1
|
Dou DR, Zhao Y, Belk JA, Zhao Y, Casey KM, Chen DC, Li R, Yu B, Srinivasan S, Abe BT, Kraft K, Hellström C, Sjöberg R, Chang S, Feng A, Goldman DW, Shah AA, Petri M, Chung LS, Fiorentino DF, Lundberg EK, Wutz A, Utz PJ, Chang HY. Xist ribonucleoproteins promote female sex-biased autoimmunity. Cell 2024; 187:733-749.e16. [PMID: 38306984 PMCID: PMC10949934 DOI: 10.1016/j.cell.2023.12.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/28/2023] [Revised: 10/03/2023] [Accepted: 12/31/2023] [Indexed: 02/04/2024]
Abstract
Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.
Collapse
Affiliation(s)
- Diana R Dou
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanding Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Derek C Chen
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bingfei Yu
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Suhas Srinivasan
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian T Abe
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ceke Hellström
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Ronald Sjöberg
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Sarah Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ami A Shah
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorinda S Chung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - David F Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Emma K Lundberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden; Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Anton Wutz
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Zurich, Switzerland
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
2
|
Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun 2023; 14:2300. [PMID: 37085539 PMCID: PMC10121654 DOI: 10.1038/s41467-023-38044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
Collapse
Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Owen Chapman
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sameena Wani
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abhijit Chakraborty
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Meghana Pagadala
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Rosalind Bump
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sahaana Chandran
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Derek Reid
- Arima Genomics, Inc, San Diego, CA, 92121, USA
| | | | - Monika Mauermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Edwin F Juarez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Anne Jenseit
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - James T Robinson
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Petra Fiesel
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ling Morgan
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sunita Sridhar
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Michael Levy
- Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Denise Malicki
- Pathology, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Stephen Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Robert J Wechsler-Reya
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jennifer Cotter
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - George Michaiel
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Hannah Carter
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kulandaimanuvel Antony Michealraj
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany
| | - Jill P Mesirov
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Jesse R Dixon
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Lukas Chavez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA.
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA.
| |
Collapse
|
3
|
Kuenz S, Thurner S, Hoffmann D, Kraft K, Wiltafsky-Martin M, Damme K, Windisch W, Brugger D. Effects of gradual differences in trypsin inhibitor activity on the estimation of digestible amino acids in soybean expellers for broiler chickens. Poult Sci 2022; 101:101740. [PMID: 35245805 PMCID: PMC8892013 DOI: 10.1016/j.psj.2022.101740] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/16/2021] [Accepted: 01/13/2022] [Indexed: 12/04/2022] Open
Abstract
The present study investigated the effect of varying trypsin inhibitor activity (TIA) in differently processed soybean expellers on apparent prececal amino acid (AA) digestibility in male broiler chickens. Two different raw soybean batches were treated using varying processing techniques and intensities. In this way, 45 expeller extracted soybean meal (ESBM) variants were created. The processed soybean variants were then merged into a basal diet (160 g/kg crude protein [CP]) at 2 inclusion levels (15%, 30%) resulting in 90 different diets plus one basal diet (0.4 mg/g-8.5 mg/g TIA). All diets contained 0.5% titanium dioxide. A total of 5,460-day-old male broilers (Ross 308) were allocated on d 14 to 546 pens (10 birds/pen) after a starter phase (CP 215 g/kg, 14 g/kg Lysine, 12.5 MJ ME/kg). The 91 experimental diets were fed ad libitum until d 22. Subsequently, birds were euthanized and digesta of the terminal ileum was collected for determination of AA digestibility. TIA depressed the prececal digestibility of every single AA significantly in a straight linear fashion (P < 0.001). Sulfur-containing AA expressed the strongest suppression by TIA with cystine showing the lowest apparent prececal digestibility measured (10.6% at 23.6 mg/g TIA in raw ESBM). The present data demonstrate that TIA severely depresses digestibility of essential and nonessential AA in a straight linear fashion. On the one hand, this questions the usefulness of defined upper limits of TIA in soy products whereas on the other hand, TIA must be considered when testing raw components for their feed protein value in vivo.
Collapse
Affiliation(s)
- S Kuenz
- Technical University of Munich (TUM), TUM School of Life Sciences, Chair of Animal Nutrition, 85354 Freising, Germany
| | - S Thurner
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, 85354 Freising, Germany
| | - D Hoffmann
- Technical University of Munich (TUM), TUM School of Life Sciences, Chair of Animal Nutrition, 85354 Freising, Germany; Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, 85354 Freising, Germany
| | - K Kraft
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, 85354 Freising, Germany; Bavarian State Research Center for Agriculture, Department for Education and Poultry Research, 97318 Kitzingen, Germany
| | | | - K Damme
- Bavarian State Research Center for Agriculture, Department for Education and Poultry Research, 97318 Kitzingen, Germany
| | - W Windisch
- Technical University of Munich (TUM), TUM School of Life Sciences, Chair of Animal Nutrition, 85354 Freising, Germany
| | - D Brugger
- Technical University of Munich (TUM), TUM School of Life Sciences, Chair of Animal Nutrition, 85354 Freising, Germany; University of Zurich, Vetsuisse-Faculty, Institute of Animal Nutrition and Dietetics, 8057 Zurich, Switzerland.
| |
Collapse
|
4
|
Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021; 600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.
Collapse
Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joshua T Lange
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Celine Chen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria E Valieva
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ivy Tsz-Lo Wong
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor V Duffy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jun Tang
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jordan Friedlein
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Paul S Mischel
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
5
|
Okonechnikov K, Hübner JM, Chapman O, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Hidalgo RA, Mundlos S, Wechsler-Reya R, Juarez EF, Coufal N, Levy M, Crawford J, Pajtler K, Reid D, Schmitt A, Carter H, Ay F, Dixon J, Mesirov J, Pfister SM, Kool M, Chavez L. EPEN-04. ONCOGENIC 3D TUMOR GENOME ORGANIZATION IDENTIFIES NEW THERAPEUTIC TARGETS IN EPENDYMOMA. Neuro Oncol 2020. [PMCID: PMC7715851 DOI: 10.1093/neuonc/noaa222.145] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
By profiling enhancers in primary ependymoma tumors, we have recently identified putative oncogenes, molecular targets, and functional pathways. Inhibition of selected targets diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymoma. While enhancers frequently regulate the nearest gene, identification of enhancer target genes remains to be a challenge in the absence of chromosome conformation information. Consequently, we have now used HiC to map the 3-dimensional organization of tumor chromatin in the two most common and aggressive ependymoma subgroups: posterior fossa group A (PF-EPN-A) and supratentorial ependymomas with gene fusions involving the NF-κB subunit gene RELA (ST-EPN-RELA). By an integrative analysis of enhancer and gene expression in the context of the newly derived HiC data, we find that a large number of the predicted enhancer target genes are enriched for strong physical interactions. Importantly, we also identify many new putative tumor-dependency genes activated by long-range promoter-enhancer interactions and complex tumor-specific chromatin clusters of regulatory elements. Complementary to the analysis of gene-enhancer interactions, we have also leveraged the HiC data for resolving structural rearrangements underlying copy number alterations. Copy number gains of the 1q arm of chromosome 1 are especially associated with poor survival. Our preliminary results in PFA relapse samples show complex structural variants underlying 1q gain that lead to inter-chromosomal rearrangements and affect several genes that potentially contribute to poor survival. In ongoing work we are testing the relevance of the novel candidate genes for tumor cell growth and proliferation in-patient derived ependymoma models.
