1
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Beschorner N, Künzle P, Voges M, Hauber I, Indenbirken D, Nakel J, Virdi S, Bradtke P, Lory NC, Rothe M, Paszkowski-Rogacz M, Buchholz F, Grundhoff A, Schambach A, Thirion C, Mittrücker HW, Schulze zur Wiesch J, Hauber J, Chemnitz J. Preclinical toxicity analyses of lentiviral vectors expressing the HIV-1 LTR-specific designer-recombinase Brec1. PLoS One 2024; 19:e0298542. [PMID: 38457474 PMCID: PMC10923487 DOI: 10.1371/journal.pone.0298542] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/25/2024] [Indexed: 03/10/2024] Open
Abstract
Drug-based antiretroviral therapies (ART) efficiently suppress HIV replication in humans, but the virus persists as integrated proviral reservoirs in small numbers of cells. Importantly, ART cannot eliminate HIV from an infected individual, since it does not target the integrated provirus. Therefore, genome editing-based strategies that can inactivate or excise HIV genomes would provide the technology for novel curative therapies. In fact, the HIV-1 LTR-specific designer-recombinase Brec1 has been shown to remove integrated proviruses from infected cells and is highly efficacious on clinical HIV-1 isolates in vitro and in vivo, suggesting that Brec1 has the potential for clinical development of advanced HIV-1 eradication strategies in people living with HIV. In line with the preparation of a first-in-human advanced therapy medicinal product gene therapy trial, we here present an extensive preclinical evaluation of Brec1 and lentiviral vectors expressing the Brec1 transgene. This included detailed functional analysis of potential genomic off-target sites, assessing vector safety by investigating vector copy number (VCN) and the risk for potential vector-related insertional mutagenesis, as well as analyzing the potential of Brec1 to trigger an undesired strong T cell immune response. In conclusion, the antiviral designer-recombinase Brec1 is shown to lack any detectable cytopathic, genotoxic or T cell-related immunogenic effects, thereby meeting an important precondition for clinical application of the therapeutic lentiviral vector LV-Brec1 in novel HIV-1 curative strategies.
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Affiliation(s)
- Niklas Beschorner
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Paul Künzle
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Maike Voges
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Ilona Hauber
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Daniela Indenbirken
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Jacqueline Nakel
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Sanamjeet Virdi
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Peter Bradtke
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Niels Christian Lory
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Frank Buchholz
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Adam Grundhoff
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Hans-Willi Mittrücker
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Schulze zur Wiesch
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim Hauber
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Jan Chemnitz
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
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2
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Bergmann L, Balzer Le S, Hageskal G, Preuss L, Han Y, Astafyeva Y, Loevenich S, Emmann S, Perez-Garcia P, Indenbirken D, Katzowitsch E, Thümmler F, Alawi M, Wentzel A, Streit WR, Krohn I. New dienelactone hydrolase from microalgae bacterial community-Antibiofilm activity against fish pathogens and potential applications for aquaculture. Sci Rep 2024; 14:377. [PMID: 38172513 PMCID: PMC10764354 DOI: 10.1038/s41598-023-50734-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Biofilms are resistant to many traditional antibiotics, which has led to search for new antimicrobials from different and unique sources. To harness the potential of aquatic microbial resources, we analyzed the meta-omics datasets of microalgae-bacteria communities and mined them for potential antimicrobial and quorum quenching enzymes. One of the most interesting candidates (Dlh3), a dienelactone hydrolase, is a α/β-protein with predicted eight α-helices and eight β-sheets. When it was applied to one of the major fish pathogens, Edwardsiella anguillarum, the biofilm development was reproducibly inhibited by up to 54.5%. The transcriptome dataset in presence of Dlh3 showed an upregulation in functions related to self-defense like active genes for export mechanisms and transport systems. The most interesting point regarding the biotechnological potential for aquaculture applications of Dlh3 are clear evidence of biofilm inhibition and that health and division of a relevant fish cell model (CHSE-214) was not impaired by the enzyme.
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Affiliation(s)
- Lutgardis Bergmann
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Simone Balzer Le
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Gunhild Hageskal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Lena Preuss
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Simon Loevenich
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Sarah Emmann
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Pablo Perez-Garcia
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany
| | | | - Elena Katzowitsch
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Fritz Thümmler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
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3
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Peters MK, Astafyeva Y, Han Y, Macdonald JFH, Indenbirken D, Nakel J, Virdi S, Westhoff G, Streit WR, Krohn I. Novel marine metalloprotease-new approaches for inhibition of biofilm formation of Stenotrophomonas maltophilia. Appl Microbiol Biotechnol 2023; 107:7119-7134. [PMID: 37755512 PMCID: PMC10638167 DOI: 10.1007/s00253-023-12781-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Many marine organisms produce bioactive molecules with unique characteristics to survive in their ecological niches. These enzymes can be applied in biotechnological processes and in the medical sector to replace aggressive chemicals that are harmful to the environment. Especially in the human health sector, there is a need for new approaches to fight against pathogens like Stenotrophomonas maltophilia which forms thick biofilms on artificial joints or catheters and causes serious diseases. Our approach was to use enrichment cultures of five marine resources that underwent sequence-based screenings in combination with deep omics analyses in order to identify enzymes with antibiofilm characteristics. Especially the supernatant of the enrichment culture of a stony coral caused a 40% reduction of S. maltophilia biofilm formation. In the presence of the supernatant, our transcriptome dataset showed a clear stress response (upregulation of transcripts for metal resistance, antitoxins, transporter, and iron acquisition) to the treatment. Further investigation of the enrichment culture metagenome and proteome indicated a series of potential antimicrobial enzymes. We found an impressive group of metalloproteases in the proteome of the supernatant that is responsible for the detected anti-biofilm effect against S. maltophilia. KEY POINTS: • Omics-based discovery of novel marine-derived antimicrobials for human health management by inhibition of S. maltophilia • Up to 40% reduction of S. maltophilia biofilm formation by the use of marine-derived samples • Metalloprotease candidates prevent biofilm formation of S. maltophilia K279a by up to 20.
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Affiliation(s)
- Marie Kristin Peters
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Jascha F H Macdonald
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Jacqueline Nakel
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Sanamjeet Virdi
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Guido Westhoff
- Tierpark Hagenbeck, Gemeinnützige Gesellschaft mbH, Lokstedter Grenzstraße 2, 22527, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
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4
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Rožmanić C, Lisnić B, Pribanić Matešić M, Mihalić A, Hiršl L, Park E, Lesac Brizić A, Indenbirken D, Viduka I, Šantić M, Adler B, Yokoyama WM, Krmpotić A, Juranić Lisnić V, Jonjić S, Brizić I. Perinatal murine cytomegalovirus infection reshapes the transcriptional profile and functionality of NK cells. Nat Commun 2023; 14:6412. [PMID: 37828009 PMCID: PMC10570381 DOI: 10.1038/s41467-023-42182-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Infections in early life can elicit substantially different immune responses and pathogenesis than infections in adulthood. Here, we investigate the consequences of murine cytomegalovirus infection in newborn mice on NK cells. We show that infection severely compromised NK cell maturation and functionality in newborns. This effect was not due to compromised virus control. Inflammatory responses to infection dysregulated the expression of major transcription factors governing NK cell fate, such as Eomes, resulting in impaired NK cell function. Most prominently, NK cells from perinatally infected mice have a diminished ability to produce IFN-γ due to the downregulation of long non-coding RNA Ifng-as1 expression. Moreover, the bone marrow's capacity to efficiently generate new NK cells is reduced, explaining the prolonged negative effects of perinatal infection on NK cells. This study demonstrates that viral infections in early life can profoundly impact NK cell biology, including long-lasting impairment in NK cell functionality.
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Affiliation(s)
- Carmen Rožmanić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Berislav Lisnić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | | | - Andrea Mihalić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Lea Hiršl
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Eugene Park
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ana Lesac Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ina Viduka
- Department of Microbiology and Parasitology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marina Šantić
- Department of Microbiology and Parasitology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Barbara Adler
- Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Astrid Krmpotić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Vanda Juranić Lisnić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Stipan Jonjić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.
| | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.
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5
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [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: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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6
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Herrnstadt GR, Niehus CB, Ramcke T, Hagenstein J, Ehnold LI, Nosko A, Warkotsch MT, Feindt FC, Melderis S, Paust HJ, Sivayoganathan V, Jauch-Speer SL, Wong MN, Indenbirken D, Krebs CF, Huber TB, Panzer U, Puelles VG, Kluger MA, Steinmetz OM. The CCR6/CCL20 axis expands RORγt + Tregs to protect from glomerulonephritis. Kidney Int 2023; 104:74-89. [PMID: 36924892 DOI: 10.1016/j.kint.2023.02.027] [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: 04/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/17/2023]
Abstract
Previous studies have identified a unique Treg population, which expresses the Th17 characteristic transcription factor RORγt. These RORγt+ Tregs possess enhanced immunosuppressive capacity, which endows them with great therapeutic potential. However, as a caveat, they are also capable of secreting pro-inflammatory IL-17A. Since the sum function of RORγt+ Tregs in glomerulonephritis (GN) remains unknown, we studied the effects of their absence. Purified CD4+ T cell populations, containing or lacking RORγt+ Tregs, were transferred into immunocompromised RAG1 knockout mice and the nephrotoxic nephritis model of GN was induced. Absence of RORγt+ Tregs significantly aggravated kidney injury, demonstrating overall kidney-protective properties. Analyses of immune responses showed that RORγt+ Tregs were broadly immunosuppressive with no preference for a particular type of T cell response. Further characterization revealed a distinct functional and transcriptional profile, including enhanced production of IL-10. Expression of the chemokine receptor CCR6 marked a particularly potent subset, whose absence significantly worsened GN. As an underlying mechanism, we found that chemokine CCL20 acting through receptor CCR6 signaling mediated expansion and activation of RORγt+ Tregs. Finally, we also detected an increase of CCR6+ Tregs in kidney biopsies, as well as enhanced secretion of chemokine CCL20 in 21 patients with anti-neutrophil cytoplasmic antibody associated GN compared to that of 31 healthy living donors, indicating clinical relevance. Thus, our data characterize RORγt+ Tregs as anti-inflammatory mediators of GN and identify them as promising target for Treg directed therapies.
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Affiliation(s)
- Georg R Herrnstadt
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph B Niehus
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Torben Ramcke
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Hagenstein
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura-Isabell Ehnold
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Nosko
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias T Warkotsch
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederic C Feindt
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Melderis
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hans-Joachim Paust
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Varshi Sivayoganathan
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Milagros N Wong
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Christian F Krebs
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulf Panzer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte A Kluger
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Oliver M Steinmetz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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7
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Albertini S, Martuscelli L, Borgogna C, Virdi S, Indenbirken D, Lo Cigno I, Griffante G, Calati F, Boldorini R, Fischer N, Gariglio M. Cancer-Associated Fibroblasts Exert Proangiogenic Activity in Merkel Cell Carcinoma. J Invest Dermatol 2022; 143:965-976.e15. [PMID: 36572089 DOI: 10.1016/j.jid.2022.12.006] [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] [Received: 09/22/2021] [Revised: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 12/25/2022]
Abstract
The tumor microenvironment is a complex niche enveloping a tumor formed by extracellular matrix, blood vessels, immune cells, and fibroblasts constantly interacting with cancer cells. Although tumor microenvironment is increasingly recognized as a major player in cancer initiation and progression in many tumor types, its involvement in Merkel cell carcinoma (MCC) pathogenesis is currently unknown. In this study, we provide a molecular and functional characterization of cancer-associated fibroblasts (CAFs), the major tumor microenvironment component, in patient-derived xenografts of patients with MCC. We show that subcutaneous coinjection of patient-derived CAFs and human MCC MKL-1 cells into severe combined immunodeficient mice significantly promotes tumor growth and metastasis. These fast-growing xenografts are characterized by areas densely populated with human CAFs, mainly localized around blood vessels. We provide evidence that the growth-promoting activity of MCC-derived CAFs is mediated by the aminopeptidase A/angiotensin II and III/angiotensin II type 1 receptor axis, with the expression of aminopeptidase A in CAFs being a triggering event. Together, our findings point to aminopeptidase A as a potential marker for MCC prognostic stratification and as a candidate for therapeutic intervention.
