tbuckley/cabot-search huggingface dataset:
Abstract 2095: Peptide-based pivoting of p53 to target metastatic breast cancer
Authors: Diana Putavet, Marjolein P. Baar, Johannes H. Lehmann, Antoine Khalil, Tao Shi, Thijs Koorman, Tobias B. Dansen, Patrick WB Derksen, Michael Teifel, Tobias Madl, Nicholas Sarlis
Journal: Cancer Research (2024)

Abstract The inability to target distant metastases limits the treatment of late-stage cancers. At least in part, this is due to the lack of optimal targeted therapies and treatment resistance to the remaining standard of care consisting of chemo-/radio- therapy. Here, we show that cancer cells that are irreparably damaged can withstand cell death through a process we define as “scarring”. In scarred cells, p53 is phosphorylated at Ser46 and Ser392 and localizes into progressive multifocal leukemia (PML) nuclear bodies. We have identified scarring in over a quarter of metastatic breast, colon, stomach and ovarian cancer. Thus, pivoting scarred p53 towards cell death in scarred cancer could establish a novel broad-range therapeutic opportunity against metastatic cancer. Targeting p53 with small molecules has proven challenging. We developed cell-penetrating peptides that selectively bind scarred p53. One of our lead compounds, CL04177 dissociates p53 from its PML scaffold leading to its a nuclear exclusion and initiation of the transcription-independent mitochondrial apoptosis. To examine the role of scarring as a therapeutic target, we focused on triple-negative breast cancer (TNBC). TNBC cells are marked by the expression of p53 and PML compared to other breast cancer subtypes. In cytotoxicity experiments, CL04177 specifically targeted TNBC over other breast cancer subtypes. Further investigation into how this compound can target metastatic cells revealed that scarred features are upregulated in metastasis-initiating cells of organoids when induced to invade in contact with collagen and that CL04177 can induce apoptosis specifically in these invading strands. In vivo, CL04177 showed favorable pharmacokinetics and -dynamics and a clear safety profile. Importantly, when dosed at 10-fold below its Maximally Tolerated Dose, CL04177 strongly reduced primary tumor mass and metastatic dissemination to the liver of TNBC cell line-derived orthotopic xenografts. This data indicates a new concept of scarred p53 in cancer progression and metastasis. Moreover, peptides that release scarring markers from nuclear structures can eliminate aggressive cancers in vitro and, most importantly, in vivo, e.g., in p53-mutated, metastatic TNBC. This ability introduces a conceptually new therapeutic option, especially for types of cancer for which there is a high unmet medical need. Citation Format: Diana Putavet, Marjolein P. Baar, Johannes H. Lehmann, Antoine Khalil, Tao Shi, Thijs Koorman, Tobias B. Dansen, Patrick WB Derksen, Michael Teifel, Tobias Madl, Nicholas Sarlis. Peptide-based pivoting of p53 to target metastatic 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 2095.
Abstract 492: Investigating solute carrier SLC46A3 to enhance nanotherapeutic delivery for cancer
Authors: Julianna Kenny-Serrano, Elizabeth B. Nelson, Gil Covarrubias, Namita Nabar, Joelle Straehla, Aanchal Gupta, Natalie Boehnke, Paula Hammond
Journal: Cancer Research (2024)