Collapse
Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens-Martin Hübner
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Owen Chapman
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, San Diego, CA, USA
| | - Meghana Pagadala
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Rosalind Bump
- Salk Institute for Biological Studies, San Diego, CA, USA
| | | | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | | | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Research Discovery Institute, San Diego, USA
| | - Edwin F Juarez
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Nicole Coufal
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Michael Levy
- Department of Neurosurgery, University of California San Diego – Rady Children’s Hospital, San Diego, CA, USA
| | - John Crawford
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
- Department of Neurosciences, University of California San Diego – Rady Children’s Hospital, San Diego, CA, USA
| | - Kristian Pajtler
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Hannah Carter
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, San Diego, CA, USA
| | - Jesse Dixon
- Salk Institute for Biological Studies, San Diego, CA, USA
| | - Jill Mesirov
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Stefan M Pfister
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| |
Collapse
|
6
|
Sommer S, Decker Y, Oberhoffer R, Grab D, Scholz C, Kraft K. Fallbericht einer 31-jährigen GII/PI Gravida mit fetaler Aortenbogenhypoplasie und Aortenisthmusstenose. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718320] [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: 10/23/2022] Open
Affiliation(s)
- S Sommer
- München Klinik Harlaching, Frauenklinik
| | - Y Decker
- München Klinik Harlaching, Frauenklinik
| | - R Oberhoffer
- Technische Universität München, Präventive Pädiatrie
| | - D Grab
- München Klinik Harlaching, Frauenklinik
| | - C Scholz
- München Klinik Harlaching, Frauenklinik
| | - K Kraft
- München Klinik Harlaching, Frauenklinik
| |
Collapse
|
7
|
Kraft K, Friedl T, Schlanstedt P, Bode H, Janni W, Scholz C, Reister F. Das Timing der antenataler Kortikosteroidgabe beeinflusst neonatale Outcome nach Frühgeburt. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1717942] [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: 10/23/2022] Open
Affiliation(s)
- K Kraft
- München Klinik Harlaching, Frauenklinik
| | | | | | - H Bode
- Uniklinikum Ulm, Sozialpädiatrisches Zentrum
| | - W Janni
- Unifrauenklinik Ulm, Frauenklinik
| | - C Scholz
- München Klinik Harlaching, Frauenklinik
| | | |
Collapse
|
8
|
Decker Y, Sommer S, Oberhoffer R, Grab D, Scholz C, Kraft K. Fallbericht einer 36-jährigen IVG/IP mit Rhabdomyom des II. Fetus bei Di-Di Geminigravidität. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718256] [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: 10/23/2022] Open
Affiliation(s)
- Y Decker
- München Klinik Harlaching, Gynäkologie und Geburtshilfe
| | - S Sommer
- München Klinik Harlaching, Gynäkologie und Geburtshilfe
| | - R Oberhoffer
- Technische Universität München, Präventive Pädiatrie
| | - D Grab
- München Klinik Harlaching, Gynäkologie und Geburtshilfe
| | - C Scholz
- München Klinik Harlaching, Gynäkologie und Geburtshilfe
| | - K Kraft
- München Klinik Harlaching, Gynäkologie und Geburtshilfe
| |
Collapse
|
9
|
Affiliation(s)
- C Vollbracht
- University Medicine Rostock, Rostock
- Address correspondence to C. Vollbracht, University Medicine Rostock, Rostock, Germany.
| | | | - K Kraft
- University Medicine Rostock, Rostock
| |
Collapse
|
10
|
Okonechnikov K, Hübner JM, Chapman O, Chakraborty A, Bump R, Chandran S, Kraft K, Acuna Hidalgo R, Mundlos S, Coufal N, Levy M, Crawford J, Ay F, Mesirov J, Pajtler K, Dixon J, Pfister S, Kool M, Chavez L. GENE-15. TARGETING OF EPENDYMOMA AS INFORMED BY ONCOGENIC 3D GENOME ORGANIZATION. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.417] [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: 11/13/2022] Open
Abstract
Abstract
By profiling enhancers in primary ependymoma tumors, we have recently identified putative oncogenes, molecular targets, and functional pathways. Inhibition of selected targets diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymoma. While enhancers frequently regulate the nearest gene, unambiguous identification of enhancer target genes remains to be a challenge in the absence of chromosome conformation information. Consequently, we have now used HiC to map the 3-dimensional organization of tumor chromatin in the two most common and aggressive ependymoma subgroups: posterior fossa group A (PF-EPN-A) and supratentorial ependymomas with gene fusions involving the NF-κB subunit gene RELA (ST-EPN-RELA). By an integrative analysis of enhancer and gene expression in the context of the newly derived HiC data, we find that a large amount of the previously predicted enhancer target genes can be confirmed by physical interactions. Importantly, we also identify many new putative tumor-dependency genes activated by long-range promoter-enhancer interactions. Complementary to the analysis of gene-enhancer interactions, we have also leveraged the HiC data for resolving structural rearrangements underlying copy number alterations frequently observed in PF-EPN-A tumors. Especially copy number gains of the 1q arm of chromosome 1 are associated with poor survival. Our preliminary results reveal complex structural variants that underlie 1q gains, which lead to inter-chromosomal rearrangements and affect several genes that potentially contribute to poor survival. We now aim to test the relevance of the novel candidate tumor-dependency genes for tumor cell growth and proliferation in patient derived ependymoma models.
