1
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Moosburner M, Alibegovic L, Hasselmann K, Gaiderov A, Hildebrand J, Philippou-Massier J, Blum H, Fischer L, Dreyling M, Silkenstedt E. Combined treatment with crizotinib and temsirolimus is an effective strategy in mantle cell lymphoma and can overcome acquired resistance to temsirolimus. Hematol Oncol 2023; 41:858-868. [PMID: 37300279 DOI: 10.1002/hon.3194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Constitutive activation of the PI3K/AKT/mTOR-pathway plays an important role in the pathogenesis of mantle cell lymphoma (MCL), leading to approval of the mTOR inhibitor temsirolimus for relapsed or refractory MCL. Yet, despite favorable initial response rates, early relapses under treatment have been observed. Therefore, understanding the underlying mechanisms of temsirolimus resistance and developing strategies to overcome it is highly warranted. Here, we established a new temsirolimus-resistant MCL cell line to evaluate the molecular background of resistance to this drug. Transcriptome profiling and gene set enrichment analysis comparing temsirolimus-sensitive and -resistant cell lines showed significant upregulation of PI3K/AKT/mTor-, RAS signaling- and the RTK-dependent PDGFR-, FGFR-, Met- and ALK-signaling-pathways in the resistant cells. Furthermore, MET, known as important proto-oncogene and mediator of drug resistance, was among the most upregulated genes in the resistant cells. Importantly, Met protein was overexpressed in both, MCL cells with acquired as well as intrinsic temsirolimus resistance, but could not be detected in any of the temsirolimus sensitive ones. Combined pharmacological inhibition of mTOR and Met signaling with temsirolimus and the RTK inhibitor crizotinib significantly restored sensitivity to temsirolimus. Furthermore, this combined treatment proved to be synergistic in all MCL cell lines investigated and was also active in primary MCL cells. In summary, we showed for the first time that overexpression of MET plays an important role for mediating temsirolimus resistance in MCL and combined treatment with temsirolimus and crizotinib is a very promising therapeutic approach for MCL and an effective strategy to overcome temsirolimus resistance.
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Affiliation(s)
- Marie Moosburner
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Lamija Alibegovic
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Korbinian Hasselmann
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Anton Gaiderov
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Johannes Hildebrand
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Luca Fischer
- Department of Medicine III, LMU University Hospital Großhadern of the Ludwig-Maximilians-University, Munich, Germany
| | - Martin Dreyling
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
- Department of Medicine III, LMU University Hospital Großhadern of the Ludwig-Maximilians-University, Munich, Germany
| | - Elisabeth Silkenstedt
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
- Department of Medicine III, LMU University Hospital Großhadern of the Ludwig-Maximilians-University, Munich, Germany
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2
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Kufner CL, Krebs S, Fischaleck M, Philippou-Massier J, Blum H, Bucher DB, Braun D, Zinth W, Mast CB. Sequence dependent UV damage of complete pools of oligonucleotides. Sci Rep 2023; 13:2638. [PMID: 36788271 PMCID: PMC9929323 DOI: 10.1038/s41598-023-29833-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.
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Affiliation(s)
- Corinna L. Kufner
- grid.38142.3c000000041936754XHarvard-Smithsonian Center for Astrophysics, Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, MA 02138 USA
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Marlis Fischaleck
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Julia Philippou-Massier
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dominik B. Bucher
- grid.6936.a0000000123222966Chemistry Department, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Dieter Braun
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Wolfgang Zinth
- grid.5252.00000 0004 1936 973XBiomolecular Optics and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
| | - Christof B. Mast
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
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3
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Simmet K, Kurome M, Zakhartchenko V, Reichenbach HD, Springer C, Bähr A, Blum H, Philippou-Massier J, Wolf E. OCT4/POU5F1 is indispensable for the lineage differentiation of the inner cell mass in bovine embryos. FASEB J 2022; 36:e22337. [PMID: 35486003 DOI: 10.1096/fj.202101713rrr] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/10/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023]
Abstract
The mammalian blastocyst undergoes two lineage segregations, that is, formation of the trophectoderm and subsequently differentiation of the hypoblast (HB) from the inner cell mass, leaving the epiblast (EPI) as the remaining pluripotent lineage. To clarify the expression patterns of markers specific for these lineages in bovine embryos, we analyzed day 7, 9, and 12 blastocysts completely produced in vivo by staining for OCT4, NANOG, SOX2 (EPI), and GATA6, SOX17 (HB) and identified genes specific for these developmental stages in a global transcriptomics approach. To study the role of OCT4, we generated OCT4-deficient (OCT4 KO) embryos via somatic cell nuclear transfer or in vitro fertilization. OCT4 KO embryos reached the expanded blastocyst stage by day 8 but lost NANOG and SOX17 expression, while SOX2 and GATA6 were unaffected. Blastocysts transferred to recipient cows from day 6 to 9 expanded, but the OCT4 KO phenotype was not rescued by the uterine environment. Exposure of OCT4 KO embryos to exogenous FGF4 or chimeric complementation with OCT4 intact embryos did not restore NANOG or SOX17 in OCT4-deficient cells. Our data show that OCT4 is required cell autonomously for the maintenance of pluripotency of the EPI and differentiation of the HB in bovine embryos.