Abstract BACKGROUND: Nanoparticle therapeutics have multifaceted potential to improve efficacy and decrease toxicity of cancer treatments. Nanotherapeutics can encapsulate a range of cargos and have tunable surface chemistry that can enhance drug delivery to tumors. Cellular features also play a role in successful drug delivery, and predictive biomarkers may improve patient selection for clinical trials. In previous work, we identified SLC46A3, a poorly characterized lysosomal solute carrier, as a strong negative regulator of lipid-based nanoparticle uptake across many cancer models. We hypothesize that the expression of SLC46A3 will act as a predictive biomarker for therapeutic nanoparticles. METHODS: To test this hypothesis, we used two engineered model systems to probe the relationship between SLC46A3 expression and therapeutic response: lentiviral overexpression in a natively low-expressing melanoma model and genetic deactivation in a natively high-expressing breast cancer model. A library of FDA-approved and experimental therapeutic nanoparticles were screened in both models under a range of conditions. Liposomal formulations of chemotherapeutics were included with high and low surface functionalization of polyethylene glycol to investigate the impact of this ubiquitous ‘stealth’ polymer on our biomarker of interest. Solid lipid nanoparticles with nucleic acid cargo were also included. Orthogonal methods were used to probe these interactions and the therapeutic efficacy of nanotherapeutics, including pulsed dosing viability assays and label-free live-cell imaging. RESULTS: We found that SLC46A3 expression is a class-specific biomarker of lipid-based nanoparticle uptake and is predictive of distinctive patterns of response to therapy-loaded nanoparticles in both formulation and time-dependent manners. Additionally, we present a new technology for long-term, live cell imaging of nanoparticle uptake and trafficking that can discriminate mechanisms of cytotoxicity, accelerating the study of nano-bio interactions. These findings highlight a promising approach for the functional validation of nanoparticle-specific biomarkers using clinically relevant formulations that have the potential for rapid repurposing. Citation Format: Julianna Kenny-Serrano, Elizabeth B. Nelson, Gil Covarrubias, Namita Nabar, Joelle Straehla, Aanchal Gupta, Natalie Boehnke, Paula Hammond. Investigating solute carrier SLC46A3 to enhance nanotherapeutic delivery for 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 492.
Abstract 4978: Genomic characterization of metastatic pancreatic cancer according to tumor sample sites
Authors: Suleyman Y. Goksu, Muhammet Ozer, Busra Bacik Goksu, Nina N. Sanford, Amy Jones, Nilesh Verma, Syed Kazmi
Journal: Cancer Research (2024)

Abstract Background: Our research aimed to evaluate and compare the genetic variations in the primary and metastatic sites of patients with metastatic pancreatic cancer. Methods: In this study, we selected individuals with metastatic pancreatic cancer from the data provided by the American Association for Cancer Research Project GENIE (version 14.1). The comparison of genetic mutations between primary and metastatic tumor sites was conducted using the Fisher exact test, augmented with the Benjamini-Hochberg adjustment technique. Results: In a study of 3,108 patients with metastatic pancreatic cancer, 38.9% had metastatic site tumor samples, while 61.1% had samples from the primary tumor. The most frequent mutations were KRAS (89.4%), TP53 (72.9%), SMAD4 (21.2%), and CDKN2A (17.4%). Metastatic samples showed higher rates of CDKN2A, CDKN2B, and MTAP mutations compared to primary site samples (40.1% vs. 29.1%; 20.3% vs. 10.4%; and 20.8% vs. 8.9%, respectively, all with p&amp;lt;0.001 and q&amp;lt;0.001). In patients with young-onset pancreatic cancer (younger than 50 years), there was no notable difference in gene mutations between the two sample groups. Conclusion: Our findings corroborate the notion that identifying the precise genes that contribute to the development of metastatic pancreatic cancer is vital for gaining a more comprehensive understanding of the biological mechanisms. Moreover, genomic profiling could be a key in pinpointing potential biomarkers for diagnosis and therapy. Citation Format: Suleyman Y. Goksu, Muhammet Ozer, Busra Bacik Goksu, Nina N. Sanford, Amy Jones, Nilesh Verma, Syed Kazmi. Genomic characterization of metastatic pancreatic cancer according to tumor sample sites [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 4978.
Abstract 4106: A novel synthetic long peptide vaccine composition targeting multiple PD-L1 T-cell epitopes exhibits anti-tumor efficacy in a syngeneic mouse colorectal cancer model
Authors: Kenneth Nansheng Lin, Melvin Toh
Journal: Cancer Research (2024)

