1
|
de Bortoli T, Benary M, Horak P, Lamping M, Stintzing S, Tinhofer I, Leyvraz S, Schäfer R, Klauschen F, Keller U, Stenzinger A, Fröhling S, Kurzrock R, Keilholz U, Rieke DT, Jelas I. Tumour mutational burden and survival with molecularly matched therapy. Eur J Cancer 2023; 190:112925. [PMID: 37544709 DOI: 10.1016/j.ejca.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND The impact of tumour mutational burden (TMB) on outcome with molecularly matched therapy is unknown. Higher TMB could predict resistance to molecularly matched therapy through co-occurring driver mutations. METHODS One hundred and four patients with advanced cancers underwent molecular profiling in the DKTK-MASTER program. Fifty-five patients received systemic therapy excluding immunotherapy. Patients with molecularly matched (n = 35) or non-molecularly informed therapy (n = 20) were analysed for TMB and survival. Results were validated in an independent cohort of patients receiving molecularly matched (n = 68) or non-molecularly informed therapy (n = 40). Co-occurring driver mutations and TMB were analysed in the exploratory cohort and The Cancer Genome Atlas (TCGA) datasets. RESULTS Patients were stratified by the median TMB of 1.67 mutations per Megabase (mut/Mb) of 35 patients receiving molecularly matched therapy into TMB-high or TMB-low groups. Median overall survival (4 months [95% CI, 3.3-7.6] versus 12.8 months [95% CI, 10-not reached], p < 0.001) and progression-free survival (1.8 months [95% CI, 1.1-3.7] versus 7.9 months [95% CI, 2.8-17.0], p = 0.003) were significantly shorter in the TMB-high group compared to the TMB-low group. In the validation cohort, shorter OS and PFS were identified in the TMB-high group (TMB cut-off of 4 mut/Mb) treated with molecularly matched therapy. No differences were observed in patients receiving non-molecularly informed systemic therapy. A significant correlation between co-occurring driver mutations and TMB (n = 104, r = 0.78 [95% CI, 0.68-0.85], p < 0.001) was found in the exploratory cohort as well as the majority (24/33) of TCGA studies. CONCLUSION A high TMB was associated with unfavourable outcome in patients receiving molecularly matched therapy, indicating untargeted resistance pathways. Therefore, TMB should be further investigated as a predictive biomarker in precision oncology programs.
Collapse
Affiliation(s)
- Till de Bortoli
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Manuela Benary
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter Horak
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mario Lamping
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Sebastian Stintzing
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Serge Leyvraz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ulrich Keller
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) Association-WIN Consortium, Villejuif, France
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany
| | - Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Sites Berlin and Heidelberg, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Ivan Jelas
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| |
Collapse
|
2
|
Ahmed SM, Ragunathan P, Shin J, Peter S, Kleissle S, Neuenschwander M, Schäfer R, Kries JPV, Grüber G, Dröge P. The FGFR inhibitor PD173074 binds to the C-terminus of oncofetal HMGA2 and modulates its DNA-binding and transcriptional activation functions. FEBS Lett 2023; 597:1977-1988. [PMID: 37259564 DOI: 10.1002/1873-3468.14675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/20/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
The architectural chromatin factor high-mobility group AT-hook 2 (HMGA2) is causally involved in several human malignancies and pathologies. HMGA2 is not expressed in most normal adult somatic cells, which renders the protein an attractive drug target. An established cell-based compound library screen identified the fibroblast growth factor receptor (FGFR) inhibitor PD173074 as an antagonist of HMGA2-mediated transcriptional reporter gene activation. We determined that PD173074 binds the C-terminus of HMGA2 and interferes with functional coordination of the three AT-hook DNA-binding domains mediated by the C-terminus. The HMGA2-antagonistic effect of PD173074 on transcriptional activation may therefore result from an induced altered DNA-binding mode of HMGA2. PD173074 as a novel HMGA2-specific antagonist could trigger the development of derivates with enhanced attributes and clinical potential.
Collapse
Affiliation(s)
- Syed Moiz Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Sabrina Kleissle
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Berlin, Germany
| | | | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Jens Peter V Kries
- Leibniz-Forschungsinstitut fűr Molekulare Pharmakologie, Berlin, Germany
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- LambdaGen Pte Ltd, Singapore City, Singapore
| |
Collapse
|
3
|
Macion A, Schäfer R. Ionization potentials of metal clusters studied with a broad range, tunable vacuum ultraviolet light source. Rev Sci Instrum 2023; 94:063101. [PMID: 37862487 DOI: 10.1063/5.0151238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 10/22/2023]
Abstract
In this work, we present an alternative to complex laser setups or synchrotron light sources to accurately measure the ionization potentials of metal clusters. The setup is based on a commercial Xe flash lamp, combined with a vacuum monochromator, and has been applied to determine the ionization potentials of Snn clusters with n = 8-12 atoms. The uncertainty in the determination of the ionization potentials is mainly caused by the bandwidth of the monochromator. The adiabatic ionization potentials (AIPs) are extracted from experimental photoionization efficiency curves. Franck-Condon simulations are additionally used to interpret the shape and onset of the photo-ion yield. The obtained AIPs are (all energies are in eV) Sn8 (6.53 ± 0.05), Sn9 (6.69 ± 0.04), Sn10 (6.93 ± 0.03), Sn11 (6.34 ± 0.05), and Sn12 (IsoI 6.64 ± 0.04 and IsoIII 6.36 ± 0.05). Furthermore, the impact of multiple isomers present in the experiment on the photo-ion yield is addressed and compared with other experimental data in the literature.
Collapse
Affiliation(s)
- A Macion
- Technical University of Darmstadt, Eduard-Zintl-Institut, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - R Schäfer
- Technical University of Darmstadt, Eduard-Zintl-Institut, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| |
Collapse
|
4
|
Kendzia S, Franke S, Kröhler T, Golob-Schwarzl N, Schweiger C, Toeglhofer AM, Skofler C, Uranitsch S, El-Heliebi A, Fuchs J, Punschart A, Stiegler P, Keil M, Hoffmann J, Henderson D, Lehrach H, Yaspo ML, Reinhard C, Schäfer R, Keilholz U, Regenbrecht C, Schicho R, Fickert P, Lax SF, Erdmann F, Schulz MH, Kiemer AK, Haybaeck J, Kessler SM. A combined computational and functional approach identifies IGF2BP2 as a driver of chemoresistance in a wide array of pre-clinical models of colorectal cancer. Mol Cancer 2023; 22:89. [PMID: 37248468 PMCID: PMC10227963 DOI: 10.1186/s12943-023-01787-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
AIM Chemoresistance is a major cause of treatment failure in colorectal cancer (CRC) therapy. In this study, the impact of the IGF2BP family of RNA-binding proteins on CRC chemoresistance was investigated using in silico, in vitro, and in vivo approaches. METHODS Gene expression data from a well-characterized cohort and publicly available cross-linking immunoprecipitation sequencing (CLIP-Seq) data were collected. Resistance to chemotherapeutics was assessed in patient-derived xenografts (PDXs) and patient-derived organoids (PDOs). Functional studies were performed in 2D and 3D cell culture models, including proliferation, spheroid growth, and mitochondrial respiration analyses. RESULTS We identified IGF2BP2 as the most abundant IGF2BP in primary and metastastatic CRC, correlating with tumor stage in patient samples and tumor growth in PDXs. IGF2BP2 expression in primary tumor tissue was significantly associated with resistance to selumetinib, gefitinib, and regorafenib in PDOs and to 5-fluorouracil and oxaliplatin in PDX in vivo. IGF2BP2 knockout (KO) HCT116 cells were more susceptible to regorafenib in 2D and to oxaliplatin, selumitinib, and nintedanib in 3D cell culture. Further, a bioinformatic analysis using CLIP data suggested stabilization of target transcripts in primary and metastatic tumors. Measurement of oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) revealed a decreased basal OCR and an increase in glycolytic ATP production rate in IGF2BP2 KO. In addition, real-time reverse transcriptase polymerase chain reaction (qPCR) analysis confirmed decreased expression of genes of the respiratory chain complex I, complex IV, and the outer mitochondrial membrane in IGF2BP2 KO cells. CONCLUSIONS IGF2BP2 correlates with CRC tumor growth in vivo and promotes chemoresistance by altering mitochondrial respiratory chain metabolism. As a druggable target, IGF2BP2 could be used in future CRC therapy to overcome CRC chemoresistance.
Collapse
Affiliation(s)
- Sandra Kendzia
- Institute of Pharmacy, Experimental Pharmacology for Natural Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Susanne Franke
- Institute of Pharmacy, Experimental Pharmacology for Natural Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Tarek Kröhler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Nicole Golob-Schwarzl
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
- Department of Dermatology and Venereology, Medical University of Graz, Graz, Austria
| | - Caroline Schweiger
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anna M Toeglhofer
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Christina Skofler
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Stefan Uranitsch
- Department of Surgery, Hospital Brothers of Charity Graz, Graz, Austria
| | - Amin El-Heliebi
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Julia Fuchs
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- Division of Medical Physics and Biophysics, Medical University Graz, Graz, Austria
| | | | - Philipp Stiegler
- Department of Surgery, Medical University of Graz, Graz, Austria
| | - Marlen Keil
- Experimental Pharmacology & Oncology, Berlin GmbH-Berlin-Buch, Germany
| | - Jens Hoffmann
- Experimental Pharmacology & Oncology, Berlin GmbH-Berlin-Buch, Germany
| | | | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Christoph Reinhard
- Eli Lilly & Company, Indianapolis, USA
- CELLphenomics GmbH, Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Regenbrecht
- CELLphenomics GmbH, Berlin, Germany
- Institute for Pathology, University Hospital Göttingen, Göttingen, Germany
| | - Rudolf Schicho
- Division of Pharmacology, Medical University of Graz, Graz, Austria
| | - Peter Fickert
- Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Sigurd F Lax
- Department of Pathology, Hospital Graz South-West and School of Medicine, Johannes Kepler University Linz, Linz, Austria
| | - Frank Erdmann
- Institute of Pharmacy, Experimental Pharmacology for Natural Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Frankfurt, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Johannes Haybaeck
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sonja M Kessler
- Institute of Pharmacy, Experimental Pharmacology for Natural Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany.
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany.
- Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria.
- Halle Research Centre for Drug Therapy (HRCDT), Halle, Germany.
| |
Collapse
|
5
|
Scheel CH, Schäfer R. Editorial: Hallmark of cancer: Evasion of growth suppressors. Front Oncol 2023; 13:1170115. [PMID: 36994210 PMCID: PMC10040857 DOI: 10.3389/fonc.2023.1170115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/15/2023] Open
Affiliation(s)
- Christina H. Scheel
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
- *Correspondence: Christina H. Scheel, ; Reinhold Schäfer,
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Universitaetsmedizin Berlin, Berlin, Germany
- *Correspondence: Christina H. Scheel, ; Reinhold Schäfer,
| |
Collapse
|
6
|
Motta S, Christensen JB, Togno M, Schäfer R, Safai S, Lomax AJ, Yukihara EG. Characterization of LiF:Mg,Ti thermoluminescence detectors in low-LET proton beams at ultra-high dose rates. Phys Med Biol 2023; 68. [PMID: 36696696 DOI: 10.1088/1361-6560/acb634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/25/2023] [Indexed: 01/26/2023]
Abstract
Objective.This work aims at characterizing LiF:Mg,Ti thermoluminescence detectors (TLDs) for dosimetry of a 250 MeV proton beam delivered at ultra-high dose rates (UHDR). Possible dose rate effects in LiF:Mg,Ti, as well as its usability for dosimetry of narrow proton beams are investigated.Approach.LiF:Mg,Ti (TLD-100TMMicrocubes, 1 mm × 1 mm × 1 mm) was packaged in matrices of 5 × 5 detectors. The center of each matrix was irradiated with single-spot low-LET (energy >244 MeV) proton beam in the (1-4500) Gy s-1average dose rates range. A beam reconstruction procedure was applied to the detectors irradiated at the highest dose rate (Gaussian beam sigma <2 mm) to correct for volumetric averaging effects. Reference dosimetry was carried out with a diamond detector and radiochromic films. The delivered number of protons was measured by a Faraday cup, which was employed to normalize the detector responses.Main results.The lateral beam spread obtained from the beam reconstruction agreed with the one derived from the radiochromic film measurements. No dose rates effects were observed in LiF:Mg,Ti for the investigated dose rates within 3% (k= 1). On average, the dose response of the TLDs agreed with the reference detectors within their uncertainties. The largest deviation (-5%) was measured at 4500 Gy s-1.Significance.The dose rate independence of LiF:Mg,Ti TLDs makes them suitable for dosimetry of UHDR proton beams. Additionally, the combination of a matrix of TLDs and the beam reconstruction can be applied to determine the beam profile of narrow proton beams.