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Affiliation(s)
- Kilian Simmet
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Mayuko Kurome
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Valeri Zakhartchenko
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | | | - Claudia Springer
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Andrea Bähr
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany.,Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Poing, Germany
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4
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Flenkenthaler F, Ländström E, Shashikadze B, Backman M, Blutke A, Philippou-Massier J, Renner S, Hrabe de Angelis M, Wanke R, Blum H, Arnold GJ, Wolf E, Fröhlich T. Differential Effects of Insulin-Deficient Diabetes Mellitus on Visceral vs. Subcutaneous Adipose Tissue-Multi-omics Insights From the Munich MIDY Pig Model. Front Med (Lausanne) 2021; 8:751277. [PMID: 34888323 PMCID: PMC8650062 DOI: 10.3389/fmed.2021.751277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
Adipose tissue (AT) is no longer considered to be responsible for energy storage only but is now recognized as a major endocrine organ that is distributed across different parts of the body and is actively involved in regulatory processes controlling energy homeostasis. Moreover, AT plays a crucial role in the development of metabolic disease such as diabetes. Recent evidence has shown that adipokines have the ability to regulate blood glucose levels and improve metabolic homeostasis. While AT has been studied extensively in the context of type 2 diabetes, less is known about how different AT types are affected by absolute insulin deficiency in type 1 or permanent neonatal diabetes mellitus. Here, we analyzed visceral and subcutaneous AT in a diabetic, insulin-deficient pig model (MIDY) and wild-type (WT) littermate controls by RNA sequencing and quantitative proteomics. Multi-omics analysis indicates a depot-specific dysregulation of crucial metabolic pathways in MIDY AT samples. We identified key proteins involved in glucose uptake and downstream signaling, lipogenesis, lipolysis and β-oxidation to be differentially regulated between visceral and subcutaneous AT in response to insulin deficiency. Proteins related to glycogenolysis, pyruvate metabolism, TCA cycle and lipogenesis were increased in subcutaneous AT, whereas β-oxidation-related proteins were increased in visceral AT from MIDY pigs, pointing at a regionally different metabolic adaptation to master energy stress arising from diminished glucose utilization in MIDY AT. Chronic, absolute insulin deficiency and hyperglycemia revealed fat depot-specific signatures using multi-omics analysis. The generated datasets are a valuable resource for further comparative and translational studies in clinical diabetes research.
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Affiliation(s)
- Florian Flenkenthaler
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,German Center for Diabetes Research (DZD), Oberschleißheim, Germany
| | - Erik Ländström
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Gene Center, Graduate School of Quantitative Biosciences Munich (QBM), Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Mattias Backman
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Gene Center, Graduate School of Quantitative Biosciences Munich (QBM), Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Andreas Blutke
- Helmholtz Zentrum München, Institute of Experimental Genetics, Oberschleißheim, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,German Center for Diabetes Research (DZD), Oberschleißheim, Germany
| | - Simone Renner
- German Center for Diabetes Research (DZD), Oberschleißheim, Germany.,Department of Veterinary Sciences, Gene Center, Institute for Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität (LMU) Munich, Oberschleißheim, Germany
| | - Martin Hrabe de Angelis
- German Center for Diabetes Research (DZD), Oberschleißheim, Germany.,Helmholtz Zentrum München, Institute of Experimental Genetics, Technical University of Munich, Munich, Germany
| | - Rüdiger Wanke
- Center for Clinical Veterinary Medicine, Institute of Veterinary Pathology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,German Center for Diabetes Research (DZD), Oberschleißheim, Germany.,Department of Veterinary Sciences, Gene Center, Institute for Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität (LMU) Munich, Oberschleißheim, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
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5
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Holtkamp SJ, Ince LM, Barnoud C, Schmitt MT, Sinturel F, Pilorz V, Pick R, Jemelin S, Mühlstädt M, Boehncke WH, Weber J, Laubender D, Philippou-Massier J, Chen CS, Holtermann L, Vestweber D, Sperandio M, Schraml BU, Halin C, Dibner C, Oster H, Renkawitz J, Scheiermann C. Circadian clocks guide dendritic cells into skin lymphatics. Nat Immunol 2021; 22:1375-1381. [PMID: 34663979 PMCID: PMC8553624 DOI: 10.1038/s41590-021-01040-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022]
Abstract
Migration of leukocytes from the skin to lymph nodes (LNs) via afferent lymphatic vessels (LVs) is pivotal for adaptive immune responses1,2. Circadian rhythms have emerged as important regulators of leukocyte trafficking to LNs via the blood3,4. Here, we demonstrate that dendritic cells (DCs) have a circadian migration pattern into LVs, which peaks during the rest phase in mice. This migration pattern is determined by rhythmic gradients in the expression of the chemokine CCL21 and of adhesion molecules in both mice and humans. Chronopharmacological targeting of the involved factors abrogates circadian migration of DCs. We identify cell-intrinsic circadian oscillations in skin lymphatic endothelial cells (LECs) and DCs that cogovern these rhythms, as their genetic disruption in either cell type ablates circadian trafficking. These observations indicate that circadian clocks control the infiltration of DCs into skin lymphatics, a process that is essential for many adaptive immune responses and relevant for vaccination and immunotherapies.
