tbuckley/cabot-search huggingface dataset:
Abstract 1931: The first circulating tumor cell detection technique from frozen PBMCs
Authors: Heming Li, Izhar Singh Batth, Xueqing Xia, Frank J. Hsu, Neeta Somaiah, Keila Enitt Torres, Ruoyu Wang, Shulin Li
Journal: Cancer Research (2017)

Abstract Circulating tumor cells (CTCs) enter the vasculature or lymphatic system after shedding from the primary tumor. CTCs may serve as “seed” cells for tumor metastasis. The utility of CTCs in clinical application is not fully investigated, partly due to the necessity for fresh blood samples and the lack of CTC specific antibody. Of note, there is no CTC detection tool for pediatric tumors. To overcome these drawbacks, we developed a protocol for CTC capture from frozen peripheral blood mononuclear cells (PBMCs) based on the cell-surface vimentin (CSV) antibody 84-1. CSV is a unique marker compared to others such as EpCAM because it is only specific to tumor cells and has been demonstrated to be a viable target for isolation and enumeration of CTCs across tumor types. In this study, we report the first CTC isolation technology from frozen PBMCs of osteosarcoma patients using the CSV antibody 84-1. The CTCs captured using this new protocol were validated by single cell gene sequencing analysis and mesenchymal marker α-SMA staining. Moreover, spiking analysis was also performed to ensure the specificity and sensitivity of this unique CTC capture analysis. Linear regression analysis yielded a positive correlation between the number of detected sarcoma cells and the number of sarcoma cells spiked in both fresh and frozen PBMCs. In summary, our results demonstrate for the first time, a technology to specifically detect and isolate mesenchymal origin CTCs from frozen PBMCs. This technology can be easily expanded to other types of cancers including pediatric tumors because the antibody used is universal and CTC specific. Such a technology will boost the feasibility and utility of CTC-based diagnosis and therapeutic treatment monitoring in a centralized laboratory. Citation Format: Heming Li, Izhar Singh Batth, Xueqing Xia, Frank J. Hsu, Neeta Somaiah, Keila Enitt Torres, Ruoyu Wang, Shulin Li. The first circulating tumor cell detection technique from frozen PBMCs [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 1931. doi:10.1158/1538-7445.AM2017-1931
Abstract 5432: Characterization of metabolic fuel dependency in multidrug resistant breast cancer cells
Authors: Yoonseok Kam, Natalia Romero, Pamela Swain, Brian P. Dranka
Journal: Cancer Research (2017)

Abstract Multidrug resistance (MDR) is a common resistant mechanism of cancer cells to cytotoxic drugs in systemic therapy. MDR is characterized by increased expression of ATP-dependent drug exporting pumps which remove cytotoxic compounds from the cytosol. However, the mechanism whereby cancer cells rapidly respond to this increased ATP demand is not fully understood although the glycolytic nature of MDR phenotype has been evidenced repeatedly by previous reports. We thus hypothesized that flexibility and dependency on mitochondrial fuels would be altered in concert with the switch to glycolysis. In order to more accurate analyze glycolytic pathway, we newly developed an assay to improve glycolytic rate measurements by accounting for TCA-dependent CO2 contribution to extracellular acidification and to correlate Seahorse extracellular flux data with lactate production. In a comparison of glycolytic rates between MCF7 breast cancer cell line and its MDR variant MCF7/Dox using this new assay, we confirmed that in MCF7/Dox cells glycolysis rate under basal conditions is significantly increased compared to wild type cells. Furthermore, MCF7Dox presents a significant increase in compensatory glycolysis when mitochondrial ATP production is blocked. This metabolic profile switch is accompanied by a decreased dependency on glutamine to fuel mitochondrial respiration an increased tolerance of the MCF7/Dox cells to glutamine deprivation as compared to the MCF7 wild type. In contrast, dependency on glucose and fatty acids mitochondrial-oxidation was largely unchanged in MDR cells. Additionally, an increase in long chain fatty acid oxidation is observed when glucose and glutamine oxidation is blocked indicating that MDR cells has higher mitochondrial flexibility to compensate for inhibition of alternative fuels utilization although it preferentially uses glucose. Together these data demonstrate that acquisition of multidrug resistance in MCF7 cells fundamentally changes their metabolism from a glutamine-driven, oxidative phosphorylation dependent phenotype to a highly glycolytic and glucose-dependent phenotype. These findings have potential therapeutic relevance in the context of inhibition of specific mitochondrial fuel pathways to prevent therapy resistance. Citation Format: Yoonseok Kam, Natalia Romero, Pamela Swain, Brian P. Dranka. Characterization of metabolic fuel dependency in multidrug resistant breast 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 5432. doi:10.1158/1538-7445.AM2017-5432
Abstract 1828: Are callipers obsolute? A novel 3D scanning technology to measure subcutaneous tumor volume
Authors: Zena Wilson, Juan Delgado, Michael Davies, Rebecca Whiteley, Jennifer Hare, Amar Rahi, Stephen Marshall, Andrew Smith, Stephen Atkinson, Jarno Ralli, Adeala Zabair, Adeala Zabair, Jane Kendrew
Journal: Cancer Research (2017)