Collapse
Affiliation(s)
- S Motta
- Department of Radiation Safety and Security, Paul Scherrer Institute, Villigen PSI, Switzerland.,Department of Physics, ETH Zürich, Zürich, Switzerland
| | - J B Christensen
- Department of Radiation Safety and Security, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - M Togno
- Center for Proton Therapy, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - R Schäfer
- Center for Proton Therapy, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - S Safai
- Center for Proton Therapy, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - A J Lomax
- Center for Proton Therapy, Paul Scherrer Institute, Villigen PSI, Switzerland.,Department of Physics, ETH Zürich, Zürich, Switzerland
| | - E G Yukihara
- Department of Radiation Safety and Security, Paul Scherrer Institute, Villigen PSI, Switzerland
| |
Collapse
|
7
|
Sers C, Schäfer R. Silencing effects of mutant RAS signalling on transcriptomes. Adv Biol Regul 2023; 87:100936. [PMID: 36513579 DOI: 10.1016/j.jbior.2022.100936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Mutated genes of the RAS family encoding small GTP-binding proteins drive numerous cancers, including pancreatic, colon and lung tumors. Besides the numerous effects of mutant RAS gene expression on aberrant proliferation, transformed phenotypes, metabolism, and therapy resistance, the most striking consequences of chronic RAS activation are changes of the genetic program. By performing systematic gene expression studies in cellular models that allow comparisons of pre-neoplastic with RAS-transformed cells, we and others have estimated that 7 percent or more of all transcripts are altered in conjunction with the expression of the oncogene. In this context, the number of up-regulated transcripts approximates that of down-regulated transcripts. While up-regulated transcription factors such as MYC, FOSL1, and HMGA2 have been identified and characterized as RAS-responsive drivers of the altered transcriptome, the suppressed factors have been less well studied as potential regulators of the genetic program and transformed phenotype in the breadth of their occurrence. We therefore have collected information on downregulated RAS-responsive factors and discuss their potential role as tumor suppressors that are likely to antagonize active cancer drivers. To better understand the active mechanisms that entail anti-RAS function and those that lead to loss of tumor suppressor activity, we focus on the tumor suppressor HREV107 (alias PLAAT3 [Phospholipase A and acyltransferase 3], PLA2G16 [Phospholipase A2, group XVI] and HRASLS3 [HRAS-like suppressor 3]). Inactivating HREV107 mutations in tumors are extremely rare, hence epigenetic causes modulated by the RAS pathway are likely to lead to down-regulation and loss of function.
Collapse
Affiliation(s)
- Christine Sers
- Laboratory of Molecular Tumor Pathology and systems Biology, Institute of Pathology, Charité Universitätstmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| |
Collapse
|
8
|
Togno M, Nesteruk KP, Schäfer R, Psoroulas S, Meer D, Grossmann M, Christensen JB, Yukihara EG, Lomax AJ, Weber DC, Safai S. Ultra-high dose rate dosimetry for pre-clinical experiments with mm-small proton fields. Phys Med 2022; 104:101-111. [PMID: 36395638 DOI: 10.1016/j.ejmp.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/10/2022] [Accepted: 10/23/2022] [Indexed: 11/15/2022] Open
Abstract
PURPOSE To characterize an experimental setup for ultra-high dose rate (UHDR) proton irradiations, and to address the challenges of dosimetry in millimetre-small pencil proton beams. METHODS At the PSI Gantry 1, high-energy transmission pencil beams can be delivered to biological samples and detectors up to a maximum local dose rate of ∼9000 Gy/s. In the presented setup, a Faraday cup is used to measure the delivered number of protons up to ultra-high dose rates. The response of transmission ion-chambers, as well as of different field detectors, was characterized over a wide range of dose rates using the Faraday cup as reference. RESULTS The reproducibility of the delivered proton charge was better than 1 % in the proposed experimental setup. EBT3 films, Al2O3:C optically stimulated luminescence detectors and a PTW microDiamond were used to validate the predicted dose. Transmission ionization chambers showed significant volume ion-recombination (>30 % in the tested conditions) which can be parametrized as a function of the maximum proton current density. Over the considered range, EBT3 films, inorganic scintillator-based screens and the PTW microDiamond were demonstrated to be dose rate independent within ±3 %, ±1.8 % and ±1 %, respectively. CONCLUSIONS Faraday cups are versatile dosimetry instruments that can be used for dose estimation, field detector characterization and on-line dose verification for pre-clinical experiments in UHDR proton pencil beams. Among the tested detectors, the commercial PTW microDiamond was found to be a suitable option to measure real time the dosimetric properties of narrow pencil proton beams for dose rates up to 2.2 kGy/s.
Collapse
Affiliation(s)
- M Togno
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland.
| | - K P Nesteruk
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - R Schäfer
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland
| | - S Psoroulas
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland
| | - D Meer
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland
| | - M Grossmann
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland
| | - J B Christensen
- Department of Radiation Safety and Security, Paul Scherrer Institut, Villigen, Switzerland
| | - E G Yukihara
- Department of Radiation Safety and Security, Paul Scherrer Institut, Villigen, Switzerland
| | - A J Lomax
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland; Department of Physics, ETH Zurich, Zurich, Switzerland
| | - D C Weber
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland; Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland; Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - S Safai
- Center for Proton Therapy, Paul Scherrer Institut, Villigen, Switzerland
| |
Collapse
|
9
|
Leyvraz S, Schütte M, Kessler T, Lamping M, Burock S, Ochsenreither S, Amstislavskiy V, Risch T, Jelas I, Ulrich C, Dobos G, Klauschen F, Schäfer R, Lange B, Klinghammer K, Yaspo ML, Keilholz U. 847P Precision oncology for resistant acral, mucosal and cutaneous melanomas: A prospective broad high throughput genomics feasibility study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
10
|
Xu Y, Pachnikova G, Wang H, Wu Y, Przybilla D, Schäfer R, Chen Z, Zhu S, Keilholz U. IC50: an unsuitable measure for large-sized prostate cancer spheroids in drug sensitivity evaluation. Bosn J Basic Med Sci 2022; 22:580-592. [PMID: 35694767 PMCID: PMC9392968 DOI: 10.17305/bjbms.2022.7279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/09/2022] [Indexed: 02/02/2023] Open
Abstract
Preclinical models of tumors have the potential to become valuable tools for commercial drug research and development, and 3D culture systems are gaining traction in this area, particularly in prostate cancer (PCa) research. However, nearly all 3D drug design and screening assessments are based on 2D experiments, suggesting limitations of 3D drug testing. To simulate the natural response of human cells to the drug, we detected the half-maximal inhibitory concentration (IC50) changes of 2D/3D LNCaP cells in the drug docetaxel, as well as the sensitivity of different morphologies of 2D/3D LNCaP to docetaxel treatment. In contrast to 2D LNCaP cells, the evaluation of LNCaP spheroids' susceptibility to treatment was more complicated; the fitness of IC50 curves of 2D and 3D tumor cell preclinical models differs significantly. IC50 curves were unsuitable for large-sized LNCaP spheroids. More evaluation indexes (such as max inhibition) and experiments (such as spheroids formation) should be explored and performed to evaluate the susceptibility systematically.
Collapse
Affiliation(s)
- Yipeng Xu
- Department of Urology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China,The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou, China,Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Gabriela Pachnikova
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - He Wang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Zhejiang, China
| | - Yaoyao Wu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Zhejiang, China
| | - Dorothea Przybilla
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Zihao Chen
- Department of Urology, Southern Medical University, Guangzhou, China
| | - Shaoxing Zhu
- Department of Urology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China,The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou, China,Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China,Corresponding authors: Shaoxing Zhu, Department of Urology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China; The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou, China; Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China. E-mail:
| | - Ulrich Keilholz
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany,
Ulrich Keilholz; Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. E-mail:
| |
Collapse
|
11
|
Kumbrink J, Bohlmann L, Mamlouk S, Redmer T, Peilstöcker D, Li P, Lorenzen S, Algül H, Kasper S, Hempel D, Kaiser F, Michl M, Bartsch H, Neumann J, Klauschen F, von Bergwelt-Baildon M, Modest DP, Stahler A, Stintzing S, Jung A, Kirchner T, Schäfer R, Heinemann V, Holch JW. Serial Analysis of Gene Mutations and Gene Expression during First-Line Chemotherapy against Metastatic Colorectal Cancer: Identification of Potentially Actionable Targets within the Multicenter Prospective Biomarker Study REVEAL. Cancers (Basel) 2022; 14:cancers14153631. [PMID: 35892888 PMCID: PMC9367450 DOI: 10.3390/cancers14153631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The emergence of resistant cells remains a major obstacle for chemotherapy treatment of metastatic colorectal cancers. Improvement of the therapeutic response requires a thorough understanding of the mechanisms of resistance as well as informative biomarkers. In the REVEAL study, we have systematically compared the mutational patterns and expression profiles of primary tumor specimens before and after first-line chemotherapy treatment in the metastatic situation. In addition, we analyzed liquid biopsies pre, during, and after treatment. Alterations in gene expression appeared as the major drivers of chemotherapy resistance. We identified a gene expression signature differentiating primary tumors and metastases and validated this signature in two independent patient cohorts. Moreover, we evaluated the expression of two signature genes, SFRP2 and SPP1, as prognostic and potentially druggable biomarkers. Abstract Most metastatic colorectal cancer (mCRC) patients succumb to refractory disease due to secondary chemotherapy resistance. To elucidate the molecular changes associated with secondary resistance, we recruited 64 patients with mCRC and hepatic metastases before standard first-line chemotherapy between 2014 and 2018. We subjected DNA from primary tumor specimens (P), hepatic metastasis specimens after treatment (M), and liquid biopsies (L) taken prior to (pre), during (intra), and after (post) treatment to next generation sequencing. We performed Nanostring expression analysis in P and M specimens. Comparative bioinformatics and statistical analysis revealed typical mutational patterns with frequent alterations in TP53, APC, and KRAS in P specimens (n = 48). P and pre-L (n = 42), as well as matched P and M (n = 30), displayed a similar mutation spectrum. In contrast, gene expression profiles classified P (n = 31) and M (n = 23), distinguishable by up-regulation of immune/cytokine receptor and autophagy programs. Switching of consensus molecular subtypes from P to M occurred in 58.3% of cases. M signature genes SFRP2 and SPP1 associated with inferior survival, as validated in an independent cohort. Molecular changes during first-line treatment were detectable by expression profiling rather than by mutational tumor and liquid biopsy analyses. SFRP2 and SPP1 may serve as biomarkers and/or actionable targets.
Collapse
Affiliation(s)
- Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Correspondence:
| | - Lisa Bohlmann
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Soulafa Mamlouk
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Pathology, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Torben Redmer
- Institute of Medical Biochemistry, University of Veterinary Medicine Vienna, 1210 Vienna, Austria;
| | - Daniela Peilstöcker
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Pan Li
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Sylvie Lorenzen
- Klinik und Poliklinik für Innere Medizin III, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany;
| | - Hana Algül
- School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- Comprehensive Cancer Center Munich, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Stefan Kasper
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, 45147 Essen, Germany;
| | - Dirk Hempel
- Steinbeishochschule Berlin, 12489 Berlin, Germany;
- Steinbeis Transfer Institute Clinical Hematology-Oncology, 86609 Donauwörth, Germany
| | | | - Marlies Michl
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
- Comprehensive Cancer Center, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Harald Bartsch
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
| | - Jens Neumann
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Frederick Klauschen
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Michael von Bergwelt-Baildon
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
| | - Dominik Paul Modest
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Arndt Stahler
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sebastian Stintzing
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Hematology, Oncology and Cancer Immunology (CCM), Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Andreas Jung
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich (LMU), 80337 Munich, Germany; (L.B.); (D.P.); (P.L.); (H.B.); (J.N.); (F.K.); (A.J.); (T.K.)
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
| | - Reinhold Schäfer
- Partner Site Berlin, German Cancer Consortium (DKTK), 10117 Berlin, Germany; (S.M.); (D.P.M.); (A.S.); (S.S.); (R.S.)
- Charité Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Volker Heinemann
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
- Comprehensive Cancer Center, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Julian W. Holch
- Partner Site Munich, German Cancer Consortium (DKTK), 80336 Munich, Germany; (M.v.B.-B.); (V.H.); (J.W.H.)
