tbuckley/cabot-search huggingface dataset:
Abstract 5769: Modeling the tumor invasion front using 3D fluidic tumoroid culture of cancer cells
Authors: Koh Meng Aw Yong, Christopher Oliver, Megan Altemus, Zhi Fen Wu, Sofia Merajver
Journal: Cancer Research (2017)

Abstract To realize the promise of precision medicine, it is important to integrate phenotypic assessment of cell populations to genomic data. The analysis of invading leader cells at the tumor invasion front is of interest as they may be guided by a targetable molecular phenotype. However, there is a lack of suitable platforms on which to analyze the tumor invasion front. In this study, we have designed and constructed a fluidic device for long-term (several days to weeks) 3-dimensional tumoroid culture of diverse cancer cells. Using this device, we can recapitulate the tumor invasion front and at the same time quantify the invasive potential of different breast cancer cell line models. Analyses of the tumor invasion front indicated a region of higher proliferation and suggest that the leader cells possess a different molecular phenotype from the tumoroid mass. Interestingly, significant heterogeneity among invading cells was still observed, suggesting that there could be: 1) the presence of multiple subpopulations of invasive cells, each with a different clonal genetic signature; and/or 2) reversible phenotypic switching occurring among invading cells due to phenotypic plasticity. These results obtained using this innovative device highlight and present a promising solution to the challenges developing adequate therapeutics accounting for tumor phenotypic heterogeneity. There is potential for the device for use in personalized medicine at diagnosis, allowing for both the quantification of disease progression risk as well as the molecular characterization of the invasive subpopulations from patient samples and their response to tailored therapies. Citation Format: Koh Meng Aw Yong, Christopher Oliver, Megan Altemus, Zhi Fen Wu, Sofia Merajver. Modeling the tumor invasion front using 3D fluidic tumoroid culture of cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5769. doi:10.1158/1538-7445.AM2017-5769
Abstract 5402: Single cell sequencing of high grade serous ovarian cancer
Authors: Timothy K. Starr, Boris Winterhoff, Makayla Maile, Kenneth Beckman, Jerry Daniel, Melissa Geller, Martina Bazzaro, Molly Klein, Raffaele Hellweg, Juan Abrahante, Amit K. Mitra, Atilla Sebe, Sally A. Mullany
Journal: Cancer Research (2017)

Abstract We performed RNA sequencing of single cells derived from a high grade serous ovarian cancer (HGSOC) specimen to determine the extent of heterogeneity and to determine if it was feasible to identify cancer stem cells or gene expression signatures of chemo resistance. To perform RNA sequencing we enzymatically digested a fresh specimen from an HGSOC derived from the ovary. Immune cells were depleted by flow cytometry and single cell sequencing was performed using the Fluidigm C1 chip in tandem with Illumina HiSeq 2500 sequencing. Multiple bioinformatics tools were used to identify subgroups and activated pathways. Immunohistochemistry was performed on an adjacent tumor section to analyze markers of epithelium, stroma and stem cells. We found that gene expression patterns in single cells could be used to separate cells into stroma-like and epithelial-like groups. Gene set enrichment analysis identified proliferative genesets (oxidative phosphorylation and MYC targets) associated with the epithelial-like cells while epithelial-to-mesenchymal-transition (EMT) genes associated with the stroma-like cells. Neither group was significantly associated with genesets derived from chemo-resistant cells. Using known marker analysis, we could identify a small percentage of cells that expressed ovarian cancer stem cell markers and we could group cells into functional categories. Using four molecular subtypes established from large-scale bulk sequencing studies we show that single cells from a single patient are heterogeneous and each molecular subtype is represented. In conclusion, we show the feasibility