Publications by authors named "Stephan Wolf"

79 Publications

Autonomic Nervous System Activity during Refractory Rise in Intracranial Pressure.

J Neurotrauma 2021 Jan 12. Epub 2021 Jan 12.

Brain Division of Neurosurgery, Department of Clinical Neurosciences, Physics Laboratory, Department of Medicine, University of Cambridge, Cambridge, United Kingdom.

Refractory intracranial hypertension (RIH) is a dramatic increase in intracranial pressure (ICP) that cannot be controlled by treatment. Recent reports suggest that the autonomic nervous system (ANS) activity may be altered during changes in ICP. Our study aimed to assess ANS activity during RIH and the causal relationship between rising in ICP and autonomic activity. We reviewed retrospectively 24 multicenter (Cambridge, Tromso, Berlin) patients in whom RIH developed as a pre-terminal event after acute brain injury (ABI). They were monitored with ICP, arterial blood pressure (ABP), and electrocardiography (ECG) using ICM+ software. Parameters reflecting autonomic activity were computed in time and frequency domain through the measurement of heart rate variability (HRV) and baroreflex sensitivity (BRS). Our results demonstrated that a rise in ICP was associated to a significant rise in HRV and BRS with a higher significance level in the high-frequency HRV ( < 0.001). This increase was followed by a significant decrease in HRV and BRS above the upper-breakpoint of ICP where ICP pulse-amplitude starts to decrease whereas the mean ICP continues to rise. Temporality measured with a Granger test suggests a causal relationship from ICP to ANS. The above results suggest that a rise in ICP interacts with ANS activity, mainly interfacing with the parasympathetic-system. The ANS seems to react to the rise in ICP with a response possibly focused on maintaining the cerebrovascular homeostasis. This happens until the critical threshold of ICP is reached above which the ANS variables collapse, probably because of low perfusion of the brain and the central autonomic network.
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http://dx.doi.org/10.1089/neu.2020.7091DOI Listing
January 2021

Global differences in the treatment of Legg-Calvé-Perthes disease: a comprehensive review.

Arch Orthop Trauma Surg 2021 Jan 14;141(1):1-16. Epub 2020 Mar 14.

Department of Orthopedics, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria.

Introduction: Global discussions regarding the treatment of Legg-Calvé-Perthes disease (LCPD) are still controversial. The aim of this study was to characterize the worldwide regional differences in nonoperative and operative treatment for LCPD.

Materials And Methods: Based on a comprehensive literature search, 123 studies describing the results of nonoperative and operative treatment for LCPD were included. Overall, disease and outcome parameters of 6,968 hips were recorded and compared among the continents-Europe, North America, Asia, Africa, South America, and Australia.

Results: Our results showed that the continents differed regarding initial disease progression and therapeutic decision-making, but the final outcome was comparable. The reported proportion of affected hips with mild presentation tended to be higher in Europe, North America, and Africa, whereas disease progression was more severe in Asia, Australia, and South America. Nonoperative treatment was reported more frequently in Europe and North America, while operative management was more common in the rest of the world. Femoral osteotomy was performed more frequently than pelvic osteotomy worldwide, but pelvic osteotomy was comparably more common in North America, Australia, and South America.

Conclusions: The continents differed in terms of therapies for LCPD, while the final outcome was similar. Studies with greater evidence and larger sample size are needed to evaluate the effect of therapeutic measures on LCPD outcome.

Level Of Evidence: III (systematic review of level III studies).
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http://dx.doi.org/10.1007/s00402-020-03392-9DOI Listing
January 2021

The molecular landscape of ETMR at diagnosis and relapse.

Nature 2019 12 4;576(7786):274-280. Epub 2019 Dec 4.

Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.

Embryonal tumours with multilayered rosettes (ETMRs) are aggressive paediatric embryonal brain tumours with a universally poor prognosis. Here we collected 193 primary ETMRs and 23 matched relapse samples to investigate the genomic landscape of this distinct tumour type. We found that patients with tumours in which the proposed driver C19MC was not amplified frequently had germline mutations in DICER1 or other microRNA-related aberrations such as somatic amplification of miR-17-92 (also known as MIR17HG). Whole-genome sequencing revealed that tumours had an overall low recurrence of single-nucleotide variants (SNVs), but showed prevalent genomic instability caused by widespread occurrence of R-loop structures. We show that R-loop-associated chromosomal instability can be induced by the loss of DICER1 function. Comparison of primary tumours and matched relapse samples showed a strong conservation of structural variants, but low conservation of SNVs. Moreover, many newly acquired SNVs are associated with a mutational signature related to cisplatin treatment. Finally, we show that targeting R-loops with topoisomerase and PARP inhibitors might be an effective treatment strategy for this deadly disease.
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http://dx.doi.org/10.1038/s41586-019-1815-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908757PMC
December 2019

Nanoscale deformation mechanics reveal resilience in nacre of Pinna nobilis shell.

