bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1576: Clonal diversity revealed by morphoproteomic and copy number profiles of single prostate cancer cells at diagnosis
Authors: Malihi Paymaneh D. , Morikado Michael , Welter Lisa , Carlsson Anders , Velasco Carmen Ruiz , Kolatkar Anand , Rodriguez-Lee Mariam , Hicks James , Kuhn Peter , Liu Sandy T. , Miller Eric T. , Cadaneanu Radu M. , Knudsen Beatrice S. , Lewis Michael S. , Garraway Isla P. 
Published: August 2018

Abstract
Tumor heterogeneity is prevalent in both treatment-naïve and end-stage metastatic castration-resistant prostate cancer (PCa), and may contribute to the broad range of clinical presentation, treatment response, and disease progression. To characterize molecular heterogeneity associated with de novo metastatic PCa, multiplatform single cell profiling was performed using High Definition Single Cell Analysis (HD-SCA). HD-SCA enabled morphoproteomic and morphogenomic profiling of single cells from touch preparations of tissue cores (prostate and bone marrow biopsies) as well as liquid samples (peripheral blood and bone marrow aspirate). Morphology, nuclear features, copy number alterations, and protein expression were analyzed. Tumor cells isolated from prostate tissue touch preparation (PTTP) and bone marrow touch preparation (BMTP) as well as metastatic tumor cells (MTCs) isolated from bone marrow aspirate were characterized by morphology and cytokeratin expression. Although peripheral blood was examined, circulating tumor cells were not definitively observed. Targeted proteomics of PTTP, BMTP, and MTCs revealed cell lineage and luminal prostate epithelial differentiation associated with PCa, including co-expression of EpCAM, PSA, and PSMA. Androgen receptor expression was highest in MTCs. Hallmark PCa copy number alterations, including PTEN and ETV6 deletions and NCOA2 amplification, were observed in cells within the primary tumor and bone marrow biopsy samples. Genomic landscape of MTCs revealed to be a mix of both primary and bone metastatic tissue. This multiplatform analysis of single cells reveals several clonal origins of metastatic PCa in a newly diagnosed, untreated patient with polymetastatic disease. This case demonstrates that real-time molecular profiling of cells collected through prostate and bone marrow biopsies is feasible and has the potential to elucidate the origin and evolution of metastatic tumor cells. Altogether, biological and genomic data obtained through longitudinal biopsies can be used to reveal the properties of PCa and can impact clinical management.
Citation Format: Paymaneh D. Malihi, Michael Morikado, Lisa Welter, Anders Carlsson, Carmen Ruiz Velasco, Anand Kolatkar, Mariam Rodriguez-Lee, James Hicks, Peter Kuhn, Sandy T. Liu, Eric T. Miller, Radu M. Cadaneanu, Beatrice S. Knudsen, Michael S. Lewis, Isla P. Garraway. Clonal diversity revealed by morphoproteomic and copy number profiles of single prostate cancer cells at diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1576.
Abstract 1579: IMI's CANCER-ID: Implications of liquid biopsy technology standardization for its clinical use
Authors: Pantel Klaus , Terstappen Leon W. , Baggiani Barbara , Krahn Thomas , Panabières Catherine , Lianidou Evi , Naume Bjørn , Farace Françoise , Schlange Thomas 
Published: August 2018

Abstract
Liquid biopsies offer the opportunity to improve the diagnosis and timely adaption of therapy options to the progression and heterogeneity of cancer. The CANCER-ID (www.cancer-id.eu) consortium was established in early 2015 as part of the Innovative Medicines Initiative (IMI) and has currently 37 partners from 14 countries, including the USA and Singapore. The goal of the CANCER-ID program is to foster implementation of liquid biopsy technologies in multicenter clinical studies and the potential regulatory approval of devices or protocols in the field. Within the project best practice protocols for using technologies aiming at the enrichment, isolation and analysis of Circulating Tumor Cells (CTCs), circulating free tumor DNA (ctDNA) and microRNAs (miRNAs) are being developed and benchmarking data for the performance of different technologies are collected. To this end defined standards for the different biomarker classes are crucial and their introduction and design is being supported by CANCER-ID. Another integral part of our work is the development of integrated workflows from patient sample collection, pre-analytical sample handling, sample and bioinformatics analyses down to the actionable information guiding patient selection and personalized treatment.