of performing single cell sequencing on an epithelial ovarian cancer and reveal a heterogeneous population of cells. Expanding these findings to a larger cohort of patients could allow for identification of targetable sub-populations of cells that were previously undetectable in studies that use bulk samples to interrogate the transcriptome and genome of ovarian cancer patients. Citation Format: Timothy K. Starr, Boris Winterhoff, Makayla Maile, Kenneth Beckman, Jerry Daniel, Melissa Geller, Martina Bazzaro, Molly Klein, Raffaele Hellweg, Juan Abrahante, Amit K. Mitra, Atilla Sebe, Sally A. Mullany. Single cell sequencing of high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5402. doi:10.1158/1538-7445.AM2017-5402
Abstract 807: A novel immunodeficient rat for modeling human cancer
Authors: Fallon K. Noto, Angela Arey, Christopher McClain, Wei Zhang, Tseten Yeshi
Journal: Cancer Research (2017)

Abstract Animal models of human cancer offer the potential to study human tumor growth kinetics, genetic variance among human cancers, and provide in vivo platforms for drug efficacy testing. In particular, immunodeficient mouse models have been invaluable in modeling a wide range of human cancers. However, some cancer lines don’t grow well in the available mouse models or show variability in growth kinetics from mouse to mouse, making drug efficacy studies difficult due to differences in tumor size at the onset of treatment. These challenges are also seen in patient derived xenograft (PDX) models, in addition to long timeframes to obtain sufficient mice with PDX tissue growth for drug efficacy studies. Mice are also limited in tumor growth potential with regard to humane endpoints and small size also limits the volume of blood that can be collected for analysis. An immunodeficient rat model could provide a solution to some of these issues. A rat model would allow for larger tumor size, easier surgical manipulation, and greater volume of tissue and blood sampling for downstream analysis. In addition, large tumors from rats could be serially transplanted into mice for drug efficacy testing and could provide a large number of transplanted mice in a shorter period of time compared with serially transplanting from mouse to mouse. We have created an immunodeficient rat model with a functional deletion of the Rag2 gene. This knockout, created using spermatogonial stem cells, lacks mature B and T cells. To assess the capability of the Rag2 knockout rat to accept human xenografts, we transplanted 2 commercially available human cancer cell lines into our animals. The human REH acute lymphocytic leukemia cell line was transplanted via intravenous injection and the human glioblastoma cell line U87MG was transplanted subcutaneously. Both cell lines survived in the Rag2 knockout rat and resulted in the growth of tumors comprised of human cells. Studies are underway to characterize the Rag2 knockout rat’s ability to grow other human cell lines, including those that do not grow well in mice, and PDX tissues. Citation Format: Fallon K. Noto, Angela Arey, Christopher McClain, Wei Zhang, Tseten Yeshi. A novel immunodeficient rat for modeling human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 807. doi:10.1158/1538-7445.AM2017-807
Abstract 2847: Loss of heterozygosity (LOH) within the hypoxia inducible factor 3A (<i>HIF3A</i>) locus in liver metastasis (LM) from primary colorectal cancer (CRC)
Authors: Takahito Kitajima, Minoru Koi, Alexander Worix, John M. Carethers
Journal: Cancer Research (2017)