Nat Commun 2019 10 23;10(1):4822. Epub 2019 Oct 23.

Department of Materials Science & Engineering, University of Michigan, Ann Arbor, MI, USA.

The combination of soft nanoscale organic components with inorganic nanograins hierarchically designed by natural organisms results in highly ductile structural materials that can withstand mechanical impact and exhibit high resilience on the macro- and nano-scale. Our investigation of nacre deformation reveals the underlying nanomechanics that govern the structural resilience and absorption of mechanical energy. Using high-resolution scanning/transmission electron microscopy (S/TEM) combined with in situ indentation, we observe nanoscale recovery of heavily deformed nacre that restores its mechanical strength on external stimuli up to 80% of its yield strength. Under compression, nacre undergoes deformation of nanograins and non-destructive locking across organic interfaces such that adjacent inorganic tablets structurally join. The locked tablets respond to strain as a continuous material, yet the organic boundaries between them still restrict crack propagation. Remarkably, the completely locked interface recovers its original morphology without any noticeable deformation after compressive contact stresses as large as 1.2 GPa.
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http://dx.doi.org/10.1038/s41467-019-12743-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811596PMC
October 2019

Bioinspired Materials: From Living Systems to New Concepts in Materials Chemistry.

Materials (Basel) 2019 Jul 1;12(13). Epub 2019 Jul 1.

Department of Materials Science and Engineering (WW), Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nuremberg (FAU), Martensstrasse 5, D-91058 Erlangen, Germany.

Nature successfully employs inorganic solid-state materials (i.e., biominerals) and hierarchical composites as sensing elements, weapons, tools, and shelters. Optimized over hundreds of millions of years under evolutionary pressure, these materials are exceptionally well adapted to the specifications of the functions that they perform. As such, they serve today as an extensive library of engineering solutions. Key to their design is the interplay between components across length scales. This hierarchical design-a hallmark of biogenic materials-creates emergent functionality not present in the individual constituents and, moreover, confers a distinctly increased functional density, i.e., less material is needed to provide the same performance. The latter aspect is of special importance today, as climate change drives the need for the sustainable and energy-efficient production of materials. Made from mundane materials, these bioceramics act as blueprints for new concepts in the synthesis and morphosynthesis of multifunctional hierarchical materials under mild conditions. In this review, which also may serve as an introductory guide for those entering this field, we demonstrate how the pursuit of studying biomineralization transforms and enlarges our view on solid-state material design and synthesis, and how bioinspiration may allow us to overcome both conceptual and technical boundaries.
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http://dx.doi.org/10.3390/ma12132117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651889PMC
July 2019

Polymer-Functionalised Nanograins of Mg-Doped Amorphous Calcium Carbonate via a Flow-Chemistry Approach.

Materials (Basel) 2019 Jun 4;12(11). Epub 2019 Jun 4.

Department of Materials Science and Engineering (WW), Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nuremberg (FAU), Martensstrasse 5, D-91058 Erlangen, Germany.

Calcareous biominerals typically feature a hybrid nanogranular structure consisting of calcium carbonate nanograins coated with organic matrices. This nanogranular organisation has a beneficial effect on the functionality of these bioceramics. In this feasibility study, we successfully employed a flow-chemistry approach to precipitate Mg-doped amorphous calcium carbonate particles functionalized by negatively charged polyelectrolytes-either polyacrylates (PAA) or polystyrene sulfonate (PSS). We demonstrate that the rate of Mg incorporation and, thus, the ratio of the Mg dopant to calcium in the precipitated amorphous calcium carbonate (ACC), is flow rate dependent. In the case of the PAA-functionalized Mg-doped ACC, we further observed a weak flow rate dependence concerning the hydration state of the precipitate, which we attribute to incorporated PAA acting as a water sorbent; a behaviour which is not present in experiments with PSS and without a polymer. Thus, polymer-dependent phenomena can affect flow-chemistry approaches, that is, in syntheses of functionally graded materials by layer-deposition processes.
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http://dx.doi.org/10.3390/ma12111818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6601056PMC
June 2019

Conical Nanoindentation Allows Azimuthally Independent Hardness Determination in Geological and Biogenic Minerals.

Materials (Basel) 2019 May 18;12(10). Epub 2019 May 18.

Department of Materials Science and Engineering, Institute of Glass and Ceramics, Friedrich-Alexander University Erlangen-Nuremberg, Martensstrasse 5, D-91058 Erlangen, Germany.