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany;
- Comprehensive Cancer Center, University Hospital, LMU Munich, 81377 Munich, Germany
| |
Collapse
|
12
|
Leyvraz S, Konietschke F, Peuker C, Schütte M, Kessler T, Ochsenreither S, Ditzhaus M, Sprünken ED, Dörpholz G, Lamping M, Rieke DT, Klinghammer K, Burock S, Ulrich C, Poch G, Schäfer R, Klauschen F, Joussen A, Yaspo ML, Keilholz U. Biomarker-driven therapies for metastatic uveal melanoma: A prospective precision oncology feasibility study. Eur J Cancer 2022; 169:146-155. [DOI: 10.1016/j.ejca.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 02/07/2023]
|
13
|
Regan JL, Schumacher D, Staudte S, Steffen A, Lesche R, Toedling J, Jourdan T, Haybaeck J, Golob-Schwarzl N, Mumberg D, Henderson D, Győrffy B, Regenbrecht CR, Keilholz U, Schäfer R, Lange M. Identification of a Neural Development Gene Expression Signature in Colon Cancer Stem Cells Reveals a Role for EGR2 in Tumorigenesis. iScience 2022; 25:104498. [PMID: 35720265 PMCID: PMC9204726 DOI: 10.1016/j.isci.2022.104498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/28/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
Recent evidence demonstrates that colon cancer stem cells (CSCs) can generate neurons that synapse with tumor innervating fibers required for tumorigenesis and disease progression. Greater understanding of the mechanisms that regulate CSC driven tumor neurogenesis may therefore lead to more effective treatments. RNA-sequencing analyses of ALDHPositive CSCs from colon cancer patient-derived organoids (PDOs) and xenografts (PDXs) showed CSCs to be enriched for neural development genes. Functional analyses of genes differentially expressed in CSCs from PDO and PDX models demonstrated the neural crest stem cell (NCSC) regulator EGR2 to be required for tumor growth and to control expression of homebox superfamily embryonic master transcriptional regulator HOX genes and the neural stem cell and master cell fate regulator SOX2. These data support CSCs as the source of tumor neurogenesis and suggest that targeting EGR2 may provide a therapeutic differentiation strategy to eliminate CSCs and block nervous system driven disease progression. Colon cancer stem cells (CSCs) are enriched for nervous system development genes Colon cancer cells express nerve cell markers EGR2 is required for CSC survival and tumor growth and regulates SOX2 and HOX genes Targeting EGR2 may block cancer neurogenesis and stop disease progression
Collapse
|
14
|
Borsato M, Cid Vidal X, Tsai Y, Vázquez Sierra C, Zurita J, Alonso-Álvarez G, Boyarsky A, Brea Rodríguez A, Buarque Franzosi D, Cacciapaglia G, Casais Vidal A, Du M, Elor G, Escudero M, Ferretti G, Flacke T, Foldenauer P, Hajer J, Henry L, Ilten P, Kamenik J, Kishor Jashal B, Knapen S, Kostiuk I, Redi FL, Low M, Liu Z, Oyanguren Campos A, Polycarpo E, Ramos M, Ramos Pernas M, Salvioni E, Rangel MS, Schäfer R, Sestini L, Soreq Y, Tran VQ, Timiryasov I, van Veghel M, Westhoff S, Williams M, Zupan J. Unleashing the full power of LHCb to probe stealth new physics. Rep Prog Phys 2022; 85:024201. [PMID: 34942603 DOI: 10.1088/1361-6633/ac4649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
In this paper, we describe the potential of the LHCb experiment to detect stealth physics. This refers to dynamics beyond the standard model that would elude searches that focus on energetic objects or precision measurements of known processes. Stealth signatures include long-lived particles and light resonances that are produced very rarely or together with overwhelming backgrounds. We will discuss why LHCb is equipped to discover this kind of physics at the Large Hadron Collider and provide examples of well-motivated theoretical models that can be probed with great detail at the experiment.
Collapse
Affiliation(s)
- M Borsato
- Physikalisches Institut, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - X Cid Vidal
- Instituto Galego de Física de Altas Enerxías (IGFAE), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Y Tsai
- Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, MD 20742-4111, United States of America
- Department of Physics, University of Notre Dame, South Bend, IN 46556, United States of America
| | - C Vázquez Sierra
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - J Zurita
- Instituto de Física Corpuscular (CSIC-UV), Valencia, Spain
| | - G Alonso-Álvarez
- Department of Physics & McGill Space Institute, McGill University, 3600 Rue University, Montréal, QC, H3A 2T8, Canada
| | - A Boyarsky
- Intituut-Lorentz, Leiden University, 2333 CA Leiden, The Netherlands
| | - A Brea Rodríguez
- Instituto Galego de Física de Altas Enerxías (IGFAE), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - D Buarque Franzosi
- Department of Physics, Chalmers University of Technology, Fysikgården, 41296 Göteborg, Sweden
- Physics Department, University of Gothenburg, 41296 Göteborg, Sweden
| | - G Cacciapaglia
- University of Lyon, Université Claude Bernard Lyon 1, F-69001 Lyon, France
- Institut de Physique des 2 Infinis (IP2I) de Lyon, CNRS/UMR5822, F-69622 Villeurbanne, France
| | - A Casais Vidal
- Instituto Galego de Física de Altas Enerxías (IGFAE), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M Du
- Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - G Elor
- Department of Physics, University of Washington, Seattle, WA 98195, United States of America
| | - M Escudero
- Physik-Department, Technische Universität, München, James-Franck-Straße, 85748 Garching, Germany
| | - G Ferretti
- Department of Physics, Chalmers University of Technology, Fysikgården, 41296 Göteborg, Sweden
| | - T Flacke
- Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - P Foldenauer
- Institute for Particle Physics Phenomenology, Durham University, Durham DH1 3LE, United Kingdom
| | - J Hajer
- Centre for Cosmology, Particle Physics and Phenomenology, Université catholique de Louvain, Louvain-la-Neuve B-1348, Belgium
- Department of Physics, Universität Basel, Klingelbergstraße 82, CH-4056 Basel, Switzerland
| | - L Henry
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
- Instituto de Física Corpuscular (CSIC-UV), Valencia, Spain
- INFN Sezione di Milano, Milano, Italy
| | - P Ilten
- Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
| | - J Kamenik
- Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | | | - S Knapen
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Igor Kostiuk
- Nikhef National Institute for Subatomic Physics, Amsterdam, The Netherlands
| | - F L Redi
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - M Low
- Theoretical Physics Department, Fermilab, PO Box 500, Batavia, IL 60510, United States of America
| | - Z Liu
- Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
- Center for High Energy Physics, Peking University, Beijing 100871, People's Republic of China
- CAS Center for Excellence in Particle Physics, Beijing 100049, People's Republic of China
| | | | - E Polycarpo
- Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - M Ramos
- CAFPE and Departamento de Física Teórica y del Cosmos, Universidad de Granada, Campus de Fuentenueva, E-18071 Granada, Spain
- Laboratório de Instrumentaçao e Física Experimental de Partículas, Departamento de Física da Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M Ramos Pernas
- Department of Physics, University of Warwick, Coventry, United Kingdom
| | - E Salvioni
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - M S Rangel
- Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Schäfer
- Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - L Sestini
- Istituto Nazionale di Fisica Nucleare (INFN), Padova Division, Padova, Italy
| | - Y Soreq
- Physics Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - V Q Tran
- Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - I Timiryasov
- Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - M van Veghel
- Van Swinderen Institute, University of Groningen, Groningen, The Netherlands
| | - S Westhoff
- Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - M Williams
- Laboratory for Nuclear Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - J Zupan
- Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
| |
Collapse
|
15
|
Xu Y, Pachnikova G, Przybilla D, Schäfer R, Cui Y, Zhou D, Chen Z, Zhao A, Keilholz U. Evaluation of JQ1 Combined With Docetaxel for the Treatment of Prostate Cancer Cells in 2D- and 3D-Culture Systems. Front Pharmacol 2022; 13:839620. [PMID: 35185589 PMCID: PMC8850784 DOI: 10.3389/fphar.2022.839620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Prostate cancer (PCa) is dependent on coupled androgen-androgen receptor (AR) signaling for growth and progression. Significant efforts have been made in this research field, as hormonal therapies have greatly improved the survival of patients with metastatic PCa (mPCa). The drug treatment agent JQ1, which potently abrogates bromodomain 4 (BRD4) localization to the AR target loci and therefore significantly impairs AR-mediated gene transcription, is a potent therapeutic option for patients with advanced PCa. In this study, we aimed to investigate the inhibitory effect of JQ1 combined with docetaxel on PCa cells in vitro for the first time. Furthermore, the 3D spheroid culture system was modeled to more accurately simulate the response of PCa cells to drugs.Methods: We established and measured 3D LNCaP spheroids in vitro in order to evaluate the susceptibility of 2D- and 3D-cultured LNCaP cells exposed to the same anti-cancer drug.Results: We demonstrated that JQ1 was an effective drug for promoting cell inhibition after docetaxel treatment in 2D- and 3D- cultured LNCaP cells. Inhibition of 3D cultured formation in the combined treatment group was significantly higher than that in docetaxel or JQ1 alone. Under the same conditions of drug solubility, the drug resistance of 3D spheroids was significantly higher than that of 2D cells. Moreover, dmax and lg volume were suitable parameters for LNCaP cells/spheroid size displaying and evaluating cell viability.Conclusion: 3D cultured spheroids of PCa are an effective tool for studying PCa drug trials. JQ1 combined with docetaxel may be an effective treatment for advanced PCa. This combination therapy strategy deserves further evaluation in clinical trials.
Collapse
Affiliation(s)
- Yipeng Xu
- Department of Urology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Gabriela Pachnikova
- Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Dorothea Przybilla
- Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Yingying Cui
- Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Dan Zhou
- Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Zihao Chen
- Department of Urology, Southern Medical University, Guangzhou, China
| | - An Zhao
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
- *Correspondence: An Zhao, ; Ulrich Keilholz,
| | - Ulrich Keilholz
- Comprehensive Cancer Center, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- *Correspondence: An Zhao, ; Ulrich Keilholz,
| |
Collapse
|
16
|
Liu S, Medina-Perez P, Ha-Thi MC, Wieland A, Stecklum M, Hoffmann J, Tchernitsa O, Sers C, Schäfer R. Rapid testing of candidate oncogenes and tumour suppressor genes in signal transduction and neoplastic transformation. Adv Biol Regul 2021; 83:100841. [PMID: 34866037 DOI: 10.1016/j.jbior.2021.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/18/2022]
Abstract
The COSMIC database (version 94) lists 576 genes in the Cancer Gene Census which have a defined function as drivers of malignancy (oncogenes) or as tumour suppressors (Tier 1). In addition, there are 147 genes with similar functions, but which are less well characterised (Tier 2). Furthermore, next-generation sequencing projects in the context of precision oncology activities are constantly discovering new ones. Since cancer genes differ from their wild-type precursors in numerous molecular and biochemical properties and exert significant differential effects on downstream processes, simple assays that can uncover oncogenic or anti-oncogenic functionality are desirable and may precede more sophisticated analyses. We describe simple functional assays for PTPN11 (protein-tyrosine phosphatase, non-receptor-type 11)/SHP2 mutants, which are typically found in RASopathies and exhibit potential oncogenic activity. We have also designed a functional test for lysyl oxidase (LOX), a prototypical class II tumour suppressor gene whose loss of function may contribute to neoplastic transformation by RAS oncogenes. Moreover, we applied this test to analyse three co-regulated, RAS-responsive genes for transformation-suppressive activity. The integration of these tests into systems biology studies will contribute to a better understanding of cellular networks in cancer.
