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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 76, No. 14_Supplement ( 2016-07-15), p. 513-513
    Abstract: Within the European Innovative Medicines Initiative (IMI) consortium CANCER-ID (www.cancer-id.eu), scientists at academic, clinical and industrial sites across Europe and in the US joined forces to evaluate innovative technologies in the field of liquid cancer biopsies. This project aims at implementing standard operating procedures (SOPs) for pre-analytical sample handling, enrichment, isolation and analysis of Circulating Tumor Cells (CTCs), circulating free tumor DNA (ctDNA) and microRNAs (miRNAs) as novel blood-based biomarkers, with a focus on Non-Small Cell Lung Cancer (NSCLC) and HER2-treatment refractory breast cancer. In order to determine sensitivity and specificity of different technologies for CTC isolation and analysis (e.g. detection of mutations, amplifications, protein phosphorylation), complex samples comprising a mixture of NSCLC or breast cancer cell lines spiked in healthy donor blood were distributed to different CANCER-ID partner sites. These cell lines have been selected based on their molecular/genetic properties to reflect clinically relevant subtypes of the disease and have been further characterized in terms of cell-surface marker expression and cell size distribution. The use of complex spiked samples better models the heterogeneity of real-life patient material. Furthermore, healthy donor and patient derived plasma samples are investigated using different technology platforms to validate tumor-specific miRNA or ctDNA profiles that might characterize molecular tumor subtypes. To this end, differences in exosome-derived versus free circulating miRNAs are of special interest. As for CTCs the development of ctDNA and miRNA standards that can be used to compare and validate different technologies are in the focus of this effort. In summary, our results pave the way for the next phase of CANCER-ID, which includes the analysis of cancer patient samples in clinical studies using different technologies and thereby advance the concept of liquid biopsy particularly in indications in which conventional tissue biopsies are difficult to obtain. Citation Format: Thomas Schlange, Nikolas Stoecklein, Rui P. Neves, Sabrina Pleier, Sebastian Bender, Nora Brychta, Merlin V. Luetke-Eversloh, Kiki Andree, Leon Terstappen, Thomas Krahn, Thomas Krahn. Standardization of technologies for CTC, ctDNA and miRNA enrichment, isolation and analysis for liquid biopsies during the first year of IMI's CANCER-ID. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 513.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
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  • 2
    Online Resource
    Online Resource
    Elsevier BV ; 2020
    In:  Molecular Aspects of Medicine Vol. 72 ( 2020-04), p. 100844-
    In: Molecular Aspects of Medicine, Elsevier BV, Vol. 72 ( 2020-04), p. 100844-
    Type of Medium: Online Resource
    ISSN: 0098-2997
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
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  • 3
    In: Current Biology, Elsevier BV, Vol. 9, No. 16 ( 1999-08), p. 911-S1
    Type of Medium: Online Resource
    ISSN: 0960-9822
    Language: English
    Publisher: Elsevier BV
    Publication Date: 1999
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 3786-3786
    Abstract: Metastasis represents the deadliest feature of cancer, which is fueled by circulating tumor cells (CTCs) being released into the bloodstream from the primary tumor. In addition to the clinical value of CTC enumeration for metastatic risk assessment, CTCs are considered to be a minimally invasive source for studying the molecular and genetic features of the disease as well as response to anticancer therapy. Given the molecular heterogeneity of CTCs, which includes loss of epithelial surface marker expression, several microfluidic and filtration technology platforms were developed to overcome the limitations of surface marker dependent CTC enrichment. Here we describe the efforts of the Innovative Medicines Initiative (IMI) consortium CANCER-ID (www.cancer-id.eu), which represents a joint undertaking of experts from academia and pharmaceutical industry, in generating comparative data using different CTC enrichment platforms in a multicenter ring trial. To address clinically relevant subtypes of Non-Small Cell Lung Cancer (NSCLC), different NSCLC cell lines were profiled for genetic aberrations (mutations and copy number aberrations), expression of epithelial markers (epithelial cell adhesion molecule (EPCAM) and cytokeratins) as well as cell size. Cell lines were selected to generate spike-in samples using blood of healthy volunteers with informed consent in a centralized way. Analysis was performed by at least three CANCER-ID partners using different CTC enrichment technologies including the Siemens filtration device, the Parsortix PR1, VyCap filtration and the CellSearch system. To ensure quality and comparability of results, CANCER-ID partners established standard operation procedures (SOPs) for pre-analytic sample handling including sample fixation, storage and shipment. Special attention was paid on the development of SOPs for the actual CTC enrichment procedure and the integration of downstream applications including single cell isolation by DEPArray™ followed by Ampli1™ WGA and molecular and genetic characterization of isolated cells. Epitope-independent enrichment by filtration or microfluidic devices was evaluated by using NSCLC cells with substantially different cell size. In addition, comparative data on spike-in samples was generated using the EPCAM-expression dependent CellSearch system, which failed to detect EPCAM-negative tumor cells. In conclusion, the evaluation of different CTC enrichment technologies and the integration of workflows for downstream analysis of single cells blaze the trail for the next phase of IMI’s CANCER-ID, which includes the analysis of real-life NSCLC patient material. This work is supported by IMI JU & EFPIA (grant no. 115749). Citation Format: Sebastian Bender, Merlin V. Lütke-Eversloh, Rui P. Neves, NNikolas H. Stoecklein, Leon W. Terstappen, Barbara Baggiani, Martin H. Neumann, Thomas Krahn, Klaus Pantel, Thomas Schlange, Leonie L. Zeune. Multicenter evaluation of technology platforms for the enumeration of circulating tumor 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 3786. doi:10.1158/1538-7445.AM2017-3786
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 5
    Online Resource
    Online Resource
    Elsevier BV ; 2018
    In:  Computational and Structural Biotechnology Journal Vol. 16 ( 2018), p. 190-195
    In: Computational and Structural Biotechnology Journal, Elsevier BV, Vol. 16 ( 2018), p. 190-195
    Type of Medium: Online Resource
    ISSN: 2001-0370
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2018
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  • 6
    In: Clinical Chemistry, Oxford University Press (OUP), Vol. 65, No. 9 ( 2019-09-01), p. 1132-1140
    Abstract: In human body fluids, microRNA (miRNA) can be found as circulating cell-free miRNA (cfmiRNA), as well as secreted into extracellular vesicles (EVmiRNA). miRNAs are being intensively evaluated as minimally invasive liquid biopsy biomarkers in patients with cancer. The growing interest in developing clinical assays for circulating miRNA necessitates careful consideration of confounding effects of preanalytical and analytical parameters. METHODS By using reverse transcription quantitative real-time PCR and next-generation sequencing (NGS), we compared extraction efficiencies of 5 different protocols for cfmiRNA and 2 protocols for EVmiRNA isolation in a multicentric manner. The efficiency of the different extraction methods was evaluated by measuring exogenously spiked cel-miR-39 and 6 targeted miRNAs in plasma from 20 healthy individuals. RESULTS There were significant differences between the tested methods. Although column-based extraction methods were highly effective for the isolation of endogenous miRNA, phenol extraction combined with column-based miRNA purification and ultracentrifugation resulted in lower quality and quantity of isolated miRNA. Among all extraction methods, the ubiquitously expressed miR-16 was represented with high abundance when compared with other targeted miRNAs. In addition, the use of miR-16 as an endogenous control for normalization of quantification cycle values resulted in a decreased variability of column-based cfmiRNA extraction methods. Cluster analysis of normalized NGS counts clearly indicated a method-dependent bias. CONCLUSIONS The choice of plasma miRNA extraction methods affects the selection of potential miRNA marker candidates and mechanistic interpretation of results, which should be done with caution, particularly across studies using different protocols.
