tbuckley/cabot-search huggingface dataset:
Abstract 2332: Enhanced analysis of CO-Detection by indEXing (CODEX) imaging through a novel image processing technique utilizing two-dimensional Fourier transform for stitching artifact detection
Authors: Afrooz Jahedi, Aliya Khan, Kasthuri Kannan, Krishna Bhat
Journal: Cancer Research (2024)

Abstract Objective: The objective of this study is to address the challenge of stitching artifacts in CODEX imaging, which hinders the accurate spatial quantification of positive cell locations—a critical step for reliable spatial analysis in computational pathology. Methods: Our algorithm applies 2D-FT and inverse transformations to process pathological images. We tested the algorithm on 16 different histology images, each containing 5 or more regions. Within these regions, we evaluated 29 protein markers, culminating in the analysis of over 2800 images. Results: The algorithm demonstrated a recall rate of over 85 percent, indicating a high likelihood of accurately identifying true positive regions with stitching artifacts. However, the precision varied, suggesting further investigation is needed to understand the variability and improve consistency. Conclusion: The proposed method significantly improves CODEX imaging reliability by detecting and quantifying stitching artifacts. The method's high recall rates are promising, but the variable precision indicates the necessity for ongoing refinement to ensure consistent diagnostic accuracy across diverse and extensive image sets. Keywords: Computational pathology, Fourier transform, Image stitching, CODEX, Spatial analysis, Diagnostic precision, Recall. Citation Format: Afrooz Jahedi, Aliya Khan, Kasthuri Kannan, Krishna Bhat. Enhanced analysis of CO-Detection by indEXing (CODEX) imaging through a novel image processing technique utilizing two-dimensional Fourier transform for stitching artifact detection [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 2332.
Abstract 3092: MICRO-TAG: A novel fluorescence-based real-time cellular target engagement platform for drug discovery
Authors: Ivan Babic, Nikolas Bryan, Claire Cunningham, Avery Sampson, Daniel Starczynowski, Elmar Nurmemmedov
Journal: Cancer Research (2024)

Abstract Success of drug discovery programs can be amplified by adopting emerging technologies that can interrogate drug targets within their physiological context. Cell target engagement (CTE) presents a combined biological &amp; biophysical method, which provides quantitative evaluation of target-drug interaction within the native environment of the cell. The currently available luminescence-based CTE methods are limited to measurement of end-point signal and poor resolution, thereby limiting their mechanistic and stoichiometric insight. We have developed MICRO-TAG, a novel fluorescence-based CTE platform, which relies on complementation of split-RNAse A. It enables interrogation of target engagement without interfering with folding, localization and function of target proteins - all within the physiological milieu of the cell. Uniquely, this new platform allows for quantitation and monitoring of CTE in real- time in the cell. It enables extraction of important parameters from target-drug interaction: target thermal profile and temperature of aggregation (Tagg), time required to reach equilibrium (teq), apparent association rate (Kon) and physiologically relevant drug:target binding affinity (KD). We provide data demonstrating potential and utility of MICRO-TAG platform on drug targets, such as KRAS, MTH1, EGFR, and UBE2N. The platform demonstrates relevance for discovery of novel drug candidates targeting challenging drug targets such as transcription factors. This highly scalable and quantitative novel method for assessing drug-target interaction within cells can enhance drug discovery programs, and offers potential to rapidly identify clinically relevant hit compounds for challenging drug targets. Citation Format: Ivan Babic, Nikolas Bryan, Claire Cunningham, Avery Sampson, Daniel Starczynowski, Elmar Nurmemmedov. MICRO-TAG: A novel fluorescence-based real-time cellular target engagement platform for drug discovery [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 3092.
Abstract 4194: An in-silico approach to identify genes required for polyamine transport
Authors: Victoria Millington, Laurence von Kalm
Journal: Cancer Research (2024)

