macrophages. Conclusion: Our experimental results demonstrated that isoxanthohumol effectively inhibits LPS-induced inflammatory responses in macrophages, suggesting that isoxanthohumol might have benefits for attenuating inflammation. Citation Format: Tzu-Han Kao, Chia-yang Li. Isoxanthohumol inhibits LPS-induced inflammatory responses in macrophages [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 7477.
Abstract 3238: Therapeutic targeting of the genome guardian sirtuins in metastatic prostate cancer
Authors: Subhajit Giri
Journal: Cancer Research (2024)

Abstract Introduction: The effective treatment paradigm for the lethal form of metastatic prostate cancer (mPCa) remains challenging. Almost all mPCas eventually develops therapy resistance against androgen receptor (AR) inhibitors (e.g., Enzalutamide, Abiraterone) or to poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors (Olaparib, Niraparib, Talazoparib) (HRRd) when used as monotherapy. Although the patients in the ARSi+PARPi combination produced significantly longer radiologic progression-free survival (rPFS), a substantial number had attained therapy resistance by the end of the study tenure. So, a newer therapy is urgently needed. In recent years, a new targetable therapeutics development domain has been unfolding with an expanding understanding of the role of SIRTuins in prostate cancer cell survival, invasion, and progression to an aggressive metastatic state. Here, we will investigate the therapeutic efficacy of SIRT1/7 inhibitor (SIRT1/7i) and determine synergy with DNA-damaging PARP inhibitor combinations through a battery of cell and molecular assays using various prostate cancer cellular models. Methods: We have treated the mPCa cell lines 22Rv1, LAPC4, PC3 and LnCAP as well as prostate epithelial cell line RWPE1 with SIRT1 inhibitor SIRT1-IN-2 (MedChemExpress, HY-146689), SIRT7 inhibitor 97491 (MedChemExpress, HY-135899) and AR inhibitor Enzalutamide individually as well as in combination of PARP inhibitor Olaparib. The treatment of the SIRT1 and SIRT7 monotherapy arm was 72 hours long, and combination therapy continued for 7 days. The cell viability was assessed with CellTiter-Glo® 2.0 Cell Viability Assay (Promega). The cell cycle progression and proliferation analysis were done using flow cytometry through Propidium iodide staining and AnnexinV-FITC apoptosis detection chemistry. Cell survival was orthogonally assessed using colony counting assays. We adopt RAD51 foci counting assays and COMET assays for evaluating treatment-induced genome instability. Results: The preliminary result suggested that the SIRT1i+Olaparib and SIRT7i+Olaparib combination significantly sensitized the mPCa cell lines 22Rv1, PC3, and LnCAP for cell death compared to the prostate epithelial cell RWPE1. Upon the combination treatment, the mPCa cell lines showed elevated apoptotic cell death, reconfirmed through colony counting assay. Conclusion: Therapeutic combination treatment of SIRT1 and SIRT7 inhibition with Olaparib could be an effective treatment option for aggressive metastatic prostate cancer. Citation Format: Subhajit Giri. Therapeutic targeting of the genome guardian sirtuins in metastatic 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 3238.
Abstract 1668: Association of stem cell-like phenotype with isoform specific functions of AKTs in hepatocytes
Authors: Ielyzaveta Slarve, Yushan Wang, Mario Alba, Lina He, Bangyan Stiles
Journal: Cancer Research (2024)