Abstract Most preclinical oncology studies (xenograft, PDX, GEMMS) involve monitoring tumour growth rates, measuring them with callipers, and calculating the volume. Volume is calculated from the width and the length to estimate a 3D volume and is directly used to assess treatment efficacy. Although this technique is useful, it is unable to accurately assess non-uniformly shaped or very small tumours and introduces a systematic bias by assuming that tumours present with spheroid shape. Furthermore callipers do not inform of the tumour condition, which is dependent upon a visual estimation. Here we describe the development and validation of a 3D scanner as an alternative method to callipers to monitor tumour progression in rodents. The resulting 3D scanner solution made up of hardware and software, has the potential to impact on the 3Rs guiding principles underpinning the humane use of animals in oncology research. The 3Rs benefits identified are primarily through reduction of animals via improved data accuracy allowing reduction in group sizes or the ability to include irregularly shaped tumours to test. In addition the scanner system described will make it possible to record tumour measurements in a rapid, minimally invasive, morphology-independent, and human-bias-free way, removing interoperator variability. This photo-based technique captures external symptoms of redness, paleness, ulceration of tumours, etc., which could ultimately be used to detect early toxicities of compounds or determine scales of animal welfare. We describe the development and early validation of the scanner system within our laboratories. Using the 3D scanner alongside tumour callipers to monitor tumour growth of Oncology tumour studies we demonstrated that we can accurately measure tumour size parameters (length, width and volume) in multiple mouse strains and across a range of tumour models. 3D scanning tumour data is comparable to tumour measures generated from tumour callipers If successful the introduction of this system to replace tumour callipers could have a large impact for groups running oncology in-vivo tumour studies. Citation Format: Zena Wilson, Juan Delgado, Michael Davies, Rebecca Whiteley, Jennifer Hare, Amar Rahi, Stephen Marshall, Andrew Smith, Stephen Atkinson, Jarno Ralli, Adeala Zabair, Adeala Zabair, Jane Kendrew. Are callipers obsolute? A novel 3D scanning technology to measure subcutaneous tumor volume [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 1828. doi:10.1158/1538-7445.AM2017-1828
Abstract 1407: Translational regulation of RPA2 via IRES by UNR and eIF3a
Authors: Jia-Jia Cui, Lei-Yun Wang, Ji-Ye Yin
Journal: Cancer Research (2017)