The remarkable mechanical performance of biominerals often relies on distinct crystallographic textures, which complicate the determination of the nanohardness from indentations with the standard non-rotational-symmetrical Berkovich punch. Due to the anisotropy of the biomineral to be probed, an azimuthal dependence of the hardness arises. This typically increases the standard deviation of the reported hardness values of biominerals and impedes comparison of hardness values across the literature and, as a result, across species. In this paper, we demonstrate that an azimuthally independent nanohardness determination can be achieved by using a conical indenter. It is also found that conical and Berkovich indentations yield slightly different hardness values because they result in different pile-up behaviors and because of technical limitations on the fabrication of perfectly equivalent geometries. For biogenic crystals, this deviation of hardness values between indenters is much lower than the azimuthal variation in non-rotational-symmetrical Berkovich indentations.
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http://dx.doi.org/10.3390/ma12101630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566684PMC
May 2019

Defective homologous recombination DNA repair as therapeutic target in advanced chordoma.

Nat Commun 2019 04 9;10(1):1635. Epub 2019 Apr 9.

German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.

Chordomas are rare bone tumors with few therapeutic options. Here we show, using whole-exome and genome sequencing within a precision oncology program, that advanced chordomas (n = 11) may be characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair and alterations affecting HR-related genes, including, for example, deletions and pathogenic germline variants of BRCA2, NBN, and CHEK2. A mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and co-occurred with genomic instability. The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells, led to prolonged clinical benefit in a patient with refractory chordoma, and whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain. These findings uncover a therapeutic opportunity in chordoma that warrants further exploration, and provide insight into the mechanisms underlying PARP inhibitor resistance.
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http://dx.doi.org/10.1038/s41467-019-09633-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456501PMC
April 2019

Designing Solid Materials from Their Solute State: A Shift in Paradigms toward a Holistic Approach in Functional Materials Chemistry.

J Am Chem Soc 2019 Mar 22;141(11):4490-4504. Epub 2019 Feb 22.

Department of Materials Science and Engineering, Institute of Glass and Ceramics and Interdisciplinary Center for Functional Particle Systems , Friedrich-Alexander-University Erlangen-Nuremberg , 91058 Erlangen , Germany.

"Non-classical" notions consider formation pathways of crystalline materials where larger species than monomeric chemical constituents, i.e., ions or single molecules, play crucial roles, which are not covered by the classical theories dating back to the 1870s and 1920s. Providing an outline of "non-classical" nucleation, we demonstrate that prenucleation clusters (PNCs) can lie on alternative pathways to phase separation, where the very event of demixing is primarily based on not the sizes of the species forming, as in the classical view, but their dynamics. Rationalizing, on the other hand, that precursors that can be analytically detected in pre-nucleation stages and that play a role in phase separation must be considered PNCs and cannot be explained by classical notions, we outline a variety of systems where PNCs are important. Indeed, in recent years, with the advent of "non-classical" theories, a primary focus of research concentrated on the fundamental understanding of oligomeric/polymeric and particulate species involved in nucleation and crystallization processes, respectively. At the same time, the near-to unfathomable potential of "non-classical" routes for the synthesis of inorganic functional materials slowly unfolds. An overview of recent developments in the fundamental and mechanistic understanding of "non-classical" nucleation and crystallization in this Perspective then allows us to map out the potential of cluster/particle-driven mineralization pathways to intrinsically tailor the properties of inorganic functional (hybrid) materials via structuration from the nano- to the mesoscale. This is of utter importance for the functionality and performance of materials, as it may even confer emergent properties such as self-healing. Biominerals-often formed via particle accretion mechanisms-demonstrate this impressively and thus can serve as a further source of inspiration how to exploit nonclassical crystallization routes for syntheses of structured and functional materials. These new avenues to synthetic approaches may finally provide a holistic material concept, in which fundamental chemistry and materials science synergistically alloy.
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http://dx.doi.org/10.1021/jacs.8b13231DOI Listing
March 2019

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation.

Cancer Cell 2019 01 27;35(1):95-110.e8. Epub 2018 Dec 27.

Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address:

Biallelic inactivation of SMARCB1, encoding a member of the SWI/SNF chromatin remodeling complex, is the hallmark genetic aberration of atypical teratoid rhabdoid tumors (ATRT). Here, we report how loss of SMARCB1 affects the epigenome in these tumors. Using chromatin immunoprecipitation sequencing (ChIP-seq) on primary tumors for a series of active and repressive histone marks, we identified the chromatin states differentially represented in ATRTs compared with other brain tumors and non-neoplastic brain. Re-expression of SMARCB1 in ATRT cell lines enabled confirmation of our genome-wide findings for the chromatin states. Additional generation of ChIP-seq data for SWI/SNF and Polycomb group proteins and the transcriptional repressor protein REST determined differential dependencies of SWI/SNF and Polycomb complexes in regulation of diverse gene sets in ATRTs.
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http://dx.doi.org/10.1016/j.ccell.2018.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341227PMC
January 2019

Bioinspired Supertough Graphene Fiber through Sequential Interfacial Interactions.

ACS Nano 2018 09 20;12(9):8901-8908. Epub 2018 Jul 20.

Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beijing Advanced Innovation Center for Biomedical Engineering , Beihang University , Beijing 100191 , P. R. China.