Collapse
Affiliation(s)
- Sha Liu
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Paula Medina-Perez
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Minh-Cam Ha-Thi
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Anja Wieland
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Maria Stecklum
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Str. 10, D-13125, Berlin-Buch, Germany
| | - Jens Hoffmann
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Str. 10, D-13125, Berlin-Buch, Germany
| | - Oleg Tchernitsa
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Christine Sers
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany; Charité Comprehensive Cancer Center Berlin, Germany.
| |
Collapse
|
17
|
Regan JL, Schumacher D, Staudte S, Steffen A, Lesche R, Toedling J, Jourdan T, Haybaeck J, Mumberg D, Henderson D, Győrffy B, Regenbrecht CRA, Keilholz U, Schäfer R, Lange M. RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence. iScience 2021; 24:102618. [PMID: 34142064 PMCID: PMC8185225 DOI: 10.1016/j.isci.2021.102618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Recent data suggest that therapy-resistant quiescent cancer stem cells (qCSCs) are the source of relapse in colon cancer. Here, using colon cancer patient-derived organoids and xenografts, we identify rare long-term label-retaining qCSCs that can re-enter the cell cycle to generate new tumors. RNA sequencing analyses demonstrated that these cells display the molecular hallmarks of quiescent tissue stem cells, including expression of p53 signaling genes, and are enriched for transcripts common to damage-induced quiescent revival stem cells of the regenerating intestine. In addition, we identify negative regulators of cell cycle, downstream of p53, that we show are indicators of poor prognosis and may be targeted for qCSC abolition in both p53 wild-type and mutant tumors. These data support the temporal inhibition of downstream targets of p53 signaling, in combination with standard-of-care treatments, for the elimination of qCSCs and prevention of relapse in colon cancer. Colon tumors contain therapy-resistant quiescent cancer stem cells (qCSCs) qCSC gene expression mirrors that of quiescent stem cells of the regenerating gut qCSCs are enriched for p53 signaling genes qCSC elimination may be achieved by inhibiting downstream targets of p53 signaling
Collapse
Affiliation(s)
- Joseph L Regan
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Dirk Schumacher
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Stephanie Staudte
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany.,Department of Radiation Oncology and Radiotherapy, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Andreas Steffen
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Ralf Lesche
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Nuvisan ICB GmbH, 13353 Berlin, Germany
| | - Joern Toedling
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Nuvisan ICB GmbH, 13353 Berlin, Germany
| | - Thibaud Jourdan
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria.,Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - David Henderson
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary.,TTK Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary
| | - Christian R A Regenbrecht
- Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,CELLphenomics GmbH, 13125 Berlin, Germany.,Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Martin Lange
- Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.,Nuvisan ICB GmbH, 13353 Berlin, Germany
| |
Collapse
|
18
|
Klotz-Noack K, Klinger B, Rivera M, Bublitz N, Uhlitz F, Riemer P, Lüthen M, Sell T, Kasack K, Gastl B, Ispasanie SSS, Simon T, Janssen N, Schwab M, Zuber J, Horst D, Blüthgen N, Schäfer R, Morkel M, Sers C. SFPQ Depletion Is Synthetically Lethal with BRAF V600E in Colorectal Cancer Cells. Cell Rep 2021; 32:108184. [PMID: 32966782 DOI: 10.1016/j.celrep.2020.108184] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 04/28/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022] Open
Abstract
Oncoproteins such as the BRAFV600E kinase endow cancer cells with malignant properties, but they also create unique vulnerabilities. Targeting of BRAFV600E-driven cytoplasmic signaling networks has proved ineffective, as patients regularly relapse with reactivation of the targeted pathways. We identify the nuclear protein SFPQ to be synthetically lethal with BRAFV600E in a loss-of-function shRNA screen. SFPQ depletion decreases proliferation and specifically induces S-phase arrest and apoptosis in BRAFV600E-driven colorectal and melanoma cells. Mechanistically, SFPQ loss in BRAF-mutant cancer cells triggers the Chk1-dependent replication checkpoint, results in decreased numbers and reduced activities of replication factories, and increases collision between replication and transcription. We find that BRAFV600E-mutant cancer cells and organoids are sensitive to combinations of Chk1 inhibitors and chemically induced replication stress, pointing toward future therapeutic approaches exploiting nuclear vulnerabilities induced by BRAFV600E.
Collapse
Affiliation(s)
- Kathleen Klotz-Noack
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bertram Klinger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Maria Rivera
- EPO Experimentelle Pharmakologie und Onkologie Berlin-Buch GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Natalie Bublitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Uhlitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Pamela Riemer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Mareen Lüthen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Sell
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Katharina Kasack
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bastian Gastl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Sylvia S S Ispasanie
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Tincy Simon
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany; University of Tuebingen, 72074 Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany; Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Auf der Morgenstelle 8, 72074 Tuebingen, Germany; German Cancer Consortium (DKTK), Partner Site Tuebingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria; Medical University of Vienna, VBC, 1030 Vienna, Austria
| | - David Horst
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nils Blüthgen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; IRI Life Sciences & Institute of Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reinhold Schäfer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany; Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christine Sers
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health. Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
19
|
Willer H, Thielemann C, Elvers-Hornung S, Spohn G, Delorme, Giesen M, Schäfer R, Bieback K. Repeated administration of human bone marrow derived MSC expanded in virally inactivated human platelet lysate improves wound healing in diabetic rats. Cytotherapy 2021. [DOI: 10.1016/s1465324921003406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Schmidt T, Schlander D, Jüchter V, Baranyai J, Neuberger F, Schäfer R. Design of a compact and versatile radiation heater with an additively manufactured Nb radiation shield for UHV high-temperature sample preparation. Rev Sci Instrum 2021; 92:025111. [PMID: 33648129 DOI: 10.1063/5.0023982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
A compact, ultrahigh vacuum, radiative heater based on pyrolytic boron nitride that efficiently directs nearly all of its radiation to the sample was designed and constructed. It is shown that the heater reaches temperatures of 1300 K experimentally at 60% of its maximum power. A COMSOL Multiphysics® simulation and an analytical model predict an ultimate temperature of up to 1500 K. Furthermore, the heater does not introduce any contamination to the sample. This is accomplished by a custom-made Nb radiation shield, which was manufactured by selective laser melting and holds a flag-style sample holder. Before manufacturing, the whole assembly was simulated with COMSOL Multiphysics to validate the design of the radiation shield.
Collapse
Affiliation(s)
- T Schmidt
- Eduard-Zintl-Institut, TU Darmstadt, 64287 Darmstadt, Germany
| | - D Schlander
- Eduard-Zintl-Institut, TU Darmstadt, 64287 Darmstadt, Germany
| | - V Jüchter
- Heraeus Additive Manufacturing GmbH, 63405 Hanau, Germany
| | - J Baranyai
- Eduard-Zintl-Institut, TU Darmstadt, 64287 Darmstadt, Germany
| | - F Neuberger
- Eduard-Zintl-Institut, TU Darmstadt, 64287 Darmstadt, Germany
| | - R Schäfer
- Eduard-Zintl-Institut, TU Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
21
|
Schumacher D, Regan JL, Przybilla D, Schäfer R. Generation of Patient-Derived Colorectal Cancer Organoids for RAS Studies. Methods Mol Biol 2021; 2262:349-360. [PMID: 33977489 DOI: 10.1007/978-1-0716-1190-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Human cell line models have been widely used for testing of novel anticancer compounds and for predicting clinical response to monotherapies and combinatorial therapies. For many years, standard monolayer culture conditions were used as gold standard, only surpassed by in vivo testing of mouse models. Recently, the incorporation of three-dimensional culture has been shown to further improve predictive compound testing. In view of the renewed interest in anti-RAS cancer therapy, we provide a protocol for establishing colorectal cancer organoids which are characterized by a high prevalence of KRAS mutations.
Collapse
Affiliation(s)
- Dirk Schumacher
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Joseph L Regan
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Dorothea Przybilla
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center Heidelberg, Heidelberg, Germany.
| |
Collapse
|
22
|
Kuhn N, Klinger B, Uhlitz F, Sieber A, Rivera M, Klotz-Noack K, Fichtner I, Hoffmann J, Blüthgen N, Falk C, Sers C, Schäfer R. Mutation-specific effects of NRAS oncogenes in colorectal cancer cells. Adv Biol Regul 2020; 79:100778. [PMID: 33431353 DOI: 10.1016/j.jbior.2020.100778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022]
Abstract
In colorectal cancer (CRC), the prevalence of NRAS mutations (5-9%) is inferior to that of KRAS mutations (40-50%). NRAS mutations feature lately during tumour progression and drive resistance to anti-EGFR therapy in KRAS wild-type tumours. To elucidate specific functions of NRAS mutations in CRC, we expressed doxycycline-inducible G12D and Q61K mutations in the CRC cell line Caco-2. A focused phospho-proteome analysis based on the Bio-Plex platform, which interrogated the activity of MAPK, PI3K, mTOR, STAT, p38, JNK and ATF2, did not reveal significant differences between Caco-2 cells expressing NRASG12D, NRASQ61K and KRASG12V. However, phenotypic read-outs were different. The NRAS Q61K mutation promoted anchorage-independent proliferation and tumorigenicity, similar to features driven by canonical KRAS mutations. In contrast, expression of NRASG12D resulted in reduced proliferation and apoptosis. At the transcriptome level, we saw upregulation of cytokines and chemokines. IL1A, IL11, CXCL8 (IL-8) and CCL20 exhibited enhanced secretion into the culture medium. In addition, RNA sequencing results indicated activation of the IL1-, JAK/STAT-, NFκB- and TNFα signalling pathways. These results form the basis for an NRASG12D-driven inflammatory phenotype in CRC.
Collapse
Affiliation(s)
- Natalia Kuhn
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Bertram Klinger
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Florian Uhlitz
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Anja Sieber
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Maria Rivera
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Robert-Rössle-Str. 10, D-13125, Berlin, Buch, Germany
| | - Kathleen Klotz-Noack
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Iduna Fichtner
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Robert-Rössle-Str. 10, D-13125, Berlin, Buch, Germany
| | - Jens Hoffmann
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Robert-Rössle-Str. 10, D-13125, Berlin, Buch, Germany
| | - Nils Blüthgen
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, Philippstraße 13, Building 18, D-10115, Berlin, Germany
| | - Christine Falk
- Institute of Transplant Immunology, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Christine Sers
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Reinhold Schäfer
- Laboratory of Molecular Tumor Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany; Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany.
| |
Collapse
|
23
|
Charid I, Kessler M, Darb-Esfahani S, Zemojtel T, Abobaker S, Tyuarets S, Schrauwen S, Atmani-Kilani D, Benaida-Debbache N, Schäfer R, Castillo-Tong DC, Atmani D, Cherbal F, Amant F, Sehouli J, Kulbe H, Braicu EI. Pretreatment with methanolic extract of Pistacia lentiscus L. increases sensitivity to DNA damaging drugs in primary high-grade serous ovarian cancer cells. Eur J Integr Med 2020. [DOI: 10.1016/j.eujim.2020.101163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
24
|
Lorenz KW, Schäfer R. [TEG-guided treatment of a dabigatran overdose in a patient with acute kidney failure]. Anaesthesist 2020; 69:573-578. [PMID: 32564188 DOI: 10.1007/s00101-020-00801-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 11/25/2022]
Abstract
This article presents the case of a multimorbid male patient with an accidental dabigatran overdose caused by kidney failure in the context of an acute intestinal disorder. After effective initial antagonizing of the dabigatran effect using idarucizumab a dabigatran rebound was detected caused by a single hemodialysis leading to a severe intrapulmonary hemorrhage. As dabigatran plasma level testing was not available and conventional coagulation analysis was out of interpretable range due to the impact of dabigatran, continuous thrombelastography (TEG) was used to detect the effect of dabigatran and monitor the treatment results. The most significant parameter used in the kaolin activated clotting time was the R‑time parameter, which was massively prolonged by the interrupted coagulation cascade.
Collapse
Affiliation(s)
- K-W Lorenz
- Klinik für Anästhesie, operative Intensiv- und Palliativmedizin, Klinikum Würzburg Mitte - Standort Juliusspital, Juliuspromenade 19, 97070, Würzburg, Deutschland.
| | - R Schäfer
- Klinik für Anästhesie, operative Intensiv- und Palliativmedizin, Klinikum Würzburg Mitte - Standort Juliusspital, Juliuspromenade 19, 97070, Würzburg, Deutschland
| |
Collapse
|
25
|
Lamping M, Benary M, Leyvraz S, Messerschmidt C, Blanc E, Kessler T, Schütte M, Lenze D, Jöhrens K, Burock S, Klinghammer K, Ochsenreither S, Sers C, Schäfer R, Tinhofer I, Beule D, Klauschen F, Yaspo ML, Keilholz U, Rieke DT. Support of a molecular tumour board by an evidence-based decision management system for precision oncology. Eur J Cancer 2020; 127:41-51. [PMID: 31982633 DOI: 10.1016/j.ejca.2019.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Reliable and reproducible interpretation of molecular aberrations constitutes a bottleneck of precision medicine. Evidence-based decision management systems may improve rational therapy recommendations. To cope with an increasing amount of complex molecular data in the clinical care of patients with cancer, we established a workflow for the interpretation of molecular analyses. METHODS A specialized physician screened results from molecular analyses for potential biomarkers, irrespective of the diagnostic modality. Best available evidence was retrieved and categorized through establishment of an in-house database and interrogation of publicly available databases. Annotated biomarkers were ranked using predefined evidence levels and subsequently discussed at a molecular tumour board (MTB), which generated treatment recommendations. Subsequent translation into patient treatment and clinical outcomes were followed up. RESULTS One hundred patients were discussed in the MTB between January 2016 and May 2017. Molecular data were obtained for 70 of 100 patients (50 whole exome/RNA sequencing, 18 panel sequencing, 2 immunohistochemistry (IHC)/microsatellite instability analysis). The MTB generated a median of two treatment recommendations each for 63 patients. Thirty-nine patients were treated: 6 partial responses and 12 stable diseases were achieved as best responses. Genetic counselling for germline events was recommended for seven patients. CONCLUSION The development of an evidence-based workflow allowed for the clinical interpretation of complex molecular data and facilitated the translation of personalized treatment strategies into routine clinical care. The high number of treatment recommendations in patients with comprehensive genomic data and promising responses in patients treated with combination therapy warrant larger clinical studies.
