bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 625: Selective inhibition of NF1 loss-of-function driven oncogenic signaling in melanomas
Authors: Abecunas Cara , Fallahi-Sichani Mohammad , Leopold Judith , Whitehead Christopher , Ziemke Elizabeth 
Published: September 2020

Abstract
Oncogenic activation of the MAPK signaling pathway occurs across &gt;90% of melanomas, motivating the clinical evaluation of MAPK-targeted therapies in these tumors. However, only BRAFV600E/K-mutated melanomas show consistent clinical responses to MAPK-targeted therapies. Inactivation of the tumor suppressor gene neurofibromin 1 (NF1) is among the mechanisms that drive hyperactivated RAS signaling in &gt;10% of melanomas. These tumors, however, have variable dependency on RAS-mediated pathways, such as MAPK and PI3K/mTOR, and thus exhibit inconsistent sensitivity to targeted inhibitors of these pathways. It is of paramount importance, therefore, to identify new therapeutic strategies to block tumor cell growth or improve MAPK- or PI3K-targeted therapy response in NF1 loss-of-function (NF1LoF) melanomas. To identify actionable vulnerabilities in NF1LoF melanoma cells, we apply a systematic approach, combining multiplexed high-throughput immunofluorescence microscopy, single-cell measurements and computational analysis, to study the responses of differentially mutated human melanoma cell lines to a variety of RAS-related pathway inhibitors. Our analysis led to the identification of a multi-kinase inhibitor, MTX-216, which is efficacious in induction of tumor cell death and inhibition of NF1LoF melanoma growth both in vitro and in vivo, but does not exhibit cytotoxicity in BRAFV600E melanomas and wild-type melanocytes. Single-cell analysis of downstream RAS-mediated signaling markers (e.g. phospho-S6) and proliferation markers (e.g. Ki-67) demonstrated cell-to-cell heterogeneity in NF1LoF melanoma cells treated with commercially available kinase inhibitors, resulting in incomplete drug responses. MTX-216 reduces this single-cell variability, providing evidence that co-suppression of signaling and proliferation pathways is correlated with drug-induced cytotoxicity. Our systematic analysis, together with ongoing studies to uncover the mechanism of action of MTX-216 in NF1LoF melanomas, has the potential to identify new and effective treatment strategies for NF1-mutant melanomas.
Citation Format: Cara Abecunas, Mohammad Fallahi-Sichani, Judith Leopold, Christopher Whitehead, Elizabeth Ziemke. Selective inhibition of NF1 loss-of-function driven oncogenic signaling in melanomas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 625.
Abstract 6281: Differential response of irradiated breast carcinoma cells to DNA-PK inhibition: Spheroid response is governed by cell adhesion effects rather than changes in radiosensitivity
Authors: Yu Jing , Lu Ryan , Nedrow Jessie , Sgouros George 
Published: September 2020

Abstract
Agents that increase tumor radiosensitivity are of interest in improving outcomes in radiotherapy (XRT). DNA-PKcs inhibitors lead to radiosensitization and also to alterations in cell adhesion proteins. Using a HER2 positive mammary carcinoma cell line, NT2.5, we investigated the impact of Nu7441, a potent and selective DNA-PKcs inhibitor together with external beam irradiation in both 2D monolayer and 3D spheroid cell culture systems. Colony formation assays were performed for cells irradiated as monolayers and also for cells disaggregated from spheroids. Cells grown in monolayer culture and as spheroids were incubated with Nu7441 (5 µM) for 24 h after different doses of external beam irradiation. In monolayer culture cells, α/β increased from 3.0 ± 0.2 Gy (XRT alone) to 6.9 ± 0.2 Gy when XRT was followed by Nu7441 incubation. Corresponding α/β values for cells obtained by disaggregating treated spheroids were 3.6 ± 0.7 Gy (XRT alone) and 3.5 ± 0.2 Gy (XRT+Nu7441). In contrast to the minimal change in α/β, spheroids survival was highly sensitive to Nu7441 incubation. 21 days after 0, 2, 4, 6, 8, or 10 Gy XRT alone 100, 83, 75, 63, 56, and 31%, respectively, of the irradiated spheroids remained intact; when Nu7441 treatment was involved, 56% remained intact at 2 Gy and 13% at 4 Gy, no spheroids survived to 3 weeks at 6 Gy or more. We also found a progressive increase in fragmentation for spheroids exposed only to Nu7441 (0 Gy): 3/24, 9/24 and 17/24 fragmented after 14, 21 and 28 days of incubation, respectively. The discrepancy between the minimal change in α/β from cells derived from spheroids and the spheroid growth response was not related to poor penetration of Nu7441 since the colony formation assay results for different sizes of spheroids (180 to 400 µm) treated with 4 Gy with or without Nu7441were not significantly different. The results suggest that spheroid response to DNA-PKcs inhibitors is driven by their known inhibition of cell-cell adhesion pathways and potentially less so by radiosensitization.
Citation Format: Jing Yu, Ryan Lu, Jessie Nedrow, George Sgouros. Differential response of irradiated breast carcinoma cells to DNA-PK inhibition: Spheroid response is governed by cell adhesion effects rather than changes in radiosensitivity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6281.
Abstract 6309: Development of protein conformational array ELISA for p53 and SHP2 allosteric regulator screening and analysis
Authors: Wang Xing 
Published: September 2020