Natural nacre exhibits extraordinary functional and structural diversity, combining high strength and toughness. The mechanical properties of nacre are attributed to (i) a highly arranged hierarchical layered structure of inorganic minerals (95 vol %) containing a small amount only of organic materials (5 vol %), (ii) abundant synergistic interfacial interactions, and (iii) formation under ambient temperature. Herein, inspired by these three design principles originating from natural nacre, the supertough bioinspired graphene-based nanocomposite fibers (BGNFs) are prepared under room temperature via sequential interfacial interactions of ionic bonding and π-π interactions. The resultant synergistic effect leads to a super toughness of 18.7 MJ m as well as a high tensile strength of 740.1 MPa. In addition, the electrical conductivity of these supertough BGNFs is as high as 384.3 S cm. They can retain almost 80% of this conductivity even after 1000 cycles of loading-unloading testing, which makes these BGNFs promising candidates for application in flexible and stable electrical devices, such as strain sensors and actuators.
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http://dx.doi.org/10.1021/acsnano.8b04322DOI Listing
September 2018

Author Correction: The landscape of genomic alterations across childhood cancers.

Nature 2018 07;559(7714):E10

Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.

In this Article, author Benedikt Brors was erroneously associated with affiliation number '8' (Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA); the author's two other affiliations (affiliations '3' and '7', both at the German Cancer Research Center (DKFZ)) were correct. This has been corrected online.
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http://dx.doi.org/10.1038/s41586-018-0167-2DOI Listing
July 2018

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell.

Sci Adv 2018 03 30;4(3):eaar3219. Epub 2018 Mar 30.

Faculty of Dentistry, McGill University, Montreal, Quebec H3A 0C7, Canada.

Avian (and formerly dinosaur) eggshells form a hard, protective biomineralized chamber for embryonic growth-an evolutionary strategy that has existed for hundreds of millions of years. We show in the calcitic chicken eggshell how the mineral and organic phases organize hierarchically across different length scales and how variation in nanostructure across the shell thickness modifies its hardness, elastic modulus, and dissolution properties. We also show that the nanostructure changes during egg incubation, weakening the shell for chick hatching. Nanostructure and increased hardness were reproduced in synthetic calcite crystals grown in the presence of the prominent eggshell protein osteopontin. These results demonstrate the contribution of nanostructure to avian eggshell formation, mechanical properties, and dissolution.
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http://dx.doi.org/10.1126/sciadv.aar3219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930395PMC
March 2018

The landscape of genomic alterations across childhood cancers.

Nature 2018 03 28;555(7696):321-327. Epub 2018 Feb 28.

Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.

Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7-8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
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http://dx.doi.org/10.1038/nature25480DOI Listing
March 2018

Evolution of Cytogenetically Normal Acute Myeloid Leukemia During Therapy and Relapse: An Exome Sequencing Study of 50 Patients.

Clin Cancer Res 2018 04 12;24(7):1716-1726. Epub 2018 Jan 12.

Department of Medicine III, University Hospital, LMU Munich, München, Germany.

To study mechanisms of therapy resistance and disease progression, we analyzed the evolution of cytogenetically normal acute myeloid leukemia (CN-AML) based on somatic alterations. We performed exome sequencing of matched diagnosis, remission, and relapse samples from 50 CN-AML patients treated with intensive chemotherapy. Mutation patterns were correlated with clinical parameters. Evolutionary patterns correlated with clinical outcome. Gain of mutations was associated with late relapse. Alterations of epigenetic regulators were frequently gained at relapse with recurring alterations of constituting a mechanism of cytarabine resistance. Low expression correlated with adverse clinical outcome, particularly in male patients. At complete remission, persistent mutations representing preleukemic lesions were observed in 48% of patients. The persistence of mutations correlated with shorter time to relapse. Chemotherapy resistance might be acquired through gain of mutations. Insights into the evolution during therapy and disease progression lay the foundation for tailored approaches to treat or prevent relapse of CN-AML. .
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http://dx.doi.org/10.1158/1078-0432.CCR-17-2344DOI Listing
April 2018

Integrative genomic and transcriptomic analysis of leiomyosarcoma.

Nat Commun 2018 01 10;9(1):144. Epub 2018 Jan 10.

Division of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.

Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic options. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown. Here we show, using whole-exome and transcriptome sequencing, that LMS tumors are characterized by substantial mutational heterogeneity, near-universal inactivation of TP53 and RB1, widespread DNA copy number alterations including chromothripsis, and frequent whole-genome duplication. Furthermore, we detect alternative telomere lengthening in 78% of cases and identify recurrent alterations in telomere maintenance genes such as ATRX, RBL2, and SP100, providing insight into the genetic basis of this mechanism. Finally, most tumors display hallmarks of "BRCAness", including alterations in homologous recombination DNA repair genes, multiple structural rearrangements, and enrichment of specific mutational signatures, and cultured LMS cells are sensitive towards olaparib and cisplatin. This comprehensive study of LMS genomics has uncovered key biological features that may inform future experimental research and enable the design of novel therapies.
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http://dx.doi.org/10.1038/s41467-017-02602-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762758PMC
January 2018

Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing.

