tbuckley/cabot-search huggingface dataset:
Abstract 3449: A novel rapid zebrafish model for validation of potential therapies for fatal pediatric brain tumors
Authors: Harpreet Kaur, Huizi Guo, Kevin Emmerich, David White, Peter Green, Alara Michelle Hector, Sepehr Akhtarkhavari, Anukriti Bhargava, Allison Martin, Smit Shah, Charles G. Eberhart, Jeffrey Mumm, Eric H. Raabe
Journal: Cancer Research (2020)

Abstract Diffuse intrinsic pontine glioma (DIPG) and atypical teratoid/rhabdoid tumors (AT/RT) are deadly pediatric brain tumors. There is an urgent need of better therapeutics for improving survival and quality of life for these patients. Additionally, we need improved animal models to accelerate identification of novel therapeutics and improve through-put. In line with our long-term interests of validating therapies and developing model systems for pediatric brain tumors, we tested a repurposed drug quinacrine as a potential therapy using a new and faster model system in zebrafish. Quinacrine is a safe and widely used treatment for pediatric malaria and parasitic infections. We hypothesized that quinacrine will increase tumor cell death and decrease tumorigenicity of DIPG and ATRT. We used quinacrine in six patient-derived cell lines: three AT/RT (BT37, CHLA-05, CHLA-266) and three DIPG (JHHDIPG1, SUDIPGXIII, SF7761). In all tumor cell lines, quinacrine caused a dose-dependent reduction in proliferation (BrdU) and increase in apoptosis (cleaved caspase-3 and cleaved PARP) compared to vehicle-treated cells (P&amp;lt;0.01). Quinacrine had no effect on growth of normal hindbrain neural stem and progenitor cells. Using quinacrine fluorescence as a surrogate, we achieved micromolar concentration of quinacrine in the mouse and zebrafish brain without overt toxicity. Treatment of mice bearing ATRT flank tumors with quinacrine resulted in decreased tumor volume compared to vehicle-treated mice (P&amp;lt;0.05). To validate quinacrine orthotopically in DIPG, we developed a novel model in zebrafish wherein we injected fluorescent DIPG cells into the developing zebrafish blastula. Two days post injection, DIPG cells had homed to the zebrafish brain. Treatment of xenografted zebrafish with quinacrine for 72 hours decreased DIPG growth by 40% as measured by fluorescence, suggesting that minor groove binding drugs like quinacrine are a viable treatment strategy for these tumors. Using this new system, we were able to validate a potential therapeutic in 7 days versus 7 months in mice. Future studies are aimed at investigating the mechanism of quinacrine in these tumors and optimizing our zebrafish model for high-throughput screening of potential drugs. Citation Format: Harpreet Kaur, Huizi Guo, Kevin Emmerich, David White, Peter Green, Alara Michelle Hector, Sepehr Akhtarkhavari, Anukriti Bhargava, Allison Martin, Smit Shah, Charles G. Eberhart, Jeffrey Mumm, Eric H. Raabe. A novel rapid zebrafish model for validation of potential therapies for fatal pediatric brain tumors [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 3449.