Abstract
P53 and SHP2 plays important role during cancer development. For p53, more than 50% of cancers were shown to have gene mutation in this tumor suppressor, however how these gene mutations impact the p53 protein conformation and function have not be studies in much detail. A Protein Conformational Array ELISA was developed with 17 polyclonal antibodies covering the whole p53 molecule, by measuring the linear epitope distribution on the surface of the p53 protein, the conformational (Higher Order Structure or HOS) can be described quantitively. Initial studies have shown that in lung cancer cells, the level of p53 is significantly increased and more interestingly, the p53 HOS has changed at its N-terminal as compared with the wild type. For SHP2, a protein phosphatase, a 27-antibody panel was developed to characterize the HOS changes. Because of the generic nature of the phosphate binding site, it has been very challenging to develop phosphatase inhibitors, however studies have shown that allosteric regulators can be identified with excellent anti-tumor activities. Currently, some of the allosteric regulators identified are being tested in the clinic. The SHP2 Conformational Array ELISA will provide a robust platform for the screening and testing of potential allosteric regulators with its molecular resolution and high-throughput capability. This presentation will describe the development of the two conformational arrays and their applications in the study of p53 and SHP2 from different cancer cell lines and the characterization of the allosteric regulators identified.
Citation Format: Xing Wang. Development of protein conformational array ELISA for p53 and SHP2 allosteric regulator screening and analysis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6309.
Abstract 6311: An enabling technology to detect low abundance targets in cells and tissues
Authors: Patel Deven , Liu Jixiang , Dong Pengfei , Kan Shu , Wu Haiyan , Zhao Qin , Diwu Zhenjun 
Published: September 2020

Abstract
The rapid advances in sequencing, genomics and bioinformatics have generated a huge amount of genomic data available at our disposal. However, some proteins, the products of those genes, are expressed in cells or tissues at extremely low levels, making the identification and characterization of proteins the bottle neck for biomedical research field. Approximately, 65% of the human proteome is expressed at less than a few thousand copies. Thus, the availability of protein detection probes and tools becomes a critical element to measure lower abundance protein targets in the cells and tissues to identify clinical significance of the particular target proteins. There are several common signal amplification methods available for detecting low abundance protein targets. However, in some cases, their sensitivities are still not satisfactory. Biotin/avidin amplification system has been predominantly used to enhance detection sensitivity but it is still sometimes not sufficient, leading to extremely challenging to accurately measure the low expressed protein targets. There is urgently unmet need to develop a new signal amplification system with enhanced detection sensitivity. We develop the Power Styramide Signal Amplification (PSA) system that can detect extremely low-abundance targets in cells and tissues. The PSA technique is much more sensitive than the traditionally used biotin/avidin and TSA amplification methods. PSA uses a concept that utilizes the catalytic activity of horseradish peroxide (HRP) for covalent deposition of Styramide in situ. The radicals generated from the Styramide based substrates have much higher reactivity towards the target, thus producing a more robust signal and achieve much higher sensitivity towards lower expressed targets. When this technique was compared to directly conjugated antibody, we saw a significant increase in the signal and improved detection limit by 10-100 folds. Another advantage using Styramide-based substrates is that the need of either primary or secondary antibodies gets significantly reduced. You can get robust signal just by using very little antibodies without sacrificing the quality of the fluorescent images. Overall, this new technology enables us to detect low expressed targets in cells or tissues using lower antibody concentration with high detection limit.
Citation Format: Deven Patel, Jixiang Liu, Pengfei Dong, Shu Kan, Haiyan Wu, Qin Zhao, Zhenjun Diwu. An enabling technology to detect low abundance targets in cells and tissues [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6311.
Abstract 6346: Optimizing precision combination therapies based on single-cell profiling of brain tumor biopsies
Authors: Babikir Husam , Wang Lin , Shamardani Karin , Catalan Francisca , Kohanbash Gary , Aghi Manish K. , Phillips Joanna J. , Diaz Aaron A. 
Published: September 2020