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Affiliation(s)
- Stephan J Holtkamp
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Louise M Ince
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Coline Barnoud
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Madeleine T Schmitt
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
- Laboratory 'Cell Biology of the Immune System', Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Flore Sinturel
- Department of Medicine, Division of Endocrinology, Diabetes, Nutrition and Patient Education, University Hospitals of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Violetta Pilorz
- Institute of Neurobiology, University of Lübeck, Lübeck, Germany
| | - Robert Pick
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stéphane Jemelin
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michael Mühlstädt
- Division of Dermatology and Venereology, Department of Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Wolf-Henning Boehncke
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Dermatology and Venereology, Department of Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Jasmin Weber
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | | | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Chien-Sin Chen
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Leonie Holtermann
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Dietmar Vestweber
- Department of Vascular Cell Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Markus Sperandio
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Barbara U Schraml
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Cornelia Halin
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Charna Dibner
- Department of Medicine, Division of Endocrinology, Diabetes, Nutrition and Patient Education, University Hospitals of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Henrik Oster
- Institute of Neurobiology, University of Lübeck, Lübeck, Germany
| | - Jörg Renkawitz
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
- Laboratory 'Cell Biology of the Immune System', Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany
| | - Christoph Scheiermann
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Germany.
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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6
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Wolfien M, Klatt D, Salybekov AA, Ii M, Komatsu-Horii M, Gaebel R, Philippou-Massier J, Schrinner E, Akimaru H, Akimaru E, David R, Garbade J, Gummert J, Haverich A, Hennig H, Iwasaki H, Kaminski A, Kawamoto A, Klopsch C, Kowallick JT, Krebs S, Nesteruk J, Reichenspurner H, Ritter C, Stamm C, Tani-Yokoyama A, Blum H, Wolkenhauer O, Schambach A, Asahara T, Steinhoff G. Hematopoietic stem-cell senescence and myocardial repair - Coronary artery disease genotype/phenotype analysis of post-MI myocardial regeneration response induced by CABG/CD133+ bone marrow hematopoietic stem cell treatment in RCT PERFECT Phase 3. EBioMedicine 2020; 57:102862. [PMID: 32629392 PMCID: PMC7339012 DOI: 10.1016/j.ebiom.2020.102862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/02/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Background Bone marrow stem cell clonal dysfunction by somatic mutation is suspected to affect post-infarction myocardial regeneration after coronary bypass surgery (CABG). Methods Transcriptome and variant expression analysis was studied in the phase 3 PERFECT trial post myocardial infarction CABG and CD133+ bone marrow derived hematopoetic stem cells showing difference in left ventricular ejection fraction (∆LVEF) myocardial regeneration Responders (n=14; ∆LVEF +16% day 180/0) and Non-responders (n=9; ∆LVEF -1.1% day 180/0). Subsequently, the findings have been validated in an independent patient cohort (n=14) as well as in two preclinical mouse models investigating SH2B3/LNK antisense or knockout deficient conditions. Findings 1. Clinical: R differed from NR in a total of 161 genes in differential expression (n=23, q<0•05) and 872 genes in coexpression analysis (n=23, q<0•05). Machine Learning clustering analysis revealed distinct RvsNR preoperative gene-expression signatures in peripheral blood acorrelated to SH2B3 (p<0.05). Mutation analysis revealed increased specific variants in RvsNR. (R: 48 genes; NR: 224 genes). 