Abstract 1211: Recurrent germline mutations in RAD51D and PALB2 are present in Colombian hereditary breast and ovarian cancer families
Authors: Maria Carolina Sanabria-Salas, Ana Lucía Rivera-Herrera, Ana Milena Gómez-Camargo, Luis G. Carvajal-Carmona, Martha Lucía Serrano-López
Journal: Cancer Research (2020)

Abstract Hereditary breast cancer (BC) syndromes corresponds to 10% - 15% of all cases diagnosed worldwide. Most of these cases are due to deleterious germline genetic variants in BRCA1/2 genes; nevertheless, multipanel testing have contribute to the identification of other risk genes, including other homologous recombination (HR) repair genes, such as PALB2, ATM, CHEK2 and RAD51D. Here we explore the mutation spectrum of Hereditary Breast and Ovarian Cancer (HBOC) Colombian cases as part of the Hereditary Cancer Program from the National Cancer Institute from Colombia, the largest reference cancer center in the country, that seeks to identified high risk families to offer preventive measures and screening recommendations. A total of 358 patients fulfilling criteria for HBOC have been so far analyzed with Next Generation Sequencing using a multigene panel. Overall, 47% have negative results and in the 33% we identified VUSs. In general, 20% have a pathogenic or potentially pathogenic genetic variant; from those, BRCA1 (n = 17) and BRCA2 (n = 17) were the most frequently mutated genes (47.2% among all positive results). Deleterious mutations in RAD51D and PALB2 (also important HR repair genes) were found in 7% and 5.6% of the cases tested. Interestingly, genotype:phenotype correlations were found for these genes, as breast cancer molecular subtypes were distributed differently depending on the gene affected. In concordance with other reports, triple negative breast cancers (TNBC) were more frequent in BRCA1 (9/17, 53%) and PALB2 (4/4, 100%) carriers, and luminal subtypes were more frequent in BRCA2 carriers (10/17, 59%). Mutations in RAD51D: c.94_95del (p.Val32Phefs*67) and PALB2: c.2288_2291del (p.Leu763Ter), were both recurrent mutations in our Colombian cases. Further haplotype analysis will help us to determine if mutation carriers shared a common ancestry. Citation Format: Maria Carolina Sanabria-Salas, Ana Lucía Rivera-Herrera, Ana Milena Gómez-Camargo, Luis G. Carvajal-Carmona, Martha Lucía Serrano-López. Recurrent germline mutations in RAD51D and PALB2 are present in Colombian hereditary breast and ovarian cancer families [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 1211.
Abstract 840: Pathway enrichment analysis of gene expression data from formalin-fixed paraffin embedded (FFPE) samples using the GeoMx™ DSP Platform
Authors: Tressa R. Hood, Jason Reeves, Zach Norgaard, Margaret Hoang, Sarah Warren, Erin Piazza, Rich Boykin, Joseph Beechem
Journal: Cancer Research (2020)

Abstract The GeoMx Digital Spatial Profiling (DSP) Platform enables robust detection of high-plex protein and RNA expression from user-defined sections within FFPE samples. As the number of targets detected within such tissues increases, it becomes important to apply systems biology strategies in order to better interpret the complex biology of the tumor microenvironment. In this study, we investigated the expression profiles of more than 1600 genes by utilizing more than 10,000 DSP-specific in situ hybridized (ISH) probes on FFPE samples. The bioinformatics tools we have development are enabling us to move beyond single-gene profiling to a better understanding of pathway-based expression. Our study includes colorectal cancer patient samples from which we have matching bulk RNA sequencing and NanoString analysis to compare. The panel of genes profiled have a strong focus around capturing biological signaling along canonical signaling pathways and cell-intrinsic signaling from immune cells and other cell types. We demonstrate the ability to leverage foundational pathway interrogation tools, including Reactome, with the data to capture spatially-resolved pathway interactions and signaling within FFPE tissues. As we look towards the future of the GeoMx platform and high-plex RNA profiling of tissue samples, these experiments highlight not only the need but the capacity for this platform to derive deep understanding of the biology within and across a single slide of tissue. These experiments are being used to drive development of the software features within the GeoMx ecosystem, which will provide further support for pathway-level exploration of expression when working with highly multiplexed reagents in future platform offerings. GeoMx™ DSP technology is for Research Use Only and not for use in diagnostic procedures. Citation Format: Tressa R. Hood, Jason Reeves, Zach Norgaard, Margaret Hoang, Sarah Warren, Erin Piazza, Rich Boykin, Joseph Beechem. Pathway enrichment analysis of gene expression data from formalin-fixed paraffin embedded (FFPE) samples using the GeoMx™ DSP Platform [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 840.
