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Hart T, Brown KR, Sircoulomb F, Rottapel R, Moffat J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol Syst Biol 2014; 10:733. [PMID: 24987113 PMCID: PMC4299491 DOI: 10.15252/msb.20145216] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Technological advancement has opened the door to systematic genetics in mammalian cells.
Genome-scale loss-of-function screens can assay fitness defects induced by partial gene knockdown,
using RNA interference, or complete gene knockout, using new CRISPR techniques. These screens can
reveal the basic blueprint required for cellular proliferation. Moreover, comparing healthy to
cancerous tissue can uncover genes that are essential only in the tumor; these genes are targets for
the development of specific anticancer therapies. Unfortunately, progress in this field has been
hampered by off-target effects of perturbation reagents and poorly quantified error rates in
large-scale screens. To improve the quality of information derived from these screens, and to
provide a framework for understanding the capabilities and limitations of CRISPR technology, we
derive gold-standard reference sets of essential and nonessential genes, and provide a Bayesian
classifier of gene essentiality that outperforms current methods on both RNAi and CRISPR screens.
Our results indicate that CRISPR technology is more sensitive than RNAi and that both techniques
have nontrivial false discovery rates that can be mitigated by rigorous analytical methods.
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Affiliation(s)
- Traver Hart
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Kevin R Brown
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Fabrice Sircoulomb
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, ON, Canada
| | - Robert Rottapel
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, ON, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada Division of Rheumatology, Department of Medicine, St. Michael's Hospital, Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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52
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Toniatti C, Jones P, Graham H, Pagliara B, Draetta G. Oncology Drug Discovery: Planning a Turnaround. Cancer Discov 2014; 4:397-404. [DOI: 10.1158/2159-8290.cd-13-0452] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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53
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Targeting components of the alternative NHEJ pathway sensitizes KRAS mutant leukemic cells to chemotherapy. Blood 2014; 123:2355-66. [PMID: 24505083 DOI: 10.1182/blood-2013-01-477620] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Activating KRAS mutations are detected in a substantial number of hematologic malignancies. In a murine T-cell acute lymphoblastic leukemia (T-ALL) model, we previously showed that expression of oncogenic Kras induced a premalignant state accompanied with an arrest in T-cell differentiation and acquisition of somatic Notch1 mutations. These findings prompted us to investigate whether the expression of oncogenic KRAS directly affects DNA damage repair. Applying divergent, but complementary, genetic approaches, we demonstrate that the expression of KRAS mutants is associated with increased expression of DNA ligase 3α, poly(ADP-ribose) polymerase 1 (PARP1), and X-ray repair cross-complementing protein 1 (XRCC1), all essential components of the error-prone, alternative nonhomologous end-joining (alt-NHEJ) pathway. Functional studies revealed delayed repair kinetics, increased misrepair of DNA double-strand breaks, and the preferential use of microhomologous DNA sequences for end joining. Similar effects were observed in primary murine T-ALL blasts. We further show that KRAS-mutated cells, but not KRAS wild-type cells, rely on the alt-NHEJ repair pathway on genotoxic stress. RNA interference-mediated knockdown of DNA ligase 3α abolished resistance to apoptotic cell death in KRAS-mutated cells. Our data indicate that targeting components of the alt-NHEJ pathway sensitizes KRAS-mutated leukemic cells to standard chemotherapeutics and represents a promising approach for inducing synthetic lethal vulnerability in cells harboring otherwise nondruggable KRAS mutations.
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54
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Finding effective cancer therapies through loss of function genetic screens. Curr Opin Genet Dev 2014; 24:23-9. [DOI: 10.1016/j.gde.2013.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/12/2013] [Accepted: 11/13/2013] [Indexed: 01/27/2023]
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55
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Bryant KL, Mancias JD, Kimmelman AC, Der CJ. KRAS: feeding pancreatic cancer proliferation. Trends Biochem Sci 2014; 39:91-100. [PMID: 24388967 DOI: 10.1016/j.tibs.2013.12.004] [Citation(s) in RCA: 510] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 02/08/2023]
Abstract
Oncogenic KRAS mutation is the signature genetic event in the progression and growth of pancreatic ductal adenocarcinoma (PDAC), an almost universally fatal disease. Although it has been appreciated for some time that nearly 95% of PDAC harbor mutationally activated KRAS, to date no effective treatments that target this mutant protein have reached the clinic. A number of studies have shown that oncogenic KRAS plays a central role in controlling tumor metabolism by orchestrating multiple metabolic changes including stimulation of glucose uptake, differential channeling of glucose intermediates, reprogrammed glutamine metabolism, increased autophagy, and macropinocytosis. We review these recent findings and address how they may be applied to develop new PDAC treatments.
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Affiliation(s)
- Kirsten L Bryant
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph D Mancias
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Alec C Kimmelman
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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56
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Abstract
Mutations in the Ras family of small GTPases are among the most frequent oncogenic events in human cancer. Difficulties in targeting Ras itself and the limited efficacy in targeting its effector kinases have spurred the search for Ras synthetic lethal genes that could shed new light on the biology of Ras-driven cancer and lead to new therapeutic strategies. Advances in mammalian RNAi technology have enabled high-throughput functional screens for Ras synthetic lethal interactions. In this chapter, we summarize the strategies and findings from these screens and discuss future improvement for Ras synthetic lethality studies.