Collapse
Affiliation(s)
- Mario Lamping
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
| | - Manuela Benary
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; IRI Life Sciences, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Serge Leyvraz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Thomas Kessler
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany
| | - Moritz Schütte
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany
| | - Dido Lenze
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Korinna Jöhrens
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Sebastian Ochsenreither
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Christine Sers
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; Department of Radiooncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Frederick Klauschen
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Marie-Laure Yaspo
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany; Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestraße 63, 14195, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany; Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany.
| |
Collapse
|
26
|
Schäfer R. [RAS mutations at the molecular tumor conference]. Pathologe 2019; 40:355-359. [PMID: 31754788 DOI: 10.1007/s00292-019-00702-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Members of the rat sarcoma (RAS) gene family belong to the most frequently mutated genes that drive pathogenesis and therapy response. As the discovery of their malignant potential dates back more than three decades, cellular mutated RAS genes and their products belong to the best characterized cancer genes. Despite urgent clinical needs, RAS therapies are still elusive and limited to preclinical studies. However, very recently, novel and promising approaches have become a reality in clinical applications and trials. In the near future, interesting therapeutic options will emerge that are capable of targeting "undruggable" RAS. This will be even more important as the detection of RAS mutations has already been an integral part of routine molecular diagnostics for many years.
Collapse
Affiliation(s)
- R Schäfer
- Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
- Deutsches Krebsforschungszentrum Heidelberg, Deutsches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Deutschland.
| |
Collapse
|
27
|
Ševa J, Wiegandt DL, Götze J, Lamping M, Rieke D, Schäfer R, Jähnichen P, Kittner M, Pallarz S, Starlinger J, Keilholz U, Leser U. VIST - a Variant-Information Search Tool for precision oncology. BMC Bioinformatics 2019; 20:429. [PMID: 31419935 PMCID: PMC6697931 DOI: 10.1186/s12859-019-2958-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/18/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient's genome. This analysis relies on previously published information regarding the association of variations to disease progression and possible interventions. Clinicians to a large degree use biomedical search engines to obtain such information; however, the vast majority of scientific publications focus on basic science and have no direct clinical impact. We develop the Variant-Information Search Tool (VIST), a search engine designed for the targeted search of clinically relevant publications given an oncological mutation profile. RESULTS VIST indexes all PubMed abstracts and content from ClinicalTrials.gov. It applies advanced text mining to identify mentions of genes, variants and drugs and uses machine learning based scoring to judge the clinical relevance of indexed abstracts. Its functionality is available through a fast and intuitive web interface. We perform several evaluations, showing that VIST's ranking is superior to that of PubMed or a pure vector space model with regard to the clinical relevance of a document's content. CONCLUSION Different user groups search repositories of scientific publications with different intentions. This diversity is not adequately reflected in the standard search engines, often leading to poor performance in specialized settings. We develop a search engine for the specific case of finding documents that are clinically relevant in the course of cancer treatment. We believe that the architecture of our engine, heavily relying on machine learning algorithms, can also act as a blueprint for search engines in other, equally specific domains. VIST is freely available at https://vist.informatik.hu-berlin.de/.
Collapse
Affiliation(s)
- Jurica Ševa
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany
| | - David Luis Wiegandt
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany
| | - Julian Götze
- University Hospital Tübingen, Hoppe-Seyler-Straße 3, Tübingen, 72076, Germany
| | - Mario Lamping
- Charité Comprehensive Cancer Center, Charitéplatz 1, Berlin, 10117, Germany
| | - Damian Rieke
- Charité Comprehensive Cancer Center, Charitéplatz 1, Berlin, 10117, Germany
- Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité Unviersitätsmedizin Berlin, Hindenburgdamm 30, Berlin, 12203, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, 10117, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charitéplatz 1, Berlin, 10117, Germany
- German Cancer Consortium (DKTK), DKFZ Heidelberg, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Patrick Jähnichen
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany
| | - Madeleine Kittner
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany
| | - Steffen Pallarz
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany
| | - Johannes Starlinger
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charitéplatz 1, Berlin, 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Department of Computer Science, Humboldt-Universität zu Berlin, Rudower Chaussee 25, Berlin, 12489, Germany.
| |
Collapse
|
28
|
Pallarz S, Benary M, Lamping M, Rieke D, Starlinger J, Sers C, Wiegandt DL, Seibert M, Ševa J, Schäfer R, Keilholz U, Leser U. Comparative Analysis of Public Knowledge Bases for Precision Oncology. JCO Precis Oncol 2019; 3:PO.18.00371. [PMID: 32914021 PMCID: PMC7446431 DOI: 10.1200/po.18.00371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2019] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Precision oncology depends on the availability of up-to-date, comprehensive, and accurate information about associations between genetic variants and therapeutic options. Recently, a number of knowledge bases (KBs) have been developed that gather such information on the basis of expert curation of the scientific literature. We performed a quantitative and qualitative comparison of Clinical Interpretations of Variants in Cancer, OncoKB, Cancer Gene Census, Database of Curated Mutations, CGI Biomarkers (the cancer genome interpreter biomarker database), Tumor Alterations Relevant for Genomics-Driven Therapy, and the Precision Medicine Knowledge Base. METHODS We downloaded each KB and restructured their content to describe variants, genes, drugs, and gene-drug associations in a common format. We normalized gene names to Entrez Gene IDs and drug names to ChEMBL and DrugBank IDs. For the analysis of clinically relevant gene-drug associations, we obtained lists of genes affected by genetic alterations and putative drug therapies for 113 patients with cancer whose cases were presented at the Molecular Tumor Board (MTB) of the Charité Comprehensive Cancer Center. RESULTS Our analysis revealed that the KBs are largely overlapping but also that each source harbors a notable amount of unique information. Although some KBs cover more genes, others contain more data about gene-drug associations. Retrospective comparisons with findings of the Charitè MTB at the gene level showed that use of multiple KBs may considerably improve retrieval results. The relative importance of a KB in terms of cancer genes was assessed in more detail by logistic regression, which revealed that all but one source had a notable impact on result quality. We confirmed these findings using a second data set obtained from an independent MTB. CONCLUSION To date, none of the existing publicly available KBs on gene-drug associations in precision oncology fully subsumes the others, but all of them exhibit specific strengths and weaknesses. Consideration of multiple KBs, therefore, is essential to obtain comprehensive results.
Collapse
Affiliation(s)
| | - Manuela Benary
- Humboldt-Universität zu Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mario Lamping
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Rieke
- Charité – Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | | | - Christine Sers
- Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Jurica Ševa
- Humboldt-Universität zu Berlin, Berlin, Germany
| | - Reinhold Schäfer
- Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | | | - Ulf Leser
- Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
29
|
Pfohl U, Silvestri A, Schumacher D, Boehnke K, Haybaeck J, Bashir S, Kühn R, Keil M, Schäfer R, Walther W, Regenbrecht C. Abstract 4525: Modulating chemoresistance: Uncovering the role of mutant SMAD4R361H in colorectal cancer using PDO and PDX models. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mutations in the transforming growth factor-β (TGF-β) pathway occur frequently in colorectal cancers (CRC). TGF-β is integral for key cellular processes, including proliferation, migration, differentiation and apoptosis. TGF-β/SMAD4 controls the activation of the pathway. A previously described R361H mutation in SMAD4 has been correlated with decreased overall survival and is suspected to modulate chemoresistance. The aim of the present study is to generate CRISPR-engineered SMAD4R361H CRC organoids and to utilize them as in vitro and in vivo models to investigate the effect of SMAD4R361H mutation on drug response. We have established independent organoid (PDO) and matching patient-derived xenograft (PDX) models from 5 different regions of a chemo-naïve CRC. By targeted amplicon sequencing using a cancer hot spot gene panel, we identified the SMAD4R361H mutation in two of the 5 subpopulations, whereas three of the PDOs were SMAD4wt. Semi-automated compound screening revealed a strong resistance phenotype to afatinib, sapitinib and gefitinib as compared to the wild-type models in vitro. Similar drug response was observed in in vivo testing. To investigate the mechanism of drug resistance, we have engineered isogenic organoids (SMAD4R361H/CRISPR) from SMAD4wt organoids using CRISPR-Cas9 genome-editing. In brief, SMAD4wt organoids were transfected with an all-in-one spCas9-sgRNA-vector and a ssODN as repair template bearing the R361H point mutation. To increase homologous-directed repair, we co-transfected the organoids with a plasmid vector containing i53-bpA, an inhibitor of 53BP1. Single clones were then isolated and genotyped by locus specific PCR to confirm the particular R361H point mutation. We were able to achieve up to 50 % knock-in efficiency in these organoids. Utilizing CRISPR-Cas9, engineered SMAD4R361H/CRISPR organoids were established. These PDOs were subjected with both, native SMAD4wt and SMAD4R361H PDOs, to an in vitro drug screening, allowing for a direct comparison of their drug sensitivity. Based on these results, confirmatory in vivo experiments were designed to investigate how SMAD4 may be involved in modulating resistance in CRC organoids. These models have a prominent role in discovering the connection between genotype and phenotype in complex PDO and PDX models. While this approach is not limited to studying the role of the R361H mutation, it has a broad range of applications in understanding cancer biology, intra-tumor heterogeneity, drug response and may eventually lead to new clinical insights, including design of new therapeutic strategies.
Citation Format: Ulrike Pfohl, Alessandra Silvestri, Dirk Schumacher, Karsten Boehnke, Johannes Haybaeck, Sanam Bashir, Ralf Kühn, Marlen Keil, Reinhold Schäfer, Wolfgang Walther, Christian Regenbrecht. Modulating chemoresistance: Uncovering the role of mutant SMAD4R361H in colorectal cancer using PDO and PDX models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4525.
Collapse
Affiliation(s)
- Ulrike Pfohl
- 1Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin, Germany
| | | | - Dirk Schumacher
- 3German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Sanam Bashir
- 6Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
| | - Ralf Kühn
- 6Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
| | - Marlen Keil
- 1Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Reinhold Schäfer
- 3German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Walther
- 1Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin, Germany
| | | |
Collapse
|
30
|
Janssen G, Pourhassan M, Lenzen-Großimlinghaus R, Jäger M, Schäfer R, Spamer C, Cuvelier I, Volkert D, Wirth R. The Refeeding Syndrome revisited: you can only diagnose what you know. Eur J Clin Nutr 2019; 73:1458-1463. [PMID: 31127188 DOI: 10.1038/s41430-019-0441-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND/OBJECTIVES The Refeeding Syndrome (RFS) is a serious complication in patients receiving nutrition support after a period of severe malnutrition. We frequently recognize and diagnose the RFS due to increased awareness. Thus, we observe that many physicians do not know the RFS and that it is rarely diagnosed. The aim of the study was to determine whether physicians in Germany know the RFS. SUBJECTS/METHODS A questionnaire with a case vignette about an older person who developed the RFS after initiation of nutritional therapy was submitted to German physicians and fifth year medical students, who were participants of educational lectures. RESULTS Of the 281 participants who answered the respective question, 40 participants (14%) correctly diagnosed the RFS of the case vignette and 21 participants (8%) gave nearly correct answers. Indeed, the majority of the participants did not diagnose the RFS. CONCLUSIONS Although the RFS may lead to fatal complications, it is unknown to the majority of the queried physicians. Therefore, there is a call to implement the RFS in respective curricula and increase systematic education on this topic.