Collapse
Affiliation(s)
| | - Jens-Martin Hübner
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | | | | | - Rosalind Bump
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | - Stefan Mundlos
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | | | | | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Kristian Pajtler
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Jesse Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Stefan Pfister
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | | |
Collapse
|
11
|
Kraft K, Alum A, Abbaszadegan M. Environmental algal phage isolates and their impact on production potential for food and biofuel applications. J Appl Microbiol 2019; 128:182-190. [PMID: 31606918 DOI: 10.1111/jam.14487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/11/2019] [Revised: 08/07/2019] [Accepted: 09/14/2019] [Indexed: 11/28/2022]
Abstract
AIMS The United States Department of Energy is aiming to bring microalgal biofuels into commercial use by 2030 at the price of $3 per gasoline gallon equivalent. Large-scale production of biofuel faces many challenges including naturally occurring algal phages; and characterizing this threat is the aim of this study. METHODS AND RESULTS Bench-scale experiments were performed to study the impact of viral infectivity on the production of microalgal in bioreactors. All environmental samples were tested positive for algal phages which showed various levels of infectivity against Synechocystis PCC 6803 and the environmental isolates of microalgae. The viral attachment to algal cells was observed under transmission electron microscopy (TEM) and to determine the shape and size of the viral particles. All the viruses detected were c. 50-60 nm icosahedral particles. Viral infection resulted in 48% reduction in the biomass of the infected algal culture in 22 days. CONCLUSIONS This study has lead to the conclusion that the microalgal phages prevalent in natural environment may cause infections in broad range of microalgae used for biofuel production. SIGNIFICANCE AND IMPACT OF THE STUDY This study has detected and quantified the phages that can infect algal populations in natural freshwater habitats and laboratory cultures of microalgal strains. The impact of viral threat to health of commercial algal production operations has been identified in this study.
Collapse
Affiliation(s)
- K Kraft
- Civil, Environmental & Sustainable Engineering, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - A Alum
- Civil, Environmental & Sustainable Engineering, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - M Abbaszadegan
- Civil, Environmental & Sustainable Engineering, School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
12
|
Holman A, Haydar B, Kraft K, Park J. Infant spinal anesthesia: a safe, efficient, and worthwhile collaboration. J Pediatr Urol 2019; 15:583-584. [PMID: 31401223 DOI: 10.1016/j.jpurol.2019.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 11/20/2022]
Affiliation(s)
- A Holman
- Department of Anesthesiology, Division of Pediatric Anesthesiology, University of Michigan, C. S. Mott Children's Hospital, 1540 E. Hospital Drive, Ann Arbor, MI, 48109, USA.
| | - B Haydar
- Department of Anesthesiology, Division of Pediatric Anesthesiology, University of Michigan, C. S. Mott Children's Hospital, 1540 E. Hospital Drive, Ann Arbor, MI, 48109, USA
| | - K Kraft
- Department of Urology, Division of Pediatric Urology, University of Michigan, C. S. Mott Children's Hospital, 1540 E. Hospital Drive, Ann Arbor, MI, 48109, USA
| | - J Park
- Department of Urology, Division of Pediatric Urology, University of Michigan, C. S. Mott Children's Hospital, 1540 E. Hospital Drive, Ann Arbor, MI, 48109, USA
| |
Collapse
|
13
|
Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell 2019; 176:816-830.e18. [PMID: 30595451 PMCID: PMC6546437 DOI: 10.1016/j.cell.2018.11.036] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [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: 03/12/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
Collapse
Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Marco Michalski
- Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nicolas P Holcomb
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jesse L Turner
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
| |
Collapse
|
14
|
McCarthy J, Lupo PJ, Kovar E, Rech M, Bostwick B, Scott D, Kraft K, Roscioli T, Charrow J, Schrier Vergano SA, Lose E, Smiegel R, Lacassie Y, Schaaf CP. Schaaf-Yang syndrome overview: Report of 78 individuals. Am J Med Genet A 2018; 176:2564-2574. [PMID: 30302899 PMCID: PMC6585857 DOI: 10.1002/ajmg.a.40650] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 08/01/2018] [Revised: 08/23/2018] [Accepted: 09/07/2018] [Indexed: 01/12/2023]
Abstract
Schaaf-Yang Syndrome (SYS) is a genetic disorder caused by truncating pathogenic variants in the paternal allele of the maternally imprinted, paternally expressed gene MAGEL2, located in the Prader-Willi critical region 15q11-15q13. SYS is a neurodevelopmental disorder that has clinical overlap with Prader-Willi Syndrome in the initial stages of life but becomes increasingly distinct throughout childhood and adolescence. Here, we describe the phenotype of an international cohort of 78 patients with nonsense or frameshift mutations in MAGEL2. This cohort includes 43 individuals that have been reported previously, as well as 35 newly identified individuals with confirmed pathogenic genetic variants. We emphasize that intellectual disability/developmental delay, autism spectrum disorder, neonatal hypotonia, infantile feeding problems, and distal joint contractures are the most consistently shared features of patients with SYS. Our results also indicate that there is a marked prevalence of infantile respiratory distress, gastroesophageal reflux, chronic constipation, skeletal abnormalities, sleep apnea, and temperature instability. While there are many shared features, patients with SYS are characterized by a wide phenotypic spectrum, including a variable degree of intellectual disability, language development, and motor milestones. Our results indicate that the variation in phenotypic severity may depend on the specific location of the truncating mutation, suggestive of a genotype-phenotype association. This evidence may be useful in both prenatal and pediatric genetic counseling.