Abstract Background and Aims: HIF3α is a hypoxia-regulated transcription factor that represses the effects of HIF1α and HIF2α under hypoxia at transcriptional and posttranslational levels. We previously found that LOH at the HIF3A locus is frequent in LM (59%) and the expression of HIF3A protein is reduced in LM compared to primary CRC. At present, the smallest overlapping LOH (SOL-LOH) region has been mapped to the intron 8 of the HIF3A, spanning from 46,312,911 to 46,315,651 on chromosome 19 in LMs. This genomic region contains multiple FOXA1 binding sites embedded in the two DNase I hypersensitive sites (UCSC Genome Browser, https://genome.UCSC.edu). About 30% of the human population carries a deletion within our SOL-LOH region (1000 Genomes Consortium: esv3644527, Chr19: 46,314,109-46,315,478). In this study, we determined whether esv3644527 deletion affects on the expressions of HIF3A, HIF2A, HIF1A and their target genes under normoxic and hypoxic conditions. Methods: For LOH mapping, 75 resected LMs derived from primary CRC were analyzed for LOH using 8 polymorphic markers. We obtained three EBV-transformed B cell lines with heterozygous esv3644527 deletion and the one with the homozygous deletion from the Coriell Institute. The expression levels of 23 genes related to HIF pathways were determined by qRT-PCR. Results and Discussion: The expression levels of HIF3A mRNA were too low to compare among these B cell lines by qRT-PCR. However, the expression levels of HIF2A and its target gene, angiopoietin 2 (ANGPT2), are significantly elevated in B cells with a homozygous deletion compared to B cells with a heterozygous deletion under both normoxic and hypoxic conditions. These observations are compatible with the results obtained from a previous study where pulmonary endothelial cells from HIF3A-knockout mice expressed elevated levels of HIF2A and ANGPT2 (Kobayashi-S et al., Genes Cells, 2015, 20:224-241), suggesting that deletion of the FOXA1 sites present in this region may regulate the HIF3A expression. Conclusions: Our results show that about 60% of LMs exhibit LOH in the 2.7 Kb region surrounding intron 8 of the HIF3A locus. Deletion within this region may lead to upregulation of HIF2A and ANGPT2 by negatively regulating HIF3A expression. To prove our hypothesis, colon cancer cell lines with deleted FOXA1 sites will be assessed. Citation Format: Takahito Kitajima, Minoru Koi, Alexander Worix, John M. Carethers. Loss of heterozygosity (LOH) within the hypoxia inducible factor 3A (HIF3A) locus in liver metastasis (LM) from primary colorectal cancer (CRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2847. doi:10.1158/1538-7445.AM2017-2847
Conformation-switchable helical polypeptide eliciting selective pro-apoptotic activity for cancer therapy
Authors: DaeYong Lee, Soo-Hwan Lee, Youjin Na, Ilkoo Noh, JongHoon Ha, Jisang Yoo, Hyun Bae Bang, Jong Hyun Park, Ki Jun Jeong, Chae-Ok Yun, Yeu-Chun Kim
Journal: Journal of Controlled Release (2017)
Abstract 5701: Innovative approach for isolation of circulating cell-free DNA from liquid biopsies
Authors: Andrei Malykh, Vladimir Evtushenko
Journal: Cancer Research (2017)

Abstract We developed a new approach for isolation of circulating cell-free DNA (cfDNA) from liquid biopsies (plasma or serum). Our technology is based on using the proprietary bi-functional substance X (SubX®) that binds DNA under physiological conditions (e.g. directly in biological liquids), followed by adsorption of [DNA- SubX®] complex on a solid phase matrix. Since SubX®) captures DNA via phosphate groups it allows for elimination of bias related to both AT/CG content and DNA fragments length, thus improving extraction efficacy and accuracy of downstream applications. All currently available commercial kits are [silica-chaotropic salt]-based and exhibit bias for either short or long DNA fragments, as well as for the GC content. In addition, such systems require at least 4- fold dilution of starting volume of bio liquid with concentrated (~5.0 M) guanidine thiocyanate (GTC) to keep resulted GTC concentration at about least 3.0 M. Thus, already low concentrations of cfDNA are significantly reduced and may negatively influence extraction efficacy of low abundance DNA fragments. Since our method does not require chaotropic salt for DNA capture, no dilution of starting material (and thus cfDNA) takes place. DNA-binding matrix SubX® allows either scaling the procedure to either large volumes of starting material or extra low volumes and adaptation of the protocol for 96/384 well format. Separation of cfDNA from the bulk of proteins occurs in a single vortex-spin step without employing chaotropic agents thus speeding-up isolation procedure and reducing the costs. The whole procedure can be completed within an hour and cfDNA is eluted in small volume of TE buffer. Average DNA yield from 0.2 ml of double centrifuged blood plasma from normal donors, cancer and multiple sclerosis patients was 7.5±4.2 ng (n=96). Citation Format: Andrei Malykh, Vladimir Evtushenko. Innovative approach for isolation of circulating cell-free DNA from liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5701. doi:10.1158/1538-7445.AM2017-5701