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Affiliation(s)
- Silvia Albertini
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Licia Martuscelli
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Cinzia Borgogna
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Sanamjeet Virdi
- Technology Platform Next Generation Sequencing, Leibniz Institute for Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute for Virology, Hamburg, Germany
| | - Irene Lo Cigno
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Gloria Griffante
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Federica Calati
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Renzo Boldorini
- Pathology Unit, Department of Health Sciences, Novara Medical School, Novara, Italy
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marisa Gariglio
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara, Italy.
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8
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Perner M, Wallmann K, Adam-Beyer N, Hepach H, Laufer-Meiser K, Böhnke S, Diercks I, Bange HW, Indenbirken D, Nikeleit V, Bryce C, Kappler A, Engel A, Scholz F. Environmental changes affect the microbial release of hydrogen sulfide and methane from sediments at Boknis Eck (SW Baltic Sea). Front Microbiol 2022; 13:1096062. [PMID: 36620042 PMCID: PMC9822571 DOI: 10.3389/fmicb.2022.1096062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Anthropogenic activities are modifying the oceanic environment rapidly and are causing ocean warming and deoxygenation, affecting biodiversity, productivity, and biogeochemical cycling. In coastal sediments, anaerobic organic matter degradation essentially fuels the production of hydrogen sulfide and methane. The release of these compounds from sediments is detrimental for the (local) environment and entails socio-economic consequences. Therefore, it is vital to understand which microbes catalyze the re-oxidation of these compounds under environmental dynamics, thereby mitigating their release to the water column. Here we use the seasonally dynamic Boknis Eck study site (SW Baltic Sea), where bottom waters annually fall hypoxic or anoxic after the summer months, to extrapolate how the microbial community and its activity reflects rising temperatures and deoxygenation. During October 2018, hallmarked by warmer bottom water and following a hypoxic event, modeled sulfide and methane production and consumption rates are higher than in March at lower temperatures and under fully oxic bottom water conditions. The microbial populations catalyzing sulfide and methane metabolisms are found in shallower sediment zones in October 2018 than in March 2019. DNA-and RNA profiling of sediments indicate a shift from primarily organotrophic to (autotrophic) sulfide oxidizing Bacteria, respectively. Previous studies using data collected over decades demonstrate rising temperatures, decreasing eutrophication, lower primary production and thus less fresh organic matter transported to the Boknis Eck sediments. Elevated temperatures are known to stimulate methanogenesis, anaerobic oxidation of methane, sulfate reduction and essentially microbial sulfide consumption, likely explaining the shift to a phylogenetically more diverse sulfide oxidizing community based on RNA.
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Affiliation(s)
- Mirjam Perner
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany,*Correspondence: Mirjam Perner,
| | - Klaus Wallmann
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Nicole Adam-Beyer
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Helmke Hepach
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Katja Laufer-Meiser
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Isabel Diercks
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Hermann W. Bange
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - Verena Nikeleit
- Department of Geomicrobiology and Geosciences, University of Tübingen, Tübingen, Germany
| | - Casey Bryce
- Department of Geomicrobiology and Geosciences, University of Tübingen, Tübingen, Germany,School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Andreas Kappler
- Department of Geomicrobiology and Geosciences, University of Tübingen, Tübingen, Germany
| | - Anja Engel
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Florian Scholz
- Department of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
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9
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Albertini S, Martuscelli L, Borgogna C, Virdi S, Indenbirken D, Boldorini R, Gariglio M, Fischer N. Cancer-associated fibroblasts exert a pro-angiogenic activity in Merkel cell carcinoma. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Sirocko KT, Angstmann H, Papenmeier S, Wagner C, Spohn M, Indenbirken D, Ehrhardt B, Kovacevic D, Hammer B, Svanes C, Rabe KF, Roeder T, Uliczka K, Krauss-Etschmann S. Early-life exposure to tobacco smoke alters airway signaling pathways and later mortality in D. melanogaster. Environ Pollut 2022; 309:119696. [PMID: 35780997 DOI: 10.1016/j.envpol.2022.119696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/31/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Early life environmental influences such as exposure to cigarette smoke (CS) can disturb molecular processes of lung development and thereby increase the risk for later development of chronic respiratory diseases. Among the latter, asthma and chronic obstructive pulmonary disease (COPD) are the most common. The airway epithelium plays a key role in their disease pathophysiology but how CS exposure in early life influences airway developmental pathways and epithelial stress responses or survival is poorly understood. Using Drosophila melanogaster larvae as a model for early life, we demonstrate that CS enters the entire larval airway system, where it activates cyp18a1 which is homologues to human CYP1A1 to metabolize CS-derived polycyclic aromatic hydrocarbons and further induces heat shock protein 70. RNASeq studies of isolated airways showed that CS dysregulates pathways involved in oxidative stress response, innate immune response, xenobiotic and glutathione metabolic processes as well as developmental processes (BMP, FGF signaling) in both sexes, while other pathways were exclusive to females or males. Glutathione S-transferase genes were further validated by qPCR showing upregulation of gstD4, gstD5 and gstD8 in respiratory tracts of females, while gstD8 was downregulated and gstD5 unchanged in males. ROS levels were increased in airways after CS. Exposure to CS further resulted in higher larval mortality, lower larval-pupal transition, and hatching rates in males only as compared to air-exposed controls. Taken together, early life CS induces airway epithelial stress responses and dysregulates pathways involved in the fly's branching morphogenesis as well as in mammalian lung development. CS further affected fitness and development in a highly sex-specific manner.
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Affiliation(s)
- Karolina-Theresa Sirocko
- Division for Invertebrate Models, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | | | - Stephanie Papenmeier
- Division for Invertebrate Models, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Christina Wagner
- Division for Invertebrate Models, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany; Division of Innate Immunity, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Michael Spohn
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Draginja Kovacevic
- DZL Laboratory - Experimental Microbiome Research, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany; Division of Early Origins of Chronic Lung Disease
| | - Barbara Hammer
- DZL Laboratory - Experimental Microbiome Research, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany; Division of Early Origins of Chronic Lung Disease
| | - Cecilie Svanes
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway; Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - Klaus F Rabe
- LungenClinic, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany; Department of Medicine, Christian Albrechts University, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Kiel, Germany
| | - Thomas Roeder
- Division of Molecular Physiology, Institute of Zoology, Christian-Albrechts University Kiel, Kiel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Germany
| | - Karin Uliczka
- Division of Innate Immunity, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany; Division of Early Origins of Chronic Lung Disease
| | - Susanne Krauss-Etschmann
- Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany; Division of Early Origins of Chronic Lung Disease.
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11
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Zech ATL, Prondzynski M, Singh SR, Pietsch N, Orthey E, Alizoti E, Busch J, Madsen A, Behrens CS, Meyer-Jens M, Mearini G, Lemoine MD, Krämer E, Mosqueira D, Virdi S, Indenbirken D, Depke M, Salazar MG, Völker U, Braren I, Pu WT, Eschenhagen T, Hammer E, Schlossarek S, Carrier L. ACTN2 Mutant Causes Proteopathy in Human iPSC-Derived Cardiomyocytes. Cells 2022; 11:cells11172745. [PMID: 36078153 PMCID: PMC9454684 DOI: 10.3390/cells11172745] [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: 08/09/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variants in α-actinin-2 (ACTN2) are associated with several forms of (cardio)myopathy. We previously reported a heterozygous missense (c.740C>T) ACTN2 gene variant, associated with hypertrophic cardiomyopathy, and characterized by an electro-mechanical phenotype in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Here, we created with CRISPR/Cas9 genetic tools two heterozygous functional knock-out hiPSC lines with a second wild-type (ACTN2wt) and missense ACTN2 (ACTN2mut) allele, respectively. We evaluated their impact on cardiomyocyte structure and function, using a combination of different technologies, including immunofluorescence and live cell imaging, RNA-seq, and mass spectrometry. This study showed that ACTN2mut presents a higher percentage of multinucleation, protein aggregation, hypertrophy, myofibrillar disarray, and activation of both the ubiquitin-proteasome system and the autophagy-lysosomal pathway as compared to ACTN2wt in 2D-cultured hiPSC-CMs. Furthermore, the expression of ACTN2mut was associated with a marked reduction of sarcomere-associated protein levels in 2D-cultured hiPSC-CMs and force impairment in engineered heart tissues. In conclusion, our study highlights the activation of proteolytic systems in ACTN2mut hiPSC-CMs likely to cope with ACTN2 aggregation and therefore directs towards proteopathy as an additional cellular pathology caused by this ACTN2 variant, which may contribute to human ACTN2-associated cardiomyopathies.
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Affiliation(s)
- Antonia T. L. Zech
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Maksymilian Prondzynski
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia R. Singh
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Niels Pietsch
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Ellen Orthey
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Erda Alizoti
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Josefine Busch
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Alexandra Madsen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Charlotta S. Behrens
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Moritz Meyer-Jens
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Giulia Mearini
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Marc D. Lemoine
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
- Department of Cardiology, University Heart and Vascular Center, 20246 Hamburg, Germany
| | - Elisabeth Krämer
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Diogo Mosqueira
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Sanamjeet Virdi
- Heinrich-Pette-Institute, Leibniz Institute of Virology, 20246 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute of Virology, 20246 Hamburg, Germany
| | - Maren Depke
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Manuela Gesell Salazar
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Ingke Braren
- Vector Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Elke Hammer
- Department for Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Saskia Schlossarek
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Lucie Carrier
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
- Correspondence: ; Tel.: +49-40-7410-57208
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12
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Astafyeva Y, Gurschke M, Qi M, Bergmann L, Indenbirken D, de Grahl I, Katzowitsch E, Reumann S, Hanelt D, Alawi M, Streit WR, Krohn I. Microalgae and Bacteria Interaction-Evidence for Division of Diligence in the Alga Microbiota. Microbiol Spectr 2022; 10:e0063322. [PMID: 35913168 PMCID: PMC9430724 DOI: 10.1128/spectrum.00633-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 02/18/2022] [Accepted: 07/07/2022] [Indexed: 11/20/2022] Open
Abstract
Microalgae are one of the most dominant forms of life on earth that is tightly associated with a distinct and specialized microbiota. We have previously shown that the microbiota of Scenedesmus quadricauda harbors less than 10 distinct microbial species. Here, we provide evidence that dominant species are affiliated with the genera of Variovorax, Porphyrobacter, and Dyadobacter. Experimental and transcriptome-based evidence implies that within this multispecies interaction, Dyadobacter is a key to alga growth and fitness and is highly adapted to live in the phycosphere. While presumably under light conditions the alga provides the energy source to the bacteria, Dyadobacter produces and releases mainly a large variety of polysaccharides modifying enzymes. This is coherent with high-level expression of the T9SS in alga cocultures. The transcriptome data further imply that quorum-quenching proteins (QQ) and biosynthesis of vitamins B1, B2, B5, B6, and B9 are expressed by Dyadobacter at high levels in comparison to Variovorax and Porphyrobacter. Notably, Dyadobacter produces a significant number of leucine-rich repeat (LRR) proteins and enzymes involved in bacterial reactive oxygen species (ROS) tolerance. Complementary to this, Variovorax expresses the genes of the biosynthesis of vitamins B2, B5, B6, B7, B9, and B12, and Porphyrobacter is specialized in the production of vitamins B2 and B6. Thus, the shared currency between partners are vitamins, microalgae growth-promoting substances, and dissolved carbon. This work significantly enlarges our knowledge on alga-bacteria interaction and demonstrates physiological investigations of microalgae and associated bacteria, using microscopy observations, photosynthetic activity measurements, and flow cytometry. IMPORTANCE The current study gives a detailed insight into mutualistic collaboration of microalgae and bacteria, including the involvement of competitive interplay between bacteria. We provide experimental evidence that Gram-negative bacteria belonging to the Dyadobacter, Porphyrobacter, and Variovorax are the key players in a Scenedesmus quadricauda alga-bacteria interaction. We impart strong evidence that Dyadobacter produces and releases polysaccharides degradation enzymes and leucine-rich repeat proteins; Variovorax supplies the consortium with auxins and vitamin B12, while Porphyrobacter produces a broad spectrum of B vitamins. We show not only that the microalgae collaborate with the bacteria and vice versa but also that the bacteria interact with each other via quorum-sensing and secretion system mechanisms. The shared currency between partners appears to be vitamins, microalgae growth-promoting substances, and dissolved carbon.