Methods Mol Biol 2018 ;1708:105-122

Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

Aberrations of the DNA methylome contribute to onset and progression of diseases. Whole genome bisulfite sequencing (WGBS) is the only analytical method covering the complete methylome. Alternative methods requiring less DNA than WGBS analyze only a minor portion of the methylome and do not cover important regulatory features like enhancers and noncoding RNAs. In tagmentation-based WGBS (TWGBS), several DNA and time-consuming steps of the conventional WGBS library preparation are circumvented by the use of a hyperactive transposase, which simultaneously fragments DNA and appends sequencing adapters. TWGBS requires only nanogram amounts of DNA and, thus, is well suited to study precious biological specimens such as sorted cells or micro-dissected tissue samples.
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http://dx.doi.org/10.1007/978-1-4939-7481-8_6DOI Listing
July 2018

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.

Nature 2017 08 16;548(7668):456-460. Epub 2017 Aug 16.

Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany.

Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure.
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http://dx.doi.org/10.1038/nature23653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905670PMC
August 2017

The whole-genome landscape of medulloblastoma subtypes.

Nature 2017 07;547(7663):311-317

Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target KBTBD4 and 'enhancer hijacking' events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.
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http://dx.doi.org/10.1038/nature22973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905700PMC
July 2017

Universal structure motifs in biominerals: a lesson from nature for the efficient design of bioinspired functional materials.

Interface Focus 2017 Aug 16;7(4):20160120. Epub 2017 Jun 16.

Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Martensstrasse 5, 91058 Erlangen, Germany.

Biominerals are typically indispensable structures for their host organism in which they serve varying functions, such as mechanical support and protection, mineral storage, detoxification site, or as a sensor or optical guide. In this perspective article, we highlight the occurrence of both structural diversity and uniformity within these biogenic ceramics. For the first time, we demonstrate that the universality-diversity paradigm, which was initially introduced for proteins by Buehler . (Cranford & Buehler 2012 ; Cranford 2013 , 802-824 (doi:10.1002/adma.201202553); Ackbarow & Buehler 2008 , 1193-1204 (doi:10.1166/jctn.2008.001); Buehler & Yung 2009 , 175-188 (doi:10.1038/nmat2387)), is also valid in the realm of biomineralization. A nanogranular composite structure is shared by most biominerals which rests on a common, non-classical crystal growth mechanism. The nanogranular composite structure affects various properties of the macroscale biogenic ceramic, a phenomenon we attribute to emergence. Emergence, in turn, is typical for hierarchically organized materials. This is a clear call to renew comparative studies of even distantly related biomineralizing organisms to identify further universal design motifs and their associated emergent properties. Such universal motifs with emergent macro-scale properties may represent an unparalleled toolbox for the efficient design of bioinspired functional materials.
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http://dx.doi.org/10.1098/rsfs.2016.0120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474032PMC
August 2017

Precision oncology based on omics data: The NCT Heidelberg experience.

Int J Cancer 2017 09 21;141(5):877-886. Epub 2017 Jun 21.

Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Precision oncology implies the ability to predict which patients will likely respond to specific cancer therapies based on increasingly accurate, high-resolution molecular diagnostics as well as the functional and mechanistic understanding of individual tumors. While molecular stratification of patients can be achieved through different means, a promising approach is next-generation sequencing of tumor DNA and RNA, which can reveal genomic alterations that have immediate clinical implications. Furthermore, certain genetic alterations are shared across multiple histologic entities, raising the fundamental question of whether tumors should be treated by molecular profile and not tissue of origin. We here describe MASTER (Molecularly Aided Stratification for Tumor Eradication Research), a clinically applicable platform for prospective, biology-driven stratification of younger adults with advanced-stage cancer across all histologies and patients with rare tumors. We illustrate how a standardized workflow for selection and consenting of patients, sample processing, whole-exome/genome and RNA sequencing, bioinformatic analysis, rigorous validation of potentially actionable findings, and data evaluation by a dedicated molecular tumor board enables categorization of patients into different intervention baskets and formulation of evidence-based recommendations for clinical management. Critical next steps will be to increase the number of patients that can be offered comprehensive molecular analysis through collaborations and partnering, to explore ways in which additional technologies can aid in patient stratification and individualization of treatment, to stimulate clinically guided exploratory research projects, and to gradually move away from assessing the therapeutic activity of targeted interventions on a case-by-case basis toward controlled clinical trials of genomics-guided treatments.
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http://dx.doi.org/10.1002/ijc.30828DOI Listing
September 2017

Integration of genomics and histology revises diagnosis and enables effective therapy of refractory cancer of unknown primary with amplification.