Abstract 6293: Novel approach for automated sequential immunoassay for quantitation and characterization of PI3K-Akt pathway proteins
Authors: Irina G. Kazakova, Crystal Tran, Anita Silver, Jessica Dermody
Journal: Cancer Research (2020)

Abstract The PI3K-Akt signaling pathway modulates cell growth, survival and apoptosis, and this pathway is frequently altered in human cancers, contributing resistance to radiation and chemotherapy treatment. Akt is a target for specific inhibition and recently, a number of small molecules have been developed to improve the pharmacologic properties of known inhibitors like wortmannin and LY294002. However, pan-Akt inhibitors can result in unanticipated side effects due to the lack of specificity for Akt isoforms 1, 2, and 3. Therefore, detection and quantitation of Akt isoforms and their downstream targets for both expression levels and phosphorylation states is crucial for therapeutic drug development. Here we demonstrate application of the Multiple Detection Approach to characterize the PI3K-Akt signaling pathway. This approach uses sequential analysis of proteins separated and immobilized in a capillary, by performing either dual immunoassays or immunoassay with total protein on the Simple Western platform using chemiluminescence detection. Assays with control and LY294002 inhibitor-treated samples were developed. Proteins were first separated based on molecular weight via capillary electrophoresis, followed by immobilization via UV-crosslinking. Next, PI3K-Akt pathway targets were sequentially probed in the same capillary with total and phospho-specific antibodies, to determine the phosphorylated fraction relative to the total fraction. Primary antibodies from the first immunoprobe were removed after the detection step with &amp;gt;95% efficiency, as confirmed by re-probing with the same secondary antibody. Target protein loss was negligible due to covalent immobilization to the capillary wall, which was confirmed with re-probing, thus validating the quantitative data generated using this sequential approach. In addition, total protein normalization was performed in tandem with the immunoassay in the same capillary. This approach enables normalization of phosphorylation levels and/or target abundance in cell line or tissue samples, correcting for change in protein content due to treatment, loading, and/or other systematic errors. These results present the utility of the Multiple Detection Approach to quickly characterize and quantify proteins involved in signaling pathways targeted during development of cancer therapies. Citation Format: Irina G. Kazakova, Crystal Tran, Anita Silver, Jessica Dermody. Novel approach for automated sequential immunoassay for quantitation and characterization of PI3K-Akt pathway proteins [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 6293.
Abstract LB-204: Oncogenic Ras signaling requires serine protease hepsin to induce invasive breast cancer phenotype
Authors: Shishir Mani Pant, Topi Tervonen, Denis Belitskin, Johanna Englund, Emmy Verschuren, Panu Kovanen, Juha Klefstrom
Journal: Cancer Research (2020)

Abstract Invasive cancer growth occurs when epithelial tumor cells individually or collectively detach from the primary tumor and migrate into the adjacent healthy tissue. This process starts a gradual tumor progression that may lead to life-threatening metastatic disease. Hepsin is a type II transmembrane serine protease that is frequently overexpressed in breast, prostate, and other epithelial cancers. It promotes tumor progression through activating growth factors and disrupting cell-cell and cell-basement membrane (BM) junctions. Although hepsin participates in pericellular cancer degradome, the oncogenic upstream mechanisms that activate hepsin in cancer are not well known. We found that oncogenic Ras proteins by activating MAPK pathway signaling alter the ratio of hepsin and HAI-1 to increase the proteolytic activity of hepsin. In 3D epithelial culture models of Ras-driven cancer, depletion of hepsin by shRNA restored desmosomes, BM defects, and glandular morphology but not the apical polarity. Mechanistically, Ras-MAPK pathway affected hepsin/HAI-1 via two distinct downstream pathways: Hepsin protein was stabilized via Ras-induced and heat shock transcription factor-1-mediated stress pathway, whereas HAI-1 was down-regulated by Ras via tumor suppressor LKB1 and PI3K-dependent pathways. Altogether, the results suggest that abnormal activation of Ras-MAPK pathway elevates hepsin activity to execute early steps of breast cancer invasion. Citation Format: Shishir Mani Pant, Topi Tervonen, Denis Belitskin, Johanna Englund, Emmy Verschuren, Panu Kovanen, Juha Klefstrom. Oncogenic Ras signaling requires serine protease hepsin to induce invasive breast cancer phenotype [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 LB-204.