Abstract Background Cancer immunotherapy targeting immune checkpoints has shown promising clinical anti-tumor efficacy over the past decades. Monoclonal antibodies against PD-1 or PD-L1 have demonstrated clinical efficacy in a wide spectrum of cancer types. Despite the clinical success of therapies using immune checkpoint inhibitors (ICI), only a subset of patients shows long-lasting tumor remission, while resistance and toxicities to these agents remain to be addressed. This supports the need to explore alternative immunotherapeutic approaches or additional therapies for synergistic combinations to augment the anti-tumor efficacy for cancer patients receiving ICI therapies. Methods As an active immunotherapy approach, we developed a blend of four novel synthetic peptide vaccines each containing one PD-L1 T-cell epitope with individual covalent conjugation of the carrier protein, keyhole limpet haemocyanin (KLH), which is to break immune tolerance towards self-molecules. The four PD-L1 epitopes range from 30 to 40 amino acids in length, which target different domains of mouse PD-L1 protein. The PD-L1 peptides were synthesized using the technique of solid-phase peptide synthesis and purified by high performance liquid chromatography. All naked peptides were conjugated to KLH protein by thiol-maleimide reaction, followed by dialysis for purification. The peptide vaccines were formulated with a Toll-like receptor 9 agonist CpG ODN 1826 and aluminum hydroxide gel for animal immunization. Results These synthetic long PD-L1 peptide vaccines are highly immunogenic in a syngeneic BALB/c mouse model for a cell-mediated immune response when admixed and formulated with adjuvants. The vaccine composition is well tolerated by the mice with no evidence of toxicity and autoimmunity. In vivo administration of the vaccine formulation can elicit a positive PD-L1-specific T cell response in splenocytes with an IFN-γ ELISPOT assay. Moreover, in vivo vaccination of these PD-L1 peptide vaccines in a CT26 syngeneic mouse preventive colorectal cancer model exhibits a potent anti-tumor activity, with a 54% tumor growth inhibition (p&amp;lt;0.001) in tumor volume compared to that of the adjuvant-control group at the end of the study. Conclusions Taken together, our data demonstrate a proof-of-concept that T cell-based PD-L1 peptide vaccines are a promising therapeutic strategy for inducing anti-tumor immunity to combat cancers. Citation Format: Kenneth Nansheng Lin, Melvin Toh. A novel synthetic long peptide vaccine composition targeting multiple PD-L1 T-cell epitopes exhibits anti-tumor efficacy in a syngeneic mouse colorectal cancer 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 4106.
Abstract 4977: The prevalence of key oncogenic driver mutations in stage I-III non-small cell lung cancer: Results from the AACR GENIE BPC dataset
Authors: Ke Zu, Jiemin Ma, Cai Chen, Christine Pierce
Journal: Cancer Research (2024)

Abstract Background: While there is growing interest in targeted therapy for non-small cell lung cancer (NSCLC) in perioperative settings, data on key oncogenic driver mutations is limited in early-stage NSCLC. This real-world database study aims to evaluate the prevalence of select genomic alterations in stage I-III NSCLC. Methods: From the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) V2.1-consortium dataset, we included adult patients with a confirmed diagnosis of NSCLC who had genomic testing using stage I-III NSCLC tissue samples. Descriptive statistics were used to summarize baseline characteristics and the prevalence of select genomic alterations. Results: A total of 465 patients were included in this study, of whom 61% were female, 85% were white, 19% were never smokers, and 77% had adenocarcinoma. Less than 2% of the study population had BRAF V600E, HER2 activating mutations, HER2 amplification, MET amplification, HER3 amplification, RET fusion, ALK fusion, or ROS1 fusion. Among genomic alterations with a prevalence of 2% or higher, such as EGFR sensitizing mutations, KRAS G12C, MET exon 14 skipping, STK11, KEAP1, and TP53, some variations in prevalence were observed across baseline patient and disease characteristics such as race, smoking status, and histology (Table 1). Conclusion: The prevalence of key oncogenic drivers and its relationship to select baseline disease characteristics among patients with early-stage NSCLC are similar to those of advanced NSCLC observed in other real-world clinico-genomic databases. Table 1. Prevalence of Select Genomic Alterations in Stage I-III NSCLC (N=465) Prevalence of Positive Biomarker Status (%) EGFR KRAS G12C MET Exon 14 Skipping STK11* KEAP1* TP53 Overall 17.6 12.7 4.5 16.0 11.0 52.7 Gender Male 7.1 9.3 5.5 18.5 18.5 59.6 Female 24.5 15.9 3.9 14.3 6.3 48.2 Race White 15.6 14.1 4.5 16.5 12.0 53.7 Black 15.0 5.0 5.0 22.2 11.1 60.0 Asian 44.0 4.0 8.0 8.3 4.2 44.0 Smoking Status Never smoker 41.4 1.2 6.9 4.7 1.2 36.8 Former smoker 13.7 16.0 4.6 17.4 12.9 52.4 Current smoker 5.7 12.9 1.4 23.9 15.4 72.9 Histology Adenocarcinoma 20.1 14.3 4.6 18.1 10.4 46.0 Squamous cell carcinoma 0 2.9 4.4 4.6 14.1 86.8 *The numbers of patients tested for STK11 and KEAP1 were 457 and 445, respectively. Citation Format: Ke Zu, Jiemin Ma, Cai Chen, Christine Pierce. The prevalence of key oncogenic driver mutations in stage I-III non-small cell lung cancer: Results from the AACR GENIE BPC dataset [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 4977.
Abstract 4923: A systematic framework for predicting adverse drug reaction signals using medical data
Authors: Junhyeok Jeon, Eujin Hong, Hyun Uk Kim
Journal: Cancer Research (2024)