Abstract The purpose of this study was to use an in-silico approach to identify genes required for polyamine transport. Polyamines are small positively charged molecules that control vital cellular processes including cell proliferation and growth. Cells obtain polyamines by biosynthesis or transport from the extracellular environment. Cancer cells require high levels of polyamines to sustain rapid growth, and therapies aimed at polyamine depletion are considered promising. The FDA approved drug difluoromethylorthinine (DFMO) blocks polyamine biosynthesis, however, in most cases malignant cells evade the biosynthetic block by increasing transport. Thus, a dual therapy that simultaneously targets polyamine biosynthesis and transport is needed. The mechanism of polyamine transport is poorly understood in multicellular eukaryotes and identification of genes involved in polyamine transport has largely relied on an inefficient hit-or-miss ‘educated guess’ approach. To increase the probability of identifying genes involved in polyamine transport, we adopted an in-silico approach comparing protein-protein interactions with the protein product of the human ATP13A3 gene across multiple databases. We used ATP13A3 because our work, and the work of others, has shown that ATP13A3 and its Drosophila ortholog ‘anne’ are required for polyamine transport. We searched for high confidence protein interactors with ATP13A3 in four databases, BioGRID, STRING, NextProt, and GPS-Prot, prioritizing hits that occurred in more than one database. We next asked if any of the high priority hits had orthologs in Drosophila. We chose to study the candidate genes in Drosophila because we have utilized the sophisticated genetic resources available in this organism to develop novel assays to identify positive and negative regulators of polyamine transport. Using the criteria described, we identified four candidates that occurred in three databases, and one that occurred in two databases. In addition, a very high confidence match to the human gene SLC15A was observed in one database and included in the group of candidate genes. To determine the validity of our candidate gene enrichment approach we are currently testing each gene for roles in polyamine transport. Citation Format: Victoria Millington, Laurence von Kalm. An in-silico approach to identify genes required for polyamine transport [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 4194.
Abstract 416: Development of substituted oxindole derivatives as a Ku-targeted DNA-PK inhibitors for cancer therapy
Authors: Dineshsinha Chauhan, Pamela L. Mendoza-Munoz, Narva Deshwar Kushwaha, Hariprasad Aruri, John J. Turchi, Navnath S. Gavande
Journal: Cancer Research (2024)

Abstract DNA double strand breaks (DSBs) are the most cytotoxic type of DNA damage. DSB repair pathway deficiency, often observed in cancer cells, results in translocations and genetic mutations that contribute to genomic instability. The generation of DNA DSBs is the primary mechanism of numerous chemo- and radio-therapeutic strategies used to treat various cancers. Modulating DSB repair pathways can have a profound impact on the clinical efficacy of DNA damaging therapies. DNA-dependent protein kinase (DNA-PK), which is composed of a DNA-PK catalytic subunit (DNA-PKcs) and Ku80-Ku70 heterodimer, acts as the molecular sensor for DSB and plays a prime role in DSB repair through non-homologous end joining (NHEJ). DNA-PK inhibitors become an attractive therapeutic target for cancer in combination with DSB-inducing radiotherapy and chemotherapy. There are at least 6-7 DNA-PK inhibitors in the preclinical and clinical stages which exhibit potential as treatment for various cancers. However, we have taken a unique and innovative approach to inhibiting DNA-PK via blocking the Ku70/80 heterodimer interaction with DNA, an essential step in DNA-PK activation and phosphorylation activity. Exploiting this unique mechanism of kinase activation, we have expanded our structure-activity relationships of pyrrolone derivatives. Modified synthetic schemes have been developed to allow a series of modifications to the X80 core structure. We have prepared furan, thiophene and pyrrole derivatives that enabled the identification of pharmacophores that impact in vitro potency and cellular off-target toxicity. Towards addressing cellular uptake and bioavailability, we identified substituted oxindole derivatives as potent Ku and DNA-PK inhibitors. These oxindole derivatives exhibited a better cellular uptake while retaining potent Ku inhibitory activity. Our data demonstrate that the cellular effects observed are a function of Ku inhibition and that this novel class of DNA-PK inhibitors can be further developed as anti-cancer therapeutics that can be used as an adjuvant to, or concomitant with radiotherapy and other cancer therapies that induce DNA damage. Citation Format: Dineshsinha Chauhan, Pamela L. Mendoza-Munoz, Narva Deshwar Kushwaha, Hariprasad Aruri, John J. Turchi, Navnath S. Gavande. Development of substituted oxindole derivatives as a Ku-targeted DNA-PK inhibitors for cancer therapy [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 416.
Abstract 4765: Tumor, serum and plasma metabolome in patients with high-grade bladder cancer
Authors: Maria-Malvina Tsamouri, Akshaya Karthikeyan, Christopher A. Lucchesi, Blythe P. Durbin-Johnson, Marc A. Dall'Era, Paramita M. Ghosh
Journal: Cancer Research (2024)