2. Preclinical:SH2B3/LNK-silenced hematopoietic stem cell (HSC) clones displayed significant overgrowth of myeloid and immune cells in bone marrow, peripheral blood, and tissue at day 160 after competitive bone-marrow transplantation into mice. SH2B3/LNK−/− mice demonstrated enhanced cardiac repair through augmenting the kinetics of bone marrow-derived endothelial progenitor cells, increased capillary density in ischemic myocardium, and reduced left ventricular fibrosis with preserved cardiac function. 3. Validation: Evaluation analysis in 14 additional patients revealed 85% RvsNR (12/14 patients) prediction accuracy for the identified biomarker signature. Interpretation Myocardial repair is affected by HSC gene response and somatic mutation. Machine Learning can be utilized to identify and predict pathological HSC response. Funding German Ministry of Research and Education (BMBF): Reference and Translation Center for Cardiac Stem Cell Therapy - FKZ0312138A and FKZ031L0106C, German Ministry of Research and Education (BMBF): Collaborative research center - DFG:SFB738 and Center of Excellence - DFG:EC-REBIRTH), European Social Fonds: ESF/IV-WM-B34-0011/08, ESF/IV-WM-B34-0030/10, and Miltenyi Biotec GmbH, Bergisch-Gladbach, Germany. Japanese Ministry of Health : Health and Labour Sciences Research Grant (H14-trans-001, H17-trans-002) Trial registration ClinicalTrials.gov NCT00950274
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Affiliation(s)
- Markus Wolfien
- Department of Systems Biology and Bioinformatics, University Rostock, Institute of Computer Science, Ulmenstrasse 69, 18057 Rostock, Germany.
| | - Denise Klatt
- Hannover Medical School, Institute of Experimental Hematology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
| | - Amankeldi A Salybekov
- Department of Advanced Medicine Science, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa 259-1143, Japan
| | - Masaaki Ii
- Nanobridge, LLC. 1-3-5-202, Sawaragi-Nishi Ibaraki Osaka 567-0868, Japan.
| | - Miki Komatsu-Horii
- Institute of Biomedical Research and Innovation, 2-2 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Ralf Gaebel
- Reference and Translation Center for Cardiac Stem Cell Therapy, Department Life, Light and Matter and Department of cardiac surgery, University Medicine Rostock, Schillingallee 35, 18055 Rostock, Germany.
| | - Julia Philippou-Massier
- Ludwig-Maximilians-Universität München, LAFUGA Genomics, Gene Center, Feodor-Lynen-Strasse 25, 81377 Muenchen, Germany.
| | - Eric Schrinner
- University Medical Center Goettingen, Institute for Diagnostic and Interventional Radiology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.
| | - Hiroshi Akimaru
- Institute of Biomedical Research and Innovation, 2-2 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Erika Akimaru
- Institute of Biomedical Research and Innovation, 2-2 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Robert David
- Reference and Translation Center for Cardiac Stem Cell Therapy, Department Life, Light and Matter and Department of cardiac surgery, University Medicine Rostock, Schillingallee 35, 18055 Rostock, Germany.
| | - Jens Garbade
- Department of Cardiac Surgery, Heart Center University Medicine Leipzig, Strümpellstrasse 39, 04289 Leipzig, Germany.
| | - Jan Gummert
- Heart and diabetes center North Rhine Westfalia, University hospital of the Ruhr university Bochum, Georgstraße 11, 32545 Bad Oeynhausen, Germany.
| | - Axel Haverich
- Medical school Hannover, Department of heart-, thoracic- and vascular surgery, Carl Neuberg Strasse 1, 30625 Hannover, Germany.
| | - Holger Hennig
- Department of Systems Biology and Bioinformatics, University Rostock, Institute of Computer Science, Ulmenstrasse 69, 18057 Rostock, Germany.
| | - Hiroto Iwasaki
- Department of cardiothoracic surgery, Osaka city university, 1-4-3, Asahimachi, Abeno. Osaka, 545-8585. Japan.
| | - Alexander Kaminski
- Reference and Translation Center for Cardiac Stem Cell Therapy, Department Life, Light and Matter and Department of cardiac surgery, University Medicine Rostock, Schillingallee 35, 18055 Rostock, Germany.
| | - Atsuhiko Kawamoto
- Institute of Biomedical Research and Innovation, 2-2 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Christian Klopsch
- Reference and Translation Center for Cardiac Stem Cell Therapy, Department Life, Light and Matter and Department of cardiac surgery, University Medicine Rostock, Schillingallee 35, 18055 Rostock, Germany.