Abstract Introduction: Liver cancer is the sixth most common cancer and the third leading cause of cancer-related deaths worldwide. It is associated with abnormal activation of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway, which is implicated in regulation of cancer stem cells (CSCs). The present study investigated the effects of AKT loss on stem cell-like phenotype in immortalized mouse hepatocytes. Methods: Immortalized hepatocytes were established from mice with Akt1 (Akt1−/−; Akt1-null) or Akt2 (Akt2−/−; Akt2-null) whole-body deletion. Cell morphology was assessed via microscopy. Cell proliferation was evaluated with hemacytometer count and MTT assay. Cell migration towards a chemoattractant was assessed via transwell assay. Cell viability was evaluated in response to chemotherapy treatment. The ability of cells to Results: When compared to WT cells, which exhibited cuboidal epithelial-like features, Akt1-null and Akt2-null cells demonstrated elongated mesenchymal-like morphology. Loss of either isoform was associated with a significantly decreased cell growth (p&amp;lt;0.05). Akt1-null cells migrated faster towards a chemoattractant in the transwell assay, were significantly more resistant to sorafenib, and formed a significantly higher number of spheres in the sphere formation assay (p&amp;lt;0.01). Proteomic analysis revealed that both Akt1-null and Akt2-null cells exhibited increased expression of CSC marker CD44, along with other proteins associated with liver cancer, including PDGFRA, CDH2, MMP14, and COX2 (p&amp;lt;0.05). Additionally, Akt1-null cells exhibited elevated levels of ANXA1 and ANXA3 (p&amp;lt;0.01). Conclusions: Loss of both AKT isoforms resulted in decreased cell proliferation and elevated expression of proteins with a previously reported role in liver cancer invasion, migration, and epithelial-mesenchymal transition. AKT1 loss correlated with an enhanced stem cell-like phenotype, including increased migration towards a chemoattractant, higher resistance to chemotherapy, and enhanced ability to form spheres. These results contribute to the understanding of the role of AKT isoforms in regulating stemness in liver cancer and may serve as a basis for investigation into isoform specific inhibitors. Further investigation into cellular mechanisms governing these phenotypes is required. Citation Format: Ielyzaveta Slarve, Yushan Wang, Mario Alba, Lina He, Bangyan Stiles. Association of stem cell-like phenotype with isoform specific functions of AKTs in hepatocytes [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 1668.
Abstract 3254: Development of novel luminescent assays for sensitive and specific quantitation of double-stranded RNA in mRNA vaccines
Authors: Rich Moravec, Jun Wang, Jim Hartnett, Mei Cong, Jamison Grailer
Journal: Cancer Research (2024)

Abstract mRNA-based therapeutics have shown clinical efficacy, evidenced by the success of the mRNA vaccines for SARS-CoV-2. Personalized mRNA vaccines containing patient-derived tumor mutations are now entering the clinic and have shown promise. Delivery of mRNA-encoded therapeutic proteins (e.g., antibodies) is also under development. mRNA drug substance is typically generated by in vitro transcription (IVT). One byproduct and contaminant of IVT is the formation of double-stranded RNA (dsRNA). dsRNA is highly immunogenic, can induce inflammation and cell death, and inhibit protein translation, including the protein encoded by the therapeutic mRNA. As such, dsRNA must be measured for all IVT products to ensure safety and efficacy. However, existing dot bot and ELISA technology to detect dsRNA is neither sensitive nor quantitative. Herein, we describe the development of novel assays for sensitive and specific quantitation of dsRNA in IVT products and following encapsulation of IVT products in lipid nanoparticles (LNPs). First, NanoBiT® split luciferase technology was applied to detect dsRNA in IVT products. dsRNA binding domains were genetically attached to either SmBiT or LgBiT. In the presence of dsRNA, the SmBiT and LgBiT constructs bind via the dsRNA binding domains, resulting in dimerization and the complementation of functional NanoBiT® luciferase. NanoBiT® then generates light which is proportional to the amount of dsRNA in the sample. The assay detects dsRNA greater than or equal to 30 base pairs and is independent of the size and sequence of the dsRNA contaminant. The assay does not cross-react with single-stranded RNA or DNA and is highly sensitive, with a limit of detection less than 100 pg/ml. As a complementary tool to the biochemical assay, we developed a cell-based bioassay to detect dsRNA encapsulated in LNPs. dsRNA/LNPs are taken up by endocytosis where Toll-like receptor 3 (TLR3) detects dsRNA. Activation of TLR3 initiates a signaling pathway that is detected by a TLR3 pathway-specific promoter driving luciferase expression. This pathway likely represents the most physiologically-relevant readout of dsRNA bioactivity. Both assays are developed in “add-mix-read” format with no wash steps or media transfer, and exhibit robust, sensitive, and repeatable performance for specific detection of dsRNA in mixed solutions. Citation Format: Rich Moravec, Jun Wang, Jim Hartnett, Mei Cong, Jamison Grailer. Development of novel luminescent assays for sensitive and specific quantitation of double-stranded RNA in mRNA vaccines [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 3254.
Abstract 3225: Profiling the DNA regulome to discover direct inhibitors of the brachyury transcription factor
Authors: Alexander Joel Federation, Yang Gao, Brian McEllin, Tonibelle Gatbonton-Schwager, Andrea Gutierrez, Julia Robbins, Bodhi Hueffmeier, Erin Broderick, Daniele Canzani, William Fondrie, Lindsay Pino
Journal: Cancer Research (2024)