CANCER-ID partners are currently planning clinical studies to assess the clinical utility of analyzing PD-L1 expression on CTCs in their core indications Non-Small Cell Lung Cancer (NSCLC) and metastatic breast cancer. While the benefit of immune checkpoint inhibition has been impressively demonstrated in NSCLC, most advanced breast cancer patients do not benefit from targeting PD-1 with the exception of the triple-negative disease type. The liquid biopsy workflows established by the CANCER-ID consortium will be used to correlate CTC PD-L1 expression in patients treated with PD-1 blocking antibodies with clinical response and in parallel perform mutational load analysis in blood. The aim will be to attempt to develop a liquid biopsy-based rationale for patient selection guiding effective immune checkpoint therapies. The study plan and current status of this multicenter effort will be presented.
This work is supported by IMI JU & EFPIA (grand no. 115749, CANCER-ID). Samples from patients and healthy volunteers, respectively, were collected under signed informed consent.
Citation Format: Klaus Pantel, Leon W. Terstappen, Barbara Baggiani, Thomas Krahn, Catherine Panabières, Evi Lianidou, Bjørn Naume, Françoise Farace, Thomas Schlange. IMI's CANCER-ID: Implications of liquid biopsy technology standardization for its clinical use [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1579.
Abstract 1583: Clinical significance of PIK3CA, AKT1, and ESR1 mutation in plasma cell-free DNA from estrogen receptor-positive breast cancer patients
Authors: Takeshita Takashi , Tomiguchi Mai , Sueta Aiko , Yamamoto-Ibusuki Mutsuko , Yamamoto Yutaka , Iwase Hirotaka 
Published: August 2018

Abstract
Background: In endocrine therapy (ET) resistance mechanisms, PI3K / AKT pathway abnormality and ESR1 mutation are drawing attention. In recent large-scale clinical trials, it was revealed that identification of these genetic abnormalities in cell-free DNA (cfDNA) was useful for rapid assessment and monitoring of the therapeutic effect in ET-resistant breast cancer (BC). However, the frequency of them per treatment line and its clinical significance have not been verified. Here we studied the clinical significance of PIK3CA, AKT1, and ESR1 mutation according to the treatment line in estrogen receptor (ER)-positive BC.
METHODS: From 2003 to 2017, a total of 251 plasma specimens were collected from 128 patients with ER positive BC treated at our hospital. The breakdown were 133 plasma samples from 73 primary BC (PBC) patients and 118 plasma samples from 68 metastatic BC (MBC) patients. CfDNA was extracted from 500 μL of plasma. The hotspot of PIK3CA, AKT1, and ESR1 mutation in plasma cfDNA was verified using multiplex digital PCR method.
RESULTS: In the PBC patient group, PIK3CA mutation was recognized at 15.1%, AKT1 mutation at 1.4%, and ESR1 mutation at 2.7%. The presence or absence of PIK3CA mutation did not affect clinical outcome. In the MBC patient group, the frequency of PIK3CA mutation increased from 16% to 32% and that of ESR1 mutation increased from 23% to 41.9% as the treatment line advanced. Furthermore, we examined the time to treatment failure (TTF) by dividing into early treatment line and late treatment line. In the early treatment group, patients with PIK3CA mutation had significantly shorter TTF (P = 0.035). However, the presence or absence of ESR1 mutation did not affect TTF. On the other hand, in the late treatment group, patients with ESR1 mutation had significantly shorter TTF (P = 0.048). However, the presence or absence of PIK3CA mutation did not affect TTF. Since AKT1 mutation was rare in both PBC patients and MBC patients, its clinical significance was unknown.
CONCLUSION: We showed clinical significance of verification of PIK3CA, AKT1, and ESR1 mutation in cfDNA according to treatment line in ER positive BC patients.