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Affiliation(s)
- Yekaterina Astafyeva
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Marno Gurschke
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Minyue Qi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
| | - Lutgardis Bergmann
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Imke de Grahl
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Plant Biochemistry and Infection Biology, Hamburg, Germany
| | - Elena Katzowitsch
- University of Würzburg, Core Unit Systems Medicine, Würzburg, Germany
| | - Sigrun Reumann
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Plant Biochemistry and Infection Biology, Hamburg, Germany
| | - Dieter Hanelt
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Malik Alawi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Core, Hamburg, Germany
| | - Wolfgang R. Streit
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Ines Krohn
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Microbiology and Biotechnology, Hamburg, Germany
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13
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Vollmers S, Lobermeyer A, Niehrs A, Fittje P, Indenbirken D, Nakel J, Virdi S, Brias S, Trenkner T, Sauer G, Peine S, Behrens GM, Lehmann C, Meurer A, Pauli R, Postel N, Roider J, Scholten S, Spinner CD, Stephan C, Wolf E, Wyen C, Richert L, Norman PJ, Sauter J, Schmidt AH, Hoelzemer A, Altfeld M, Körner C. Host KIR/HLA-C Genotypes Determine HIV-Mediated Changes of the NK Cell Repertoire and Are Associated With Vpu Sequence Variations Impacting Downmodulation of HLA-C. Front Immunol 2022; 13:922252. [PMID: 35911762 PMCID: PMC9334850 DOI: 10.3389/fimmu.2022.922252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/13/2022] [Indexed: 12/29/2022] Open
Abstract
NK cells play a pivotal role in viral immunity, utilizing a large array of activating and inhibitory receptors to identify and eliminate virus-infected cells. Killer-cell immunoglobulin-like receptors (KIRs) represent a highly polymorphic receptor family, regulating NK cell activity and determining the ability to recognize target cells. Human leukocyte antigen (HLA) class I molecules serve as the primary ligand for KIRs. Herein, HLA-C stands out as being the dominant ligand for the majority of KIRs. Accumulating evidence indicated that interactions between HLA-C and its inhibitory KIR2DL receptors (KIR2DL1/L2/L3) can drive HIV-1-mediated immune evasion and thus may contribute to the intrinsic control of HIV-1 infection. Of particular interest in this context is the recent observation that HIV-1 is able to adapt to host HLA-C genotypes through Vpu-mediated downmodulation of HLA-C. However, our understanding of the complex interplay between KIR/HLA immunogenetics, NK cell-mediated immune pressure and HIV-1 immune escape is still limited. Therefore, we investigated the impact of specific KIR/HLA-C combinations on the NK cell receptor repertoire and HIV-1 Vpu protein sequence variations of 122 viremic, untreated HIV-1+ individuals. Compared to 60 HIV-1- controls, HIV-1 infection was associated with significant changes within the NK cell receptor repertoire, including reduced percentages of NK cells expressing NKG2A, CD8, and KIR2DS4. In contrast, the NKG2C+ and KIR3DL2+ NK cell sub-populations from HIV-1+ individuals was enlarged compared to HIV-1- controls. Stratification along KIR/HLA-C genotypes revealed a genotype-dependent expansion of KIR2DL1+ NK cells that was ultimately associated with increased binding affinities between KIR2DL1 and HLA-C allotypes. Lastly, our data hinted to a preferential selection of Vpu sequence variants that were associated with HLA-C downmodulation in individuals with high KIR2DL/HLA-C binding affinities. Altogether, our study provides evidence that HIV-1-associated changes in the KIR repertoire of NK cells are to some extent predetermined by host KIR2DL/HLA-C genotypes. Furthermore, analysis of Vpu sequence polymorphisms indicates that differential KIR2DL/HLA-C binding affinities may serve as an additional mechanism how host genetics impact immune evasion by HIV-1.
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Affiliation(s)
| | | | | | - Pia Fittje
- Leibniz Institute of Virology, Hamburg, Germany
| | | | | | | | - Sebastien Brias
- Leibniz Institute of Virology, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Gabriel Sauer
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Sven Peine
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georg M.N. Behrens
- Department for Rheumatology and Clinical Immunology, Hannover Medical School, Hannover, Germany
| | - Clara Lehmann
- Department I for Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Anja Meurer
- Center for Internal Medicine and Infectiology, Munich, Germany
| | - Ramona Pauli
- Medizinisches Versorgungszentrum (MVZ) am Isartor, Munich, Germany
| | - Nils Postel
- Prinzmed, Practice for Infectious Diseases, Munich, Germany
| | - Julia Roider
- Department of Internal Medicine IV, Department of Infectious Diseases, Ludwig-Maximilians University Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | | | - Christoph D. Spinner
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Christoph Stephan
- Infectious Diseases Unit, Goethe-University Hospital Frankfurt, Frankfurt, Germany
| | | | - Christoph Wyen
- Department I for Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, Cologne, Germany
- Praxis am Ebertplatz, Cologne, Germany
| | - Laura Richert
- University of Bordeaux, Inserm U1219 Bordeaux Population Health, Inria Sistm, Bordeaux, France
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | | | | | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marcus Altfeld
- Leibniz Institute of Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Christian Körner
- Leibniz Institute of Virology, Hamburg, Germany
- *Correspondence: Christian Körner,
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14
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Baier C, Huang J, Reumann K, Indenbirken D, Thol F, Koenecke C, Ebadi E, Heim A, Bange FC, Haid S, Pietschmann T, Fischer N. Target capture sequencing reveals a monoclonal outbreak of respiratory syncytial virus B infections among adult hematologic patients. Antimicrob Resist Infect Control 2022; 11:88. [PMID: 35729671 PMCID: PMC9210056 DOI: 10.1186/s13756-022-01120-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) causes community-acquired respiratory tract infections during winter. However, outbreaks in hospitals also occur repeatedly. In particular, patients with hematologic malignancies are at an increased risk for a severe and potentially fatal course of RSV infection. Here we present the investigation of an RSV outbreak in a hematology ward for adults following the ORION statement. Methods An epidemiologic and molecular outbreak analysis was performed. We developed and employed a minimal oligonucleotide probe set in target capture probe sequencing that allows cost-effective RSV-A or -B capturing to reconstruct RSV genomes from clinical samples. Results Four adult patients were involved in the outbreak caused by RSV-B in March 2019. The enforcement of the pre-existing infection control measures by effective training of hospital staff contributed to a successful containment. PCR-based RSV screening on the ward enabled early detection of new cases and rapid isolation measures. The molecular analysis demonstrated that the outbreak sequences were highly related and distinct to other RSV-B strains circulating at the same time. Conclusions A multimodal infection control concept is essential for the timely detection and control of RSV outbreaks in patients with hematological disease. Among other measures, preventive screening for respiratory viruses is recommended. Furthermore, the integration of conventional and molecular epidemiology, such as whole-genome sequencing and variant calling, significantly contributes to the understanding of transmission pathways. Based on this, appropriate conclusions can be drawn for targeted prevention measures that have prepared us for the COVID-19 pandemic beyond the RSV approach described here. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01120-z.
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15
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Czech-Sioli M, Günther T, Robitaille A, Roggenkamp H, Büttner H, Indenbirken D, Christner M, Lütgehetmann M, Knobloch J, Aepfelbacher M, Grundhoff A, Fischer N. Integration of Sequencing and Epidemiologic Data for Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections in a Tertiary-Care Hospital. Clin Infect Dis 2022; 76:e263-e273. [PMID: 35717654 PMCID: PMC9214157 DOI: 10.1093/cid/ciac484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The ongoing coronavirus disease 2019 pandemic significantly burdens hospitals and other healthcare facilities. Therefore, understanding the entry and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for effective prevention and preparedness measures. We performed surveillance and analysis of testing and transmission of SARS-CoV-2 infections in a tertiary-care hospital in Germany during the second and third pandemic waves in fall/winter 2020. METHODS Between calendar week 41 in 2020 and calendar week 1 in 2021, 40%, of all positive patient and staff samples (284 total) were subjected to full-length viral genome sequencing. Clusters were defined based on similar genotypes indicating common sources of infection. We integrated phylogenetic, spatial, and temporal metadata to detect nosocomial infections and outbreaks, uncover transmission chains, and evaluate containment measures' effectiveness. RESULTS Epidemiologic data and contact tracing readily recognize most healthcare-associated (HA) patient infections. However, sequencing data reveal that temporally preceding index cases and transmission routes can be missed using epidemiologic methods, resulting in delayed interventions and serially linked outbreaks being counted as independent events. While hospital-associated transmissions were significantly elevated at a moderate rate of community transmission during the second wave, systematic testing and high vaccination rates among staff have led to a substantial decrease in HA infections at the end of the second/beginning of the third wave despite high community transmissions. CONCLUSIONS While epidemiologic analysis is critical for immediate containment of HA SARS-CoV-2 outbreaks, integration of genomic surveillance revealed weaknesses in identifying staff contacts. Our study underscores the importance of high testing frequency and genomic surveillance to detect, contain and prevent SARS-CoV-2-associated infections in healthcare settings.
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Affiliation(s)
| | - Thomas Günther
- Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alexis Robitaille
- Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Hannes Roggenkamp
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Henning Büttner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Mark Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Johannes Knobloch
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | | | - Nicole Fischer
- Corresponding author: Nicole Fischer, Institute for Medical Microbiology, Virology and Hygiene University Medical Center Hamburg-Eppendorf Martinistrasse 52 20246 Hamburg, Germany
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16
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Carlsen L, Büttner H, Christner M, Franke G, Indenbirken D, Knobling B, Lütgehetmann M, Knobloch J. High burden and diversity of carbapenemase-producing Enterobacterales observed in wastewater of a tertiary care hospital in Germany. Int J Hyg Environ Health 2022; 242:113968. [PMID: 35390565 DOI: 10.1016/j.ijheh.2022.113968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022]
Abstract
Hospitals are one of the main reservoirs of multi-resistant Enterobacterales (MRE). As MRE are resistant to the most frequently used antibiotics, therapy for patients with MRE infections is challenging. It has been previously described that MRE from hospital wastewater can pass into municipal wastewater and even surface water. In this study, we investigated the diversity and epidemiology of MRE in the wastewater of a large tertiary care hospital. Wastewater samples were collected for a four-day period and tested for the presence of Enterobacterales resistant to 3rd gen. cephalosporins. Representative isolates were further characterized by whole genome sequencing. In 120 β-glucuronidase-producing isolates, 68 Escherichia coli and, interestingly, also 52 Citrobacter freundii were identified. In 120 β-glucosidase-producing isolates 45 Serratia marcescens, 34 Klebsiella oxytoca, 32 Enterobacter cloacae and 9 Klebsiella pneumoniae were observed. For all species various MLST sequence types and different clusters of resistance genes were determined, showing a great diversity within the different Enterobacterales, further corroborated by clonal analysis performed by cgMLST. The most prominent clone was wastewater associated E. coli ST635, which accounted for 47.1% of all E. coli isolates. Interestingly, 45.6% of E. coli, 88.5% of C. freundii, 95.6% of S. marcescens, 91.2% of K. oxytoca, 96.9% of E. cloacae and 88.9% of K. pneumoniae isolates carried a carbapenemase gene, indicating a high burden with carbapenemase-producing Enterobacterales. Comparison with clinical isolates from the same hospital displayed few clonal matches. One wastewater isolate of K. pneumoniae was identified to be closely related compared to a clone that had been introduced into the hospital during an outbreak four years earlier. One E. coli isolate was identified as identical to an isolate from a patient, with inpatient stay during the sampling period. The data obtained in this study highlight the problem of antibiotic resistance of Enterobacterales in hospital wastewater. In particular, the clustered occurrence of carbapenemase genes is of great concern and underscores the problem of increasingly scarce antibiotic options against these bacteria.