Abstract 3686: Generation of an off-the-shelf cell-based platform (PDC-vac) for active antitumor immunotherapy
Authors: Joel Plumas, Kevin Lenogue, Alexandre Walencik, Jean-Paul Molens, Laurence Chaperot, Martin Pule
Journal: Cancer Research (2017)

Abstract The development of efficient vaccines for the treatment of cancers in combination or not with other agents such as checkpoint inhibitors represents a major public health issue but remains a challenge. A dozen of vaccine drug products is expected to be marketed in the next few years. In this context, off-the-shelf and potent platforms are more attractive than individualized vaccines that are tailored to each patient in many aspects. We have recently developed a new cell-based vaccine approach named PDC*vac (formerly GeniusVac). This cell-based vaccine was developed thanks to the establishment, from leukemic PDC, of unique human PDC line (PDC*line). We have previously shown the potential of peptide-loaded PDC*line to induce strong and fully functional HLA-A*02:01-restricted anti-tumor immunity in vitro and in vivo (Aspord et al, 2010, 2012). PDC*mel (GenusVac-Mel4), our first product is currently developed for the treatment of melanoma patients (NCT01863108). The high efficiency of PDC*vac renders the strategy very attractive for further clinical developments in active immunotherapy field. Our aim is to optimize PDC*vac technology by passing use peptides and render the vaccine easier to manufacture. We engineered our PDC*line using retrovirus to force the endogenous expression of one or more tumor or viral antigenic peptides or whole tumor/viral proteins (gp100, tyrosinase, Melan-A, Mage-A3, CMVpp65, flu, EBV) that broaden the panel of antigens presented. Data obtaining with different polypeptide and protein gene coding constructions and the expansion of multi-specific antigen-specific T-cells at the same time will be presented. Moreover, we will present how we succeed to obtain 100% of efficacy in antigen presentation by the PDC*line engineered to express tumor proteins or polyepitopes. We have validated the use of retrovirus constructs to create a new generation of an “off-the-shelf” cancer vaccines highly potent to stimulate antitumor-specific T-cells. Citation Format: Joel Plumas, Kevin Lenogue, Alexandre Walencik, Jean-Paul Molens, Laurence Chaperot, Martin Pule. Generation of an off-the-shelf cell-based platform (PDC-vac) for active antitumor immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3686. doi:10.1158/1538-7445.AM2017-3686
Abstract 1228: Nintedanib selectively inhibits the activation and tumor-promoting effects of fibroblasts from lung adenocarcinoma patients
Authors: Jordi Alcaraz, Marta Gabasa, Rafael Ikemori, Noemí Reguart
Journal: Cancer Research (2017)

Abstract Nintedanib (BIBF 1120) is a multikinase inhibitor recently approved to treat lung adenocarcinoma (ADC) patients based on the therapeutic benefits reported in clinical trials on ADC but not on squamous cell carcinoma (SCC), which are the two most common lung cancer subtypes. However, the biological processes underlying the selective anticancer function of nintedanib in ADC remain obscure. To shed light on this gap of knowledge, we examined the role of tumor-associated fibroblasts (TAFs) in the differential effects of nintedanib in ADC and SCC. Because TAFs are largely quiescent and activated in vivo, we focused on the antifibrotic effects of nintedanib on TAFs stimulated with TGF-β1, which is a potent fibroblast activator frequently upregulated in lung cancer. Nintedanib dose-dependently inhibited the TGF-β1-induced expression of activation markers in both ADC-TAFs