Collapse
Affiliation(s)
- John McCarthy
- Institute of Human Genetics, University Hospital Cologne, Köln, Germany
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Erin Kovar
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Megan Rech
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bret Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Daryl Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Katerina Kraft
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tony Roscioli
- Department of Clinical Genetics, Sydney Children's Hospital, Sydney, Australia.,Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, Australia
| | - Joel Charrow
- Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia
| | - Edward Lose
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert Smiegel
- Department of Social Pediatrics, Wroclaw Medical University, Poland
| | - Yves Lacassie
- Department of Pediatrics, LSU Health Sciences Center and Children's Hospital, New Orleans, Louisiana
| | - Christian P Schaaf
- Institute of Human Genetics, University Hospital Cologne, Köln, Germany.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Center for Molecular Medicine Cologne, University of Cologne, Köln, Germany.,Center for Rare Diseases, University Hospital Cologne, Köln, Germany
| |
Collapse
|
15
|
Kraft K, Handke-Vesely A, Stuck D, Bauer E, Hüner B, Janni W, Reister F. „Sekundäre Präeklampsie“: Fallbericht eine atypische Präsentation. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671271] [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: 10/28/2022] Open
Affiliation(s)
- K Kraft
- Universitätsklinikum Ulm, Frauenklinik, Ulm, Deutschland
| | | | - D Stuck
- Universitätsklinikum Ulm, Frauenklinik, Ulm, Deutschland
| | - E Bauer
- Universitätsklinikum Ulm, Frauenklinik, Ulm, Deutschland
| | - B Hüner
- Universitätsklinikum Ulm, Frauenklinik, Ulm, Deutschland
| | - W Janni
- Universitätsklinikum Ulm, Frauenklinik, Ulm, Deutschland
| | - F Reister
- Universitätsklinikum Ulm, Frauenklinik, Ulm, Deutschland
| |
Collapse
|
16
|
Kraft K, Hüner B, Handke-Vesely A, Janni W, Reister F. Geburtsmodus bei Frühgeborenen: Eine retrospektive Single Center Erhebung. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671656] [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: 10/28/2022] Open
Affiliation(s)
- K Kraft
- Universitätsfrauenklinik Ulm, Geburtshilfe und Gynäkologie, Ulm, Deutschland
| | - B Hüner
- Universitätsfrauenklinik Ulm, Geburtshilfe und Gynäkologie, Ulm, Deutschland
| | - A Handke-Vesely
- Universitätsfrauenklinik Ulm, Geburtshilfe und Gynäkologie, Ulm, Deutschland
| | - W Janni
- Universitätsfrauenklinik Ulm, Geburtshilfe und Gynäkologie, Ulm, Deutschland
| | - F Reister
- Universitätsfrauenklinik Ulm, Geburtshilfe und Gynäkologie, Ulm, Deutschland
| |
Collapse
|
17
|
Puhl A, Weiss C, Schneid A, Zahn E, Kraft K, Pretscher J, Faschingbauer F, Beckmann MW, Kehl S. Vergleich der Geburtseinleitung wegen einem frühen vorzeitigen Blasensprung und einem vorzeitigen Blasensprung. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671436] [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: 10/28/2022] Open
Affiliation(s)
- A Puhl
- Klinikverbund Kempten-Oberallgäu gGmbH, Klinik für Frauenheilkunde und Geburtshilfe, Kempten, Deutschland
| | - C Weiss
- Universitätsmedizin Mannheim, Universität Heidelberg, Medizinische Statistik, Biomathematik und Informationsverarbeitung, Mannheim, Deutschland
| | - A Schneid
- Klinikverbund Kempten-Oberallgäu gGmbH, Klinik für Frauenheilkunde und Geburtshilfe, Kempten, Deutschland
| | - E Zahn
- Klinikverbund Kempten-Oberallgäu gGmbH, Klinik für Frauenheilkunde und Geburtshilfe, Kempten, Deutschland
| | - K Kraft
- Universitätsfrauenklinik Ulm, Ulm, Deutschland
| | - J Pretscher
- Universitätsklinikum Erlangen, Frauenklinik, Erlangen, Deutschland
| | - F Faschingbauer
- Universitätsklinikum Erlangen, Frauenklinik, Erlangen, Deutschland
| | - MW Beckmann
- Universitätsklinikum Erlangen, Frauenklinik, Erlangen, Deutschland
| | - S Kehl
- Universitätsklinikum Erlangen, Frauenklinik, Erlangen, Deutschland
| |
Collapse
|
18
|
Kraft K, Hüner B, Handke-Vesely A, Janni W, Reister F. Vorzeitiger Blasensprung vor der 20. Schwangerschaftswoche: Eine Analyse von 29 Fällen über 3 Jahre. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1660650] [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: 10/28/2022] Open
Affiliation(s)
- K Kraft
- Universitätsfrauenklinik Ulm
| | - B Hüner
- Universitätsfrauenklinik Ulm
| | | | - W Janni
- Universitätsfrauenklinik Ulm
| | | |
Collapse
|
19
|
Bianco S, Lupiáñez DG, Chiariello AM, Annunziatella C, Kraft K, Schöpflin R, Wittler L, Andrey G, Vingron M, Pombo A, Mundlos S, Nicodemi M. Polymer physics predicts the effects of structural variants on chromatin architecture. Nat Genet 2018; 50:662-667. [DOI: 10.1038/s41588-018-0098-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/27/2018] [Indexed: 01/08/2023]
|
20
|
Kraft K. The WHO traditional medicine strategy – a way to better medical care. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608319] [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: 10/18/2022]
Affiliation(s)
- K Kraft
- Center for Internal Medicine, Universitätsmedizin Rostock, Rostock, Germany
| |
Collapse
|
21
|
Müller J, Fink C, Rabini S, Kelber O, Nieber K, Kraft K, Storr MA. The herbal medicine STW 5 is efficacious in functional dyspepsia also in the elderly – a meta-analysis of randomized controlled trials. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608491] [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: 10/18/2022]
Affiliation(s)
- J Müller
- Medical and Clinical Affairs Phytomedicines, Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany, Darmstadt, Germany
| | - C Fink
- Medical and Clinical Affairs Phytomedicines, Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany, Darmstadt, Germany
| | - S Rabini
- Medical and Clinical Affairs Phytomedicines, Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany, Darmstadt, Germany
| | - O Kelber
- Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany, Darmstadt, Germany
| | - K Nieber
- Pharmaceutical Institute, Leipzig University, Leipzig, Germany, Leipzig, Germany
| | - K Kraft
- Chair for Naturopathy, Center for Internal Medicine, University Medicine Rostock, Rostock, Germany, Rostock, Germany
| | - MA Storr
- Center for Endoscopy, Starnberg, Germany
| |
Collapse
|
22
|
Fink C, Müller J, Kelber O, Nieber K, Kraft K. Dry cough associated with pharyngeal irritation: Survey on Althea officinalis L. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608589] [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: 10/18/2022]
Affiliation(s)
- C Fink
- Medical and Clinical Affairs Phytomedicines, Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany
| | - J Müller
- Medical and Clinical Affairs Phytomedicines, Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany
| | - O Kelber
- Innovation and Development, Phytomedicines Supply and Development Center, Bayer Consumer Health Division, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany
| | - K Nieber
- Pharmaceutical Institute, Leipzig University, Leipzig, Germany
| | - K Kraft
- Chair for Naturopathy, Center for Internal Medicine, University Medicine Rostock, Rostock, Germany
| |
Collapse
|
23
|
Kraft K, Mooz H, Puhl A, Graf M, Renz H, Haller M, Karch M, Felberbaum R. Tako-Tsubo cardiomyopathy after cardiopulmonary resuscitation during emergency Cesarean section in a 28 year old patient in the 31st week of pregnancy. Geburtshilfe Frauenheilkd 2016. [DOI: 10.1055/s-0036-1593213] [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
|
24
|
Kraft K. 59-jährige Frau mit Karzinosarkom (Müller-Mischtumor). Geburtshilfe Frauenheilkd 2016. [DOI: 10.1055/s-0036-1580665] [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: 10/21/2022] Open
|
25
|
Lorenz KJ, Kraft K, Graf F, Pröpper C, Steinestel K. [Importance of cellular tight junction complexes in the development of periprosthetic leakage after prosthetic voice rehabilitation]. HNO 2015; 63:171-2, 174-8, 180-1. [PMID: 25515126 DOI: 10.1007/s00106-014-2951-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND The use of voice prostheses is currently the gold standard in voice rehabilitation after total laryngectomy. This method combines low complication rates and excellent rehabilitation results; however, approximately 30% of patients show periprosthetic leakage or severe fistula enlargement after laryngectomy and prosthetic voice restoration within the first 4 years. The development of this enlargement is controversially discussed in the literature but recently published studies have shown that high esophageal reflux plays a key role in this process, which leads to an inflammatory reaction and disturbs the intercellular tight junctions in the sense of an epithelial mesenchymal transition (EMT). MATERIAL AND METHODS A total of 44 patients underwent 24 h pH monitoring, a sample biopsy from the region of the fistula and a subsequent biomolecular examination for intracellular junction proteins as well as a correlation between the severity of reflux and tracheoesophageal fistula problems before and after antireflux therapy with proton pump inhibitors (PPI). RESULTS Immunohistochemical staining revealed decreases in membrane E-cadherin and β-catenin and a significant increase in the cytoplasmic fraction, depending on the severity of inflammation in the fistula tissue. In patients with an improvement of clinical fistula problems under oral PPI treatment an increase of membrane E-cadherin could be shown, whereas patients with persisting fistula enlargement demonstrated a further decrease of E-cadherin. CONCLUSION The data indicate a central role of EMT in the development of fistula enlargement after total laryngectomy. Patients with periprosthetic leakage showed a loss of membrane bound E-cadherin and β-catenin with an up-regulation of vimentin expression. In patients with mild or no leakage problems EMT could be resolved by aggressive antireflux treatment, whereas patients without any effect of PPI treatment on the fistula showed no reversal of EMT. These data contribute to the understanding of treatment resistant fistula enlargement after total laryngectomy.