Abstract Background: The human genome encodes more than 1,600 transcription factors (TFs), along with additional cofactors, chromatin regulators, and structural proteins that collectively execute the regulatory instructions encoded within the nuclear DNA. Dysfunctions of these proteins, collectively known as the Regulome, are known to drive multiple conditions such as cancer, autoimmune conditions, and fibrosis. Despite their importance, many of these proteins are considered undruggable due to challenges in modeling their activity in vitro. Methods: We have addressed these shortcomings by implementing a live-cell Regulome profiling approach that quantifies the global activity of TFs without the need for cell manipulation or genome engineering, called TF-Scan. The technology coupled rapid, automated purification of the DNA-bound proteome coupled to scalable Data Independent Acquisition (DIA) quantitative mass spectrometry proteomics and machine learning. Results: We completed a screen of covalent compounds across 8 tissue types to discover hotspot sites on TFs that control their DNA-binding activity. A chordoma cell line was included in this screen. The screen identified compounds capable of binding to and disrupting the activity of several previously undruggable transcription factors, including brachyury. Hit validation and hit-to-lead medicinal chemistry resulted in a covalent chemical probe for brachyury, with activity in cell line models of chordoma. Conclusion: Phenotypic drug discovery in live, unmodified human cells with systematic regulome profiling enables the discovery of compounds that disrupt previously undruggable targets by multiple mechanisms of action. Citation Format: Alexander Joel Federation, Yang Gao, Brian McEllin, Tonibelle Gatbonton-Schwager, Andrea Gutierrez, Julia Robbins, Bodhi Hueffmeier, Erin Broderick, Daniele Canzani, William Fondrie, Lindsay Pino. Profiling the DNA regulome to discover direct inhibitors of the brachyury transcription factor [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 3225.
Abstract 321: Optimized RNA Seq library preparation for fusion calling from FFPE samples
Authors: Giulia Corbet, Josh Haimes, Travis Sanders, Martin Ranik, Thomas Harrison, Eduard Casas, Kailee Reed, Doug Wendel, Kristina Giorda, Ariele Hanek, Jen Pavlica, Brian Kudlow
Journal: Cancer Research (2024)

Abstract Gene fusions due to chromosomal rearrangement, duplication, or deletion can be important drivers of cancer. Detection of gene fusions plays a valuable role in selecting targeted therapies. A widely used method for detecting fusion transcripts is targeted RNA sequencing, which focuses sequencing reads on known fusions but does not allow for the detection of novel fusions. Whole transcriptome analysis (WTA), where the entire transcriptome is interrogated, offers an opportunity to detect both known and novel fusions. Herein we examine the effect of sample quality, input mass, increased reverse transcriptase (RT) and insert size on fusion calling. Libraries are prepared using the Watchmaker RNA Library Preparation Kit with or without Polaris Depletion and, for target enrichment, the Twist Exome 2.0 panel prior to paired end 2 × 150 Illumina sequencing. First, control samples, specifically Seraseq Fusion RNA v4 high quality and FFPE samples, are used to determine if any of the parameters interrogated increase the number of breakpoint spanning reads both in a WTA and targeted sequencing context. Once established, the optimized workflow is applied to real FFPE samples. Targeted sequencing results in a higher number of breakpoint spanning reads, compared to WTA, when controlling for sequencing depth, resulting in a higher number of reads supporting each fusion call. Longer insert sizes, achieved by modified SPRI ratios, maintain library complexity and may enhance fusion calling. Taken together, these data demonstrate an optimized protocol for fusion calling from FFPE and demonstrate the utility of both WTA and targeted sequencing for fusion detection. Citation Format: Giulia Corbet, Josh Haimes, Travis Sanders, Martin Ranik, Thomas Harrison, Eduard Casas, Kailee Reed, Doug Wendel, Kristina Giorda, Ariele Hanek, Jen Pavlica, Brian Kudlow. Optimized RNA Seq library preparation for fusion calling from FFPE samples [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 321.