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Affiliation(s)
- Laura Carlsen
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Henning Büttner
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Martin Christner
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Gefion Franke
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Biology, Martinistraße 52, 20251, Hamburg, Germany
| | - Birte Knobling
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Johannes Knobloch
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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17
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Nakel J, Robitaille A, Günther T, Rosenau L, Czech-Sioli M, Plenge-Bönig A, Bühler S, Wille A, Jakubowski E, Pruskil S, Wahlen M, Indenbirken D, Nörz D, Lütgehetmann M, Aepfelbacher M, Grundhoff A, Grolle B, Fischer N. Comparing susceptibility and contagiousness in concurrent outbreaks with a non-VOC and the VOC SARS-CoV-2 variant B.1.1.7 in daycare centers in Hamburg, Germany. Int J Hyg Environ Health 2022; 240:113928. [PMID: 35093719 PMCID: PMC8784653 DOI: 10.1016/j.ijheh.2022.113928] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/04/2022] [Accepted: 01/17/2022] [Indexed: 12/03/2022]
Abstract
We describe two outbreaks of SARS-CoV-2 in daycare centers in the metropolitan area of Hamburg, Germany. The outbreaks occurred in rapid chronological succession, in neighborhoods with a very similar sociodemographic structure, thus allowing for cross-comparison of these events. We combined classical and molecular epidemiologic investigation methods to study infection entry, spread within the facilities, and subsequent transmission of infections to households. Epidemiologic and molecular evidence suggests a superspreading event with a non-variant of concern (non-VOC) SARS CoV-2 strain at the root of the first outbreak. The second outbreak involved two childcare facilities experiencing infection activity with the variant of concern (VOC) B.1.1.7 (Alpha). We show that the index cases in all outbreaks had been childcare workers, and that children contributed substantially to secondary transmission of SARS-CoV-2 infection from childcare facilities to households. The frequency of secondary transmissions in households originating from B.1.1.7-infected children was increased compared to children with non-VOC infections. Self-reported symptoms, particularly cough and rhinitis, occurred more frequently in B.1.1.7-infected children. Especially in light of the rapidly spreading VOC B.1.617.2 (Delta), our data underline the notion that rigorous SARS-CoV-2 testing in combination with screening of contacts regardless of symptoms is an important measure to prevent SARS-CoV-2 infection of unvaccinated individuals in daycare centers and associated households.
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18
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Krohn I, Bergmann L, Qi M, Indenbirken D, Han Y, Perez-Garcia P, Katzowitsch E, Hägele B, Lübcke T, Siry C, Riemann R, Alawi M, Streit WR. Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion. Front Microbiol 2021; 12:722259. [PMID: 34675897 PMCID: PMC8525681 DOI: 10.3389/fmicb.2021.722259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022] Open
Abstract
Microbial contamination of fuels, associated with a wide variety of bacteria and fungi, leads to decreased product quality and can compromise equipment performance by biofouling or microbiologically influenced corrosion. Detection and quantification of microorganisms are critical in monitoring fuel systems for an early detection of microbial contaminations. To address these challenges, we have analyzed six metagenomes, one transcriptome, and more than 1,200 fluid and swab samples taken from fuel tanks or kerosene. Our deep metagenome sequencing and binning approaches in combination with RNA-seq data and qPCR methods implied a metabolic symbiosis between fungi and bacteria. The most abundant bacteria were affiliated with α-, β-, and γ-Proteobacteria and the filamentous fungi Amorphotheca. We identified a high number of genes, which are related to kerosene degradation and biofilm formation. Surprisingly, a large number of genes coded enzymes involved in polymer degradation and potential bio-corrosion processes. Thereby, the transcriptionally most active microorganisms were affiliated with the genera Methylobacteria, Pseudomonas, Kocuria, Amorpotheka, Aspergillus, Fusarium, and Penicillium. Many not yet cultured bacteria and fungi appeared to contribute to the biofilm transcriptional activities. The largest numbers of transcripts were observed for dehydrogenase, oxygenase, and exopolysaccharide production, attachment and pili/flagella-associated proteins, efflux pumps, and secretion systems as well as lipase and esterase activity.
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Affiliation(s)
- Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Lutgardis Bergmann
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Pablo Perez-Garcia
- Institute of General Microbiology, Molecular Microbiology, Kiel University, Kiel, Germany
| | - Elena Katzowitsch
- Faculty of Medicine, Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | | | - Tim Lübcke
- T/TQ-MN, Lufthansa Technik AG HAM, Hamburg, Germany
| | | | - Ralf Riemann
- T/TQ-MN, Lufthansa Technik AG HAM, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
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19
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Šustić M, Cokarić Brdovčak M, Lisnić B, Materljan J, Juranić Lisnić V, Rožmanić C, Indenbirken D, Hiršl L, Busch DH, Brizić I, Krmpotić A, Jonjić S. Memory CD8 T Cells Generated by Cytomegalovirus Vaccine Vector Expressing NKG2D Ligand Have Effector-Like Phenotype and Distinct Functional Features. Front Immunol 2021; 12:681380. [PMID: 34168650 PMCID: PMC8218728 DOI: 10.3389/fimmu.2021.681380] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/12/2021] [Indexed: 01/17/2023] Open
Abstract
Viral vectors have emerged as a promising alternative to classical vaccines due to their great potential for induction of a potent cellular and humoral immunity. Cytomegalovirus (CMV) is an attractive vaccine vector due to its large genome with many non-essential immunoregulatory genes that can be easily manipulated to modify the immune response. CMV generates a strong antigen-specific CD8 T cell response with a gradual accumulation of these cells in the process called memory inflation. In our previous work, we have constructed a mouse CMV vector expressing NKG2D ligand RAE-1γ in place of its viral inhibitor m152 (RAE-1γMCMV), which proved to be highly attenuated in vivo. Despite attenuation, RAE-1γMCMV induced a substantially stronger CD8 T cell response to vectored antigen than the control vector and provided superior protection against bacterial and tumor challenge. In the present study, we confirmed the enhanced protective capacity of RAE-1γMCMV as a tumor vaccine vector and determined the phenotypical and functional characteristics of memory CD8 T cells induced by the RAE-1γ expressing MCMV. RNAseq data revealed higher transcription of numerous genes associated with effector-like CD8 T cell phenotype in RAE-1γMCMV immunized mice. CD8 T cells primed with RAE-1γMCMV were enriched in TCF1 negative population, with higher expression of KLRG1 and lower expression of CD127, CD27, and Eomes. These phenotypical differences were associated with distinct functional features as cells primed with RAE-1γMCMV showed inferior cytokine-producing abilities but comparable cytotoxic potential. After adoptive transfer into naive hosts, OT-1 cells induced with both RAE-1γMCMV and the control vector were equally efficient in rejecting established tumors, suggesting the context of latent infection and cell numbers as important determinants of enhanced anti-tumor response following RAE-1γMCMV vaccination. Overall, our results shed new light on the phenotypical and functional distinctness of memory CD8 T cells induced with CMV vector expressing cellular ligand for the NKG2D receptor.
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Affiliation(s)
- Marko Šustić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | | | - Berislav Lisnić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Jelena Materljan
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Vanda Juranić Lisnić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Carmen Rožmanić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Lea Hiršl
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Astrid Krmpotić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Stipan Jonjić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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20
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Holdhof D, Schoof M, Al-Kershi S, Spohn M, Kresbach C, Göbel C, Hellwig M, Indenbirken D, Moreno N, Kerl K, Schüller U. Brahma-related gene 1 has time-specific roles during brain and eye development. Development 2021; 148:268382. [PMID: 34042968 DOI: 10.1242/dev.196147] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022]
Abstract
During development, gene expression is tightly controlled to facilitate the generation of the diverse cell types that form the central nervous system. Brahma-related gene 1 (Brg1, also known as Smarca4) is the catalytic subunit of the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex that regulates transcription. We investigated the role of Brg1 between embryonic day 6.5 (E6.5) and E14.5 in Sox2-positive neural stem cells (NSCs). Being without major consequences at E6.5 and E14.5, loss of Brg1 between E7.5 and E12.5 resulted in the formation of rosette-like structures in the subventricular zone, as well as morphological alterations and enlargement of neural retina (NR). Additionally, Brg1-deficient cells showed decreased survival in vitro and in vivo. Furthermore, we uncovered distinct changes in gene expression upon Brg1 loss, pointing towards impaired neuron functions, especially those involving synaptic communication and altered composition of the extracellular matrix. Comparison with mice deficient for integrase interactor 1 (Ini1, also known as Smarcb1) revealed that the enlarged NR was Brg1 specific and was not caused by a general dysfunction of the SWI/SNF complex. These results suggest a crucial role for Brg1 in NSCs during brain and eye development.
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Affiliation(s)
- Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Sina Al-Kershi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany.,Bioinformatics Facility, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Malte Hellwig
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Natalia Moreno
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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21
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Kveštak D, Juranić Lisnić V, Lisnić B, Tomac J, Golemac M, Brizić I, Indenbirken D, Cokarić Brdovčak M, Bernardini G, Krstanović F, Rožmanić C, Grundhoff A, Krmpotić A, Britt WJ, Jonjić S. NK/ILC1 cells mediate neuroinflammation and brain pathology following congenital CMV infection. J Exp Med 2021; 218:e20201503. [PMID: 33630019 PMCID: PMC7918636 DOI: 10.1084/jem.20201503] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/11/2020] [Accepted: 01/29/2021] [Indexed: 12/31/2022] Open
Abstract
Congenital human cytomegalovirus (cHCMV) infection of the brain is associated with a wide range of neurocognitive sequelae. Using infection of newborn mice with mouse cytomegalovirus (MCMV) as a reliable model that recapitulates many aspects of cHCMV infection, including disseminated infection, CNS infection, altered neurodevelopment, and sensorineural hearing loss, we have previously shown that mitigation of inflammation prevented alterations in cerebellar development, suggesting that host inflammatory factors are key drivers of neurodevelopmental defects. Here, we show that MCMV infection causes a dramatic increase in the expression of the microglia-derived chemokines CXCL9/CXCL10, which recruit NK and ILC1 cells into the brain in a CXCR3-dependent manner. Surprisingly, brain-infiltrating innate immune cells not only were unable to control virus infection in the brain but also orchestrated pathological inflammatory responses, which lead to delays in cerebellar morphogenesis. Our results identify NK and ILC1 cells as the major mediators of immunopathology in response to virus infection in the developing CNS, which can be prevented by anti-IFN-γ antibodies.