Collapse
Affiliation(s)
- K J Lorenz
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf-Hals-Chirurgie, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081, Ulm, Deutschland,
| | | | | | | | | |
Collapse
|
26
|
Capsec J, Lefebvre C, Chupe F, Heitzmann P, Raveneau C, Giraud VD, Sauger C, Lagasse J, Kraft K, Linassier C, Dorval E. 2136 Non-organizational factors associated with delayed adjuvant chemotherapy (AC) in colon cancer (CC): An epidemiological study in “Region Centre”, France. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31057-7] [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: 11/17/2022]
|
27
|
Mühlmeier G, Hausch R, Arndt A, Kraft K, Danz B, Maier H. [Respiratory epithelial adenomatoid hamartoma of the nose and nasal sinuses : a rare differential diagnosis of nasal polyposis]. HNO 2015; 62:813-7. [PMID: 25312591 DOI: 10.1007/s00106-014-2914-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Hamartomas are benign tumor-like lesions resulting from incorrectly differentiated germplasm and can manifest in different organ systems. In the nasal cavity and the sinuses these lesions are rare. Only few data on etiology, epidemiology and clinical significance of these tumors exist to date. MATERIALS AND METHODS In a retrospective study, material from patients treated in the Clinic for Otorhinolaryngology, Head and Neck Surgery of the Ulm Military Hospital was screened on the incidence and clinical courses of respiratory epithelial adenomatoid hamartomas (REAH) of the nose and nasal cavity. Furthermore, for cases of REAH, formalin-fixated paraffin-embedded tissue samples were re-evaluated and examined for human papillomavirus (HPV) DNA by PCR. RESULTS Tissue samples from 8145 surgical interventions on the nose and nasal sinuses from 2003 to 2012 were included. A total of 22 patients (3 female, 19 male; median age 57.5 years) diagnosed with REAH could be identified. Major complaints were nasal blockage (91 %), sinusitis (82 %), rhinorrhea (36 %) and cephalgia (23 %). Nasal endoscopy showed polyps in 68 % of patients. Native nasal sinus CT scans revealed no indications of REAH. Intraoperatively, hamartomas were found in 12 patients originating from the ethmoid bone, in 8 from the middle meatus or infundibulum and in 2 from the olfactory cleft. Macroscopic and histological examination showed compact lesions sized between 4 and 25 mm in the largest diameter containing homologous tissue, without signs of dysplasia or malignancy. HPV DNA was not identified in any case. CONCLUSION REAH of the nasal cavity and sinuses are rare benign local tissue lesions, usually without any autonomous proliferation. Clinical signs and findings correspond to those in polypoid pansinusitis. Only with single-sided or olfactory cleft location might CT scans provide indication of a tumorous lesion. For differentiation from true neoplasms, surgical resection and histopathological clarification is indicated. On the basis of current knowledge, complete surgical resection is adequate therapy.
Collapse
Affiliation(s)
- G Mühlmeier
- Klinik für Hals-Nasen-Ohren-Heilkunde, Kopf- und Halschirurgie, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081, Ulm, Deutschland,
| | | | | | | | | | | |
Collapse
|
28
|
Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 2015; 161:1012-1025. [PMID: 25959774 DOI: 10.1016/j.cell.2015.04.004] [Citation(s) in RCA: 1294] [Impact Index Per Article: 143.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/12/2015] [Accepted: 03/24/2015] [Indexed: 12/21/2022]
Abstract
Mammalian genomes are organized into megabase-scale topologically associated domains (TADs). We demonstrate that disruption of TADs can rewire long-range regulatory architecture and result in pathogenic phenotypes. We show that distinct human limb malformations are caused by deletions, inversions, or duplications altering the structure of the TAD-spanning WNT6/IHH/EPHA4/PAX3 locus. Using CRISPR/Cas genome editing, we generated mice with corresponding rearrangements. Both in mouse limb tissue and patient-derived fibroblasts, disease-relevant structural changes cause ectopic interactions between promoters and non-coding DNA, and a cluster of limb enhancers normally associated with Epha4 is misplaced relative to TAD boundaries and drives ectopic limb expression of another gene in the locus. This rewiring occurred only if the variant disrupted a CTCF-associated boundary domain. Our results demonstrate the functional importance of TADs for orchestrating gene expression via genome architecture and indicate criteria for predicting the pathogenicity of human structural variants, particularly in non-coding regions of the human genome.