Abstract Introduction: Bladder cancer (BlCa) ranks as the sixth most prevalent cancer in the world. A number of urine based BlCa detection tests have recently been approved for clinical use, including the NMP22 tests and the bladder tumor antigen (BTA) tests for both detection and monitoring of patients with known bladder cancer. The FDA have approved them both for surveillance in BlCa only in conjunction with cystoscopy. Unfortunately, the sensitivity and specificity of these tests are poor, and cannot distinguish between aggressive and non-aggressive tumors. This project aims to identify alternate markers that can overcome these drawbacks. Methods: We characterized the global metabolome of 47 bladder tumors retrieved by radical cystectomy (RC) or TURBT, including 14 specimens with matching plasma and serum samples. All specimens were subjected to untargeted metabolomic approaches with gas chromatography- time-of-flight mass spectrometry (GC-TOF MS) to profile primary metabolites, hydrophilic interaction liquid chromatography MS (HILIC-QTOF MS) to profile biogenic amines, and liquid chromatography charged surface hybrid MS (LC-CSH-QTOF MS) to characterize complex lipids. Differentially expressed metabolites were analyzed with respect to grade, stage, metastases, and the use of neoadjuvant chemotherapy. For selected metabolites, area under the ROC curve (AUC) is calculated as % sensitivity vs. 100% specificity. Expression of highly discriminatory metabolites were then validated in the plasma and serum samples to determine which forum would provide greater specificity. Results: We first assembled a discovery cohort of 33 patients who did not have matching blood specimen for primary metabolites, biogenic amines and complex lipids. Comparison of high vs low grade tumors yielded two lipids, a sphingomyelin (SM (d38) and a phosphatidylcholine PC(p-38), that were significantly different (adjusted p-value&amp;lt;0.05, log2fold change&amp;gt;2.5). These results were validated in the 14-sample cohort with matching plasma and serum of which the latter showed significant correlation between tumor and plasma (Spearman R=0.872, adj p=0.03). Conclusions: Our results indicate that certain sphingomyelins and phosphatidylcholines may be useful as plasma markers of high grade BlCa. Further analyses are required to evaluate whether these markers are more discriminatory compared to existing urinary markers. Citation Format: Maria-Malvina Tsamouri, Akshaya Karthikeyan, Christopher A. Lucchesi, Blythe P. Durbin-Johnson, Marc A. Dall'Era, Paramita M. Ghosh. Tumor, serum and plasma metabolome in patients with high-grade bladder 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 4765.
Abstract 4163: Improving the dynamic range of pH low insertion peptides for targeted imaging of pancreatic tumors
Authors: Ryan Bynum, Emma Sanderson, Barish H. Edil, Ajay Jain, Lacey R. McNally
Journal: Cancer Research (2024)

Abstract Objective: Current intraoperative imaging modalities such as near-infrared fluorescent imaging (NIR) or ultrasound are limited due to operator experience and depth, and targeted imaging of pancreatic tumors would be beneficial. However, specific pancreatic tumor biomarkers available for targeting in a novel imaging protocol are lacking. As such, we focus on developing a novel targeted imaging paradigm utilizing multispectral optoacoustic imaging (MSOT) to target the acidic microenvironment of pancreatic tumors. Peptides know as pH low insertion peptides (pHLIPs) when bound to dye allow for contrasted imaging selectively based on pH using MSOT. We have identified the need for a pHLIP with improved dynamic range to improve imaging accuracy. Here, we synthesize the novel pHLIP V7FS for comparison to V3 with aims of improving the dynamic range of imaging with MSOT in pancreatic cancer. Methods: Using microwave chemistry, V7FS and V3 were synthesized with &amp;gt;90% purity. Peptides were conjugated to HiLyte 750 dye, and peptide-dye conjugation confirmed via spectroscopy. Intraoperative measurements of human pancreatic tumor and surrounding uninvolved tissue were obtained using a microsensor. Near-infrared fluorescent imaging was used to measure probe uptake in S2VP10 and S2013 pancreatic cancer cells lines grown in pH specific media (7.4, 6.8, 6.6) in replicates. MSOT was then used to image probes in phantoms mimicking tissue and then in mice with pancreatic tumors from orthotopically implanted S2VP10. Statistical analysis was performed using ANOVA. Results: Compared to surrounding uninvolved pancreatic tissue, human pancreatic tumor was more acidic with pH 6.2-6.7 vs 7.2-7.3 (p&amp;lt;0.01). Signal at pH 7.4, 6.8 and 6.6 was higher for V7FS-750 compared to V3-750 (p=0.0105). Signal for V7FS-750 was centered around pH 6.6 and signal for V3-750 centered around pH 6.8. Interaction between probe and pH did not reach significance (p=0.745). Peak uptake in orthotopic murine models was observed at 3 hours following intravenous injection. Conclusions: V7FS-750 was shown to have higher signal accumulation compared to V3-750 favoring a more acidic environment (pH 6.6 vs pH 6.8). This novel pHLIP was demonstrated to be viable for use in an imaging paradigm utilizing MSOT in an orthotopic murine model. Continued improvement in the dynamic range of these probes is promising for the use of pHLIPS in imaging of pancreatic cancer with MSOT. Citation Format: Ryan Bynum, Emma Sanderson, Barish H. Edil, Ajay Jain, Lacey R. McNally. Improving the dynamic range of pH low insertion peptides for targeted imaging of 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 4163.
Abstract 5093: Analysis of protein expression in head and neck cancers as therapeutic targets for antibody drug conjugates
Authors: Justin Tyler Moyers, Seth L. Smith, Miranda M. Mora, Roberto Carmagnani Pestana
Journal: Cancer Research (2024)