Abstract
Glioblastomas (GBM) display dramatic levels of intra-tumoral heterogeneity. This heterogeneity contributes significantly to resistance to standard and emerging treatments. As a result, GBM remains the deadliest primary tumor of the adult brain. Moreover, most preclinical studies of GBM use models of primary GBM, most studies of clinical specimens use tissue derived from primary GBMs, despite the fact that most clinical trials enroll patients at recurrence. There is a paucity of information about recurrent GBM. To address these critical barriers, we devised a strategy to optimize precision drug combinations based on an understanding of a patient's intratumor heterogeneity, ascertained via single-cell profiling. We conducted single-nucleus RNA sequencing (snRNA-seq) and/or single-nucleus assay for transposon-accessible chromatin (snATAC-seq) sequencing for 16 recurrent GBMs. For 6 of these cases we also derived cell lines from patient biopsies. We identified lineage hierarchies of proliferating cells and their more differentiated progeny. Based on this, we performed an in vitro drug-combination screen using FDA-approved chemotherapies, targeting pathways learned from these single-cell signatures. We found that targeting distinct cellular states in the inferred lineage hierarchy of a patient's tumor provides a more complete treatment than targeting one state alone. Additionally, we will present the results of our ongoing in vivo validation activities and profiling efforts. This work presents a novel paradigm for identifying precision combinations of chemotherapies targeted to phenotypes learned from single-cell profiling of a patient's tumor biopsy.
Citation Format: Husam Babikir, Lin Wang, Karin Shamardani, Francisca Catalan, Gary Kohanbash, Manish K. Aghi, Joanna J. Phillips, Aaron A. Diaz. Optimizing precision combination therapies based on single-cell profiling of brain tumor biopsies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6346.
Abstract 6356: Discovery of seleno allyl hybrid compounds, the Se incorporated mimics of naturally occurring garlic based allylic compounds, as potential anticancer agents
Authors: Talavera Irene , Astrain Nora , Barajas Miguel , Encío Ignacio , Sharma Arun K. , Sanmartín Carmen , Plano Daniel 
Published: September 2020

Abstract
Many synthetic derivatives of natural products have been found to exhibit biological activity towards cancer. One prominent example of such natural products are the garlic-based compounds. Given the well stablished preventive effects shown by garlic and some of its allylic components and a well-established chemopreventive and therapeutic effects shown by selenium (Se) compounds, we pursued to design Se-allyl hybrid compounds in order to increase efficacy as compared to naturally occurring allylic compounds. A total of 18 new selenoallyl (SeAl) compounds were designed following two different synthetic approaches. SeAl functionality was chosen to mimic the garlic bioactive allylic components. All the synthesized compounds were screened against colorectal (HT29 and HCT116) and mammary (MCF-7) cancer cell lines (48h treatment). Four most active compounds identified were submitted to the NCI Developmental Therapeutic Program (DTP). Two out of the four compounds were selected for the dose-response assay against a panel of 60 cancer cell lines. Both the compounds exhibited impressive cytotoxicity - lethal dose 50 (LD50) values below 9.2 µM in most of the melanoma and ovarian cancer cell lines tested (8 out of 9 for melanoma and 5 out of 7 for ovarian cancer cells for both compounds). Additionally, the Se-allyl derivative bearing an aspirin substituent presented a significant tumor size inhibition in a castration-resistant prostate cancer xenograft model at a dose of 4 mg/kg given intraperitoneally. Thus, this compound has the potential to be a promising candidate for prostate cancer treatment and potentially other cancers. To conclude, we firmly believe, based on the evidences obtained and presented herein, that structural modifications involving the hybridization approach with Se and naturally occurring allylic compounds could stand as a novel toolkit for anticancer drug development.
Citation Format: Irene Talavera, Nora Astrain, Miguel Barajas, Ignacio Encío, Arun K. Sharma, Carmen Sanmartín, Daniel Plano. Discovery of seleno allyl hybrid compounds, the Se incorporated mimics of naturally occurring garlic based allylic compounds, as potential anticancer agents [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6356.
Abstract 6494: Personalize My Treatment (PMT): A pan-Canadian initiative integrating precision oncology across Canada - PMT-001 pilot project
Authors: Marques Maud , Gambaro Karen , de Tertre Mathilde Couetoux , McNamara Suzan , Hoffer Cyrla ,   The Exactis Network, Fajzel Richard , Batist Gerald 
Published: September 2020