Collapse
Affiliation(s)
- Darío G Lupiáñez
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Verena Heinrich
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter Krawitz
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Francesco Brancati
- Medical Genetics Unit, Policlinico Tor Vergata University Hospital, 00133 Rome, Italy
| | - Eva Klopocki
- Institute of Human Genetics Biozentrum, Julius Maximilian University of Würzburg, 97070 Würzburg, Germany
| | - Denise Horn
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Hülya Kayserili
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, 34093 Istanbul, Turkey
| | - John M Opitz
- Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT 84108, USA
| | - Renata Laxova
- Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT 84108, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain; U753 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28046 Madrid, Spain
| | | | - Lars Wittler
- Department Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marina Borschiwer
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marco Osterwalder
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195 Berlin, Germany
| | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Axel Visel
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany.
| |
Collapse
|
29
|
Affiliation(s)
- K Kraft
- Bundeswehrzentralkrankenhaus, Abteilung Pathologie, Koblenz, BRD
| | | | | | | | | | | |
Collapse
|
30
|
Gretz N, Lasserre J, Kraft K, Waldherr R, Weidler B, Meisinger E, Strauch M. Efficacy and side effects of erythropoietin used in the treatment of anemia of uremic rats. Contrib Nephrol 2015; 60:236-44. [PMID: 3345672 DOI: 10.1159/000414808] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- N Gretz
- Clinic of Nephrology, Klinikum Mannheim, University of Heidelberg, FRG
| | | | | | | | | | | | | |
Collapse
|
31
|
Giovannetti S, Barsotti G, Gretz N, Kraft K. Treatment and prevention of uremic osteodystrophy. Contrib Nephrol 2015; 72:66-72. [PMID: 2743774 DOI: 10.1159/000417321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
32
|
Kraft K, Geuer S, Will AJ, Chan WL, Paliou C, Borschiwer M, Harabula I, Wittler L, Franke M, Ibrahim DM, Kragesteen BK, Spielmann M, Mundlos S, Lupiáñez DG, Andrey G. Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice. Cell Rep 2015; 10:833-839. [PMID: 25660031 DOI: 10.1016/j.celrep.2015.01.016] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 11/25/2022] Open
Abstract
Structural variations (SVs) contribute to the variability of our genome and are often associated with disease. Their study in model systems was hampered until now by labor-intensive genetic targeting procedures and multiple mouse crossing steps. Here we present the use of CRISPR/Cas for the fast (10 weeks) and efficient generation of SVs in mice. We specifically produced deletions, inversions, and also duplications at six different genomic loci ranging from 1.1 kb to 1.6 Mb with efficiencies up to 42%. After PCR-based selection, clones were successfully used to create mice via aggregation. To test the practicability of the method, we reproduced a human 500 kb disease-associated deletion and were able to recapitulate the human phenotype in mice. Furthermore, we evaluated the regulatory potential of a large genomic interval by deleting a 1.5 Mb fragment. The method presented permits rapid in vivo modeling of genomic rearrangements.
Collapse
Affiliation(s)
- Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sinje Geuer
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Anja J Will
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Wing Lee Chan
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Christina Paliou
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Izabela Harabula
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Bjørt K Kragesteen
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Darío G Lupiáñez
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| | - Guillaume Andrey
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| |
Collapse
|
33
|
Kraft K, Merom D, Steel K, Olson R, MacMillan F. Older adults’ views on sports and physical activity complexity: The match and mismatch to the professional's taxonomy. J Sci Med Sport 2014. [DOI: 10.1016/j.jsams.2014.11.304] [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]
|
34
|
Maier M, Kraft K, Steinestel K, Schramm A, Lorenz KJ, Tisch M, Schwerer M, Maier H. [Human papillomavirus in squamous cell cancer of the head and neck. A study at the Ulm Military Hospital, Germany]. HNO 2014; 61:593-601. [PMID: 23842698 DOI: 10.1007/s00106-013-2676-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There is increasing evidence worldwide that human papillomavirus is a major risk factor for head and neck cancer. Only few studies on this association have been performed in Germany to date. For the purposes of the present study, tumor specimens from 223 patients with squamous cell cancer of the oral cavity, oropharynx, hypopharynx and larynx were analyzed for HPV DNA and p16INK4a expression. The prevalence of HPV genotype 16 (HPV16) DNA in the study population was 17.5%. Further high-risk HPV types were not detected. All HPV16-positive tumors showed intense p16INK4a expression. HPV16 prevalence was highest in tonsillar carcinoma (37.5%) and lowest in laryngeal cancer (2.8%). We observed a significantly higher incidence of cervical lymph node metastases in patients with HPV16-positive tonsillar carcinoma in comparison to HPV-negative tumors (p < 0.016). Tobacco and/or alcohol consumption was significantly lower in patients with HPV-positive tumors (p < 0.0001).
Collapse
Affiliation(s)
- M Maier
- Univ.-HNO-Klinik Heidelberg.
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Kuss P, Kraft K, Stumm J, Ibrahim D, Vallecillo-Garcia P, Mundlos S, Stricker S. Regulation of cell polarity in the cartilage growth plate and perichondrium of metacarpal elements by HOXD13 and WNT5A. Dev Biol 2013; 385:83-93. [PMID: 24161848 DOI: 10.1016/j.ydbio.2013.10.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [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: 06/24/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 01/07/2023]
Abstract
The morphology of bones is genetically determined, but the molecular mechanisms that control shape, size and the overall gestalt of bones remain unclear. We previously showed that metacarpals in the synpolydactyly homolog (spdh) mouse, which carries a mutation in Hoxd13 similar to the human condition synpolydactyly (SPD), were transformed to carpal-like bones with cuboid shape that lack cortical bone and a perichondrium and are surrounded by a joint surface. Here we provide evidence that spdh metacarpal growth plates have a defect in cell polarization with a random instead of linear orientation. In parallel prospective perichondral cells failed to adopt the characteristic flattened cell shape. We observed a similar cell polarity defect in metacarpals of Wnt5a(-/-) mice. Wnt5a and the closely related Wnt5b were downregulated in spdh handplates, and HOXD13 induced expression of both genes in vitro. Concomitant we observed mislocalization of core planar cell polarity (PCP) components DVL2 and PRICKLE1 in spdh metacarpals indicating a defect in the WNT/PCP pathway. Conversely the WNT/β-CATENIN pathway, a hallmark of joint cells lining carpal bones, was upregulated in the perichondral region. Finally, providing spdh limb explant cultures with cells expressing either HOXD13 or WNT5A led to a non-cell autonomous partial rescue of cell polarity the perichondral region and restored the expression of perichondral markers. This study provides a so far unrecognized link between HOX proteins and cell polarity in the perichondrium and the growth plate, a failure of which leads to transformation of metacarpals to carpal-like structures.