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MESH Headings
- Animals
- Animals, Newborn
- Brain/immunology
- Brain/pathology
- Brain/virology
- Chemokine CXCL10/genetics
- Chemokine CXCL10/immunology
- Chemokine CXCL10/metabolism
- Chemokine CXCL9/genetics
- Chemokine CXCL9/immunology
- Chemokine CXCL9/metabolism
- Cytomegalovirus/immunology
- Cytomegalovirus/physiology
- Cytomegalovirus Infections/immunology
- Cytomegalovirus Infections/virology
- Gene Expression Regulation/immunology
- Humans
- Immunity, Innate/immunology
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/virology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocytes/immunology
- Lymphocytes/metabolism
- Mice, 129 Strain
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Microglia/immunology
- Microglia/metabolism
- Microglia/virology
- Receptors, CXCR3/genetics
- Receptors, CXCR3/immunology
- Receptors, CXCR3/metabolism
- Mice
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Affiliation(s)
- Daria Kveštak
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Vanda Juranić Lisnić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Berislav Lisnić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Jelena Tomac
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Mijo Golemac
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Giovanni Bernardini
- Department of Molecular Medicine, Faculty of Pharmacy and Medicine, University of Rome “Sapienza”, Rome, Italy
| | - Fran Krstanović
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Carmen Rožmanić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Astrid Krmpotić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - William J. Britt
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Stipan Jonjić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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22
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Holdhof D, Johann PD, Spohn M, Bockmayr M, Safaei S, Joshi P, Masliah-Planchon J, Ho B, Andrianteranagna M, Bourdeaut F, Huang A, Kool M, Upadhyaya SA, Bendel AE, Indenbirken D, Foulkes WD, Bush JW, Creytens D, Kordes U, Frühwald MC, Hasselblatt M, Schüller U. Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases. Acta Neuropathol 2021; 141:291-301. [PMID: 33331994 PMCID: PMC7847432 DOI: 10.1007/s00401-020-02250-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022]
Abstract
Atypical teratoid/rhabdoid tumors (ATRTs) are very aggressive childhood malignancies of the central nervous system. The underlying genetic cause are inactivating bi-allelic mutations in SMARCB1 or (rarely) in SMARCA4. ATRT-SMARCA4 have been associated with a higher frequency of germline mutations, younger age, and an inferior prognosis in comparison to SMARCB1 mutated cases. Based on their DNA methylation profiles and transcriptomics, SMARCB1 mutated ATRTs have been divided into three distinct molecular subgroups: ATRT-TYR, ATRT-SHH, and ATRT-MYC. These subgroups differ in terms of age at diagnosis, tumor location, type of SMARCB1 alterations, and overall survival. ATRT-SMARCA4 are, however, less well understood, and it remains unknown, whether they belong to one of the described ATRT subgroups. Here, we examined 14 ATRT-SMARCA4 by global DNA methylation analyses. We show that they form a separate group segregating from SMARCB1 mutated ATRTs and from other SMARCA4-deficient tumors like small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) or SMARCA4 mutated extra-cranial malignant rhabdoid tumors. In contrast, medulloblastoma (MB) samples with heterozygous SMARCA4 mutations do not group separately, but with established MB subgroups. RNA sequencing of ATRT-SMARCA4 confirmed the clustering results based on DNA methylation profiling and displayed an absence of typical signature genes upregulated in SMARCB1 deleted ATRT. In summary, our results suggest that, in line with previous clinical observations, ATRT-SMARCA4 should be regarded as a distinct molecular subgroup.
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Affiliation(s)
- Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
| | - Pascal D Johann
- Paediatric and Adolescent Medicine, Swabian Childrens' Cancer Center Augsburg, Augsburg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
- Institute of Pathology, Corporate Member of Freie Universität Berlin, Charité, Universitätsmedizin Berlin, Humboldt-Universität Zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sepehr Safaei
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Piyush Joshi
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Julien Masliah-Planchon
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Ben Ho
- Division of Hematology and Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Mamy Andrianteranagna
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
- INSERM U900, CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Curie Institute, Paris, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
- Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France
| | - Annie Huang
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Santhosh A Upadhyaya
- Department of Oncology, St Jude Children's Research Hospital, Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Anne E Bendel
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN, USA
| | - Daniela Indenbirken
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jonathan W Bush
- Division of Anatomical Pathology, British Columbia Children's Hospital and Women's Hospital and Health Center, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Uwe Kordes
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael C Frühwald
- Paediatric and Adolescent Medicine, Swabian Childrens' Cancer Center Augsburg, Augsburg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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23
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Pfefferle S, Günther T, Kobbe R, Czech-Sioli M, Nörz D, Santer R, Oh J, Kluge S, Oestereich L, Peldschus K, Indenbirken D, Huang J, Grundhoff A, Aepfelbacher M, Knobloch JK, Lütgehetmann M, Fischer N. SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany. Clin Microbiol Infect 2021; 27:130.e5-130.e8. [PMID: 33007476 PMCID: PMC7524521 DOI: 10.1016/j.cmi.2020.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 06/06/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters in Hamburg, Germany. METHODS Metagenomic RNA-sequencing and amplicon-sequencing and subsequent variant calling in 25 respiratory samples from SARS-CoV-2 infected patients involved in the earliest infection clusters in Hamburg. RESULTS Amplikon sequencing and cluster analyses of these SARS-CoV-2 sequences allowed the identification of the first infection cluster and five non-related infection clusters occurring at the beginning of the viral entry of SARS-CoV-2 in the Hamburg metropolitan region. Viral genomics together with epidemiological analyses revealed that the index patient acquired the infection in northern Italy and transmitted it to two out of 134 contacts. Single nucleotide polymorphisms clearly distinguished the virus variants of the index and other clusters and allowed us to track in which sequences worldwide these mutations were first described. Minor variant analyses identified the transmission of intra-host variants in the index cluster and household clusters. CONCLUSIONS SARS-CoV-2 variant tracing allows the identification of infection clusters and the follow up of infection chains occurring in the population. Furthermore, the follow up of minor viral variants in infection clusters can provide further resolution on transmission events indistinguishable at a consensus sequence level.
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Affiliation(s)
- Susanne Pfefferle
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Robin Kobbe
- I. Medical Clinic and Polyclinic, Section Infectious Diseases, University Medical Centre Eppendorf, Hamburg, Germany
| | - Manja Czech-Sioli
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Dominic Nörz
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - René Santer
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Jun Oh
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute, Leibniz Institute for Tropical Medicine, Hamburg, Germany
| | - Kersten Peldschus
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Johannes K Knobloch
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
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24
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Günther T, Czech‐Sioli M, Indenbirken D, Robitaille A, Tenhaken P, Exner M, Ottinger M, Fischer N, Grundhoff A, Brinkmann MM. SARS-CoV-2 outbreak investigation in a German meat processing plant. EMBO Mol Med 2020; 12:e13296. [PMID: 33012091 PMCID: PMC7646008 DOI: 10.15252/emmm.202013296] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [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: 08/15/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/09/2023] Open
Abstract
We describe a multifactorial investigation of a SARS-CoV-2 outbreak in a large meat processing complex in Germany. Infection event timing, spatial, climate and ventilation conditions in the processing plant, sharing of living quarters and transport, and viral genome sequences were analyzed. Our results suggest that a single index case transmitted SARS-CoV-2 to co-workers over distances of more than 8 m, within a confined work area in which air is constantly recirculated and cooled. Viral genome sequencing shows that all cases share a set of mutations representing a novel sub-branch in the SARS-CoV-2 C20 clade. We identified the same set of mutations in samples collected in the time period between this initial infection cluster and a subsequent outbreak within the same factory, with the largest number of confirmed SARS-CoV-2 cases in a German meat processing facility reported so far. Our results indicate climate conditions, fresh air exchange rates, and airflow as factors that can promote efficient spread of SARS-CoV-2 via long distances and provide insights into possible requirements for pandemic mitigation strategies in industrial workplace settings.
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Affiliation(s)
- Thomas Günther
- Heinrich Pette InstituteLeibniz Institute for Experimental VirologyHamburgGermany
| | - Manja Czech‐Sioli
- Institute for Medical Microbiology, Virology and HygieneUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Daniela Indenbirken
- Heinrich Pette InstituteLeibniz Institute for Experimental VirologyHamburgGermany
| | - Alexis Robitaille
- Heinrich Pette InstituteLeibniz Institute for Experimental VirologyHamburgGermany
| | | | - Martin Exner
- Institute of Hygiene and Public HealthUniversity of BonnBonnGermany
| | | | - Nicole Fischer
- Institute for Medical Microbiology, Virology and HygieneUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Adam Grundhoff
- Heinrich Pette InstituteLeibniz Institute for Experimental VirologyHamburgGermany
| | - Melanie M Brinkmann
- Viral Immune Modulation Research GroupHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute of GeneticsTechnische Universität BraunschweigBraunschweigGermany
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25
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Günther T, Czech-Sioli M, Indenbirken D, Robitaille A, Tenhaken P, Exner M, Ottinger M, Fischer N, Grundhoff A, Brinkmann MM. SARS-CoV-2 outbreak investigation in a German meat processing plant. EMBO Mol Med 2020. [PMID: 33012091 DOI: 10.2139/ssrn.3654517] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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] [Indexed: 05/13/2023] Open
Abstract
We describe a multifactorial investigation of a SARS-CoV-2 outbreak in a large meat processing complex in Germany. Infection event timing, spatial, climate and ventilation conditions in the processing plant, sharing of living quarters and transport, and viral genome sequences were analyzed. Our results suggest that a single index case transmitted SARS-CoV-2 to co-workers over distances of more than 8 m, within a confined work area in which air is constantly recirculated and cooled. Viral genome sequencing shows that all cases share a set of mutations representing a novel sub-branch in the SARS-CoV-2 C20 clade. We identified the same set of mutations in samples collected in the time period between this initial infection cluster and a subsequent outbreak within the same factory, with the largest number of confirmed SARS-CoV-2 cases in a German meat processing facility reported so far. Our results indicate climate conditions, fresh air exchange rates, and airflow as factors that can promote efficient spread of SARS-CoV-2 via long distances and provide insights into possible requirements for pandemic mitigation strategies in industrial workplace settings.
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Affiliation(s)
- Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Manja Czech-Sioli
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alexis Robitaille
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Martin Exner
- Institute of Hygiene and Public Health, University of Bonn, Bonn, Germany
| | | | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Melanie M Brinkmann
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
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26
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Voß H, Wurlitzer M, Smit DJ, Ewald F, Alawi M, Spohn M, Indenbirken D, Omidi M, David K, Juhl H, Simon R, Sauter G, Fischer L, Izbicki JR, Molloy MP, Nashan B, Schlüter H, Jücker M. Differential regulation of extracellular matrix proteins in three recurrent liver metastases of a single patient with colorectal cancer. Clin Exp Metastasis 2020; 37:649-656. [PMID: 33099724 PMCID: PMC7666585 DOI: 10.1007/s10585-020-10058-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/14/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) patients suffer from the second highest mortality among all cancer entities. In half of all CRC patients, colorectal cancer liver metastases (CRLM) can be observed. Metastatic colorectal cancer is associated with poor overall survival and limited treatment options. Even after successful surgical resection of the primary tumor, metachronous liver metastases occur in one out of eight cases. The only available curative intended treatment is hepatic resection, but metachronous CRLM frequently recur after approximately 1 year. In this study, we performed a proteome analysis of three recurrent liver metastases of a single CRC patient by mass spectrometry. Despite surgical resection of the primary CRC and adjuvant chemotherapy plus cetuximab treatment, the patient developed three metachronous CRLM which occurred consecutively after 9, 21 and 31 months. We identified a set of 1132 proteins expressed in the three metachronous CRLM, of which 481 were differentially regulated, including 81 proteins that were associated with the extracellular matrix (ECM). 56 ECM associated proteins were identified as upregulated in the third metastasis, 26 (46%) of which were previously described as negative prognostic markers in CRC, including tenascin C, nidogen 1, fibulin 1 and vitronectin. These data may reflect an ascending trend of malignancy from the first to the third metachronous colorectal cancer liver metastasis. Additionally, the results indicate different ECM phenotypes for recurrent metachronous metastasis, associated with different grades of malignancy and highlights the importance of individual analysis of molecular features in different, consecutive metastatic events in a single patient.
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Affiliation(s)
- Hannah Voß
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Wurlitzer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel J Smit
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Florian Ewald
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Spohn
- Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lutz Fischer
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark P Molloy
- Bowel Cancer and Biomarker Laboratory, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Björn Nashan
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Clinic of Hepato-Pancreatico-Biliary Surgery and Transplantation, First Affiliated Hospital, University of Science and Technology of China, Hefei, People's Republic of China
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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27
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Czech-Sioli M, Günther T, Therre M, Spohn M, Indenbirken D, Theiss J, Riethdorf S, Qi M, Alawi M, Wülbeck C, Fernandez-Cuesta I, Esmek F, Becker JC, Grundhoff A, Fischer N. High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms. PLoS Pathog 2020; 16:e1008562. [PMID: 32833988 PMCID: PMC7470373 DOI: 10.1371/journal.ppat.1008562] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 09/03/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022] Open
Abstract
Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses.