    Type of Medium: Online Resource
    ISSN: 0009-9147 , 1530-8561
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
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  • 7
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2018
    In:  Cancer Research Vol. 78, No. 13_Supplement ( 2018-07-01), p. 2389-2389
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 2389-2389
    Abstract: Introduction c-MET is a well-known target due to its amplification and overexpression in gastric cancer and NSCLC. Overexpression has also been reported for Head and Neck Cancer (HNSCC), but initial clinical trials with MET inhibitors in HNSCC have not been successful. Methods We investigated the expression level of MET in HNSCC and also characterized the molecular activity level based on the phosphorylation of the intracellular adaptor protein docking site, Tyrosine-1349. In a second larger cohort, we tested expression of MET and correlate it with follow-up data in order to test the prognostic relevance of MET expression in gastric cancer. All clinical samples were all obtained in compliance with clinical regulations and informed consent of every patient. Results We found MET clearly overexpressed in HNSCC. However, the signaling activity of MET was not elevated compared to normal adjacent tissue. To test the relevance of MET for growth of HNSCC cells, we tested the activity of BAY 853474 in a panel of HNSCC cell lines. In contrast to gastric cancer control cell lines which had low nanomolar IC50 values, none of the 12 HNSCC cell lines was sensitive to MET inhibition. This was in contrast to their sensitivity to Cisplatin/Fluoruracil as positive control. Compared to MET dependent cell lines from gastric cancer, HNSCC cell lines had 10 fold less MET expression. The phosphorylation was two orders of magnitude below that of responder cell lines. On the molecular level, we also compared the properties of the HNSCC cell lines with that of fresh frozen tumor biopsies from 50 patients. In this analysis, it became evident that clinical samples had strikingly lower MET expression and phosphorylation even compared to the HNSCC cell lines. Based on these findings, a clinical response to MET inhibitors cannot be expected. In a larger cohort of several hundred patients, we are currently testing whether the elevated MET expression may still be prognostic for progression and/or survival. It appears possible that MET expression may give a growth advantage to tumor cells although it is clearly not fulfilling the criteria for an oncogenic driver in this indication. The significant overexpression of MET in tumor tissue and the very strong overexpression in cell lines compared to clinical samples show that MET expression gives a selective advantage to the tumor cells. We will show whether this advantage results in shorter time to progression or overall survival. Conclusion We show that MET expression in HNSCC cell lines is not representative for the clinical situation. HNSCC does not overexpress Met and the molecular activity is low. MET is devalidated as therapeutic target in HNSCC. An analysis of the prognostic value of MET expression in HNSCC will follow and presented at the AACR meeting in 2018. Citation Format: Thomas Schlange, Martin Khan, Sami Khaznadar, arndt schmitz, Thomas Krahn, Oliver von Ahsen. Role of MET in head and neck cancer [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 2389.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 8
    Online Resource
    Online Resource
    Elsevier BV ; 2000
    In:  Mechanisms of Development Vol. 98, No. 1-2 ( 2000-11), p. 157-160
    In: Mechanisms of Development, Elsevier BV, Vol. 98, No. 1-2 ( 2000-11), p. 157-160
    Type of Medium: Online Resource
    ISSN: 0925-4773
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2000
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  • 9
    Online Resource
    Online Resource
    Elsevier BV ; 2000
    In:  Mechanisms of Development Vol. 91, No. 1-2 ( 2000-03), p. 259-270
    In: Mechanisms of Development, Elsevier BV, Vol. 91, No. 1-2 ( 2000-03), p. 259-270
    Type of Medium: Online Resource
    ISSN: 0925-4773
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2000
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  • 10
    Online Resource
    Online Resource
    Wiley ; 2003
    In:  Developmental Dynamics Vol. 228, No. 2 ( 2003-10), p. 217-230
    In: Developmental Dynamics, Wiley, Vol. 228, No. 2 ( 2003-10), p. 217-230
    Abstract: Dextral looping of the heart is regulated on multiple levels. In humans, mutations of the genes CFC and Pitx2 / RIEG result in laterality‐associated cardiac anomalies. In animal models, a common read‐out after the misexpression of laterality genes is heart looping direction. Missing in these studies is how laterality genes impact on downstream morphogenetic processes to coordinate heart looping. Previously, we showed that Pitx2 indirectly regulates flectin protein by regulating the timing of flectin expression in one heart field versus the other (Linask et al. [ 2002 ] Dev. Biol. 246:407–417). To address this question further we used a reported loss‐of‐function approach to interfere with chick CFC expression (Schlange et al. [ 2001 ] Dev. Biol. 234:376–389) and assaying for flectin expression during looping. Antisense CFC treatment results in abnormal heart looping or no looping. Our results show that regardless of the sidedness of downstream Pitx2 expression, it is the sidedness of predominant flectin protein expression in the extracellular matrix of the dorsal mesocardial folds and splanchnic mesoderm apposed to the foregut wall that is associated directly with looping direction. Thus, Pitx2 can be experimentally uncoupled from heart looping. The flectin asymmetry continues to be maintained in the secondary heart field during looping. Developmental Dynamics 228:217–230, 2003. © 2003 Wiley‐Liss, Inc.
    Type of Medium: Online Resource
    ISSN: 1058-8388 , 1097-0177
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2003
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