Abstract Purpose: Translation is a critical step in the process of genetic information expression. Internal ribosome entry site (IRES) element is a RNA sequence with a complex structure, which plays an important role in cap independent translation regulation. The activation of RPA2 IRES element can cause its abnormal expression and finally effects DNA repair pathway. We conducted series of assays to explore the mechanism of translation initiation regulation of RPA2 via IRES by UNR and eIF3a Methods: Biotin pull down assay was taken to investigate the physical interaction between RPA2 IRES and UNR. UNR was knocked down and overexpressed in H1299, A549 and SK-MES cell lines. Western blot and real-time PCR were used to detect protein level and mRNA level respectively. For interaction of eIF3a with UNR, CO-IP assay and co-localization assay were conducted. And GST pull down assay was carried out to further identify their exact binding domains. RPA2 IRES-interacting domains of UNR and eIF3a were explored with EMSA assay. Results: UNR protein could directly bind to RPA2 IRES as well as to eIF3a, and UNR regulated the protein expression of RPA2 in H1299, A549 and SK-MES cells, while the mRNA level of RPA2 remained no change. UNR interacted with the first domain of eIF3a and with RPA2 IRES via its own first domain. However, we have not found a clue for the direct interaction of eIF3a with RPA2 IRES yet. Conclusion: UNR cooperated with eIF3a to regulate the RPA2 IRES activity and hence to regulate the RPA2 protein expression. This might be a regulation mechanism of cellular internal ribosomal entry site affecting translation initiation, the rate-limiting step of translation. Citation Format: Jia-Jia Cui, Lei-Yun Wang, Ji-Ye Yin. Translational regulation of RPA2 via IRES by UNR and eIF3a [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 1407. doi:10.1158/1538-7445.AM2017-1407
Abstract 1928: The lung microenvironment promotes stem-like phenotype and behavior of breast cancer cells
Authors: Ashkan Sadri, Alison L. Allan
Journal: Cancer Research (2017)

Abstract Ninety percent of breast cancer-related mortalities result from metastasis, a process whereby the primary tumour disseminates and targets distant secondary organs. We have previously demonstrated that stem-like breast cancer cells expressing high levels of aldehyde dehydrogenase (ALDH) and CD44 are critical for metastasis. These ALDHhiCD44+ cells preferentially migrate and/or metastasize to the lung and bone microenvironments, where secondary tumours can severely impede organ function. However, the specific role of the lung and bone marrow (BM) microenvironments in supporting and/or promoting metastasis of ALDHhiCD44+ cells remains poorly understood, and this is the purpose of the current study. Using a 2D ex vivo model, lung and bone marrow (BM) conditioned media (CM) enriched in tissue-specific soluble proteins were generated from murine tissues and utilized in cell culture to assess their ability to influence the stem-like phenotype and behavior of MDA-MB-468 human breast cancer cells. Exposure to lung-CM promoted the generation of a viable, non-adherent (“floating”) breast cancer cell subpopulation that was not observed in response to BM-CM or basal media (p&amp;lt;0.05). Phenotypic analysis by flow cytometry and gene expression analysis by RT-qPCR revealed notable differences in ALDH/CD44 phenotype in whole cell populations, adherent subpopulations, and/or non-adherent subpopulations in response to 72 hour exposure to lung-CM relative to basal media. In particular, the non-adherent breast cancer cell subpopulation generated in response to lung-CM demonstrated increased CD44 and ALDH1A3 gene expression and decreased ALDH1A1 gene expression relative to the adherent subpopulation (p&amp;lt;0.05). No significant phenotypic or gene expression differences were observed in MDA-MB-468 breast cancer cells in response to BM-CM. Taken together with our previous studies, these findings suggest that while both the lung and bone microenvironments support breast cancer cells with a pre-existing ALDHhiCD44+ phenotype, the lung microenvironment may additionally help to even further promote stem-like phenotype and behavior in the secondary metastatic site. Ongoing studies are aimed at elucidating the mechanisms by which aggressive ALDHhiCD44+ breast cancer cells interact with and/or are influenced by the lung microenvironment during metastatic progression. Citation Format: Ashkan Sadri, Alison L. Allan. The lung microenvironment promotes stem-like phenotype and behavior of breast 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 1928. doi:10.1158/1538-7445.AM2017-1928
Abstract 1985:Tbk1loss in pancreatic cancer leads to changes in epithelial plasticity
Authors: Victoria Haley Burton, Rolf A. Brekken, Melissa Gross, Alberto Bremauntz
Journal: Cancer Research (2017)