Collapse
Affiliation(s)
- G Janssen
- Department for Geriatric Medicine, Marien Hospital Herne - University Hospital, Ruhr-Universität Bochum, Herne, Germany
| | - M Pourhassan
- Department for Geriatric Medicine, Marien Hospital Herne - University Hospital, Ruhr-Universität Bochum, Herne, Germany
| | | | - M Jäger
- Hüttenhospital, Dortmund, Germany
| | - R Schäfer
- GFO Kliniken Rhein-Berg, Bergisch Gladbach, Germany
| | | | - I Cuvelier
- Department of Geriatric Medicine, ViDia Christliche Kliniken Karlsruhe, Karlsruhe, Germany
| | - D Volkert
- Institute for Biomedicine of Aging, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nürnberg, Germany
| | - R Wirth
- Department for Geriatric Medicine, Marien Hospital Herne - University Hospital, Ruhr-Universität Bochum, Herne, Germany.
| | | |
Collapse
|
31
|
Lamping M, Rieke DT, Klauschen F, Jöhrens K, Anagnostopoulos I, Lenze D, Tinhofer I, Benary M, Ochsenreither S, Klinghammer KF, Burock S, Jann H, Stüven AK, Ditzen D, Beule D, Messerschmidt C, Blanc E, Schäfer R, Keilholz U. Clinical impact of comprehensive versus targeted genomic analysis for precision oncology. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13033 Background: Panel sequencing (PS) has become a standard-of-care in cancer diagnostics. More comprehensive analyses such as whole-exome (WES) or RNA sequencing (RNAseq) allow for the detection of rare and unknown genetic aberrations that are not covered by predefined assays. The clinical impact of targeted versus comprehensive genomic assays were analyzed in patients presented at the Charité Molecular Tumor Board (MTB). Methods: Patients (pts) with advanced and/or metastatic cancer for whom no standard therapy was available were discussed in the MTB to allocate diagnostic profiling and guide biomarker-based treatment (BBT). Pts had to be < 50 years of age or diagnosed with a rare tumor entity to undergo WES/RNAseq, performed on fresh tissue. If ineligible, standard PS was performed on archival tissue. BBT recommendations, ranked by pre-specified evidence levels, were made by the MTB and pts were followed up. Results: 228 patients (median age 49 years, 108 female and 120 male) were discussed in the MTB between January 2016 and February 2019. We assigned 73 and 155 pts to PS and WES/RNAseq and results were obtained for 78.1% (n = 57/73) and 54.8% (n = 85/155) pts, respectively. Sequencing failed for 11 (PS; 15.1%) and 62 (WES/RNAseq; 40%) pts, most commonly due to insufficient tissue (n = 29). Sequencing was ongoing in 5 (PS) and 8 (WES/RNAseq) pts at the time of analysis. A median of 2 BBTs were recommended for 75.4% (43/57) of PS (range r: 1-3) and 90.6% (77/85) of WES/RNAseq pts (r: 1-6) each. 22% (n = 17/77) of WES/RNAseq pts had ≥4 BBTs made by the MTB. Treatment was initiated in 30.2% (n = 13/43) of PS and 40.2% (n = 31/77) of WES/RNAseq pts. Clinical benefit rates (CBRs) were 23.1% (2 PR, 1 SD) for PS and 45.2% (2 CR, 3 PR, 9 SD) for WES/RNAseq pts. Overall survival data was immature at the time of analysis. Conclusions: Utilizing WES/RNAseq is a feasible approach to perform tumor profiling in a heterogeneous cohort. We here show a higher rate of pts receiving confident evidence-based treatment recommendations in the WES/RNAseq group and a higher rate of treatment initiation. The CBR nearly doubled in the WES/RNAseq cohort when compared to standard PS pts, thus emphasizing the need for larger comparative analyses to guide diagnostic decision-making.
Collapse
Affiliation(s)
- Mario Lamping
- Charité Comprehensive Cancer Center, Berlin, Germany
| | | | | | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | | | | | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital and German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK), Berlin, Germany
| | - Manuela Benary
- Institute for Theoretical Biology-Humboldt University Berlin, Berlin, Germany
| | | | | | | | - Henning Jann
- Department of Gastroenterology - Charité University Medicine Berlin, Berlin, Germany
| | - Anna Kathrin Stüven
- Department of Gastroenterology - Charité University Medicine Berlin, Berlin, Germany
| | - Doreen Ditzen
- Charité - University Medicine Berlin, German Cancer Consortium (DKTK), Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | | | - Eric Blanc
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | | | | |
Collapse
|
32
|
Schumacher D, Andrieux G, Boehnke K, Keil M, Silvestri A, Silvestrov M, Keilholz U, Haybaeck J, Erdmann G, Sachse C, Templin M, Hoffmann J, Boerries M, Schäfer R, Regenbrecht CRA. Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures. PLoS Genet 2019; 15:e1008076. [PMID: 30925167 PMCID: PMC6457557 DOI: 10.1371/journal.pgen.1008076] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/10/2019] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Organoid cultures derived from colorectal cancer (CRC) samples are increasingly used as preclinical models for studying tumor biology and the effects of targeted therapies under conditions capturing in vitro the genetic make-up of heterogeneous and even individual neoplasms. While 3D cultures are initiated from surgical specimens comprising multiple cell populations, the impact of tumor heterogeneity on drug effects in organoid cultures has not been addressed systematically. Here we have used a cohort of well-characterized CRC organoids to study the influence of tumor heterogeneity on the activity of the KRAS/MAPK-signaling pathway and the consequences of treatment by inhibitors targeting EGFR and downstream effectors. MAPK signaling, analyzed by targeted proteomics, shows unexpected heterogeneity irrespective of RAS mutations and is associated with variable responses to EGFR inhibition. In addition, we obtained evidence for intratumoral heterogeneity in drug response among parallel “sibling” 3D cultures established from a single KRAS-mutant CRC. Our results imply that separate testing of drug effects in multiple subpopulations may help to elucidate molecular correlates of tumor heterogeneity and to improve therapy response prediction in patients. Commonly occurring genetic alterations and patient-specific genetic features are increasingly used to predict the possible action of targeted cancer therapies. Although several lines of evidence have suggested that preclinical and clinical responses concur, the heterogeneity of tumors remains a severe obstacle in routinely translating preclinical data to patient treatments. Here we present a rapid work flow that integrates drug testing of three-dimensional patient tumor-derived (organoid) cultures and assessment of their genetic make-up as well as that of their donor tumors by amplicon sequencing and targeted proteomics. While the organoid cultures largely recapitulated the genomic profiles of donor tumors, the overall treatment responses and inhibitor effects on the intracellular signaling system were quite variable. Notably, organoid cultures obtained by synchronous multi-regional sampling of the same colorectal tumor showed an up to 30-fold difference in drug response. A combinatorial drug treatment improved the response. These data were confirmed in matched mouse xenograft models from the same tumor. Our findings may help to refine preclinical testing of individual tumors by modelling heterogeneity in cultures, to better understand therapeutic failure in clinical settings and to find ways to overcome treatment resistance.
Collapse
Affiliation(s)
- Dirk Schumacher
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Geoffroy Andrieux
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Karsten Boehnke
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Translational Research, New York, NY, United States of America
| | - Marlen Keil
- EPO Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | | | | | | | - Johannes Haybaeck
- Department of Pathology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Department of Pathology, Neuropathology, and Molecular Pathology, Medical University of Innsbruck, Austria.,Diagnostic & Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, Austria
| | - Gerrit Erdmann
- NMI TT Pharmaservices, Berlin, Germany.,ASC Oncology GmbH, Berlin, Germany
| | - Christoph Sachse
- NMI TT Pharmaservices, Berlin, Germany.,ASC Oncology GmbH, Berlin, Germany
| | - Markus Templin
- ASC Oncology GmbH, Berlin, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jens Hoffmann
- EPO Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Reinhold Schäfer
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Charité Comprehensive Cancer Center, Berlin, Germany
| | - Christian R A Regenbrecht
- cpo-Cellular Phenomics & Oncology Berlin-Buch GmbH, Berlin, Germany.,Department of Pathology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,ASC Oncology GmbH, Berlin, Germany
| |
Collapse
|
33
|
|
34
|
Bormann F, Stinzing S, Tierling S, Morkel M, Markelova MR, Walter J, Weichert W, Roßner F, Kuhn N, Perner J, Dietz J, Ispasanie S, Dietel M, Schäfer R, Heinemann V, Sers C. Epigenetic regulation of Amphiregulin and Epiregulin in colorectal cancer. Int J Cancer 2018; 144:569-581. [PMID: 30252132 DOI: 10.1002/ijc.31892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/05/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Abstract
Expression of the epidermal growth factor ligands amphiregulin (AREG) and epiregulin (EREG) is positively correlated with a response to EGFR-targeted therapies in colorectal cancer. Gene-body methylation sites, which show a strong inverse correlation with AREG and EREG gene expression, were identified in cell lines using targeted 454 FLX-bisulfite sequencing and SIRPH analyses for AREG/EREG promoters and intragenic CpGs. Upon treatment of colorectal cancer cells with 5-aza-2'-desoxycytidine, methylation decreases at specific intragenic CpGs accompanied by upregulation of AREG and EREG gene expression. The same AREG gene-body methylation was also found in human colorectal cancer samples and is independent of KRAS and NRAS mutations. Methylation is specifically decreased in the tumor epithelial compartment as compared to stromal tissue and normal epithelium. Investigation of a promoter/enhancer function of the AREG exon 2 region revealed a potential promoter function in reverse orientation. Retrospective comparison of the predictive power of AREG gene-body methylation versus AREG gene expression using samples from colorectal cancer patients treated with anti-EGFR inhibitors with complete clinical follow-up revealed that AREG expression is superior to AREG gene methylation. AREG and EREG genes undergo a complex regulation involving both intragenic methylation and promoter-dependent control.
Collapse
Affiliation(s)
- Felix Bormann
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Sebastian Stinzing
- Department of Hematology and Medical Oncology, Klinikum der Universität München (LMU); German Cancer Consortium site Munich (DKTK); German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken
| | - Markus Morkel
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | | | - Jörn Walter
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken
| | - Wilko Weichert
- DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany.,Institute of Pathology, Technical University Munich, Germany and Munich German Cancer Consortium (DKTK), German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Florian Roßner
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Natalia Kuhn
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Juliane Perner
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Johanna Dietz
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Sylvia Ispasanie
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin, Germany
| | - Manfred Dietel
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | - Reinhold Schäfer
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | - Volker Heinemann
- Department of Hematology and Medical Oncology, Klinikum der Universität München (LMU); German Cancer Consortium site Munich (DKTK); German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Christine Sers
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| |
Collapse
|
35
|
Zhou N, Schäfer R, Li T, Fang M, Liu L. A primary undifferentiated pleomorphic sarcoma of the lumbosacral region harboring a LMNA-NTRK1 gene fusion with durable clinical response to crizotinib: a case report. BMC Cancer 2018; 18:842. [PMID: 30134855 PMCID: PMC6106902 DOI: 10.1186/s12885-018-4749-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/14/2018] [Indexed: 01/13/2023] Open
Abstract
Background High-grade spindle cell sarcomas are a subtype of rare, undifferentiated pleomorphic sarcomas (UPSs) for which diagnosis is difficult and no specific treatment strategies have been established. The limited published data on UPSs suggest an aggressive clinical course, high rates of local recurrence and distant metastasis, and poor prognosis. Case presentation Here we present the unusual case of a 45-year-old male patient with a lumbosacral UPS extending into the sacrum. An initial diagnosis of a low-grade malignant spindle cell tumor was based on a tumor core biopsy. After complete extensive resection, the diagnosis of an UPS of the lumbosacral region was confirmed by excluding other types of cancers. Despite treatment with neoadjuvant radiotherapy, extensive resection, and adjuvant chemotherapy, the patient presented with multiple pulmonary metastases 3 months after surgery. The patient then began treatment with crizotinib at an oral dose of 450 mg per day, based on the detection of a LMNA-NTRK1 fusion gene in the tumor by next-generation sequencing. Over 18 months of follow-up through July 2018, the patient maintained a near-complete clinical response to crizotinib. Conclusions The LMNA-NTRK1 fusion was likely the molecular driver of tumorigenesis and metastasis in this patient, and the observed effectiveness of crizotinib treatment provides clinical validation of this molecular target. Molecular and cytogenetic evaluations are critical to accurate prognosis and treatment planning in cases of UPS, especially when treatment options are limited or otherwise exhausted. Molecularly targeted therapy of these rare but aggressive lesions represents a novel treatment option that may lead to fewer toxic side effects and better clinical outcomes. Electronic supplementary material The online version of this article (10.1186/s12885-018-4749-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ning Zhou
- Department of Abdominal Radiotherapy, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, People's Republic of China.,Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Tao Li
- Department of Bone and Soft-tissue Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, People's Republic of China
| | - Meiyu Fang
- Department of Integration of Traditional Chinese and Western Medicine, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, People's Republic of China
| | - Luying Liu
- Department of Abdominal Radiotherapy, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, 310022, People's Republic of China.