and control fibroblasts derived from uninvolved parenchyma, whereas such inhibiton was very modest in SCC-TAFs, thereby suggesting that TAF activation is regulated by different mechanisms in ADC and SCC. Remarkably, nintedanib abrogated the stimulation of growth and invasion in a panel of carcinoma cell lines induced by secreted factors from activated TAFs in ADC but not SCC. These results reveal that nintedanib is a potent inhibitor of fibrosis and its associated tumor-promoting effects in ADC, and strongly suggest that the subnormal antifibrotic response of SCC-TAFs to nintedanib may underlie the lack of therapeutic benefits of this drug in SCC. Our findings also support that preclinical models based on carcinoma-TAF interactions may help unraveling the resistance mechanisms of SCC-TAFs to nintedanib and testing new combined therapies to further expand the therapeutic effects of this drug. Citation Format: Jordi Alcaraz, Marta Gabasa, Rafael Ikemori, Noemí Reguart. Nintedanib selectively inhibits the activation and tumor-promoting effects of fibroblasts from lung adenocarcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1228. doi:10.1158/1538-7445.AM2017-1228
08.01 Heat shock protein 90 is increased in muscle tissue and plasma in idiopathic inflammatory myopathies
Authors: Hana Storkanova, Olga Krystufkova, Martin Klein, Herman Mann, Lucia Vernerova, Maja Spiritovic, Josef Zamecnik, Karel Pavelka, Ladislav Senolt, Jiri Vencovsky, Michal Tomcik
Journal: Annals of the Rheumatic Diseases (2017)

<h3>Background</h3> Heat shock proteins (Hsps) are chaperones playing important roles in skeletal muscle physiology, adaptation to exercise or stress, and activation of inflammatory cells. The aim of our study was to assess Hsp90 expression in muscle biopsies and plasma of patients with idiopathic inflammatory myopathies (IIM) and to characterise its association with IIM-related features. <h3>Methods</h3> Total of 277 patients with IIM (198 females, 79 males; mean age 54.8; disease duration 4.1 years; dermatomyositis (DM, 104)/polymyositis (PM, 104)/cancer associated myositis (CAM, 42)/necrotizing myopathy (IMNM, 27)) and 100 age-/sex-matched healthy individuals were included in plasma analysis and 50 muscle biopsy samples were stained for Hsp90 (in PM, DM, IMNM, myodystrophy, myasthenia gravis, 10 each). Plasma Hsp90 was measured by ELISA (eBioscience, Vienna). CK, LD, ALT, AST and CRP were analysed by routine techniques and IIM-specific autoantibodies by in-line blot/immunoprecipitation. Data are presented as median. <h3>Results</h3> In muscle biopsies Hsp90 expression was higher in IIM than in myodystrophy (myasthenia gravis used as another control was negative). Increased Hsp90 was detected in perifascicular degenerating and/or regenerating fibres, inflammatory cells (DM, PM), and necrotic and regenerating fibres (IMNM). Plasma Hsp90 levels were increased in IIM patients compared to healthy controls (20.2 vs. 9.2 ng/ml, p&lt;0.0001). Hsp90 levels in all patients positively correlated with LD (r=0.551, p&lt;0.0001) and AST (r=0.372, p&lt;0.0001). Increased Hsp90 was associated with decreased MMT8 values (r=−0.136, p=0.029), in particular in proximal muscles. Hsp90 positively correlated with patient and doctor disease activity (r=0.222, p=0.0004; r=0.217, p=0.0005, respectively), pulmonary (r=0.222, p=0.0004) and muscle disease activity (r=0.146, p=0.018), MITAX (r=0.175, p=0.005) and MYOACT (r=0.159, p=0.012), and with MDI extent/severity (r=0.215, p=0.003; r=0.120, p=0.041, respectively). Higher Hsp90 was found in patients with interstitial lung disease, cardiac involvement and dysphagia (25.4 vs. 18.9, p=0.004; 27.5 vs. 19.3, p=0.004; 25.0 vs. 18.2 ng/ml, p=0.018, respectively). <h3>Conclusions</h3> We demonstrate increased Hsp90 expression in IIM muscle biopsy samples, specifically in inflammatory cells, degenerating, regenerating and/or necrotic fibres. Increased Hsp90 plasma levels in IIM patients are associated with disease activity and damage, and with the involvement of proximal skeletal muscles, heart and lungs. <h3>Acknowledgement</h3> Supported by AZV-16–33542A.