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Affiliation(s)
- Bing Yu
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Ji Luo
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
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57
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Rask-Andersen M, Moschonis G, Chrousos GP, Marcus C, Dedoussis GV, Fredriksson R, Schiöth HB. The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children. PLoS One 2013; 8:e71353. [PMID: 23967198 PMCID: PMC3744548 DOI: 10.1371/journal.pone.0071353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/30/2013] [Indexed: 12/26/2022] Open
Abstract
Recent genome wide association studies (GWAS) have identified a locus on chromosome 11p15.5, closely associated with serine/threonine kinase 33 (STK33), to be associated with body mass. STK33, a relatively understudied protein, has been linked to KRAS mutation-driven cancers and explored as a potential antineoplastic drug target. The strongest association with body mass observed at this loci in GWAS was rs4929949, a single nucleotide polymorphism located within intron 1 of the gene encoding STK33. The functional implications of rs4929949 or related variants have not been explored as of yet. We have genotyped rs4929949 in two cohorts, an obesity case-control cohort of 991 Swedish children, and a cross-sectional cohort of 2308 Greek school children. We found that the minor allele of rs4929949 was associated with obesity in the cohort of Swedish children and adolescents (OR = 1.199 (95%CI: 1.002–1.434), p = 0.047), and with body mass in the cross-sectional cohort of Greek children (β = 0.08147 (95% CI: 0.1345–0.1618), p = 0.021). We observe the effects of rs4929949 on body mass to be detectable already at adolescence. Subsequent analysis did not detect any association of rs4929949 to phenotypic measurements describing body adiposity or to metabolic factors such as insulin levels, triglycerides and insulin resistance (HOMA).
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Affiliation(s)
- Mathias Rask-Andersen
- Department of Neuroscience, Functional Pharmacology, Uppsala University BMC, Uppsala, Sweden
| | - George Moschonis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - George P. Chrousos
- First Department of Pediatrics, Athens University Medical School, Aghia Sophia Children’s Hospital, Athens, Greece
| | - Claude Marcus
- Department for Clinical Science Intervention and Technology (CLINTEC), Department of Pediatrics, Karolinska University Hospital Karolinska Institutet, Huddinge, Sweden
| | - George V. Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Robert Fredriksson
- Department of Neuroscience, Functional Pharmacology, Uppsala University BMC, Uppsala, Sweden
| | - Helgi B. Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University BMC, Uppsala, Sweden
- * E-mail:
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58
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Alvarez-Calderon F, Gregory MA, DeGregori J. Using functional genomics to overcome therapeutic resistance in hematological malignancies. Immunol Res 2013; 55:100-15. [PMID: 22941562 PMCID: PMC3673782 DOI: 10.1007/s12026-012-8353-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite great advances in our understanding of the driving events involved in malignant transformation, only a small number of oncogenic drivers have been targeted and translated into tangible clinical benefit. Moreover, even when a targeted therapy can be shown to effectively inhibit an oncogenic driver, leading to cancer remission, disease persistence and/or relapse is typically inevitable. Reemergence of the cancer can result from either intrinsic or acquired resistance mechanisms that result in failure to eliminate all cancer cells. Intrinsic mechanisms of resistance include tumor heterogeneity and pathways that can compensate for the inhibition of the oncogenic driver. Acquired resistance mechanisms include mutation of the oncogenic driver to directly prevent drug-mediated inhibition and the activation of compensatory survival pathways. RNA interference (RNAi)-based screening provides a powerful approach for the interrogation of both intrinsic and acquired resistance mechanisms. The availability of short interfering (si)RNA libraries targeting all human and mouse genes has made it possible to perform large-scale unbiased screens to identify pathways that are specifically required in cancer cells of particular genotypes or following particular treatments, facilitating the design of potential new therapeutic strategies that may limit resistance mechanisms. In this review, we will discuss how RNAi screens can be used to uncover critical growth and survival pathways and aid in the identification of novel therapeutic targets for improved treatment of hematological malignancies.