| |
Collapse
|
36
|
Leyvraz S, Kessler T, Schütte M, Lamping M, Burock S, Ochsenreither S, Amstislavskiy V, Wierling C, Jöhrens K, Klauschen F, Peuker CA, Kiecker F, Schäfer R, Lange B, Lehrach H, Joussen A, Rieke DT, Klinghammer KF, Keilholz U, Yaspo ML. Treatment of metastatic uveal melanoma (mUM) directed by a comprehensive molecular tumour analysis program (CMTA). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.9566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Serge Leyvraz
- Charité Comprehensive Cancer Center, Berlin, Germany
| | | | | | - Mario Lamping
- Charité Comprehensive Cancer Center, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Berlin, Germany
| | | | - Vyacheslav Amstislavskiy
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Korinna Jöhrens
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany
| | | | - Caroline-Anna Peuker
- Departement of Hematology and Medical Oncology, Charité Universitätsmedizin, Berlin, Germany
| | - Felix Kiecker
- Dermatology Department, Charité Universitätsmedizin, Berlin, Germany
| | | | - Bodo Lange
- Alacris Theranostics GmbH, Berlin, Germany
| | | | | | | | | | | | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
37
|
Rieke DT, Lamping M, Klauschen F, Ochsenreither S, Schütte M, Kessler T, Klinghammer KF, Jöhrens K, Messerschmidt C, Lenze D, Burock S, Ditzen D, Schäfer R, Pavel M, Tinhofer I, Sers C, Beule D, Yaspo ML, Leyvraz S, Keilholz U. Efficacy of a structured workflow for the interpretation of comprehensive genomic analysis data in clinical routine. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e24164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Mario Lamping
- Charité Comprehensive Cancer Center, Berlin, Germany
| | | | | | | | | | | | - Korinna Jöhrens
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany
| | | | - Dido Lenze
- Institute of Pathology, Charite - University Medicine Berlin, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Berlin, Germany
| | - Doreen Ditzen
- Charité - University Medicine Berlin, German Cancer Consortium (DKTK), Berlin, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charite-Universitatsmedizin Berlin, Berlin, Germany
| | - Marianne Pavel
- Charite-Universitatsmedizin Berlin/Campus Virchow Klinikum, Berlin, Germany
| | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital and German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK), Berlin, Germany
| | | | - Dieter Beule
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | |
Collapse
|
38
|
Khong S, Lee M, Khong D, Kosaric N, Duscher D, Dong Y, Schäfer R, Gurtner G. 1407 Single-cell transcriptomics of human mesenchymal stem cells reveal age-related cellular subpopulation depletion and impaired regenerative gene expression. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
39
|
Schäfer R, Strnad V, Polgár C, Uter W, Hildebrandt G, Ott O, Kauer-Dorner D, Knauerhase H, Major T, Lyczek J, Guinot J, Dunst J, Gutierrez Miguelez C, Slampa P, Allgäuer M, Lössl K, Kovacs G, Fietkau R, Resch A, Kulik A, Arribas L, Niehoff P, Guedea F, Gall C, Polat B. OC-0326: QOL After APBI (Multicatheter Brachytherapy) Versus WBI: 5-Year Results, Phase 3 GEC-ESTRO Trial. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)30636-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
40
|
Shayeghi A, Pašteka LF, Götz DA, Schwerdtfeger P, Schäfer R. Spin–orbit effects in optical spectra of gold–silver trimers. Phys Chem Chem Phys 2018; 20:9108-9114. [DOI: 10.1039/c8cp00672e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photodissociation spectra of cationic gold–silver trimers are analysed using relativistic electronic structure theories paying special attention to the importance of spin–orbit and charge transfer effects.
Collapse
Affiliation(s)
- A. Shayeghi
- Vienna Center for Quantum Science and Technology
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
| | - L. F. Pašteka
- Centre for Theoretical Chemistry and Physics
- The New Zealand Institute for Advanced Study
- Massey University Auckland
- 0632 Auckland
- New Zealand
| | - D. A. Götz
- Eduard-Zintl-Institut
- Technische Universität Darmstadt
- 64287 Darmstadt
- Germany
| | - P. Schwerdtfeger
- Centre for Theoretical Chemistry and Physics
- The New Zealand Institute for Advanced Study
- Massey University Auckland
- 0632 Auckland
- New Zealand
| | - R. Schäfer
- Eduard-Zintl-Institut
- Technische Universität Darmstadt
- 64287 Darmstadt
- Germany
| |
Collapse
|
41
|
Strunk D, Lozano M, Marks DC, Loh YS, Gstraunthaler G, Schennach H, Rohde E, Laner-Plamberger S, Öller M, Nystedt J, Lotfi R, Rojewski M, Schrezenmeier H, Bieback K, Schäfer R, Bakchoul T, Waidmann M, Jonsdottir-Buch SM, Montazeri H, Sigurjonsson OE, Iudicone P, Fioravanti D, Pierelli L, Introna M, Capelli C, Falanga A, Takanashi M, Lόpez-Villar O, Burnouf T, Reems JA, Pierce J, Preslar AM, Schallmoser K. International Forum on GMP-grade human platelet lysate for cell propagation: summary. Vox Sang 2017; 113:80-87. [PMID: 29076169 DOI: 10.1111/vox.12593] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- D Strunk
- Institute of Experimental and Clinical Cell Therapy, Paracelsus Medical University, Salzburg, Austria
| | - M Lozano
- Hospital Clinic, Department of Hemotherapy and Hemostasis, Hospital Clínic University of Barcelona , Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - K Schallmoser
- Department of Blood Group Serology and Transfusion Medicine, Paracelsus Medical University Hospital Salzburg, Salzburg, Austria
| |
Collapse
|
42
|
Strunk D, Lozano M, Marks DC, Loh YS, Gstraunthaler G, Schennach H, Rohde E, Laner-Plamberger S, Öller M, Nystedt J, Lotfi R, Rojewski M, Schrezenmeier H, Bieback K, Schäfer R, Bakchoul T, Waidmann M, Jonsdottir-Buch SM, Montazeri H, Sigurjonsson OE, Iudicone P, Fioravanti D, Pierelli L, Introna M, Capelli C, Falanga A, Takanashi M, López-Villar O, Burnouf T, Reems JA, Pierce J, Preslar AM, Schallmoser K. International Forum on GMP-grade human platelet lysate for cell propagation. Vox Sang 2017; 113:e1-e25. [PMID: 29071726 DOI: 10.1111/vox.12594] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - D C Marks
- Australian Red Cross Blood Service, Research and Development, 17 O'Riordan Street, Sydney, New South Wales, 2015, Australia
| | - Y S Loh
- Australian Red Cross Blood Service, Research and Development, 17 O'Riordan Street, Sydney, New South Wales, 2015, Australia
| | - G Gstraunthaler
- Division of Physiology, Medical University Innsbruck, Schöpfstr. 41, Innsbruck, A-6020, Austria
| | - H Schennach
- Central Institute of Blood Transfusion and Immunology, University Hospital Innsbruck, Anichstr. 35, Innsbruck, A-6020, Austria
| | - E Rohde
- Department of Blood Group Serology and Transfusion Medicine, Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Lindhofstrasse 20-22, Salzburg, 5020, Austria
| | - S Laner-Plamberger
- Department of Blood Group Serology and Transfusion Medicine, Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Lindhofstrasse 20-22, Salzburg, 5020, Austria
| | - M Öller
- Department of Blood Group Serology and Transfusion Medicine, Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Lindhofstrasse 20-22, Salzburg, 5020, Austria
| | - J Nystedt
- Finnish Red Cross Blood Service, Advanced Cell Therapy Centre, Kivihaantie 7, FI-00310, Helsinki, Finland
| | - R Lotfi
- Institute for Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service, Baden-Wuerttemberg-Hessen , University Hospital Ulm, University of Ulm, Helmholtzstr. 10, Ulm, 89081, Germany
| | - M Rojewski
- Institute for Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service, Baden-Wuerttemberg-Hessen , University Hospital Ulm, University of Ulm, Helmholtzstr. 10, Ulm, 89081, Germany
| | - H Schrezenmeier
- Institute for Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service, Baden-Wuerttemberg-Hessen , University Hospital Ulm, University of Ulm, Helmholtzstr. 10, Ulm, 89081, Germany
| | - K Bieback
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Heidelberg University, Friedrich-Ebert Str. 107, Mannheim, D-68167, Germany
| | - R Schäfer
- Institute for Transfusion Medicine and Immunohematology, German Red Cross Blood Donor Service Baden-Württemberg- Hessen gGmbH, Goethe-University Hospital, Sandhofstrasse 1, Frankfurt am Main, D-60528, Germany
| | - T Bakchoul
- Center for Clinical Transfusion Medicine, Otfried-Müller-Strasse 4/1, D-72076 , Tuebingen, Germany
| | - M Waidmann
- Center for Clinical Transfusion Medicine, Otfried-Müller-Strasse 4/1, D-72076 , Tuebingen, Germany
| | - S M Jonsdottir-Buch
- The Blood Bank, Landspitali University Hospital, Snorrabraut 60, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101, Reykjavik, Iceland.,Platome Biotechnology, Alfaskeid 27, 220, Hafnarfjordur, Iceland
| | - H Montazeri
- The Blood Bank, Landspitali University Hospital, Snorrabraut 60, 101, Reykjavik, Iceland.,Platome Biotechnology, Alfaskeid 27, 220, Hafnarfjordur, Iceland
| | - O E Sigurjonsson
- The Blood Bank, Landspitali University Hospital, Snorrabraut 60, 101, Reykjavik, Iceland.,Platome Biotechnology, Alfaskeid 27, 220, Hafnarfjordur, Iceland.,School of Science and Engineering, University of Reykjavik, Menntavegur 1, 101, Reykjavik, Iceland
| | - P Iudicone
- San Camillo Forlanini Hospital, Circonvallazione Gianicolense 87, Rome, 00152, Italy
| | - D Fioravanti
- San Camillo Forlanini Hospital, Circonvallazione Gianicolense 87, Rome, 00152, Italy
| | - L Pierelli
- Department of Experimental Medicine, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185, Italy
| | - M Introna
- QP USS Centro di Terapia Cellulare 'G. Lanzani', USC Ematologia, ASST Papa Giovanni XXIII, Via Garibaldi 11/13, Bergamo, 24124, Italy
| | - C Capelli
- USS Centro di Terapia Cellulare 'G. Lanzani', USC Ematologia, ASST Papa Giovanni XXIII, Via Garibaldi 11/13, Bergamo, 24124, Italy
| | - A Falanga
- Division of Immunohematology and Transfusion Medicine, ASST Papa Giovanni XXIII, Piazza OMS 1, Bergamo, 24127, Italy
| | - M Takanashi
- Japanese Red Cross Blood Service Headquarters, 1-2-1 Shiba-koen, Minato-ku, Tokyo, 105-0011, Japan
| | - O López-Villar
- Department of Hematology, University Hospital of Salamanca, P/San Vicente 58-182, Salamanca, 37007, Spain
| | - T Burnouf
- Graduate Institute of Biomedical Materials and Tissue Engineering, International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, 250 Wu-Shin Street, Taipei, 101, Taiwan
| | - J A Reems
- Division of Hematology and Hematologic Malignancies, Department of Medicine, University of Utah Cell Therapy and Regenerative Medicine, 675 Arapeen, Suite 300, Salt Lake City, Utah, 84108, USA
| | - J Pierce
- Division of Hematology and Hematologic Malignancies, Department of Medicine, University of Utah Cell Therapy and Regenerative Medicine, 675 Arapeen, Suite 300, Salt Lake City, Utah, 84108, USA
| | - A M Preslar
- Division of Hematology and Hematologic Malignancies, Department of Medicine, University of Utah Cell Therapy and Regenerative Medicine, 675 Arapeen, Suite 300, Salt Lake City, Utah, 84108, USA
| | | |
Collapse
|
43
|
Abstract
A new technique for contrast separation in wide-field magneto-optical Kerr microscopy is introduced. Utilizing the light from eight light emitting diodes, guided to the microscope by glass fibers and being switched synchronously with the camera exposure, domain images with orthogonal in-plane sensitivity can be displayed simultaneously at real-time, and images with pure in-plane or polar contrast can be obtained. The benefit of this new method of contrast separation is demonstrated for Permalloy films, a NdFeB sinter magnet, and a cobalt crystal. Moreover, the new technique is shown to strongly enhance the sensitivity of Kerr microscopy by eliminating parasitic contrast contributions occurring in conventional setups. A doubling of the in-plane domain contrast and a sensitivity to Kerr rotations as low as 0.6 mdeg is demonstrated.