Abstract Prescribing a combination of medications is a common strategy to enhance the effectiveness of disease treatment. While this approach aims to improve therapeutic outcomes, it may lead to unintended adverse drug reactions (ADRs) due to interactions between prescribed drugs and individual factors. Recognizing the importance of ADRs, various machine learning models have been developed. However, these models face limitations, particularly in predicting reactions induced by three or more drugs and in accounting for individual patient factors, such as age and medical history. To address these limitations, we propose a systematic framework that leverages medical data for predicting ADR signals. In the framework, the MIMIC-IV database was systematically preprocessed, and a series of machine learning models were developed that predict the ADR signals. The model predictions were validated using the eICU collaborative research database. The machine learning models process multiple inputs, including information on administered drugs, age, gender, ethnicity, and underlying medical conditions to predict ADR signals. The ADR signals are determined by classifying abnormalities in 20 specific laboratory test values, such as hematocrit, creatinine, and hemoglobin. The machine learning models developed in this study hold promise as a valuable tool for assessing potential risks, such as ADRs, associated with the concurrent use of multiple drugs. Citation Format: Junhyeok Jeon, Eujin Hong, Hyun Uk Kim. A systematic framework for predicting adverse drug reaction signals using medical data [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 4923.
Abstract 4724: Optimizing 500 pooled PRISM cell lines for a 10-day assay to elucidate viability effects and mechanism of action for slower-acting therapeutics
Authors: Melissa Ronan, Blanche C. Ip, Ellen Nguyen, Ursula Widocki, Tenzin Sangpo, Alvin Kalathungal, Nashielli Diaz-Gallegos, Anthony Fazio, Aydin Golabi, Maha Naim, Ashish Bino George, YuhJong Liu, Mustafa Kocak, Rishi Puram, Matthew G. Rees, Jennifer Roth
Journal: Cancer Research (2024)

Abstract PRISM (Profiling Relative Inhibition Simultaneously in Mixtures), using DNA-barcoded cell lines cultured as ~25 cell line pools, has been an effective drug discovery screening platform to rapidly test large numbers of potential therapeutics on over 900 different cancer cell lines. However, the conventional 5-day assay may be too short to offer the resolution needed to identify the full cellular response for slower-acting therapeutics such as those directed against epigenetic pathways. Here, we describe development of the PRISM 10-day extended assay with ~500 adherent solid tumor cancer cell lines to overcome this challenge. We found that the ranges of cell line growth rates within the standard PRISM pools were too large and not amenable for a long-term assay beyond 6 days—after 10 days of growth, slower cell lines dropped below the limit of barcode detection as faster cell lines overtook the pools. We therefore regenerated pools to reduce the range of growth rates within a pool. We show that this re-pooling, coupled with seeding density optimization, enables recovery of &amp;gt; 98% of cell lines at day 10 in vehicle-treated wells, with acceptable data variability. The average estimated number of cell doublings across our cell lines, 7, is significantly greater than the number of doublings in the PRISM standard 5-day assay (~3 doublings). Importantly, we observe greater drug effects on day 10 versus day 6 when cells are treated with slow-acting DNA methyltransferase inhibitors such as decitabine; this also results in increased sensitivity to identify cellular biomarkers underlying differential response. In summary, we have successfully engineered a PRISM 10-day assay in ~500 adherent cell lines, where the extended duration can be beneficial in elucidating the effects and mechanism of action for epigenetic drug candidates. Citation Format: Melissa Ronan, Blanche C. Ip, Ellen Nguyen, Ursula Widocki, Tenzin Sangpo, Alvin Kalathungal, Nashielli Diaz-Gallegos, Anthony Fazio, Aydin Golabi, Maha Naim, Ashish Bino George, YuhJong Liu, Mustafa Kocak, Rishi Puram, Matthew G. Rees, Jennifer Roth. Optimizing 500 pooled PRISM cell lines for a 10-day assay to elucidate viability effects and mechanism of action for slower-acting therapeutics [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 4724.
Abstract 5069: Retrospective analysis of acute myeloid leukemia using next generation cytogenomics identifies variants missed at diagnosis
Authors: Stephen Eacker, Maika Malig, Mary Wood, Alexander Muratov, Olga Sala-Torra, Ivan Liachko, Cecilia Yeung, Jerald Radich
Journal: Cancer Research (2024)