Cold Spring Harb Mol Case Stud 2016 11;2(6):a001180

Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany;; Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg 69120, Germany;; German Cancer Consortium (DKTK), Heidelberg 69120, Germany.

Identification of the tissue of origin in cancer of unknown primary (CUP) poses a diagnostic challenge and is critical for directing site-specific therapy. Currently, clinical decision-making in patients with CUP primarily relies on histopathology and clinical features. Comprehensive molecular profiling has the potential to contribute to diagnostic categorization and, most importantly, guide CUP therapy through identification of actionable lesions. We here report the case of an advanced-stage malignancy initially mimicking poorly differentiated soft-tissue sarcoma that did not respond to multiagent chemotherapy. Molecular profiling within a clinical whole-exome and transcriptome sequencing program revealed a heterozygous, highly amplified G12S mutation, compound-heterozygous mutation/deletion, high mutational load, and focal high-level amplification of Chromosomes 9p (including [] and ) and 10p (including ). Integrated analysis of molecular data and histopathology provided a rationale for immune checkpoint inhibitor (ICI) therapy with pembrolizumab, which resulted in rapid clinical improvement and a lasting partial remission. Histopathological analyses ruled out sarcoma and established the diagnosis of a poorly differentiated adenocarcinoma. Although neither histopathology nor molecular data were able to pinpoint the tissue of origin, our analyses established several differential diagnoses including triple-negative breast cancer (TNBC). We analyzed 157 TNBC samples from The Cancer Genome Atlas, revealing copy number gains coinciding with excessive mRNA expression in 24% of cases. Collectively, these results illustrate the impact of multidimensional tumor profiling in cases with nondescript histology and immunophenotype, show the predictive potential of amplification for immune checkpoint inhibitors (ICIs) and suggest a targeted therapeutic strategy in Chromosome 9p24.1/-amplified cancers.
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http://dx.doi.org/10.1101/mcs.a001180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111004PMC
November 2016

Braf Mutations Initiate the Development of Rat Gliomas Induced by Postnatal Exposure to N-Ethyl-N-Nitrosourea.

Am J Pathol 2016 10;186(10):2569-76

International Agency for Research on Cancer, Lyon, France. Electronic address:

A single dose of N-ethyl-N-nitrosourea (ENU) during late prenatal or early postnatal development induces a high incidence of malignant schwannomas and gliomas in rats. Although T->A mutations in the transmembrane domain of the Neu (c-ErbB-2) gene are the driver mutations in ENU-induced malignant schwannomas, the molecular basis of ENU-induced gliomas remains enigmatic. We performed whole-genome sequencing of gliomas that developed in three BDIV and two BDIX rats exposed to a single dose of 80 mg ENU/kg body weight on postnatal day one. T:A->A:T and T:A->C:G mutations, which are typical for ENU-induced mutagenesis, were predominant (41% to 55% of all somatic single nucleotide mutations). T->A mutations were identified in all five rat gliomas at Braf codon 545 (V545E), which corresponds to the human BRAF V600E. Additional screening revealed that 33 gliomas in BDIV rats and 12 gliomas in BDIX rats all carried a Braf V545E mutation, whereas peritumoral brain tissue of either strain had the wild-type sequence. The gliomas were immunoreactive to BRAF V600E antibody. These results indicate that Braf mutation is a frequent early event in the development of rat gliomas caused by a single dose of ENU.
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http://dx.doi.org/10.1016/j.ajpath.2016.05.024DOI Listing
October 2016

Nonclassical crystallization in vivo et in vitro (II): Nanogranular features in biomimetic minerals disclose a general colloid-mediated crystal growth mechanism.

J Struct Biol 2016 11 9;196(2):260-287. Epub 2016 Sep 9.

Department of Materials Science and Engineering, Institute of Glass and Ceramics (WW3), Friedrich-Alexander-University Erlangen-Nürnberg, Martensstrasse 5, 91058 Erlangen, Germany; Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Haberstrasse 9a, 91058 Erlangen, Germany.

Recent research has shown that biominerals and their biomimetics (i) typically form via an amorphous precursor phase, and (ii) commonly display a nanogranular texture. Apparently, these two key features are closely related, underlining the fact that the formation of biominerals and their biomimetics does not necessarily follow classical crystallization routes, and leaves a characteristic nanotextural imprint which may help to disclose their origins and formation mechanisms. Here we present a general overview of the current theories and models of nonclassical crystallization and their applicability for the advance of our current understanding of biomineralization and biomimetic mineralization. We pay particular attention to the link between nonclassical crystallization routes and the resulting nanogranular textures of biomimetic CaCO mineral structures. After a general introductory section, we present an overview of classical nucleation and crystal growth theories and their limitations. Then, we introduce the Ostwald's step rule as a general framework to explain nonclassical crystallization. Subsequently, we describe nonclassical crystallization routes involving stable prenucleation clusters, dense liquid and solid amorphous precursor phases, as well as current nonclassical crystal growth models. The latter include oriented attachment, mesocrystallization and the new model based on the colloidal growth of crystals via attachment of amorphous nanoparticles. Biomimetic examples of nanostructured CaCO minerals formed via these nonclassical routes are presented which help us to show that colloid-mediated crystal growth can be regarded as a wide-spread growth mechanism. Implications of these observations for the advance in the current understanding on the formation of biomimetic materials and biominerals are finally outlined.
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http://dx.doi.org/10.1016/j.jsb.2016.09.005DOI Listing
November 2016

Optimal search patterns in honeybee orientation flights are robust against emerging infectious diseases.