| | - Johannes T Kowallick
- University Medical Center Goettingen, Institute for Diagnostic and Interventional Radiology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.
| | - Stefan Krebs
- Ludwig-Maximilians-Universität München, LAFUGA Genomics, Gene Center, Feodor-Lynen-Strasse 25, 81377 Muenchen, Germany.
| | - Julia Nesteruk
- Reference and Translation Center for Cardiac Stem Cell Therapy, Department Life, Light and Matter and Department of cardiac surgery, University Medicine Rostock, Schillingallee 35, 18055 Rostock, Germany.
| | - Hermann Reichenspurner
- Department of Cardiac and Vascular Surgery, University heart center Hamburg, Martinistraße. 52, 20246 Hamburg, Germany.
| | - Christian Ritter
- University Medical Center Goettingen, Institute for Diagnostic and Interventional Radiology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.
| | - Christof Stamm
- German Heart Center Berlin, Department of Heart-, Thoracic- and Vascular Surgery, Augustenburger Platz 1, 13353 Berlin, Germany.
| | - Ayumi Tani-Yokoyama
- Institute of Biomedical Research and Innovation, 2-2 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Helmut Blum
- Ludwig-Maximilians-Universität München, LAFUGA Genomics, Gene Center, Feodor-Lynen-Strasse 25, 81377 Muenchen, Germany.
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University Rostock, Institute of Computer Science, Ulmenstrasse 69, 18057 Rostock, Germany.
| | - Axel Schambach
- Hannover Medical School, Institute of Experimental Hematology, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
| | - Takayuki Asahara
- Department of Advanced Medicine Science, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa 259-1143, Japan.
| | - Gustav Steinhoff
- Reference and Translation Center for Cardiac Stem Cell Therapy, Department Life, Light and Matter and Department of cardiac surgery, University Medicine Rostock, Schillingallee 35, 18055 Rostock, Germany.
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7
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Hoesl C, Zanuttigh E, Fröhlich T, Philippou-Massier J, Krebs S, Blum H, Dahlhoff M. The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and induces tumorigenic properties. Biochim Biophys Acta Mol Cell Res 2020; 1867:118717. [PMID: 32283126 DOI: 10.1016/j.bbamcr.2020.118717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/20/2020] [Accepted: 04/07/2020] [Indexed: 12/21/2022]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the most prominent tumor of non-melanoma skin cancers and the most aggressive tumor among keratinocyte carcinoma of the skin, showing a high potential for local invasion and metastasis. The cSCC incidences increased dramatically in recent years and the disease occurs more commonly than any other malignancy. The secretome of cancer cells is currently the focus of many studies in order to identify new marker proteins for different types of cancer and to investigate its influence on the tumor microenvironment. In our study we evaluated whether the secretome of cSCC cells has an impact on keratinocytes, the surrounding tissue cells of cSCC. Therefore, we analyzed and compared the secretome of human A431 cancer cells and of HaCaT keratinocytes by mass spectrometry. In a second experiment, keratinocytes were exposed to the secretome of A431 cells and vice versa and the transcriptome was analyzed by next-generation sequencing. HaCaT cells incubated with A431 conditioned medium revealed a significantly activated mammalian target of rapamycin pathway with a concomitant increase in proliferation and migration. In conclusion, our data demonstrate the impact of the secretome of cancer cells on the transcription machinery of the cells surrounding the tumor, leading to a tumorigenic cell fate.
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Affiliation(s)
- Christine Hoesl
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, LMU, München, Germany
| | - Enrica Zanuttigh
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, LMU, München, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, LMU, München, Germany
| | | | - Stefan Krebs
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, LMU, München, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, LMU, München, Germany
| | - Maik Dahlhoff
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, LMU, München, Germany.