Abstract 2345: Statin use associated with reduced risk of hepatocellular carcinoma recurrence following liver resection: A systematic review and meta-analysis
Authors: Chun Philip Yeung, Siu Tim Cheung, Kwok Chai Kelvin Ng, Bo San Paul Lai, Ching Ning Charing Chong
Journal: Cancer Research (2020)

Abstract The effect of statins in preventing hepatocellular carcinoma (HCC) recurrence after curative liver resection has been controversial. Some retrospective studies identified perioperative use of statins was associated with significantly lower risk of HCC recurrence and improve recurrence-free survival (RFS) after liver resection, among patients with or without chronic hepatitis viral infection in multivariate survival analysis. However, a recent single-center study enrolled 430 cases in Taiwan revealed that the protective effect of statins was only significant in univariate analysis but not significant in multivariate analyses. To evaluate the effect of statins on the risk of HCC recurrence after curative liver resections, we performed a systematic review and meta-analysis on this topic. A systematic search of Medline, Embase, and Web of Science was conducted through December 2019. Studies were included if they evaluated perioperative exposure to statins, reported the recurrence of HCC after curative resection, and reported hazard ratios (HR) of multivariable analysis by Cox proportional hazards model. Summary HR estimates with 95% confidence intervals (CI) were calculated using the random-effects model. The analysis included 5 studies reporting the recurrence of HCC among 8,586 patients after liver resection, in which 411 of them received perioperative statins treatments. A meta-analysis of the studies showed a significant (39%) reduction in the risk of HCC recurrence among patients who took statins (adjusted HR, 0.61; 95% CI, 0.49-0.76), with no or little heterogeneity among studies (χ2=5.58, df=4, I2=28%). In conclusion, perioperative statins use may improve recurrence-free survival and decrease the risk of HCC recurrence after curative liver resection. Further prospective studies and larger randomized controlled trials (RCTs) are warranted to validate the conclusion. Statin usersNon-statin usersAdjusted Hazard RatioStudyTotalTotalWeightIV, Random, 95%CIYear of publicationWu 2012175439437.6%0.68 (0.53-0.87)2012Lee 2016132207831.2%0.66 (0.49-0.90)2016Kawaguchi 2017317037.0%0.34 (0.12-0.75)2017Nishio 20184360014.5%0.42 (0.25-0.71)2018Young 2019304009.8%0.79 (0.41-1.52)2019Total (95% CI)4118175100.0%0.61 (0.49-0.76)Heterogeneity: Tau2=0.02; Chi2=5.58, df=4 (p=0.23); I2=28%Test for overall effect: Z=4.43 (p&amp;lt;0.00001) Citation Format: Chun Philip Yeung, Siu Tim Cheung, Kwok Chai Kelvin Ng, Bo San Paul Lai, Ching Ning Charing Chong. Statin use associated with reduced risk of hepatocellular carcinoma recurrence following liver resection: A systematic review and meta-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 2345.