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Affiliation(s)
- Manja Czech-Sioli
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marlin Therre
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Spohn
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Juliane Theiss
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabine Riethdorf
- Institute of Tumorbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Corinna Wülbeck
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Irene Fernandez-Cuesta
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Franziska Esmek
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Jürgen C. Becker
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail: (AG); (NF)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (AG); (NF)
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28
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Spieck E, Sass K, Keuter S, Hirschmann S, Spohn M, Indenbirken D, Kop LFM, Lücker S, Giaveno A. Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea. Front Microbiol 2020; 11:1522. [PMID: 32849321 PMCID: PMC7365893 DOI: 10.3389/fmicb.2020.01522] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidation - the second step of nitrification - is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35-37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37°C.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Katharina Sass
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sophia Hirschmann
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Michael Spohn
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Linnea F. M. Kop
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Alejandra Giaveno
- PROBIEN (CONICET-UNCo), Departamento de Química, Facultad de Ingeniería, Universidad Nacional del Comahue, Neuquén, Argentina
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29
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Schoof M, Hellwig M, Harrison L, Holdhof D, Lauffer MC, Niesen J, Virdi S, Indenbirken D, Schüller U. The basic helix-loop-helix transcription factor TCF4 impacts brain architecture as well as neuronal morphology and differentiation. Eur J Neurosci 2020; 51:2219-2235. [PMID: 31919899 DOI: 10.1111/ejn.14674] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 12/13/2022]
Abstract
Germline mutations in the basic helix-loop-helix transcription factor 4 (TCF4) cause the Pitt-Hopkins syndrome (PTHS), a developmental disorder with severe intellectual disability. Here, we report findings from a new mouse model with a central nervous system-specific truncation of Tcf4 leading to severe phenotypic abnormalities. Furthermore, it allows the study of a complete TCF4 knockout in adult mice, circumventing early postnatal lethality of previously published mouse models. Our data suggest that a TCF4 truncation results in an impaired hippocampal architecture affecting both the dentate gyrus as well as the cornu ammonis. In the cerebral cortex, loss of TCF4 generates a severe differentiation delay of neural precursors. Furthermore, neuronal morphology was critically affected with shortened apical dendrites and significantly increased branching of dendrites. Our data provide novel information about the role of Tcf4 in brain development and may help to understand the mechanisms leading to intellectual deficits observed in patients suffering from PTHS.
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Affiliation(s)
- Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
| | - Malte Hellwig
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
| | - Luke Harrison
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
| | - Marlen C Lauffer
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Judith Niesen
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
| | - Sanamjeet Virdi
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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30
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Schoof M, Launspach M, Holdhof D, Nguyen L, Engel V, Filser S, Peters F, Immenschuh J, Hellwig M, Niesen J, Mall V, Ertl-Wagner B, Hagel C, Spohn M, Lutz B, Sedlacik J, Indenbirken D, Merk DJ, Schüller U. The transcriptional coactivator and histone acetyltransferase CBP regulates neural precursor cell development and migration. Acta Neuropathol Commun 2019; 7:199. [PMID: 31806049 PMCID: PMC6896766 DOI: 10.1186/s40478-019-0849-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
CREB (cyclic AMP response element binding protein) binding protein (CBP, CREBBP) is a ubiquitously expressed transcription coactivator with intrinsic histone acetyltransferase (KAT) activity. Germline mutations within the CBP gene are known to cause Rubinstein-Taybi syndrome (RSTS), a developmental disorder characterized by intellectual disability, specific facial features and physical anomalies. Here, we investigate mechanisms of CBP function during brain development in order to elucidate morphological and functional mechanisms underlying the development of RSTS. Due to the embryonic lethality of conventional CBP knockout mice, we employed a tissue specific knockout mouse model (hGFAP-cre::CBPFl/Fl, mutant mouse) to achieve a homozygous deletion of CBP in neural precursor cells of the central nervous system. Our findings suggest that CBP plays a central role in brain size regulation, correct neural cell differentiation and neural precursor cell migration. We provide evidence that CBP is both important for stem cell viability within the ventricular germinal zone during embryonic development and for unhindered establishment of adult neurogenesis. Prominent histological findings in adult animals include a significantly smaller hippocampus with fewer neural stem cells. In the subventricular zone, we observe large cell aggregations at the beginning of the rostral migratory stream due to a migration deficit caused by impaired attraction from the CBP-deficient olfactory bulb. The cerebral cortex of mutant mice is characterized by a shorter dendrite length, a diminished spine number, and a relatively decreased number of mature spines as well as a reduced number of synapses. In conclusion, we provide evidence that CBP is important for neurogenesis, shaping neuronal morphology, neural connectivity and that it is involved in neuronal cell migration. These findings may help to understand the molecular basis of intellectual disability in RSTS patients and may be employed to establish treatment options to improve patients’ quality of life.
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31
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Alawi M, Burkhardt L, Indenbirken D, Reumann K, Christopeit M, Kröger N, Lütgehetmann M, Aepfelbacher M, Fischer N, Grundhoff A. DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. Sci Rep 2019; 9:16841. [PMID: 31727957 PMCID: PMC6856179 DOI: 10.1038/s41598-019-52881-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.
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Affiliation(s)
- Malik Alawi
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany.,Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lia Burkhardt
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Kerstin Reumann
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Maximilian Christopeit
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,German Center for Infection Research, DZIF, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
| | - Adam Grundhoff
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany. .,German Center for Infection Research, DZIF, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
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32
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Böhnke S, Sass K, Gonnella G, Diehl A, Kleint C, Bach W, Zitoun R, Koschinsky A, Indenbirken D, Sander SG, Kurtz S, Perner M. Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO 2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments. Front Microbiol 2019; 10:2296. [PMID: 31649639 PMCID: PMC6794353 DOI: 10.3389/fmicb.2019.02296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/20/2019] [Indexed: 12/01/2022] Open
Abstract
The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO2 fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO2 fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO2 fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO2 fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.
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Affiliation(s)
- Stefanie Böhnke
- Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Katharina Sass
- Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Giorgio Gonnella
- Center for Bioinformatics (ZBH), Universität Hamburg, Hamburg, Germany
| | - Alexander Diehl
- Department of Geosciences, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Charlotte Kleint
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Wolfgang Bach
- Department of Geosciences, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Rebecca Zitoun
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Andrea Koschinsky
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sylvia G Sander
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Stefan Kurtz
- Center for Bioinformatics (ZBH), Universität Hamburg, Hamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
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33
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Neelagandan N, Gonnella G, Dang S, Janiesch PC, Miller KK, Küchler K, Marques RF, Indenbirken D, Alawi M, Grundhoff A, Kurtz S, Duncan KE. TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease. Nucleic Acids Res 2019; 47:341-361. [PMID: 30357366 PMCID: PMC6326785 DOI: 10.1093/nar/gky972] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022] Open
Abstract
The RNA-binding protein TDP-43 is heavily implicated in neurodegenerative disease. Numerous patient mutations in TARDBP, the gene encoding TDP-43, combined with data from animal and cell-based models, imply that altered RNA regulation by TDP-43 causes Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. However, underlying mechanisms remain unresolved. Increased cytoplasmic TDP-43 levels in diseased neurons suggest a possible role in this cellular compartment. Here, we examined the impact on translation of overexpressing human TDP-43 and the TDP-43A315T patient mutant protein in motor neuron-like cells and primary cultures of cortical neurons. In motor-neuron like cells, TDP-43 associates with ribosomes without significantly affecting global translation. However, ribosome profiling and additional assays revealed enhanced translation and direct binding of Camta1, Mig12, and Dennd4a mRNAs. Overexpressing either wild-type TDP-43 or TDP-43A315T stimulated translation of Camta1 and Mig12 mRNAs via their 5'UTRs and increased CAMTA1 and MIG12 protein levels. In contrast, translational enhancement of Dennd4a mRNA required a specific 3'UTR region and was specifically observed with the TDP-43A315T patient mutant allele. Our data reveal that TDP-43 can function as an mRNA-specific translational enhancer. Moreover, since CAMTA1 and DENND4A are linked to neurodegeneration, they suggest that this function could contribute to disease.
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Affiliation(s)
- Nagammal Neelagandan
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
| | - Giorgio Gonnella
- Universität Hamburg, MIN-Fakultät, ZBH-Center for Bioinformatics, Hamburg 20146, Germany
| | - Stefan Dang
- Universität Hamburg, MIN-Fakultät, ZBH-Center for Bioinformatics, Hamburg 20146, Germany
| | - Philipp C Janiesch
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
| | - Katharine K Miller
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
| | - Katrin Küchler
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
| | - Rita F Marques
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg 20251, Germany
| | - Malik Alawi
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg 20251, Germany.,Bioinformatics Core, University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg 20251, Germany
| | - Stefan Kurtz
- Universität Hamburg, MIN-Fakultät, ZBH-Center for Bioinformatics, Hamburg 20146, Germany
| | - Kent E Duncan
- Neuronal Translational Control Research Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20251, Germany
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34
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Krohn-Molt I, Alawi M, Förstner KU, Wiegandt A, Burkhardt L, Indenbirken D, Thieß M, Grundhoff A, Kehr J, Tholey A, Streit WR. Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches. Front Microbiol 2017; 8:1941. [PMID: 29067007 PMCID: PMC5641341 DOI: 10.3389/fmicb.2017.01941] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [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: 06/14/2017] [Accepted: 09/21/2017] [Indexed: 11/13/2022] Open
Abstract
Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that Chlorella saccharophila, Scenedesmus quadricauda, and Micrasterias crux-melitensis, maintained in strain collections, are associated with unique and specific microbial populations. Deep metagenome sequencing, binning approaches, secretome analyses in combination with RNA-Seq data implied fundamental differences in the gene expression profiles of the microbiota associated with the different microalga. Our metatranscriptome analyses indicates that the transcriptionally most active bacteria with respect to key genes commonly involved in plant–microbe interactions in the Chlorella (Trebouxiophyceae) and Scenedesmus (Chlorophyceae) strains belong to the phylum of the α-Proteobacteria. In contrast, in the Micrasterias (Zygnematophyceae) phycosphere biofilm bacteria affiliated with the phylum of the Bacteroidetes showed the highest gene expression rates. We furthermore show that effector molecules known from plant–microbe interactions as inducers for the innate immunity are already of relevance at this evolutionary early plant-microbiome level.
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Affiliation(s)
- Ines Krohn-Molt
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Alena Wiegandt
- Division of Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | - Lia Burkhardt
- Virus Genomics, Leibniz Institute for Experimental Virology, Heinrich-Pette-Institute, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Leibniz Institute for Experimental Virology, Heinrich-Pette-Institute, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Adam Grundhoff
- Virus Genomics, Leibniz Institute for Experimental Virology, Heinrich-Pette-Institute, Hamburg, Germany
| | - Julia Kehr
- Molecular Plant Genetics, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Andreas Tholey
- Division of Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
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35
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Engels G, Hierweger AM, Hoffmann J, Thieme R, Thiele S, Bertram S, Dreier C, Resa-Infante P, Jacobsen H, Thiele K, Alawi M, Indenbirken D, Grundhoff A, Siebels S, Fischer N, Stojanovska V, Muzzio D, Jensen F, Karimi K, Mittrücker HW, Arck PC, Gabriel G. Pregnancy-Related Immune Adaptation Promotes the Emergence of Highly Virulent H1N1 Influenza Virus Strains in Allogenically Pregnant Mice. Cell Host Microbe 2017; 21:321-333. [PMID: 28279344 DOI: 10.1016/j.chom.2017.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/20/2017] [Accepted: 02/22/2017] [Indexed: 01/13/2023]
Abstract
Pregnant women are at high risk for severe influenza disease outcomes, yet insights into the underlying mechanisms are limited. Here, we present models of H1N1 infection in syngenic and allogenic pregnant mice; infection in the latter mirrors the severe course of 2009 pandemic influenza in pregnant women. We found that the anti-viral immune response in the pregnant host was significantly restricted as compared to the non-pregnant host. This included a reduced type I interferon response as well as impaired migration of CD8+ T cells into the lung. The multi-faceted failure to mount an anti-viral response in allogenic pregnant mice resulted in a less stringent selective environment that promoted the emergence of 2009 H1N1 virus variants that specifically counteract type I interferon response and mediate increased viral pathogenicity. These insights underscore the importance of influenza vaccination compliance in pregnant women and may open novel therapeutic avenues.