Abstract Effective therapies are needed to enhance the long-term survival of patients with pancreatic ductal adenocarcinoma (PDA), which is the fourth leading cause of cancer-related deaths in the United States and eighth worldwide. Initial stages of PDA are commonly characterized by an activating mutation in K-RAS, yet direct inhibition of K-RAS through pharmacological means remains a challenge. Higher levels of TANK Binding Kinase 1 (TBK1) mRNA, a critical downstream effector of mutant active K-RAS in lung cancer, are associated with poorer overall survival in a cohort of human PDA patients. We hypothesize that TBK1 is also an effective mediator of K-RAS driven pancreatic cancer. Here we report that TBK1 is expressed and more active in human PDA cell lines relative to immortalized pancreatic epithelial lines (HPNE) and fibroblasts. We found that human PDA cell lines are sensitive to a small molecule inhibitor of TBK1 in the low micromolar range. Further mice engineered to express a mutant kinase dead form of TBK1 (Tbk1Δ/Δ) are viable and fertile yet display smaller tumors at early time points in a genetically engineered mouse model of PDA. Interestingly, tumors from Tbk1Δ/Δ: PDA mice are more epithelial in gene expression and show significantly less collagen deposition compared to Tbk1+/+: PDA tumors. Additionally, cell lines isolated from Tbk1Δ/Δ: PDA tumors are more epithelial in morphology and less migratory and invasive relative to Tbk1+/+: PDA cell lines. Current work is focused on delineating the functional contribution of TBK1 to tumor cell motility in vivo as well as mechanistic understanding of the epithelial phenotype in Tbk1Δ/Δ: PDA tumors. These results will further our understanding of Ras signaling in pancreatic cancer and are critical for exploring a new avenue of targeted therapy. Citation Format: Victoria Haley Burton, Rolf A. Brekken, Melissa Gross, Alberto Bremauntz. Tbk1 loss in pancreatic cancer leads to changes in epithelial plasticity [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 1985. doi:10.1158/1538-7445.AM2017-1985
Abstract 303: Oncogenic activity of amplified miniature chromosome maintenance 8 in human malignancies
Authors: Jian-Hua Luo, Dong-Mei He, Baoguo Ren, Yan Yu
Journal: Cancer Research (2017)

Abstract Miniature chromosome maintenance (MCM) proteins play critical roles in DNA replication licensing, initiation and elongation. MCM8, one of the MCM proteins playing critical role in DNA repairing and recombination, was found to have over-expression and increased DNA copy number in a variety of human malignancies. The gain of MCM8 is associated with aggressive clinical features of several human cancers. Increased expression of MCM8 in prostate cancer is associated with cancer recurrence. Forced expression of MCM8 in RWPE1 cells, the immortalized but non-transformed prostate epithelial cell line, exhibited fast cell growth and transformation, while knocked down of MCM8 in PC3, DU145 and LNCaP cells induced cell growth arrest, and decreased tumor volumes and mortality of severe combined immunodeficiency mice xenografted with PC3 and DU145 cells. MCM8 bound cyclin D1 and activated Rb protein phosphorylation by cyclin-dependent kinase 4 in vitro and in vivo. The cyclin D1/MCM8 interaction is required for Rb phosphorylation and for S phase entry in cancer cells. As a result, our study showed that copy number increase and overexpression of MCM8 may play critical roles in human cancer development. Note: This abstract was not presented at the meeting. Citation Format: Jian-Hua Luo, Dong-Mei He, Baoguo Ren, Yan Yu. Oncogenic activity of amplified miniature chromosome maintenance 8 in human malignancies [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 303. doi:10.1158/1538-7445.AM2017-303
Abstract 4443: SPARC overexpression alters microRNA expression profiles involved in tumor progression
Authors: Bhavesh K. Ahir, Sajani Lakka
Journal: Cancer Research (2017)