Citation Format: Takashi Takeshita, Mai Tomiguchi, Aiko Sueta, Mutsuko Yamamoto-Ibusuki, Yutaka Yamamoto, Hirotaka Iwase. Clinical significance of PIK3CA, AKT1, and ESR1 mutation in plasma cell-free DNA from estrogen receptor-positive breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1583.
Abstract 1587: Detection of PD-L1 and PD-1 positive circulating tumor cells (CTCs) in non-small cell lung cancer (NSCLC) patients treated with nivolumab
Authors: Kallergi Galatea , Koutsopoulos Anastasios , Lagoudaki Eleni , Agouraki Despoina , Vetsika Eleni-Kiriaki , Voumvouraki Anastasia , Martin Stuart S. , Koinis Filippos , Stournaras Christos , Georgoulias Vassilis , Kotsakis Athanasios 
Published: August 2018

Abstract
Introduction: Circulating tumor cells (CTCs) are considered as a “liquid biopsy” that allows the assessment of tumor changes over time. Tumor cells may escape from the immune system through the activation of PD-1/PD-L1 axis. Targeting these molecules with monoclonal antibodies has shown encouraging results at many types of cancers, including NSCLC. In the current study we investigated the expression of PD-1/PD-L1 molecules on the CTCs isolated from NSCLC patients treated with Nivolumab.
Methods: CTCs were isolated based on their size using the ISET platform from 27 patients before treatment, after 1 cycle and 3 cycles. CTCs were detected with Giemsa staining and immunofluorescence (IF) experiments, using either pancytokeratin (A45-B/B3) (CK7)/PD-1/CD45 or (A45-B/B3)(CK7)/PD-L1/CD45 combination of antibodies and analysis with the ARIOL system. Spiking experiments using the NSCLC cell lines: H460, H1299, HCC827 and SKMES in normal blood were used to evaluate the detection method.
Results: Giemsa evaluation in Nivolumab-treated patients at baseline (25 evaluable samples), after the 1st (9 evaluable samples) and the 3rd (8 evaluable patients) cycle of treatment showed that CTCs could be detected in 48% (12/25), 33.3% (3/9) and 50% (4/8) of patients, respectively. IF could also reveal the presence of CK-positive cells in 44.4% (12/27), 22% (2/9) and 75% (6/8) patients, respectively. PD-1 (+) CTCs were detected in 33.3% (4/12) of patients at baseline, in, 0% after the 1 and 16.7% (1/6) of patients after the 3rd cycle. The same percentages were identified for PD-L1 expression in the same cohort of patients. The expression of PD-1 at baseline was associated with poorer OS (p=0.022) and PFS (p=0.011), while the expression of PD-L1 was associated with shorter PFS (p=0.011). Multivariate analysis revealed that the presence of CK-positive cells is an independent prognostic factor for OS (p=0.028)
Conclusion: Nivolumab reduced the number of PD-1- and PD-L1-expressing CTCs in advanced NSCLC patients. Furthermore the expression of both markers at baseline is associated with the clinical outcome.
Citation Format: Galatea Kallergi, Anastasios Koutsopoulos, Eleni Lagoudaki, Despoina Agouraki, Eleni-Kiriaki Vetsika, Anastasia Voumvouraki, Stuart S. Martin, Filippos Koinis, Christos Stournaras, Vassilis Georgoulias, Athanasios Kotsakis. Detection of PD-L1 and PD-1 positive circulating tumor cells (CTCs) in non-small cell lung cancer (NSCLC) patients treated with nivolumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1587.