Abstract Introduction: Antibody Drug Conjugates (ADCs) represent a new category of therapeutic molecular targeting for solid tumors. To date 6 ADCs have been approved in solid tumors against 5 targets (HER2/ERBB2, Folate alpha, Tissue Factor, Nectin-4, and Trop-2). Thus far, no ADCs have been approved for head and neck cancers. Methods: We queried protein expression data from a publically available consortium of datasets (TNMPlot.com) containing protein expression data from over 56,000 tumor and normal samples from GEO, GTex, TCGA, and TARGET databases. Genes examined for protein targets, included those with ADC targets of both presently approved and investigational drugs from clinical trials.The level of overexpression was determined as the percent of tumors over the 75th percentile of expression in normal tissue. Results: Protein expression data were available for 99 HNSCC samples. Among targets with ADCs available, increased protein expression was seen in HNSCC for 0% of ERBB2 (n=0/99), 38% of FOLR1 (n=38/99), 0% of TACSTD2 (n=0/99), and 42% of F2 (n=42/99) genes.Among gene targets with investigational ADCs, increased protein expression was seen in HNSCC for 35% of of AXL (n=35/99), 13% of B7H3/CD27 (n=12/99), 50% of EGFR (n=50/99), 63% of VTCN1 (n=63/99), 10% of MSLN (n=10/99), 77% of CDH3 (n=76/99), and 39% of PDGFRA (n=39/99). Conclusion: Increased protein expression for approved ADC targets were infrequent in HNSCC. However, increased protein expression is seen for several ADCs under clinical investigation supporting the potential therapeutic approaches for investigational ADC targets. Citation Format: Justin Tyler Moyers, Seth L. Smith, Miranda M. Mora, Roberto Carmagnani Pestana. Analysis of protein expression in head and neck cancers as therapeutic targets for antibody drug conjugates [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 5093.
Abstract 5092: Development of a priming approach to enhance antigen-directed therapies in hematological malignancies and solid tumors
Authors: Kathryn E. Vanderlaag, Anukriti Dhar, Molly Volkman, Erik Werner, Transon Nguyen, Kamran Ali
Journal: Cancer Research (2024)

Abstract Clinical success of antigen-directed therapies in cancer has been limited by heterogeneous antigen expression and a narrow therapeutic window. In many patients, failure of antigen-directed therapies such as CAR T-cell therapies, antibody-drug conjugates (ADC) or radioligand therapies (RLT) has less to do with a lack of potency or specificity of the agent and more to do with variable and suboptimal antigen expression in the patient. We are developing combination therapies that introduce a priming agent designed to optimize antigen expression in the patient and improve the therapeutic window of existing antigen-directed therapies. Our high-throughput platform utilizes machine learning and automation to scale functional combinatorial screening for small molecule priming agents using cell lines and patient samples. Using this platform, we are identifying priming therapies for CD123, CD33, CD22, and CD19 in hematological malignancies including acute myeloid leukemia (AML), and HER2, HER3, and TROP2 in solid tumors including breast cancer.For our CD123 program, we have identified priming agents that selectively upregulate CD123 expression ≥2-fold on AML cells without increasing expression on normal myeloid progenitor cells, which also express CD123. AML cells treated with a CD123 priming agent in combination with a CD123 ADC showed greater tumor-cell killing compared to the ADC alone. In comparison, normal myeloid progenitor cells from healthy bone marrow treated with the same CD123 priming-ADC combination treatment did not show an increase in ADC-mediated cell killing. From our mechanistic studies, we have identified a somatic mutation associated with CD123 upregulation that may lead to selective upregulation on cancer cells and not on normal cells. Additionally, this marker can be used for patient selection. We have also observed CD123 upregulation in vivo using mouse models of AML and are currently conducting additional in vivo proof of concept studies to demonstrate that CD123 priming therapy enhances efficacy.There are two distinct advantages of a priming approach paired with an antigen-directed therapy, which include: (1) improving the durability of patient responses and (2) expanding the patient population. Our priming combination approach has the potential to overcome antigen heterogeneity and thereby improve the clinical success of antigen-directed therapies. Citation Format: Kathryn E. Vanderlaag, Anukriti Dhar, Molly Volkman, Erik Werner, Transon Nguyen, Kamran Ali. Development of a priming approach to enhance antigen-directed therapies in hematological malignancies and solid 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 5092.