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8
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Fessler E, Eckl EM, Schmitt S, Mancilla IA, Meyer-Bender MF, Hanf M, Philippou-Massier J, Krebs S, Zischka H, Jae LT. A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol. Nature 2020; 579:433-437. [PMID: 32132706 PMCID: PMC7116715 DOI: 10.1038/s41586-020-2076-4] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [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: 08/13/2019] [Accepted: 01/23/2020] [Indexed: 11/08/2022]
Abstract
Mitochondrial fidelity is tightly linked to overall cellular homeostasis and is compromised in ageing and various pathologies1-3. Mitochondrial malfunction needs to be relayed to the cytosol, where an integrated stress response is triggered by the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) in mammalian cells4,5. eIF2α phosphorylation is mediated by the four eIF2α kinases GCN2, HRI, PERK and PKR, which are activated by diverse types of cellular stress6. However, the machinery that communicates mitochondrial perturbation to the cytosol to trigger the integrated stress response remains unknown1,2,7. Here we combine genome engineering and haploid genetics to unbiasedly identify genes that affect the induction of C/EBP homologous protein (CHOP), a key factor in the integrated stress response. We show that the mitochondrial protease OMA1 and the poorly characterized protein DELE1, together with HRI, constitute the missing pathway that is triggered by mitochondrial stress. Mechanistically, stress-induced activation of OMA1 causes DELE1 to be cleaved into a short form that accumulates in the cytosol, where it binds to and activates HRI via its C-terminal portion. Obstruction of this pathway can be beneficial or adverse depending on the type of mitochondrial perturbation. In addition to the core pathway components, our comparative genetic screening strategy identifies a suite of additional regulators. Together, these findings could be used to inform future strategies to modulate the cellular response to mitochondrial dysfunction in the context of human disease.
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Affiliation(s)
- Evelyn Fessler
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eva-Maria Eckl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sabine Schmitt
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University Munich, Munich, Germany
| | - Igor Alves Mancilla
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias F Meyer-Bender
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Monika Hanf
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julia Philippou-Massier
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Krebs
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans Zischka
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University Munich, Munich, Germany
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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9
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Batcha AMN, Bamopoulos SA, Kerbs P, Kumar A, Jurinovic V, Rothenberg-Thurley M, Ksienzyk B, Philippou-Massier J, Krebs S, Blum H, Schneider S, Konstandin N, Bohlander SK, Heckman C, Kontro M, Hiddemann W, Spiekermann K, Braess J, Metzeler KH, Greif PA, Mansmann U, Herold T. Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia. Sci Rep 2019; 9:11796. [PMID: 31409822 PMCID: PMC6692371 DOI: 10.1038/s41598-019-48167-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/29/2019] [Indexed: 12/24/2022] Open
Abstract
The patho-mechanism of somatic driver mutations in cancer usually involves transcription, but the proportion of mutations and wild-type alleles transcribed from DNA to RNA is largely unknown. We systematically compared the variant allele frequencies of recurrently mutated genes in DNA and RNA sequencing data of 246 acute myeloid leukaemia (AML) patients. We observed that 95% of all detected variants were transcribed while the rest were not detectable in RNA sequencing with a minimum read-depth cut-off (10x). Our analysis focusing on 11 genes harbouring recurring mutations demonstrated allelic imbalance (AI) in most patients. GATA2, RUNX1, TET2, SRSF2, IDH2, PTPN11, WT1, NPM1 and CEBPA showed significant AIs. While the effect size was small in general, GATA2 exhibited the largest allelic imbalance. By pooling heterogeneous data from three independent AML cohorts with paired DNA and RNA sequencing (N = 253), we could validate the preferential transcription of GATA2-mutated alleles. Differential expression analysis of the genes with significant AI showed no significant differential gene and isoform expression for the mutated genes, between mutated and wild-type patients. In conclusion, our analyses identified AI in nine out of eleven recurrently mutated genes. AI might be a common phenomenon in AML which potentially contributes to leukaemogenesis.
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Affiliation(s)
- Aarif M N Batcha
- Institute of Medical Data Processing, Biometrics and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany. .,Data Integration for Future Medicine (DiFuture, www.difuture.de), LMU Munich, Munich, Germany.
| | - Stefanos A Bamopoulos
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Paul Kerbs
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Ashwini Kumar
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Vindi Jurinovic
- Institute of Medical Data Processing, Biometrics and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany.,Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Bianka Ksienzyk
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - Nikola Konstandin
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Caroline Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mika Kontro
- Department of Haematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Wolfgang Hiddemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany
| | - Klaus H Metzeler
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Mansmann
- Institute of Medical Data Processing, Biometrics and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany.,Data Integration for Future Medicine (DiFuture, www.difuture.de), LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany. .,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.