Abstract 16: A wide-spectrum analysis of angiogenesis-related factors in ovarian cancer reveals a signature potentially for prognosis and therapeutic targeting
Authors: Kuo Chih-Lin 
Published: August 2018

Abstract
Ovarian cancer is the first leading cause of death from woman gynecological malignancies worldwide. It is typically diagnosed at a late stage with a poor 5-year survival rate less than 30%. In the progress of ovarian cancer, angiogenesis-related factors not only induce neovascularization for supporting tumor growth but also accelerate ascites production, which helps the peritoneal metastasis and is associated with poor disease prognosis. Therefore, angiogenesis-related factors are thought to be particularly crucial in the persistence of ovarian cancer and have become key targets in clinical research. Although the expression of some angiogenesis-related factors in ovarian cancer has been sporadically reported, analysis of the profile of angiogenesis-related factors in a whole spectrum manner is needed to evaluate their cruciality and relationship. In our study, totally 104 angiogenesis-related factors were used to analyze their transcriptional changes along with ovarian cancer progression in the data of 601 patients obtained from TCGA datasets (AgilentG4502A_07_2 and AgilentG4502A_07_3). 33 candidates with significantly differential expression (p &lt; 0.05) between normal and any stage were initially revealed. To narrow down the candidates, these factors were ranked by the significance of expressional changes between normal and all various stages and 13 factors with the most significant difference (p &lt; 0.0001) were selected and their fold changes were further shown in a heat-map manner; these included MMP9, VEGFA, CXCL10, TIMP2, AGRP, MMP8, IGFBP-1, ENG, TEK, FGF7, CSF3, ANGPTL5, ANGPTL7. Moreover, Ingenuity Pathway Analysis (IPA) and DAVID database analysis were applied to analyze their functional categories in angiogenesis. In conclusion, we developed a signature of angiogenesis-related factors for patients with ovarian cancer. With appropriate validation, it can be applied as a prognostic index or used to select certain candidates for developing targeted therapies.
Citation Format: Chih-Lin Kuo. A wide-spectrum analysis of angiogenesis-related factors in ovarian cancer reveals a signature potentially for prognosis and therapeutic targeting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 16.
Abstract 1602: Urine cell-free DNA as early biomarker in immunotherapy response in NSCLC
Authors: Wekken Anthonie J. van der , Elst Arja ter , Miedema Anneke , Hiltermann Thijo J. , Goen Harry J. , Schuuring Ed 
Published: August 2018

Abstract
Introduction: Immunotherapy shows a durable tumor response in approximately 20% of advanced NSCLC patients. Imaging by CT is used to evaluate tumor response. PD-L1 immunohistochemistry is generally used to predict survival advantages, however with low predictive value. Therefore, it is important that alternative predictive biomarkers are investigated. Minimal invasive techniques may be a solution. The role of circulating cell-free DNA (cfDNA) was found to be an early biomarker for tumor response in KRAS positive Non-Small Cell Lung Cancer (NSCLC) patients treated with immunotherapy (N=6). In this study we will determine the role of urine cell-free DNA (ucfDNA) in an extended cohort. The non-invasive method of urine collection makes it an excellent source for mutation detection and follow-up.
Methods: In an ongoing study KRAS positive patients treated with immunotherapy, are being tested for cfDNA at baseline (before treatment, 1, 2, 4, 6 and thereafter every 12 weeks until disease progression) with a KRAS G12-13 or Q61H digital droplet PCR (ddPCR) screening assay (BioRad). In a pilot study, urine from these patients is collected in a tube with 5 ml of STRECK reagent at baseline and at 6 weeks.
Results: In 16/27 patients with KRAS positive advanced NSCLC, the mutation was detected in plasma at baseline and subsequent evaluation time points. Urine cfDNA as a predictive marker seems promising and results will be reported and presented at the AACR meeting.
Conclusion: Among patients with advanced NSCLC treated with immunotherapy plasma and urine cfDNA are collected and will be presented as non-invasive early biomarker for tumor response evaluation.
Citation Format: Anthonie J. van der Wekken, Arja ter Elst, Anneke Miedema, Thijo J. Hiltermann, Harry J. Goen, Ed Schuuring. Urine cell-free DNA as early biomarker in immunotherapy response in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1602.
Abstract 1604: Highly sensitive digital detection of circulating DNA cancer mutations using synthetic genome standards
Authors: Wood-Bouwens Christina M. , St.Onge Robert P. , Ji Hanlee P. 