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Affiliation(s)
- Géraldine Engels
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Alexandra Maximiliane Hierweger
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Julia Hoffmann
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - René Thieme
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Swantje Thiele
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Stephanie Bertram
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Carola Dreier
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Patricia Resa-Infante
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Henning Jacobsen
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Kristin Thiele
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Malik Alawi
- Research Group Viral Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Daniela Indenbirken
- Research Group Viral Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Adam Grundhoff
- Research Group Viral Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Svenja Siebels
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Violeta Stojanovska
- Department of Obstetrics and Gynaecology, University Medical Center, 9713 Groningen, NL
| | - Damián Muzzio
- Department of Obstetrics and Gynecology, University of Greifswald, 17475 Greifswald, Germany
| | - Federico Jensen
- Department of Obstetrics and Gynecology, University of Greifswald, 17475 Greifswald, Germany; Laboratory for Immunology of Pregnancy, Center for Pharmacological and Botanical Studies (CEFYBO-CONICET), School of Medicine, University of Buenos Aires, 1053 Buenos Aires, Argentina
| | - Khalil Karimi
- Institute for Hepatology and Experimental Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hans-Willi Mittrücker
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Petra Clara Arck
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Gülsah Gabriel
- Research Group Viral Zoonosis and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; Centre for Structural and Cell Biology in Medicine, University of Lübeck, 23562 Lübeck, Germany.
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36
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Nagarajan S, Bedi U, Budida A, Hamdan FH, Mishra VK, Najafova Z, Xie W, Alawi M, Indenbirken D, Knapp S, Chiang CM, Grundhoff A, Kari V, Scheel CH, Wegwitz F, Johnsen SA. BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells. Nucleic Acids Res 2017; 45:3130-3145. [PMID: 27980063 PMCID: PMC5389510 DOI: 10.1093/nar/gkw1276] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is a member of the bromo- and extraterminal (BET) domain-containing family of epigenetic readers which is under intensive investigation as a target for anti-tumor therapy. BRD4 plays a central role in promoting the expression of select subsets of genes including many driven by oncogenic transcription factors and signaling pathways. However, the role of BRD4 and the effects of BET inhibitors in non-transformed cells remain mostly unclear. We demonstrate that BRD4 is required for the maintenance of a basal epithelial phenotype by regulating the expression of epithelial-specific genes including TP63 and Grainy Head-like transcription factor-3 (GRHL3) in non-transformed basal-like mammary epithelial cells. Moreover, BRD4 occupancy correlates with enhancer activity and enhancer RNA (eRNA) transcription. Motif analyses of cell context-specific BRD4-enriched regions predicted the involvement of FOXO transcription factors. Consistently, activation of FOXO1 function via inhibition of EGFR-AKT signaling promoted the expression of TP63 and GRHL3. Moreover, activation of Src kinase signaling and FOXO1 inhibition decreased the expression of FOXO/BRD4 target genes. Together, our findings support a function for BRD4 in promoting basal mammary cell epithelial differentiation, at least in part, by regulating FOXO factor function on enhancers to activate TP63 and GRHL3 expression.
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Affiliation(s)
- Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Upasana Bedi
- Institute of Molecular Oncology, University Medical Center Göttingen, 37077 Göttingen, Germany.,Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anusha Budida
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Feda H Hamdan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Vivek Kumar Mishra
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Wanhua Xie
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.,Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.,Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.,Institute for Pharmaceutical Chemistry, Goethe University Frankfurt 60323, Germany
| | - Cheng-Ming Chiang
- University of Texas Southwestern Medical Center, Simmons Comprehensive Cancer Center, Dallas, TX 75235, USA
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Christina H Scheel
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, 37077 Göttingen, Germany
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Behrens K, Maul K, Tekin N, Kriebitzsch N, Indenbirken D, Prassolov V, Müller U, Serve H, Cammenga J, Stocking C. RUNX1 cooperates with FLT3-ITD to induce leukemia. J Exp Med 2017; 214:737-752. [PMID: 28213513 PMCID: PMC5339673 DOI: 10.1084/jem.20160927] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 06/17/2016] [Revised: 11/27/2016] [Accepted: 01/27/2017] [Indexed: 01/08/2023] Open
Abstract
Behrens et al. establish the interplay of activated FLT3 receptor and the phosphorylated RUNX1 transcription factor in uncoupling proliferation and differentiation signals in acute leukemia. These findings demonstrate that RUNX1 is a viable therapeutic target in FLT3-mutated AML. Acute myeloid leukemia (AML) is induced by the cooperative action of deregulated genes that perturb self-renewal, proliferation, and differentiation. Internal tandem duplications (ITDs) in the FLT3 receptor tyrosine kinase are common mutations in AML, confer poor prognosis, and stimulate myeloproliferation. AML patient samples with FLT3-ITD express high levels of RUNX1, a transcription factor with known tumor-suppressor function. In this study, to understand this paradox, we investigated the impact of RUNX1 and FLT3-ITD coexpression. FLT3-ITD directly impacts on RUNX1 activity, whereby up-regulated and phosphorylated RUNX1 cooperates with FLT3-ITD to induce AML. Inactivating RUNX1 in tumors releases the differentiation block and down-regulates genes controlling ribosome biogenesis. We identified Hhex as a direct target of RUNX1 and FLT3-ITD stimulation and confirmed high HHEX expression in FLT3-ITD AMLs. HHEX could replace RUNX1 in cooperating with FLT3-ITD to induce AML. These results establish and elucidate the unanticipated oncogenic function of RUNX1 in AML. We predict that blocking RUNX1 activity will greatly enhance current therapeutic approaches using FLT3 inhibitors.
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Affiliation(s)
- Kira Behrens
- Retroviral Pathogenesis, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Katrin Maul
- Retroviral Pathogenesis, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Nilgün Tekin
- Retroviral Pathogenesis, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany.,Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Neele Kriebitzsch
- Retroviral Pathogenesis, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Daniela Indenbirken
- Viral Transformation, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | | | - Ursula Müller
- Retroviral Pathogenesis, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Hubert Serve
- Department of Medicine, Hematology/Oncology, Johann Wolfgang Goethe-University, 60590 Frankfurt am Main, Germany
| | - Jörg Cammenga
- Department of Hematology, Institute for Clinical and Experimental Medicine, Linköping University, 58185 Linköping, Sweden
| | - Carol Stocking
- Retroviral Pathogenesis, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
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38
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Xie W, Nagarajan S, Baumgart SJ, Kosinsky RL, Najafova Z, Kari V, Hennion M, Indenbirken D, Bonn S, Grundhoff A, Wegwitz F, Mansouri A, Johnsen SA. RNF40 regulates gene expression in an epigenetic context-dependent manner. Genome Biol 2017; 18:32. [PMID: 28209164 PMCID: PMC5314486 DOI: 10.1186/s13059-017-1159-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/23/2017] [Indexed: 12/20/2022] Open
Abstract
Background Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. Results Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss. Furthermore, we find that decreased expression of RNF40-dependent genes is highly associated with widespread narrowing of H3K4me3 peaks. H2Bub1 promotes the broadening of H3K4me3 to increase transcriptional elongation, which together lead to increased tissue-specific gene transcription. Notably, genes upregulated following Rnf40 deletion, including Foxl2, are enriched for H3K27me3, which is decreased following Rnf40 deletion due to decreased expression of the Ezh2 gene. As a consequence, increased expression of some RNF40-“suppressed” genes is associated with enhancer activation via FOXL2. Conclusion Together these findings reveal the complexity and context-dependency whereby one histone modification can have divergent effects on gene transcription. Furthermore, we show that these effects are dependent upon the activity of other epigenetic regulatory proteins and histone modifications. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1159-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wanhua Xie
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Simon J Baumgart
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Magali Hennion
- Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Griesebachstraße 5, 37077, Göttingen, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Stefan Bonn
- Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Griesebachstraße 5, 37077, Göttingen, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Ahmed Mansouri
- Department of Molecular Cell Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg, 37077, Göttingen, Germany.,Department of Clinical Neurophysiology, University of Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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Coronado L, Liniger M, Muñoz-González S, Postel A, Pérez LJ, Pérez-Simó M, Perera CL, Frías-Lepoureau MT, Rosell R, Grundhoff A, Indenbirken D, Alawi M, Fischer N, Becher P, Ruggli N, Ganges L. Novel poly-uridine insertion in the 3'UTR and E2 amino acid substitutions in a low virulent classical swine fever virus. Vet Microbiol 2017; 201:103-112. [PMID: 28284595 DOI: 10.1016/j.vetmic.2017.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 09/30/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/24/2022]
Abstract
In this study, we compared the virulence in weaner pigs of the Pinar del Rio isolate and the virulent Margarita strain. The latter caused the Cuban classical swine fever (CSF) outbreak of 1993. Our results showed that the Pinar del Rio virus isolated during an endemic phase is clearly of low virulence. We analysed the complete nucleotide sequence of the Pinar del Rio virus isolated after persistence in newborn piglets, as well as the genome sequence of the inoculum. The consensus genome sequence of the Pinar del Rio virus remained completely unchanged after 28days of persistent infection in swine. More importantly, a unique poly-uridine tract was discovered in the 3'UTR of the Pinar del Rio virus, which was not found in the Margarita virus or any other known CSFV sequences. Based on RNA secondary structure prediction, the poly-uridine tract results in a long single-stranded intervening sequence (SS) between the stem-loops I and II of the 3'UTR, without major changes in the stem- loop structures when compared to the Margarita virus. The possible implications of this novel insertion on persistence and attenuation remain to be investigated. In addition, comparison of the amino acid sequence of the viral proteins Erns, E1, E2 and p7 of the Margarita and Pinar del Rio viruses showed that all non-conservative amino acid substitutions acquired by the Pinar del Rio isolate clustered in E2, with two of them being located within the B/C domain. Immunisation and cross-neutralisation experiments in pigs and rabbits suggest differences between these two viruses, which may be attributable to the amino acid differences observed in E2. Altogether, these data provide fresh insights into viral molecular features which might be associated with the attenuation and adaptation of CSFV for persistence in the field.
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Affiliation(s)
- Liani Coronado
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Matthias Liniger
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
| | - Sara Muñoz-González
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Alexander Postel
- EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, Hannover, Germany
| | | | - Marta Pérez-Simó
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | | | - Rosa Rosell
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Departamentd'Agricultura, Ramaderia, Pesca, Alimentació i Medi Natural, (DAAM), Generalitat de Catalunya, Spain
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Malik Alawi
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany; Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Becher
- EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, Hannover, Germany
| | - Nicolas Ruggli
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
| | - Llilianne Ganges
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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Fischer S, Cornils K, Speiseder T, Badbaran A, Reimer R, Indenbirken D, Grundhoff A, Brunswig-Spickenheier B, Alawi M, Lange C. Indication of Horizontal DNA Gene Transfer by Extracellular Vesicles. PLoS One 2016; 11:e0163665. [PMID: 27684368 PMCID: PMC5042424 DOI: 10.1371/journal.pone.0163665] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/12/2016] [Indexed: 12/27/2022] Open
Abstract
The biological relevance of extracellular vesicles (EV) in intercellular communication has been well established. Thus far, proteins and RNA were described as main cargo. Here, we show that EV released from human bone marrow derived mesenchymal stromal cells (BM-hMSC) also carry high-molecular DNA in addition. Extensive EV characterization revealed this DNA mainly associated with the outer EV membrane and to a smaller degree also inside the EV. Our EV purification protocol secured that DNA is not derived from apoptotic or necrotic cells. To analyze the relevance of EV-associated DNA we lentivirally transduced Arabidopsis thaliana-DNA (A.t.-DNA) as indicator into BM-hMSC and generated EV. Using quantitative polymerase chain reaction (qPCR) techniques we detected high copy numbers of A.t.-DNA in EV. In recipient hMSC incubated with tagged EV for two weeks we identified A.t.-DNA transferred to recipient cells. Investigation of recipient cell DNA using quantitative PCR and verification of PCR-products by sequencing suggested stable integration of A.t.-DNA. In conclusion, for the first time our proof-of-principle experiments point to horizontal DNA transfer into recipient cells via EV. Based on our results we assume that eukaryotic cells are able to exchange genetic information in form of DNA extending the known cargo of EV by genomic DNA. This mechanism might be of relevance in cancer but also during cell evolution and development.