Development of Sentinel LN Imaging with a Combination of HAase Based on a Comprehensive Analysis of the Intra-lymphatic Kinetics of LPs
Authors: Masaki Gomi, Yu Sakurai, Takaharu Okada, Naoya Miura, Hiroki Tanaka, Hidetaka Akita
Journal: Molecular Therapy (2020)

The sentinel lymph node (LN) is the first LN to which lymph fluid flows from tumor tissue. We identified the key parameters of liposomes (LPs) that affect their accumulation in regional (primary) LNs with minimum leakage to its connecting (secondary) LNs by a comprehensive analysis of the LN-to-LN trafficking of LPs with various surface charges and various sizes. We used a lymphatic flow-modified (LFM) mouse that allows for the chronological analysis of inguinal (primary) LN-to-axillary (secondary) LN at the body surface. As a result, the anionic medium-sized LPs (130 nm on average) exhibited the highest accumulation in the primary LNs. A mechanism-based analysis revealed that CD169-positive macrophages in LNs were the dominant cell population that captures anionic LPs. Sentinel LN imaging was also performed by the intratumoral injection of fluorescent medium-sized anionic LPs using a breast cancer orthotopic model. In comparison with the typically used contrast agent indocyanine green, the anionic LPs were detected in sentinel LNs with a high sensitivity. Additionally, the co-injection of hyaluronidase significantly improved the sensitivity of detection of the fluorescent LPs in sentinel LNs. In conclusion, medium-sized anionic LPs combined with hyaluronidase represents a potent strategy for investigating sentinel LNs. The sentinel lymph node (LN) is the first LN to which lymph fluid flows from tumor tissue. We identified the key parameters of liposomes (LPs) that affect their accumulation in regional (primary) LNs with minimum leakage to its connecting (secondary) LNs by a comprehensive analysis of the LN-to-LN trafficking of LPs with various surface charges and various sizes. We used a lymphatic flow-modified (LFM) mouse that allows for the chronological analysis of inguinal (primary) LN-to-axillary (secondary) LN at the body surface. As a result, the anionic medium-sized LPs (130 nm on average) exhibited the highest accumulation in the primary LNs. A mechanism-based analysis revealed that CD169-positive macrophages in LNs were the dominant cell population that captures anionic LPs. Sentinel LN imaging was also performed by the intratumoral injection of fluorescent medium-sized anionic LPs using a breast cancer orthotopic model. In comparison with the typically used contrast agent indocyanine green, the anionic LPs were detected in sentinel LNs with a high sensitivity. Additionally, the co-injection of hyaluronidase significantly improved the sensitivity of detection of the fluorescent LPs in sentinel LNs. In conclusion, medium-sized anionic LPs combined with hyaluronidase represents a potent strategy for investigating sentinel LNs.
Abstract 5833: Senescence is a central response to chemotherapy in ovarian cancer
Authors: Michael Skulimowski, Llilians Calvo-Gonzales, Shuofei Cheng, Isabelle Clément, Lise Portelance, Yu Zhan, Euridice Carmona, Manon de Ladurantaye, Julie Lafontaine, Kurosh Rahimi, Diane Provencher, Anne-Marie Mes-Masson, Francis Rodier
Journal: Cancer Research (2020)

Abstract High-grade serous ovarian carcinoma (HGSOC) commonly responds to initial therapy, but this response is rarely durable. Understanding the cell fate decisions taken by HGSOC cells in response to treatment could guide new therapeutic opportunities. Here, we find that more than 90% of tissue-derived primary HGSOC cultures, reflecting the original disease, retain the capacity to undergo stress-induced cellular senescence and primarily undergo therapy-induced senescence (TIS) in response to first-line carboplatin/taxol chemotherapy. HGSOC-TIS displays senescence-associated hallmarks, including a stable proliferation arrest, increased p16INK4A expression, persistent DNA damage, an inflammatory secretome, and senolytic sensitivity, suggesting new avenues for selective pharmacological manipulation of these cells. Comparison of pre- and post-chemotherapy patient HGSOC tissue samples revealed changes in physio-pathological senescence biomarkers supporting the occurrence of post-treatment TIS. Whether cell senescence induced by cancer therapy is beneficial or detrimental to treatment outcomes remains unknown. We find that patients with stronger TIS biomarkers in post-chemotherapy tissues have a more favorale 5-year survival, suggesting that the induction of senescence in HGSOC cells accounts, at least in part, for beneficial responses to treatment. Given that HGSOC cells almost universally retain the capacity to undergo senescence and that senescence appears beneficial in this context, senescence-centric therapeutic avenues should be further explored. Citation Format: Michael Skulimowski, Llilians Calvo-Gonzales, Shuofei Cheng, Isabelle Clément, Lise Portelance, Yu Zhan, Euridice Carmona, Manon de Ladurantaye, Julie Lafontaine, Kurosh Rahimi, Diane Provencher, Anne-Marie Mes-Masson, Francis Rodier. Senescence is a central response to chemotherapy in ovarian cancer [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 5833.