Collapse
Affiliation(s)
- I V Soldatov
- Institute for Metallic Materials, Leibniz Institute for Solid State and Materials Research (IFW) Dresden, Helmholtzstrasse 20, D-01069 Dresden, Germany and Institute of Natural Sciences, Ural Federal University, 620002 Ekaterinburg, Russia
| | - R Schäfer
- Institute for Metallic Materials, Leibniz Institute for Solid State and Materials Research (IFW) Dresden, Helmholtzstrasse 20, D-01069 Dresden, Germany and Institute for Materials Science, TU Dresden, 01062 Dresden, Germany
| |
Collapse
|
44
|
Elger B, Schmidt T, Krähling S, Neuberger F, Schäfer R. Electrostatic simulation of a complete cluster deposition apparatus. Rev Sci Instrum 2017; 88:063303. [PMID: 28667987 DOI: 10.1063/1.4984968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A complete electrostatic model of a cluster deposition apparatus is presented using SIMION. It consists of fifteen different ion optical components including a quadrupole mass filter and a quadrupole ion deflector. The accuracy of the model was tested by comparing calculated cationic cluster transmissions with experimental ion currents by varying the electrostatic potential of different components. Considering the negatively charged particles produced by the magnetron cluster source as a charged background with a density of 5⋅10-7 cm-3, the influence of the first components on cluster transmission is well reproduced in comparison to the experimental results. This background was included by increasing the charge of the clusters from zero to an elementary charge using a sigmoidal function. The inflection point of this function was found to depend on the first components' electrostatic potential but in good approximation, not on later ones. All of the calculated transmissions represent the experimental data quite well; therefore, the simulation is validated and helps us to understand the influence of the electrostatic components on cluster transmission and improve the target efficiency. Furthermore, this understanding opens the possibility for a global optimization scheme to be employed in the ion optics' geometries.
Collapse
Affiliation(s)
- B Elger
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - T Schmidt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - S Krähling
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - F Neuberger
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - R Schäfer
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| |
Collapse
|
45
|
Le LD, Mansmann UR, Jung A, Kirchner T, Schäfer R, Neureiter D, Holch JW, Heinemann V, Stintzing S. Is the primary tumor location (PTL) associated with differential gene expression profiles in patients with metastatic colorectal cancer (mCRC)? Analysis of the FIRE1-trial. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.4_suppl.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
598 Background: Site-differential molecular characteristics of PTL as well as its influence on overall survival have been reported. In our study, we investigated the association of PTL with gene- and pathway-wise RNA expression as well as its representation in RAS mutational status subgroups. Methods: The phase-III-trial FIRE-1 compared the efficacy of FuFIRI and mIROX in patients with mCRC. Formalin-fixed, paraffin-embedded pretreatment samples from 166 FIRE-I patients were collected. The splenic flexure was used for differentiation between left colon cancer (LC) and right colon cancer (RC). RAS mutated PTs (RASmut) had PCR confirmed mutations in KRAS gene (Exon 2, 3, or 4) or in NRAS gene (Exon 2, 3, or 4). RNA expression profiling used the nCounter(R) PanCancer Pathways Panel including DNA damage control and TGF-β. We also studied a set of selected genes (Aprataxin, AREG, CD3EAP, CES1, CES2, CMPK1, DPD, DUT, ERCC1, ERCC5, EREG, FGF2, GSTP1, KLC3, MTHFR, PPP1R13L, RCC1, TOPO1, TP, TS, and UGT1A1). The gene-wise analyses used Limma and the permutated t-test with appropriate multiple testing adjustment. Holistic pathway investigation used GlobalAncova and the global tests. RAS mutation status and its correlation with tumor side were included as factors in both analyses. Additionally, gene- and pathway-wise analyses were performed in RASmut and RASWTsubgroups. Results: A total of 83 (50%) of 166 patients had any RAS mutation. A total of 28 (17%) patients had PTs on the right side and 13 of those (46%) were RASmut. The top ten differentially expressed genes between LC and RC are MMP9, ERCC3, MAP3K1, RRAS2, SOCS3, RB1, TGFβ1, LEFTY1, NKD1, and CDC25B (unadjusted p-values < 0.005). Potential enrichment in the DNA damage control pathway was found (p = 0.008). The RAS subgroup analyses showed a non-overlapping top ten list. Side specific effects may exist for the TGF-β pathway and the selected gene set in RASWTpatients. Conclusions: No strong association between PTL and gene expression showed up in mCRC tumors nor RAS subgroups. Potentially differential gene expression may exist for specific genes, two pathways and our selected gene set.
Collapse
Affiliation(s)
- Lien D. Le
- Institute of Medical Informatics, Biostatistics, and Epidemiology, LMU, Munich, Germany
| | | | - Andreas Jung
- Pathologisches Institut der Ludwig-Maximilians-Universitat Munchen, Munchen, Germany
| | - Thomas Kirchner
- Department of Pathology, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charite-Universitatsmedizin Berlin, Berlin, Germany
| | | | - Julian Walter Holch
- Comprehensive Cancer Center, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Volker Heinemann
- Comprehensive Cancer Center, Ludwig-Maximilian-University of Munich, Munich, Germany
| | | |
Collapse
|
46
|
Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
Collapse
Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany.,NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| |
Collapse
|
47
|
Redmer T, Walz I, Klinger B, Khouja S, Welte Y, Schäfer R, Regenbrecht C. The role of the cancer stem cell marker CD271 in DNA damage response and drug resistance of melanoma cells. Oncogenesis 2017; 6:e291. [PMID: 28112719 PMCID: PMC5294251 DOI: 10.1038/oncsis.2016.88] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/31/2016] [Accepted: 11/25/2016] [Indexed: 12/14/2022] Open
Abstract
Several lines of evidence have suggested that stemness and acquired resistance to targeted inhibitors or chemotherapeutics are mechanistically linked. Here we observed high cell surface and total levels of nerve growth factor receptor/CD271, a marker of melanoma-initiating cells, in sub-populations of chemoresistant cell lines. CD271 expression was increased in drug-sensitive cells but not resistant cells in response to DNA-damaging chemotherapeutics etoposide, fotemustine and cisplatin. Comparative analysis of melanoma cells engineered to stably express CD271 or a targeting short hairpin RNA by expression profiling provided numerous genes regulated in a CD271-dependent manner. In-depth analysis of CD271-responsive genes uncovered the association of CD271 with regulation of DNA repair components. In addition, gene set enrichment analysis revealed enrichment of CD271-responsive genes in drug-resistant cells, among them DNA repair components. Moreover, our comparative screen identified the fibroblast growth factor 13 (FGF13) as a target of CD271, highly expressed in chemoresistant cells. Further we show that levels of CD271 determine drug response. Knock-down of CD271 in fotemustine-resistant cells decreased expression of FGF13 and at least partly restored sensitivity to fotemustine. Together, we demonstrate that expression of CD271 is responsible for genes associated with DNA repair and drug response. Further, we identified 110 CD271-responsive genes predominantly expressed in melanoma metastases, among them were NEK2, TOP2A and RAD51AP1 as potential drivers of melanoma metastasis. In addition, we provide mechanistic insight in the regulation of CD271 in response to drugs. We found that CD271 is potentially regulated by p53 and in turn is needed for a proper p53-dependent response to DNA-damaging drugs. In summary, we provide for the first time insight in a CD271-associated signaling network connecting CD271 with DNA repair, drug response and metastasis.
Collapse
Affiliation(s)
- T Redmer
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - I Walz
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - B Klinger
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - S Khouja
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Y Welte
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - R Schäfer
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - C Regenbrecht
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,CPO-Cellular Phenomics and Oncology Berlin-Buch GmbH, Berlin, Germany
| |
Collapse
|
48
|
Abstract
The scope of this project covers the storing of result data produced by generic laboratory devices during processing of analytical experiments, the data describing the examination methods, and the audit trail using the Analytical Information Markup Language (AnIML) standard. This project also considers the integration of generic devices in automated laboratory environments. AnIML is an upcoming ASTM standard format for recording analytical data and workflows with accompanying experimental metadata. Adapting this standard to existing instruments currently requires manual intervention. The goal of this project is to automate as many steps as possible in generating an AnIML document with all its essential information supplied directly by the analytical instrument. Software with such functionality could be integrated into analytical instruments or reside in firmware boxes hooked to the instruments. This would allow a smooth transition to the new standard even in complex existing environments. A set of prerequisites have to be fulfilled before the feasibility of this approach can be shown. The prototype application we describe here integrates the generic description of an instrument using the Laboratory Equipment Control Interface Specification, Object Management Group (LECIS OMG) Device Capability Dataset. Information about the device's commands and the device's data stream with its semantics can be found there. The experiment's metadata are provided by the test order. In both cases, XML schemas contain the information syntax. Using this information, we developed a generic interface that maps the result stream semantically and then transforms it into an AnIML document without manual intervention. At this time, we have completed and tested a prototype implementation and are working to support the full functionality of both the LECIS OMG and the ASTM AnIML standards. (JALA 2006;11:247–53)
Collapse
Affiliation(s)
- Alexander Roth
- National Institute of Standards and Technology, Gaithersburg, MD
- University of Applied Sciences, Wiesbaden, Germany
| | - Ronny Jopp
- National Institute of Standards and Technology, Gaithersburg, MD
- University of Applied Sciences, Wiesbaden, Germany
| | | | - Gary W. Kramer
- National Institute of Standards and Technology, Gaithersburg, MD
| |
Collapse
|
49
|
Rohr I, Sehouli J, En-Nia A, Heinrich M, Richter R, Chekerov R, Dechend R, Heidecke H, Dragun D, Schäfer R, Gorny X, Lindquist J, Brandt S, Braicu E, Mertens P. Y-box protein-1/p18 as novel serum marker for ovarian cancer diagnosis: A study by the Tumor Bank Ovarian Cancer (TOC). Geburtshilfe Frauenheilkd 2016. [DOI: 10.1055/s-0036-1593015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
50
|
Menyhárt O, Harami-Papp H, Sukumar S, Schäfer R, Magnani L, de Barrios O, Győrffy B. Guidelines for the selection of functional assays to evaluate the hallmarks of cancer. Biochim Biophys Acta Rev Cancer 2016; 1866:300-319. [PMID: 27742530 DOI: 10.1016/j.bbcan.2016.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 01/05/2023]
Abstract
The hallmarks of cancer capture the most essential phenotypic characteristics of malignant transformation and progression. Although numerous factors involved in this multi-step process are still unknown to date, an ever-increasing number of mutated/altered candidate genes are being identified within large-scale cancer genomic projects. Therefore, investigators need to be aware of available and appropriate techniques capable of determining characteristic features of each hallmark. We review the methods tailored to experimental cancer researchers to evaluate cell proliferation, programmed cell death, replicative immortality, induction of angiogenesis, invasion and metastasis, genome instability, and reprogramming of energy metabolism. Selecting the ideal method is based on the investigator's goals, available equipment and also on financial constraints. Multiplexing strategies enable a more in-depth data collection from a single experiment - obtaining several results from a single procedure reduces variability and saves time and relative cost, leading to more robust conclusions compared to a single end point measurement. Each hallmark possesses characteristics that can be analyzed by immunoblot, RT-PCR, immunocytochemistry, immunoprecipitation, RNA microarray or RNA-seq. In general, flow cytometry, fluorescence microscopy, and multiwell readers are extremely versatile tools and, with proper sample preparation, allow the detection of a vast number of hallmark features. Finally, we also provide a list of hallmark-specific genes to be measured in transcriptome-level studies. Although our list is not exhaustive, we provide a snapshot of the most widely used methods, with an emphasis on methods enabling the simultaneous evaluation of multiple hallmark features.
Collapse
Affiliation(s)
- Otília Menyhárt
- MTA TTK Lendület Cancer Biomarker Research Group, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | | | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Reinhold Schäfer
- German Cancer Consortium (DKTK), DKFZ, Im Neuenheimer Feld 280, D-69120 Heidelberg and Charité Comprehensive Cancer Center, Invalidenstr. 80, D-10115 Berlin, Germany
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Oriol de Barrios
- Group of Transcriptional Regulation of Gene Expression, Department of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Magyar tudósok körútja 2, H-1117 Budapest, Hungary; 2nd Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary.
| |
Collapse
|