Abstract Cytogenetics forms the cornerstone of diagnostic genetic testing in leukemia, providing both prognostic and diagnostic information to help guide treatment. Currently, standard-of-care cytogenetics in acute myeloid leukemia (AML) is composed of a combination of karyotyping, FISH testing, and in some cases chromosomal microarray analysis, each test offering a unique combination of advantages and weaknesses. A particular challenge for this combination of tests is the delivery of results in a timely and comprehensive manner. To overcome these limitations, we have developed OncoTerra, a proximity-ligation-sequencing based method which can rapidly detect all classes of variants detected by cytogenetics tests in a single assay. We applied OncoTerra to a cohort of more than 100 samples from a SWOG AML trial (S0106), benchmarking sensitivity and specificity of the variants. We observed an overall &amp;gt;0.95 sensitivity and a specificity of 1 for the variants identified by cytogenetics and identified numerous cryptic variants. Overall, we identified variants that changed the diagnostic risk stratification of 15% of the patient involved in the trial based on the ELN 2022 criteria. This translated into better overall prediction of outcomes of patients in the trial and has identified both known and novel variants missed by standard-of-care tools. Citation Format: Stephen Eacker, Maika Malig, Mary Wood, Alexander Muratov, Olga Sala-Torra, Ivan Liachko, Cecilia Yeung, Jerald Radich. Retrospective analysis of acute myeloid leukemia using next generation cytogenomics identifies variants missed at diagnosis [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 5069.
Abstract 5026: Microfluidic capillary electrophoresis optimization of high-throughput cfDNA and pDNA measurements for enabling cancer diagnostics and gene therapy development
Authors: Dipti Mehta, Gayatri Gautam, Adriana Coll de Pena, Menel Ben Frej, Anubhav Tripathi, James White
Journal: Cancer Research (2024)

Abstract Rapid and accurate electrophoresis characterization can be an important tool for cancer researchers and therapy manufacturers. Advances in NGS of low molecular weight cfDNA for diagnostics may benefit from high-throughput checks of cfDNA sample quality with ultra-low quantities of sample. On the other hand, high molecular weight pDNA characterization and separation of supercoiled, linear and open-linear conformations aids in quality control of these payloads for personalized medicine and in particular cancer vaccines and gene therapies. This work shows optimization of established microfluidic capillary electrophoresis to enable the measurement of cfDNA and pDNA. cfDNA study was completed on plasma reformatted from whole blood tubes using Janus G3 Blood iQ workstation. The cfDNA samples were extracted using commercial cfDNA extraction kits. Using a LabChip GX Touch Biologics Characterization system: gel optimization, marker solution dilution, and inclusion of a low molecular weight DNA standard improved the sensitivity of cfDNA detection. This afforded a new electrophoresis assay with linear dynamic range of 50-1000 pg/uL and sensitivity of &amp;lt;25 ng/uL. pDNA, supercoiled DNA and linear DNA standards were prepared according to published procedures and measured on the LabChip GX Touch Biologics Characterization system. A new ladder system was developed along with gel optimization to develop a new High Sensitivity Assay platform capable of baseline resolving each conformation and providing fragment DNA sizing and purity information. Taken together, this work provides researchers new tools to leverage automated microfluidic capillary electrophoresis for DNA analysis in both upstream and manufacturing processes. Citation Format: Dipti Mehta, Gayatri Gautam, Adriana Coll de Pena, Menel Ben Frej, Anubhav Tripathi, James White. Microfluidic capillary electrophoresis optimization of high-throughput cfDNA and pDNA measurements for enabling cancer diagnostics and gene therapy development [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 5026.