Abstract
More than 90% of cancer therapeutics in development are targeted therapies. Although the number of patients who can benefit from targeted therapies is increasing, many of the biomarkers are identified in only a small fraction of patients. Identifying and enrolling these rare cancer patient sub-populations into clinical trials presents an enormous challenge to both pharmaceutical companies and clinicians. Furthermore, in Canada, the lack of harmonized standard of care molecular testing for cancer patients results in a discordance in the number of genes tested across Hospital sites. Identifying patients with biomarkers of interest across Canada is essential to attract precision oncology clinical trials to Canada and to offer cancer patients better therapeutic options and improved outcomes. Founded in 2014, Exactis Innovation is a non-profit Academic Research Organization which aims to integrate precision oncology across Canada. Exactis has consolidated a pan-Canadian network of 13 cancer care centre sites and 4 federated laboratories. Network sites host an REB-approved molecular cancer patient registry (PMT), through which patients can be profiled, identified as carrying a biomarker, followed throughout their disease trajectory and be re-contacted if their molecular profile matches a clinical trial or an approved therapy. Here we report the results of Exactis' first profiling initiative (PMT-001), performed across 8 Exactis Network sites within 3 Canadian provinces in a four months' time period. In summary, 447 individual tumors specimens were collected from breast, colorectal, lung and ovary cancer patients and 382 were profiled using the Oncomine comprehensive assay v3 (OCAv3) panel DNA (n=365) and OCAv3 DNA/RNA (n=151). At least one aberration was identified in 346 participants. As expected, the top mutated genes across the 4 cohorts were TP53 (50%), PIK3CA(15%), KRAS (12.5%) and BRCA1/2 (12%/11%). At the fusion level, we identified EML4-ALK (5.2%), KIF5B-RET(1.7%) and MET exon 14 skipping (3.4%) in NSCLC participants and we identified RSPO3 (3%) and RSPO2 (2%) fusion in colorectal cancer participants. The profiling pilot of the PMT initiative shows how strong foundations within the Exactis pan-Canadian network is resulting in fast, high quality and meaningful molecular data for Canadian cancer patients.
Citation Format: Maud Marques, Karen Gambaro, Mathilde Couetoux de Tertre, Suzan McNamara, Cyrla Hoffer, The Exactis Network, Richard Fajzel, Gerald Batist. Personalize My Treatment (PMT): A pan-Canadian initiative integrating precision oncology across Canada - PMT-001 pilot project [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6494.
Abstract 781: Methylation-based liquid biopsy of meningioma primary and recurrent samples
Authors: Sabedot Thais S. , Malta Tathiane M. , She Ruicong , Snyder James , Walbert Tobias , Lee Ian , Kalkanis Steven , Ewing James , Castro AnaValeria , Noushmehr Houtan 
Published: September 2020

Abstract
Meningiomas are mostly benign CNS tumors however, a subset of these tumors may become atypical or malignant. The standard of care to monitor patients after diagnosis requires serial MRI assessments, which have limited value in distinguishing malignant tumors from benign disease. Therefore the discovery of non-invasive methodologies that reflect meningioma tumor burden and its dynamic evolution in real-time is highly desirable. Liquid biopsy (LB) could be used to fine-tune surveillance and treatment with minimal risk to patients. Evidence of circulating tumor cells and cell-free (cf) tumor DNA in the blood has been shown in several tumor types however, limited progress has been made for brain tumors with known biomarkers; possibly due to the unlikelihood of capturing point mutations in circulating DNA fragments. On the other hand, DNA methylation signatures are maintained even in small DNA fragments, which suggests that DNA methylation is an attractive biomarker to be studied in liquid biopsy of brain cancers. In order to identify DNA methylation-based biomarkers using archival serum and tissue specimens, we generated and analyzed the epigenome (Illumina Human EPIC array) of patients with meningioma (including primary (n=6); recurrent (n=8)) and non-meningioma (including non-tumor patients (n=5), pituitary tumor (n=13), colorectal cancer (n=2) and other CNS diseases (n=6), such as inflammatory tissue and radiation necrosis). cfDNA fragment size distribution revealed peaks with 150~200bp on average. By randomly selecting 70% of our cohort as a discovery set, we identified 500 CpGs (FDR&lt;0.05) differentially methylated between meningiomas and non-meningiomas, which show a DNA methylation profile similar to the matched meningioma tissue. Then, we trained a random-forest machine learning using the same signature and applied the model to the remaining 30% samples (validation set) from our cohort. The model was able to correctly classify samples into meningioma and non-meningiomas with a sensitivity of 100% and specificity of 100%. From this pilot data, we were able to investigate the LB methylome of meningioma patients and identify potential markers to detect tumor cells in the serum of these patients, which could eventually allow clinicians to monitor impending disease progression and recurrence.
Citation Format: Thais S. Sabedot, Tathiane M. Malta, Ruicong She, James Snyder, Tobias Walbert, Ian Lee, Steven Kalkanis, James Ewing, AnaValeria Castro, Houtan Noushmehr. Methylation-based liquid biopsy of meningioma primary and recurrent samples [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 781.