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Affiliation(s)
- Francesca Alvarez-Calderon
- Integrated Department of Immunology, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Medical Scientist Training Program, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
| | - Mark A. Gregory
- Department of Biochemistry and Molecular Genetics, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
| | - James DeGregori
- Integrated Department of Immunology, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Department of Biochemistry and Molecular Genetics, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Department of Pediatrics, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Program in Molecular Biology, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
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59
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Weïwer M, Spoonamore J, Wei J, Guichard B, Ross NT, Masson K, Silkworth W, Dandapani S, Palmer M, Scherer CA, Stern AM, Schreiber SL, Munoz B. A Potent and Selective Quinoxalinone-Based STK33 Inhibitor Does Not Show Synthetic Lethality in KRAS-Dependent Cells. ACS Med Chem Lett 2012; 3:1034-1038. [PMID: 23256033 PMCID: PMC3523537 DOI: 10.1021/ml300246r] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 10/22/2012] [Indexed: 12/31/2022] Open
Abstract
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The KRAS oncogene is found in up to 30% of all human
tumors. In
2009, RNAi experiments revealed that lowering mRNA levels of a transcript
encoding the serine/threonine kinase STK33 was selectively toxic to
KRAS-dependent cancer cell lines, suggesting that small-molecule inhibitors
of STK33 might selectively target KRAS-dependent cancers. To test
this hypothesis, we initiated a high-throughput screen using compounds
in the Molecular Libraries Small Molecule Repository (MLSMR). Several
hits were identified, and one of these, a quinoxalinone derivative,
was optimized. Extensive SAR studies were performed and led to the
chemical probe ML281 that showed low nanomolar inhibition of purified
recombinant STK33 and a distinct selectivity profile as compared to
other STK33 inhibitors that were reported in the course of these studies.
Even at the highest concentration tested (10 μM), ML281 had
no effect on the viability of KRAS-dependent cancer cells. These results
are consistent with other recent reports using small-molecule STK33
inhibitors. Small molecules having different chemical structures and
kinase-selectivity profiles are needed to fully understand the role
of STK33 in KRAS-dependent cancers. In this regard, ML281 is a valuable
addition to small-molecule probes of STK33.
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Affiliation(s)
- Michel Weïwer
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - James Spoonamore
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Jingqiang Wei
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Boris Guichard
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Nathan T. Ross
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Kristina Masson
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Whitney Silkworth
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Sivaraman Dandapani
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Michelle Palmer
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Christina A. Scherer
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Andrew M. Stern
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Stuart L. Schreiber
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Benito Munoz
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
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60
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Sacco E, Spinelli M, Vanoni M. Approaches to Ras signaling modulation and treatment of Ras-dependent disorders: a patent review (2007--present). Expert Opin Ther Pat 2012; 22:1263-87. [PMID: 23009088 DOI: 10.1517/13543776.2012.728586] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Ras proteins are small GTPases molecular switches that cycle through two alternative conformational states, a GDP-bound inactive state and a GTP-bound active state. In the active state, Ras proteins interact with and modulate the activity of several downstream effectors regulating key cellular processes including proliferation, differentiation, survival, senescence, migration and metabolism. Activating mutations of RAS genes and of genes encoding Ras signaling members have a great incidence in proliferative disorders, such as cancer, immune and inflammatory diseases and developmental syndromes. Therefore, Ras and Ras signaling represent important clinical targets for the design and development of pharmaceutically active agents, including anticancer agents. AREAS COVERED The authors summarize methods available to down-regulate the Ras pathway and review recent patents covering Ras signaling modulators, as well as methods designed to kill specifically cancer cells bearing activated RAS oncogene. EXPERT OPINION Targeted therapy approach based on direct targeting of molecules specifically altered in Ras-dependent diseases is pursued with molecules that down-regulate expression or inhibit the biological function of mutant Ras or Ras signaling members. The low success rate in a clinical setting of molecules targeting activated members of the Ras pathway may require development of novel approaches, including combined and synthetic lethal therapies.
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Affiliation(s)
- Elena Sacco
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milano, Italy
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61
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Azoitei N, Hoffmann CM, Ellegast JM, Ball CR, Obermayer K, Gößele U, Koch B, Faber K, Genze F, Schrader M, Kestler HA, Döhner H, Chiosis G, Glimm H, Fröhling S, Scholl C. Targeting of KRAS mutant tumors by HSP90 inhibitors involves degradation of STK33. ACTA ACUST UNITED AC 2012; 209:697-711. [PMID: 22451720 PMCID: PMC3328372 DOI: 10.1084/jem.20111910] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Previous efforts to develop drugs that directly inhibit the activity of mutant KRAS, the most commonly mutated human oncogene, have not been successful. Cancer cells driven by mutant KRAS require expression of the serine/threonine kinase STK33 for their viability and proliferation, identifying STK33 as a context-dependent therapeutic target. However, specific strategies for interfering with the critical functions of STK33 are not yet available. Here, using a mass spectrometry-based screen for STK33 protein interaction partners, we report that the HSP90/CDC37 chaperone complex binds to and stabilizes STK33 in human cancer cells. Pharmacologic inhibition of HSP90, using structurally divergent small molecules currently in clinical development, induced proteasome-mediated degradation of STK33 in human cancer cells of various tissue origin in vitro and in vivo, and triggered apoptosis preferentially in KRAS mutant cells in an STK33-dependent manner. Furthermore, HSP90 inhibitor treatment impaired sphere formation and viability of primary human colon tumor-initiating cells harboring mutant KRAS. These findings provide mechanistic insight into the activity of HSP90 inhibitors in KRAS mutant cancer cells, indicate that the enhanced requirement for STK33 can be exploited to target mutant KRAS-driven tumors, and identify STK33 depletion through HSP90 inhibition as a biomarker-guided therapeutic strategy with immediate translational potential.
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Affiliation(s)
- Ninel Azoitei
- Department of Internal Medicine III, Ulm University, 89081 Ulm, Germany
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