Sci Rep 2016 09 12;6:32612. Epub 2016 Sep 12.

Rothamsted Research, Harpenden, UK.

Lévy flights are scale-free (fractal) search patterns found in a wide range of animals. They can be an advantageous strategy promoting high encounter rates with rare cues that may indicate prey items, mating partners or navigational landmarks. The robustness of this behavioural strategy to ubiquitous threats to animal performance, such as pathogens, remains poorly understood. Using honeybees radar-tracked during their orientation flights in a novel landscape, we assess for the first time how two emerging infectious diseases (Nosema sp. and the Varroa-associated Deformed wing virus (DWV)) affect bees' behavioural performance and search strategy. Nosema infection, unlike DWV, affected the spatial scale of orientation flights, causing significantly shorter and more compact flights. However, in stark contrast to disease-dependent temporal fractals, we find the same prevalence of optimal Lévy flight characteristics (μ ≈ 2) in both healthy and infected bees. We discuss the ecological and evolutionary implications of these surprising insights, arguing that Lévy search patterns are an emergent property of fundamental characteristics of neuronal and sensory components of the decision-making process, making them robust against diverse physiological effects of pathogen infection and possibly other stressors.
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http://dx.doi.org/10.1038/srep32612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018844PMC
September 2016

Targeting Fibroblast Growth Factor Receptor 1 for Treatment of Soft-Tissue Sarcoma.

Clin Cancer Res 2017 Feb 17;23(4):962-973. Epub 2016 Aug 17.

Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.

Altered FGFR1 signaling has emerged as a therapeutic target in epithelial malignancies. In contrast, the role of FGFR1 in soft-tissue sarcoma (STS) has not been established. Prompted by the detection and subsequent therapeutic inhibition of amplified FGFR1 in a patient with metastatic leiomyosarcoma, we investigated the oncogenic properties of FGFR1 and its potential as a drug target in patients with STS. The frequency of amplification and overexpression, as assessed by FISH, microarray-based comparative genomic hybridization and mRNA expression profiling, SNP array profiling, and RNA sequencing, was determined in three patient cohorts. The sensitivity of STS cell lines with or without FGFR1 alterations to genetic and pharmacologic FGFR1 inhibition and the signaling pathways engaged by FGFR1 were investigated using viability assays, colony formation assays, and biochemical analysis. Increased copy number was detected in 74 of 190 (38.9%; cohort 1), 13 of 79 (16.5%; cohort 2), and 80 of 254 (31.5%; cohort 3) patients. overexpression occurred in 16 of 79 (20.2%, cohort 2) and 39 of 254 (15.4%; cohort 3) patients. Targeting of FGFR1 by RNA interference and small-molecule inhibitors (PD173074, AZD4547, BGJ398) revealed that the requirement for FGFR1 signaling in STS cells is dictated by FGFR1 expression levels, and identified the MAPK-ERK1/2 axis as critical FGFR1 effector pathway. These data identify as a driver gene in multiple STS subtypes and support FGFR1 inhibition, guided by patient selection according to the FGFR1 expression and monitoring of MAPK-ERK1/2 signaling, as a therapeutic option in this challenging group of diseases. .
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http://dx.doi.org/10.1158/1078-0432.CCR-16-0860DOI Listing
February 2017

Next-generation personalised medicine for high-risk paediatric cancer patients - The INFORM pilot study.

Eur J Cancer 2016 09 29;65:91-101. Epub 2016 Jul 29.

Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg, 69120, Germany; German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany. Electronic address:

The 'Individualized Therapy for Relapsed Malignancies in Childhood' (INFORM) precision medicine study is a nationwide German program for children with high-risk relapsed/refractory malignancies, which aims to identify therapeutic targets on an individualised basis. In a pilot phase, reported here, we developed the logistical and analytical pipelines necessary for rapid and comprehensive molecular profiling in a clinical setting. Fifty-seven patients from 20 centers were prospectively recruited. Malignancies investigated included sarcomas (n = 25), brain tumours (n = 23), and others (n = 9). Whole-exome, low-coverage whole-genome, and RNA sequencing were complemented with methylation and expression microarray analyses. Alterations were assessed for potential targetability according to a customised prioritisation algorithm and subsequently discussed in an interdisciplinary molecular tumour board. Next-generation sequencing data were generated for 52 patients, with the full analysis possible in 46 of 52. Turnaround time from sample receipt until first report averaged 28 d. Twenty-six patients (50%) harbored a potentially druggable alteration with a prioritisation score of 'intermediate' or higher (level 4 of 7). Common targets included receptor tyrosine kinases, phosphoinositide 3-kinase-mammalian target of rapamycin pathway, mitogen-activated protein kinase pathway, and cell cycle control. Ten patients received a targeted therapy based on these findings, with responses observed in some previously treatment-refractory tumours. Comparative primary relapse analysis revealed substantial tumour evolution as well as one case of unsuspected secondary malignancy, highlighting the importance of re-biopsy at relapse. This study demonstrates the feasibility of comprehensive, real-time molecular profiling for high-risk paediatric cancer patients. This extended proof-of-concept, with examples of treatment consequences, expands upon previous personalised oncology endeavors, and presents a model with considerable interest and practical relevance in the burgeoning era of personalised medicine.
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http://dx.doi.org/10.1016/j.ejca.2016.06.009DOI Listing
September 2016

Nonclassical crystallization in vivo et in vitro (I): Process-structure-property relationships of nanogranular biominerals.

J Struct Biol 2016 11 25;196(2):244-259. Epub 2016 Jul 25.

Department of Mineralogy and Petrology, University of Granada, Spain, Fuentenueva s/n, 18071 Granada, Spain.

A distinct nanogranular fine structure is shared by a wealth of biominerals from several species, classes and taxa. This nanoscopic organization affects the properties and behavior of the biogenic ceramic material and confers on them attributes that are essential to their function. We present a set of structure-relationship properties that are rooted in the nanogranular organization and we propose that they rest on a common pathway of formation, a colloid-driven and hence nonclassical mode of crystallization. With this common modus operandi, we reveal the most fundamental and wide spread process-structure-property relationship in biominerals. With the recent increase in our understanding of nonclassical crystallization in vitro and in vivo, this significant process-structure-property relationship will serve as a source for new design approaches of bio-inspired materials.
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http://dx.doi.org/10.1016/j.jsb.2016.07.016DOI Listing
November 2016

Flight performance of actively foraging honey bees is reduced by a common pathogen.

Environ Microbiol Rep 2016 Oct 7;8(5):728-737. Epub 2016 Jul 7.

Rothamsted Research, Harpenden, UK.

Sudden and severe declines in honey bee (Apis mellifera) colony health in the US and Europe have been attributed, in part, to emergent microbial pathogens, however, the mechanisms behind the impact are unclear. Using roundabout flight mills, we measured the flight distance and duration of actively foraging, healthy-looking honey bees sampled from standard colonies, before quantifying the level of infection by Nosema ceranae and Deformed Wing Virus complex (DWV) for each bee. Neither the presence nor the quantity of N. ceranae were at low, natural levels of infection had any effect on flight distance or duration, but presence of DWV reduced flight distance by two thirds and duration by one half. Quantity of DWV was shown to have a significant, but weakly positive relation with flight distance and duration, however, the low amount of variation that was accounted for suggests further investigation by dose-response assays is required. We conclude that widespread, naturally occurring levels of infection by DWV weaken the flight ability of honey bees and high levels of within-colony prevalence are likely to reduce efficiency and increase the cost of resource acquisition. Predictions of implications of pathogens on colony health and function should take account of sublethal effects on flight performance.
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http://dx.doi.org/10.1111/1758-2229.12434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5091639PMC
October 2016

ZBTB7A mutations in acute myeloid leukaemia with t(8;21) translocation.

Nat Commun 2016 06 2;7:11733. Epub 2016 Jun 2.

Department of Internal Medicine 3, University Hospital, Ludwig-Maximilians-Universität (LMU) München, 81377 München, Germany.

The t(8;21) translocation is one of the most frequent cytogenetic abnormalities in acute myeloid leukaemia (AML) and results in the RUNX1/RUNX1T1 rearrangement. Despite the causative role of the RUNX1/RUNX1T1 fusion gene in leukaemia initiation, additional genetic lesions are required for disease development. Here we identify recurring ZBTB7A mutations in 23% (13/56) of AML t(8;21) patients, including missense and truncating mutations resulting in alteration or loss of the C-terminal zinc-finger domain of ZBTB7A. The transcription factor ZBTB7A is important for haematopoietic lineage fate decisions and for regulation of glycolysis. On a functional level, we show that ZBTB7A mutations disrupt the transcriptional repressor potential and the anti-proliferative effect of ZBTB7A. The specific association of ZBTB7A mutations with t(8;21) rearranged AML points towards leukaemogenic cooperativity between mutant ZBTB7A and the RUNX1/RUNX1T1 fusion.
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http://dx.doi.org/10.1038/ncomms11733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895769PMC
June 2016