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10
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Backman M, Flenkenthaler F, Blutke A, Dahlhoff M, Ländström E, Renner S, Philippou-Massier J, Krebs S, Rathkolb B, Prehn C, Grzybek M, Coskun Ü, Rothe M, Adamski J, de Angelis MH, Wanke R, Fröhlich T, Arnold GJ, Blum H, Wolf E. Multi-omics insights into functional alterations of the liver in insulin-deficient diabetes mellitus. Mol Metab 2019; 26:30-44. [PMID: 31221621 PMCID: PMC6667734 DOI: 10.1016/j.molmet.2019.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE The liver regulates the availability of insulin to other tissues and is the first line insulin response organ physiologically exposed to higher insulin concentrations than the periphery. Basal insulin during fasting inhibits hepatic gluconeogenesis and glycogenolysis, whereas postprandial insulin peaks stimulate glycogen synthesis. The molecular consequences of chronic insulin deficiency for the liver have not been studied systematically. METHODS We analyzed liver samples of a genetically diabetic pig model (MIDY) and of wild-type (WT) littermate controls by RNA sequencing, proteomics, and targeted metabolomics/lipidomics. RESULTS Cross-omics analyses revealed increased activities in amino acid metabolism, oxidation of fatty acids, ketogenesis, and gluconeogenesis in the MIDY samples. In particular, the concentrations of the ketogenic enzyme 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2) and of retinol dehydrogenase 16 (RDH16), which catalyzes the first step in retinoic acid biogenesis, were highly increased. Accordingly, elevated levels of retinoic acid, which stimulates the expression of the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (PCK1), were measured in the MIDY samples. In contrast, pathways related to extracellular matrix and inflammation/pathogen defense response were less active than in the WT samples. CONCLUSIONS The first multi-omics study of a clinically relevant diabetic large animal model revealed molecular signatures and key drivers of functional alterations of the liver in insulin-deficient diabetes mellitus. The multi-omics data set provides a valuable resource for comparative analyses with other experimental or clinical data sets.
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Affiliation(s)
- Mattias Backman
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; Graduate School of Quantitative Biosciences Munich (QBM), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Florian Flenkenthaler
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Andreas Blutke
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Maik Dahlhoff
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany
| | - Erik Ländström
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; Graduate School of Quantitative Biosciences Munich (QBM), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Simone Renner
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Birgit Rathkolb
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; German Mouse Clinic (GMC), Institute of Experimental Genetics, 85764 Neuherberg, Germany
| | - Cornelia Prehn
- Research Unit of Molecular Endocrinology and Metabolism (MEM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michal Grzybek
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital, Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany
| | - Ünal Coskun
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital, Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany
| | | | - Jerzy Adamski
- Research Unit of Molecular Endocrinology and Metabolism (MEM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, 85764 Neuherberg, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Martin Hrabĕ de Angelis
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; German Mouse Clinic (GMC), Institute of Experimental Genetics, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, 85764 Neuherberg, Germany
| | - Rüdiger Wanke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany.
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11
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Schmähling S, Meiler A, Lee Y, Mohammed A, Finkl K, Tauscher K, Israel L, Wirth M, Philippou-Massier J, Blum H, Habermann B, Imhof A, Song JJ, Müller J. Regulation and function of H3K36 di-methylation by the trithorax-group protein complex AMC. Development 2018. [PMID: 29540501 PMCID: PMC5963871 DOI: 10.1242/dev.163808] [Citation(s) in RCA: 25] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Drosophila Ash1 protein is a trithorax-group (trxG) regulator that antagonizes Polycomb repression at HOX genes. Ash1 di-methylates lysine 36 in histone H3 (H3K36me2) but how this activity is controlled and at which genes it functions is not well understood. We show that Ash1 protein purified from Drosophila exists in a complex with MRG15 and Caf1 that we named AMC. In Drosophila and human AMC, MRG15 binds a conserved FxLP motif near the Ash1 SET domain and stimulates H3K36 di-methylation on nucleosomes. Drosophila MRG15-null and ash1 catalytic mutants show remarkably specific trxG phenotypes: stochastic loss of HOX gene expression and homeotic transformations in adults. In mutants lacking AMC, H3K36me2 bulk levels appear undiminished but H3K36me2 is reduced in the chromatin of HOX and other AMC-regulated genes. AMC therefore appears to act on top of the H3K36me2/me3 landscape generated by the major H3K36 methyltransferases NSD and Set2. Our analyses suggest that H3K36 di-methylation at HOX genes is the crucial physiological function of AMC and the mechanism by which the complex antagonizes Polycomb repression at these genes. Highlighted Article: The trithorax group protein Ash1 and its regulator MRG15 form a multiprotein complex that maintains expression of HOX and other target genes by methylating histone H3 in their chromatin.