Collapse
Affiliation(s)
- Pia Kuss
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité University Medicine, Augustenburger Platz 1, 13353 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
36
|
Kraft K, Reese S, Maierl J, Fiedler A. Einfluss eines neuartigen Biozids auf die Prävalenz von Dermatitis digitalis bei Milchkühen. Tierarztl Prax Ausg G Grosstiere Nutztiere 2013. [DOI: 10.1055/s-0038-1623179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Zusammenfassung
Gegenstand und Ziel: Es wurde untersucht, ob der Einsatz des Biozidprodukts T-Hexx Dragonhyde HBC (Fa. Hydromer, Branchburg, NJ, USA) die Prävalenz der Dermatitis digitalis (DD) beeinflusst. Material und Methoden: In einem Milchviehbetrieb (110 melkende Kühe) wurden 48 lahmheitsfreie Tiere randomisiert Versuchs- und Kontrollgruppe zugeteilt. Die mit 70–80% hohe Prävalenz der DD wurde 2 Monate lang vier Mal im Abstand von je 16–21 Tagen erfasst. Ein Punkteschema diente zur Dokumentation des Grades der DD-Läsionen an den Hinterklauen. Die Kühe der Versuchsgruppe wurden zweimal wöchentlich für zwei Melkzeiten nach Vorreinigung der Klauen mit Wasser durch ein Klauenbad mit T-Hexx-Dragonhyde geleitet, bei den Kontrolltieren erfolgte nur eine Klauenreinigung. Die Spritzer der Biozidlösung an Tieren und Umgebung wurden fotografisch dokumentiert und beurteilt. Wasser- und Biozidbad wurden nach Nutzung durch steigende Tierzahlen bakteriologisch untersucht. Ergebnisse: Statistisch signifikante Unterschiede der Prävalenzen der DD zwischen und innerhalb der beiden Gruppen waren nicht festzustellen. Die Punktebewertung der Läsionen differierte zwischen beiden Gruppen nicht. Im Wasserbad nahm mit steigender Zahl der Durchgänge die Zahl der koloniebildenden Einheiten (KBE) pro Milliliter sowie die der Enterobacteriaceae deutlich zu. Im T-Hexx-Dragonhyde-Bad ließen sich zu keinem Zeitpunkt KBE oder Enterobacteriaceae bestimmen. Die auffälligen Spritzer der Lösung waren bis in Höhe des Euters sichtbar. Schlussfolgerung und klinische Relevanz: Ein Einfluss des Biozidprodukts bei 4%- und 2%iger Badkonzentrationen auf die Prävalenz der DD konnte nicht nachgewiesen werden. Die hygienische Wirkung der Lösung war nicht gleichbedeutend mit einer erfolgreichen Keimreduktion an der Klaue. Eine mögliche Prävention der DD durch veterinärhygienische Maßnahmen könnte zukünftig bei geringerer Prävalenz und größerem Stichprobenumfang überprüft werden. Bei Anwendung von Klauenbädern besteht grundsätzlich die Gefahr einer Kontamination der Milch bzw. einer Mastitis durch Spritzer der Lösung.
Collapse
|
37
|
Fiedler A, Kraft K, Reese S, Maierl J. [Influence of a new biocidal product on the prevalence of digital dermatitis in dairy cows]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2013; 41:207-216. [PMID: 23959616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 02/20/2013] [Indexed: 06/02/2023]
Abstract
OBJECTIVE It was investigated whether usage of the biocidal product T-Hexx Dragonhyde (Hydromer, Branchburg, NJ, USA) could influence the prevalence of digital dermatitis (DD). MATERIAL AND METHODS On a dairy farm (110 milking cows) 48 dairy cows without lameness were selected randomly for a test group or a control (negative) group, respectively. A high prevalence of DD (70-80%) was documented over a period of 2 months, during which four examinations were made, with an interval of 16-21 days between each examination. The respective grade of the DD-lesion on the hind hoofs was documented according to a scoring scheme. After precleaning the claws with water, the test group passed through a hoof bath containing T-Hexx Dragonhyde on 2 days per week at two milking times on each day, whereas the claws of control animals were cleaned using only a water bath. Splashes contaminating the animals and the environment were documented photographically and evaluated. Bacteriological examinations of the water bath and the T-Hexx-bath were performed after increasing numbers of animals had passed through the baths. RESULTS Between and within groups no statistically significant differences in the prevalence of DD were found. DD-lesion scoring did not show any difference between the groups. With increasing numbers of animals having passed through the water bath, there was a significant increase in colony-forming units per millilitre and of enterobacteriaceae. In the T-Hexx Dragonhyde footbath, bacterial contamination remained below the detection limit at all times. The coloured splashes of the footbath were visible up to the level of the udder and teats. CONCLUSION AND CLINICAL RELEVANCE The prevalence of DD was not influenced by the 2% or 4% concentration of the biocidal product in the footbath. Thus the microbiocidal effect of the solution did not lead to an efficient reduction in bacteria on the hoof. To demonstrate a potential preventive effect on DD, future studies would require herds with lower prevalence and a higher sample size. However, when applying footbaths there is the general risk of milk contamination or causing mastitis.
Collapse
Affiliation(s)
- A Fiedler
- Dr. Andrea Fiedler, Heerstraße 3, 81247 München, E-Mail:
| | | | | | | |
Collapse
|
38
|
Janik H, Mau C, Kraft K. P02.104. Nonlinear parameters of heart rate variability (HRV) – suitable measures to observe physiological outcome during a peat bath in rehabilitation. Altern Ther Health Med 2012. [PMCID: PMC3373320 DOI: 10.1186/1472-6882-12-s1-p160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
39
|
Mariette C, Messager M, Lefevre JH, Pichot V, Souadka A, Thibot T, Brachet D, Carrere N, Fernandez M, Guiramand J, Tsilividis B, Flamein R, Kraft K, Balon JM, Borie F, Glaise A, d'Journo X, Peschaud F, Vandois F, Piessen G. Effect of neoadjuvant chemotherapy on survival in patients with gastric signet ring cell adenocarcinoma: A multicentric comparative study. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.4036] [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: 11/20/2022] Open
|
40
|
Reichling J, Kraft K, Gome R, Kelber O, Wegener T. Letter to the Editor Subject: Contribution of Maistro et al. in Genetics and Molecular Research (2010); 9(4): 2114-2122. Genet Mol Res 2011; 10:1092-4; author reply 1095-7. [DOI: 10.4238/vol10-2gmr1445] [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: 11/03/2022]
|
41
|
Kraft K, Delibasic M, Janik H. Evaluation of the effect of dynamic electro-neuro-stimulation (DENS)-therapy in patients with chronic neck pain in two rehabilitation hospitals. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.09.044] [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: 11/29/2022]
|
42
|
Kiene H, Brinkhaus B, Fischer G, Girke M, Hahn E, Hoppe H, Jütte R, Kraft K, Klitzsch W, Matthiessen P, Meister P, Michalsen A, Teut M, Willich S, Heimpel H. Professional treatment in the context of medical pluralism—A German perspective. Eur J Integr Med 2010. [DOI: 10.1016/j.eujim.2010.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
43
|
|
44
|
Janik H, Mau C, Kraft K. Influence of a peat bath series on heart rate variability (HRV) measures of patients with prolapse of the nucleus pulposus during an inpatient orthopaedic rehabilitation. Eur J Integr Med 2009. [DOI: 10.1016/j.eujim.2009.08.125] [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]
|
45
|
Kraft K, Balushev L. Deficits in the knowledge of relaxation techniques in German medical and economics students. Eur J Integr Med 2008. [DOI: 10.1016/j.eujim.2008.08.071] [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: 10/21/2022]
|
46
|
Richter H, Kraft K, Kleinwechter H, Demandt N, Meincke G, Dabelstein A, Weisser B. [Effects of a telephone intervention in patients with type 2 diabetes]. Dtsch Med Wochenschr 2008; 133:2203-8. [PMID: 18924053 DOI: 10.1055/s-0028-1091262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND OBJECTIVE While there are evermore therapeutic options, a continuous rise in the prevalence of type 2 diabetes mellitus has been demonstrated in epidemiological studies and is leading to an increasing financial burden on health care systems. It has been shown in a number of studies that health-related lifestyle may be influenced by a telephone intervention program. PATIENTS AND METHODS The effect of a telephone intervention on physical activity and other important cardiovascular risk factors was investigated over a period of three months in patients with type 2 diabetes. Those in the intervention group (n=22) were phoned once weekly and only matters concerning their physical activity were discussed. The patients in a matching control group (n=20) were not phoned. RESULTS Physical activity increased in the intervention group with a significant difference when compared to the control group at the end of the three months' intervention. At the end of the intervention weight, body mass index, waist circumference, systolic blood pressure, triglycerides and fasting blood sugar where either significantly different between the intervention and control groups (absolute values) or showed a significantly greater decrease in the intervention group. In addition there was a tendency (not statistically significant) towards an improvement in the intervention group regarding other risk factors (body fat, diastolic blood pressure, total cholesterol, LDL, HDL, HbA1c). CONCLUSIONS These results demonstrate that a telephone intervention can increase physical activity and reduce cardiovascular risk factors. As a result it may reduce health care-related costs.