Published: August 2018

Abstract
With the emergence of precision cancer medicine, there is an increasing need for new longitudinal diagnostic tests to evaluate patients at the initial diagnosis, during treatment, and for routine monitoring. As a general solution, we developed a single-color digital PCR assay technology that detects and quantifies circulating DNA cancer mutations collected from the plasma of cancer patients. The assay has a sensitivity of 0.1% mutation allelic fraction and can be designed for nearly any cancer mutation. In addition, this assay demonstrates design flexibility, low cost, and robust performance, making it a powerful approach for longitudinal monitoring of cancer patients during treatment.
Positive controls are a critical component for highly sensitive detection of circulating DNA cancer mutations. However, there are minimal resources for providing standard curves. Commercially available cancer cell lines cover a very limited number of cancer mutations. Amplicons or oligonucleotides pose a high risk of contamination due to the sheer number of molecules generated, an important consideration when working with rare molecular species such as cell-free DNA.
To address this challenge, we developed a novel technology that enables a single copy of synthetic human genome sequence to be introduced into a non-mammalian eukaryotic genome. The system highly-scalable and capable of producing thousands of unique clones which can be archived for future use, accessed individually, or combined to create customizable target pools on-demand. These custom designed synthetic positive controls are therefore readily renewable, require no amplification to obtain, and most importantly allow precise control over the number of molar equivalents of each target in a reaction. Using these synthetic controls, we simulate low mutation-allele fractions to validate the specificity and sensitivity of our assay.
As a proof of concept, we have designed approximately 400 cancer mutation controls in driver genes such as KRAS and EGFR, and developed a design process to generate multiplex digital PCR assays targeting these driver genes. We will validate the digital PCR assays with standard bulk PCR and will validate the template by comparing to results generated using cancer cell line derived DNA. In the era of circulating DNA diagnostics, these genome engineered synthetic controls meet a critical need for reliable and customizable positive controls.
Citation Format: Christina M. Wood-Bouwens, Robert P. St.Onge, Hanlee P. Ji. Highly sensitive digital detection of circulating DNA cancer mutations using synthetic genome standards [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1604.
Abstract 162: UBE2T: A molecular regulator for cancer stemness and drug resistance in hepatocellular carcinoma
Authors: Ho Pui Yu , Lee Kin Wah 
Published: August 2018

Abstract
Hepatocellular carcinoma (HCC) is one of the common cancers worldwide. Poor prognosis of HCC patients is attributed to high frequency of tumor relapse and chemoresistant nature of this disease. Increasing evidence showed the critical role of cancer stem cells (CSCs) on tumor relapse and therapeutic resistance. Since normal stem cells and CSCs share high similarity, we would like to identify the molecules/pathways crucial in liver CSCs by determining what molecules involved in normal liver stem cells during liver regeneration. Comparison of expression profiles between early regenerating liver and intact liver revealed the upregulation of DNA Damage Response pathways in the self-renewing liver, in which Ubiquitin Conjugating Enzyme E2 T (UBE2T) was the most significantly upregulated. This, together with the publicly available dataset (GSE5975) shows upregulation of UBE2T in EpCAM-enriched liver CSC populations, suggest the potential role of UBE2T on regulation of cancer stemness. By qPCR analysis UBE2T mRNA level was overexpressed in 91% of the clinical HCC specimens (n=56) and associated with aggressive tumor behavior and poorer patients' survival. The overexpression of UBE2T was further confirmed by western blot and immunohistochemical analysis. By lentiviral based knock-down approach, we demonstrated the role of UBE2T in regulation of liver CSC properties, including self-renewal, tumorigenicity, drug resistance and expression of liver CSC markers. In orthotopic HCC model, UBE2T was found to play pivotal role in lung metastasis in vivo. Mechanistically, UBE2T is found to interact directly with E3 ligase Mule and regulate its protein expression via ubiquitination. Since Mule is found to directly degrade β-catenin protein, we are examining whether UBE2T mediates liver T-IC function through direct regulation of Mule-mediated β-catenin degradation. In conclusion, we have uncovered the novel role of UBE2T signaling cascade in regulation liver CSCs, which provides attractive therapeutic target for potential treatment of HCC.
Citation Format: Pui Yu Ho, Kin Wah Lee. UBE2T: A molecular regulator for cancer stemness and drug resistance in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 162.