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Affiliation(s)
- Sigrun Schmähling
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Arno Meiler
- Max-Planck Institute of Biochemistry, Computational Biology, Am Klopferspitz 18 82152 Martinsried, Germany
| | - Yoonjung Lee
- Korea Advanced Institute of Science and Technology (KAIST), Department of Biological Sciences, Daejeon 34141, Korea
| | - Arif Mohammed
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Katja Finkl
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Katharina Tauscher
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lars Israel
- Zentrallabor für Proteinanalytik, BioMedical Center, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Marc Wirth
- Zentrallabor für Proteinanalytik, BioMedical Center, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Bianca Habermann
- Max-Planck Institute of Biochemistry, Computational Biology, Am Klopferspitz 18 82152 Martinsried, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, BioMedical Center, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Ji-Joon Song
- Korea Advanced Institute of Science and Technology (KAIST), Department of Biological Sciences, Daejeon 34141, Korea
| | - Jürg Müller
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
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12
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Moessinger C, Klizaite K, Steinhagen A, Philippou-Massier J, Shevchenko A, Hoch M, Ejsing CS, Thiele C. Two different pathways of phosphatidylcholine synthesis, the Kennedy Pathway and the Lands Cycle, differentially regulate cellular triacylglycerol storage. BMC Cell Biol 2014; 15:43. [PMID: 25491198 PMCID: PMC4293825 DOI: 10.1186/s12860-014-0043-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 11/17/2014] [Indexed: 02/01/2023] Open
Abstract
Background Lipids are stored within cells in lipid droplets (LDs). They consist of a core of neutral lipids surrounded by a monolayer of phospholipids, predominantly phosphatidylcholine (PC). LDs are very dynamic and can rapidly change in size upon lipid uptake or release. These dynamics require a fast adaptation of LD surface. We have recently shown that two Lands cycle PC synthesizing enyzmes, LPCAT1 and LPCAT2 can localize to the LD surface. Results Here, we show that knock-down of both enzymes leads to an increase in LD size without changes in the total amount of neutral lipids, while interference with the de-novo Kennedy pathway PC biosynthesis is associated with changes in triacylglyceride synthesis. We show that function of LPCAT1 and 2 is conserved in Drosophila melanogaster by the ortholog CG32699. Furthermore we demonstrate that modulation of the LD pool by LPCAT1 influences the release of lipoprotein from liver cells. Conclusion Activity of the Kennedy pathway regulates the balance between phospholipids and neutral lipids, while the Lands cycle regulates lipid droplet size by regulating surface availability and influencing surface to volume ratio. Differences in lipid droplet size may account for differences in lipid dynamics and be relevant to understand lipid overload diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12860-014-0043-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christine Moessinger
- Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany. .,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307, Dresden, Germany.
| | - Kristina Klizaite
- Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany.
| | - Almut Steinhagen
- Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany.
| | - Julia Philippou-Massier
- Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany. .,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307, Dresden, Germany.
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307, Dresden, Germany.
| | - Michael Hoch
- Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany.
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark.
| | - Christoph Thiele
- Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany.
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Böttcher R, Hollmann M, Merk K, Nitschko V, Obermaier C, Philippou-Massier J, Wieland I, Gaul U, Förstemann K. Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells. Nucleic Acids Res 2014; 42:e89. [PMID: 24748663 PMCID: PMC4066747 DOI: 10.1093/nar/gku289] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/26/2014] [Accepted: 03/26/2014] [Indexed: 12/26/2022] Open
Abstract
The ability to edit the genome is essential for many state-of-the-art experimental paradigms. Since DNA breaks stimulate repair, they can be exploited to target site-specific integration. The clustered, regularly interspaced, short palindromic repeats (CRISPR)/cas9 system from Streptococcus pyogenes has been harnessed into an efficient and programmable nuclease for eukaryotic cells. We thus combined DNA cleavage by cas9, the generation of homologous recombination donors by polymerase chain reaction (PCR) and transient depletion of the non-homologous end joining factor lig4. Using cultured Drosophila melanogaster S2-cells and the phosphoglycerate kinase gene as a model, we reached targeted integration frequencies of up to 50% in drug-selected cell populations. Homology arms as short as 29 nt appended to the PCR primer resulted in detectable integration, slightly longer extensions are beneficial. We confirmed established rules for S. pyogenes cas9 sgRNA design and demonstrate that the complementarity region allows length variation and 5'-extensions. This enables generation of U6-promoter fusion templates by overlap-extension PCR with a standardized protocol. We present a series of PCR template vectors for C-terminal protein tagging and clonal Drosophila S2 cell lines with stable expression of a myc-tagged cas9 protein. The system can be used for epitope tagging or reporter gene knock-ins in an experimental setup that can in principle be fully automated.
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Affiliation(s)
- Romy Böttcher
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Manuel Hollmann
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Karin Merk
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Volker Nitschko
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Christina Obermaier
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Julia Philippou-Massier
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Isabella Wieland
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Ulrike Gaul
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Klaus Förstemann
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
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