Collapse
Affiliation(s)
- H Richter
- Abteilung Sportmedizin, Institut für Sport und Sportwissenschaften der CAU zu Kiel, 24098 Kiel
| | | | | | | | | | | | | |
Collapse
|
47
|
Maier H, Mühlmeier G, Kraft K, Blumstein NM, Tisch M. [Primary malignant melanoma of the parotid gland: a case report and review of the literature]. HNO 2008; 56:627-32. [PMID: 18066514 DOI: 10.1007/s00106-007-1634-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Malignant melanomas (MMs) of the parotid gland are relatively uncommon. They occur almost invariably as metastases from a primary tumour located in the region of the scalp or the mucous membranes of the nose, paranasal sinuses, or throat. Primary MMs arising in the parotid gland are extremely rare. It is assumed that they originate in the glandular tissue or in intraglandular lymph nodes. We present a case report and review of the literature on the diagnosis, treatment, and prognosis of intraparotid malignant melanoma. Diagnosis is based primarily on B-scan ultrasonography and fine-needle aspiration cytology. Patients with a cytological diagnosis of MM are further evaluated by magnetic resonance imaging and positron emission tomography and receive a thorough ear-nose-throat and dermatological examination. The treatment of choice is total parotidectomy and selective neck dissection. The effectiveness of adjuvant treatments such as radiotherapy, chemotherapy, or immunotherapy remains controversial. Patients with primary MMs of the parotid gland appear to have a better prognosis than those with parotid metastases from melanomas of the skin or mucous membranes.
Collapse
Affiliation(s)
- H Maier
- Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081, Ulm.
| | | | | | | | | |
Collapse
|
48
|
Kraft K. Cimicifuga, Johanniskraut und andere Phytotherapeutika im Klimakterium. Gynäkologische Endokrinologie 2008. [DOI: 10.1007/s10304-008-0256-7] [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: 10/22/2022]
|
49
|
Eisele R, Vogelsang E, Kraft K, Baumgarten U, Schick RR. Screening for colorectal lesions with high-resolution video colonoscopes in a German male average-risk population at 40 to 59 years of age. Z Gastroenterol 2007; 45:952-7. [PMID: 17874357 DOI: 10.1055/s-2007-963477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND Prevalence data for colorectal neoplastic lesions obtained from screening colonoscopies have recently been reported for a U. S. American and a Polish average-risk population. However, prevalence data for a German average-risk population have not been published. METHODS From 1998 until 2003 a screening colonoscopy was offered to all male participants of a health assessment program. In a total of 618 volunteers with an average risk for colorectal cancer, polypoid lesions were identified and removed using high-resolution video colonoscopes. The histological features of the lesions were categorised according to those of the most advanced one. An advanced lesion was defined as an adenoma of at least 1 cm in diameter, a polyp with villous histological features or high-grade intraepithelial neoplasms or a cancer. Data were analysed in two groups: age 40 - 49 years (group A) and age 50 - 59 years (group B). RESULTS In group A (age 40 - 49 years, n = 285), 133 subjects (47 %) had polypoid lesions. Histological findings revealed that 57 subjects (20 %) had non-neoplastic and 76 subjects (27 %) had neoplastic lesions. In nine cases (3.2 %) polyps were classified as advanced lesions with a maximal diameter of 35 mm. In group B (age 50 - 59, n = 333), 183 subjects (55 %) had polypoid lesions. Histological findings revealed that 64 subjects (19 %) had non-neoplastic and 119 subjects (36 %) had neoplastic lesions. Among those, 34 (10.2 %) had advanced lesions with a maximal diameter of 55 mm. In neither group was an invasive cancer detected. The difference in the prevalence of neoplastic lesions between the two age groups was statistically significant (chi (2) = 5.85). An exceptionally high rate of 27 % neoplastic lesions was detected in subjects at 40 to 49 years of age. The rate of detected lesions in the group of older subjects was 36 %. CONCLUSION By using high-resolution endoscopes we found an unexpectedly large number of neoplastic lesions in the colon even in a relatively young average-risk population. The question whether screening colonoscopy should therefore not only aim at detecting early colorectal cancer but also at identifying and removing precursor adenomas at younger ages clearly deserves further attention.
Collapse
Affiliation(s)
- R Eisele
- Department of Internal Medicine, Federal Armed Forces Hospital Ulm, Ulm, Germany.
| | | | | | | | | |
Collapse
|
50
|
Völker HU, Mühlmeier G, Maier H, Kraft K, Müller-Hermelink HK, Zettl A. True malignant mixed tumour (carcinosarcoma) of submandibular gland--a rare neoplasm of monoclonal origin? Histopathology 2007; 50:795-8. [PMID: 17376173 DOI: 10.1111/j.1365-2559.2007.02646.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|