Abstract Medulloblastoma is the most common of malignant brain tumor in children. SPARC (secreted protein acidic and rich in cysteine), a multicellular non-structural glycoprotein is known to be involved in multiple processes in various cancers. Previously, we reported that SPARC expression significantly impairs medulloblastoma tumor growth in vivo and alters chemo sensitivity. MicroRNAs are a class of post-transcriptional gene regulators with critical functions in tumor progression. In addition, they also play role in regulation of vital genes that control mechanisms of chemo-resistance. Herein, we assessed microRNA (miRNA) profiling to identify the functional network and biological pathways altered in SPARC-overexpressed medulloblastoma cells. A total of 27 differentially expressed miRNAs were identified between the control and SPARC-overexpressed samples. Potential messenger RNA (mRNA) targets of the differentially expressed miRNA were identified using Ingenuity Pathway Analysis (IPA). Network-based functional analyses were performed on the available human protein interaction and miRNA-gene association data to highlight versatile miRNAs among the significantly deregulated miRNAs using the IPA, and the biological pathway analysis using the PANTHER web-based tool. We identified six miRNAs (miR-125b1*, miR-146a-5p, miR-181a-5p, miR-204-5p, miR-219-5p and miR-509-3p) which are differentially regulated with SPARC expression in medulloblastoma cells. Furthermore, pathway enrichment analysis outline that these six microRNAs mainly belong to biological processes related to cancer related signaling pathways. Collectively, these results suggest that a perturbed expression for these six miRNAs and their complex regulatory loops contribute to tumor suppressive effects in SPARC overexpressed medulloblastoma cells. Citation Format: Bhavesh K. Ahir, Sajani Lakka. SPARC overexpression alters microRNA expression profiles involved in tumor progression [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 4443. doi:10.1158/1538-7445.AM2017-4443
Abstract 3834: Tracking CAD-ALK gene translocation in urine and plasma of a colorectal cancer patient treated with ALK blockade
Authors: Giulia Siravegna, Andrea Sartore-Bianchi, Benedetta Mussolin, Laura Palmieri, Federica Tosi, Andrea Cassingena, Luca Novara, Michela Buscarino, Giorgio Corti, Giovanni Crisafulli, Alice Bartolini, Mark Erlander, Federica Di Nicolantonio, Salvatore Siena, Alberto Bardelli
Journal: Cancer Research (2017)

Abstract A metastatic colorectal cancer (mCRC) patient carrying CAD-ALK translocation achieved partial response to an experimental ALK inhibitor and then progressed after 5 months. We studied whether urine cell-free, trans-renal DNA (tr-DNA) could be used to monitor tumor burden and patient’s response. A NGS panel was developed to interrogate 52 common cancer gene rearrangements and 14 frequently mutated genes in cancer patients. A TP53 p.R248W mutation and the CAD-ALK genomic breakpoint (rearrangement) were identified in the tumor tissue and matched plasma circulating tumor DNA (ctDNA) Urine samples were longitudinally obtained from the patient during ALK inhibitor treatment in parallel with blood. To detect the CAD-ALK translocation in urine tr-DNA we designed ultra-short (51 bp amplicon) primer pairs spanning the genomic breakpoint as a unique tumor marker. This approach allowed the non-invasive monitoring of the gene fusion in urine with amounts paralleling tumor burden. Of note, CAD-ALK gene fusion was apparent in urine tr-DNA before radiological confirmation of disease progression. The same strategy was applied to plasma ctDNA and the results were compared. To detect point mutations in urine tr-DNA, we exploited a peptide nucleic acids (PNA)-CLAMP PCR coupled with droplet digital PCR (ddPCR) analysis to specifically suppress amplification of wild-type DNA fragments. Custom PNA probes were designed for TP53 codon 248, and a ddPCR assay was optimized to detect the TP53 p.R248W mutation, which was then identified in all urine tr-DNA samples, with absolute copies correlating with tumor burden throughout ALK inhibitor treatment. In conclusion, we find that urine tr-DNA can be exploited to non-invasively monitor tumor burden by detecting tumor-specific gene fusions as well as point mutations. Citation Format: Giulia Siravegna, Andrea Sartore-Bianchi, Benedetta Mussolin, Laura Palmieri, Federica Tosi, Andrea Cassingena, Luca Novara, Michela Buscarino, Giorgio Corti, Giovanni Crisafulli, Alice Bartolini, Mark Erlander, Federica Di Nicolantonio, Salvatore Siena, Alberto Bardelli. Tracking CAD-ALK gene translocation in urine and plasma of a colorectal cancer patient treated with ALK blockade [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 3834. doi:10.1158/1538-7445.AM2017-3834