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Affiliation(s)
- Stefanie Fischer
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Cornils
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Speiseder
- Research Unit Viral Transformation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Anita Badbaran
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rudolph Reimer
- Dept. Electron Microscopy, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Bärbel Brunswig-Spickenheier
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatic Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Lange
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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41
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Joosse SA, Babayan A, Prieske K, Indenbirken D, Alawi M, Burandt EC, Grundhoff A, Müller V, Pantel K. Abstract 2421: Circulating tumor cells reveal the genetic evolution of metastatic breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2421] [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: 11/16/2022]
Abstract
Abstract
BACKGROUND. Anti-cancer treatment failure is caused by the genetic and phenotypic heterogeneous properties of the disease. Early dissemination of circulating tumor cells (CTCs) into the blood circulation of cancer patients allows for parallel genetic evolution of the primary tumor and metastases. This study investigated the genomic make-up of CTCs originating from metastasis as a so called “liquid biopsy” and compared these with the different clones of the archived autologous primary tumor on single cell level.
METHODS. From two breast cancer patients, individual CTCs were isolated from blood using Ficoll density gradient followed by micromanipulation of keratin positive cells. Single cells from archived primary breast tumors from the same patients were captured by laser microdissection. DNA was isolated and amplified by whole genome amplification and copy number alterations (CNA) were obtained by shallow, whole genome next generations sequencing (NGS).
RESULTS. From the first breast cancer patient, the genomes from 50 single cells from the primary tumor were sequenced. An unsupervised phylogenetic cluster analysis based on CNA revealed five distinct subclones that displayed increasing chromosomal instability from the first to the last cluster. Using support vector machine (SVM) learning, the CNA profiles of 42 CTCs were residing mostly to the first three clones with few chromosomal aberrations, whereas only one CTC resided to the fourth clone and none to the last with many chromosomal aberrations. The tumor from a second breast cancer patient displayed the presence of three genetically distinct clones with increasing chromosomal instability after sequencing 11 single cells. CTCs (n = 12) from this patient at metastatic disease were classified to the last branch using SVM, however with low probability. After repeating unsupervised clustering on the genomes of the primary tumor tissue and CTCs, a fourth branch was formed with CTCs only.
CONCLUSION. Our results suggest that therapy resistant metastases in breast cancer patients can originate from tumor clones from early stages of tumor evolution and may genetically still be similar (patient 1). On the other hand, further genetic progression may also take place (patient 2) after which the genetic landscape of the metastasis does not resemble the primary tumor anymore. These results underline the importance of “liquid biopsy” in the diagnosis of metastatic cancer.
Citation Format: Simon A. Joosse, Anna Babayan, Katharina Prieske, Daniela Indenbirken, Malik Alawi, Eike C. Burandt, Adam Grundhoff, Volkmar Müller, Klaus Pantel. Circulating tumor cells reveal the genetic evolution of metastatic breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2421.
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Affiliation(s)
- Simon A. Joosse
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Babayan
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Malik Alawi
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eike C. Burandt
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Adam Grundhoff
- 2Heinrich-Pette-Institute for Experimental Virology, Hamburg, Germany
| | - Volkmar Müller
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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42
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Nagarajan S, Bedi U, Budida A, Xie W, Hamdan FHM, Mishra VK, Najafova Z, Alawi M, Indenbirken D, Knapp S, Chiang CM, Grundhoff A, Scheel CH, Kari V, Wegwitz F, Johnsen SA. Abstract 1982: BRD4-FOXO axis maintains differentiated mammary epithelial phenotype by regulating p63 and GRHL3 expression. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Bromodomain-containing protein 4 (BRD4) is an important epigenetic reader which promotes gene transcription to modulate cell-specific functions and is under intensive investigation for its potential as an anti-tumor therapeutic target. However, the role of BRD4 in non-transformed cells remains unclear. Using RNA sequencing and chromatin immunoprecipitation-sequencing analyses in normal basal-like breast epithelial cells, we demonstrate that BRD4 is required for the expression of epithelial-specific genes and suppression of stem cell-like properties by binding to the distal regions of epithelial-related genes. Moreover, BRD4 occupancy correlates with enhancer activity and enhancer RNA (eRNA) transcription of these genes. Interestingly, we show that BRD4 perturbation regulates the expression of p63 and Grainy Head-like transcription factor-3, GRHL3, whose depletion partially mimics BRD4 inhibition and impairs a differentiated phenotype. By binding to the distal regions of p63 and GRHL3, BRD4 promotes RNA polymerase-II occupancy and thus affects eRNA transcription. Motif analyses on cell-specific BRD4 binding sites predict the involvement of FOXO transcription factors. Consistently, inhibition of EGFR-AKT signalling activates FOXO1 function and promotes the expression of p63 and GRHL3. Activation of Src kinase signaling decreases RNA polymerase-II occupancy on BRD4 target genes and enhancers. Altogether, these findings provide evidence that BRD4 promotes a differentiated epithelial phenotype in non-transformed mammary cells at least in part through the activation of p63 and GRHL3 expression by associating with FOXO factors.
Citation Format: Sankari Nagarajan, Upasana Bedi, Anusha Budida, Wanhua Xie, Feda Hisham Moh’d Hamdan, Vivek Kumar Mishra, Zeynab Najafova, Malik Alawi, Daniela Indenbirken, Stephan Knapp, Cheng-Ming Chiang, Adam Grundhoff, Christina H. Scheel, Vijayalakshmi Kari, Florian Wegwitz, Steven A. Johnsen. BRD4-FOXO axis maintains differentiated mammary epithelial phenotype by regulating p63 and GRHL3 expression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1982.
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Affiliation(s)
- Sankari Nagarajan
- 1Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Germany; Cancer Research Centre UK, University of Cambridge, Cambridge, United Kingdom
| | - Upasana Bedi
- 2Institute for Molecular Oncology, University Medical Center Göttingen, Goettingen, Germany; Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anusha Budida
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Wanhua Xie
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Feda Hisham Moh’d Hamdan
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Vivek Kumar Mishra
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Zeynab Najafova
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Malik Alawi
- 4Bioinformatics Core, University Medical Center Hamburg-Eppendorf; Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- 5Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Stephan Knapp
- 6Structural Genomics Consortium and Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Institute for Pharmaceutical Chemistry, Goethe Universität, Frankfurt, Germany
| | - Cheng-Ming Chiang
- 7University of Texas Southwestern Medical Center, Simmons Comprehensive Cancer Center, Dallas, TX
| | - Adam Grundhoff
- 5Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Christina H. Scheel
- 8Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research, Munich, Germany
| | - Vijayalakshmi Kari
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Florian Wegwitz
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
| | - Steven A. Johnsen
- 3Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Goettingen, Germany
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Stadt UZ, Escherich G, Indenbirken D, Alawi M, Adao M, Horstmann MA. Rapid Capture Next-Generation Sequencing in Clinical Diagnostics of Kinase Pathway Aberrations in B-Cell Precursor ALL. Pediatr Blood Cancer 2016; 63:1283-6. [PMID: 27007619 DOI: 10.1002/pbc.25975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/23/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Comprehensive next-generation sequencing (NGS) applications have recently identified various recurrent kinase and cytokine receptor rearrangements in Ph-like B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) amenable to tyrosin kinase inhibitor treatment. For rapid diagnostics of kinase pathway aberrations in minimal residual disease (MRD) high-risk BCP-ALL, we developed a PCR-independent NGS custom enrichment capture panel targeting recurrent genomic alterations, which allows for the identification of unknown 5' fusion partner genes and precise mapping of variable genomic breakpoints. Using a standardized bioinformatics algorithm, we identified kinase and cytokine receptor rearrangements in the majority of ALL patients with high burden of postinduction MRD and enrichment of IKZF1 mutation or deletion (IKZF1(del) ).
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Affiliation(s)
- Udo Zur Stadt
- Center for Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Escherich
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Heinrich-Pette-Institute for Experimental Virology, Hamburg, Germany
| | - Malik Alawi
- Virus Genomics, Heinrich-Pette-Institute for Experimental Virology, Hamburg, Germany.,Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Adao
- Center for Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin A Horstmann
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center, Hamburg, Germany
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Gonnella G, Böhnke S, Indenbirken D, Garbe-Schönberg D, Seifert R, Mertens C, Kurtz S, Perner M. Endemic hydrothermal vent species identified in the open ocean seed bank. Nat Microbiol 2016; 1:16086. [DOI: 10.1038/nmicrobiol.2016.86] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/03/2016] [Indexed: 01/08/2023]
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Hossan T, Nagarajan S, Baumgart SJ, Xie W, Magallanes RT, Hernandez C, Chiaroni PM, Indenbirken D, Spitzner M, Thomas-Chollier M, Grade M, Thieffry D, Grundhoff A, Wegwitz F, Johnsen SA. Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation. Stem Cells 2016; 34:1369-76. [PMID: 27146025 DOI: 10.1002/stem.2287] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 07/15/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
Cellular differentiation is accompanied by dramatic changes in chromatin structure which direct the activation of lineage-specific transcriptional programs. Structure-specific recognition protein-1 (SSRP1) is a histone chaperone which is important for chromatin-associated processes such as transcription, DNA replication and repair. Since the function of SSRP1 during cell differentiation remains unclear, we investigated its potential role in controlling lineage determination. Depletion of SSRP1 in human mesenchymal stem cells elicited lineage-specific effects by increasing expression of adipocyte-specific genes and decreasing the expression of osteoblast-specific genes. Consistent with a role in controlling lineage specification, transcriptome-wide RNA-sequencing following SSRP1 depletion and the induction of osteoblast differentiation revealed a specific decrease in the expression of genes involved in biological processes related to osteoblast differentiation. Importantly, we observed a specific downregulation of target genes of the canonical Wnt signaling pathway, which was accompanied by decreased nuclear localization of active β-catenin. Together our data uncover a previously unknown role for SSRP1 in promoting the activation of the Wnt signaling pathway activity during cellular differentiation. Stem Cells 2016;34:1369-1376.
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Affiliation(s)
- Tareq Hossan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Simon J Baumgart
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Wanhua Xie
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Roberto Tirado Magallanes
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Céline Hernandez
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Pierre-Marie Chiaroni
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Melanie Spitzner
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Morgane Thomas-Chollier
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Denis Thieffry
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
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Stenzig J, Hirt MN, Löser A, Bartholdt LM, Hensel JT, Werner TR, Riemenschneider M, Indenbirken D, Guenther T, Müller C, Hübner N, Stoll M, Eschenhagen T. DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors. Basic Res Cardiol 2015; 111:9. [DOI: 10.1007/s00395-015-0528-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/09/2015] [Indexed: 12/11/2022]
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Postel A, Schmeiser S, Oguzoglu TC, Indenbirken D, Alawi M, Fischer N, Grundhoff A, Becher P. Close relationship of ruminant pestiviruses and classical Swine Fever virus. Emerg Infect Dis 2015; 21:668-72. [PMID: 25811683 PMCID: PMC4378490 DOI: 10.3201/eid2104.141441] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
To determine why serum from small ruminants infected with ruminant pestiviruses reacted positively to classical swine fever virus (CSFV)–specific diagnostic tests, we analyzed 2 pestiviruses from Turkey. They differed genetically and antigenically from known Pestivirus species and were closely related to CSFV. Cross-reactions would interfere with classical swine fever diagnosis in pigs.
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Ostermann E, Pawletko K, Indenbirken D, Schumacher U, Brune W. Stepwise adaptation of murine cytomegalovirus to cells of a foreign host for identification of host range determinants. Med Microbiol Immunol 2015; 204:461-9. [PMID: 25788395 DOI: 10.1007/s00430-015-0400-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 02/26/2015] [Indexed: 10/23/2022]
Abstract
Ever since their first isolation 60 years ago, cytomegaloviruses have been recognized as being highly species specific. They replicate only in cells of their own or a closely related host species, while cells of phylogenetically more distant hosts are usually not permissive for viral replication. For instance, human cytomegalovirus replicates in human and chimpanzee fibroblasts but not in rodent cells, and murine cytomegalovirus (MCMV) replicates in cells of mice and rats but not in primate cells. However, the viral and cellular factors determining the narrow host range of cytomegaloviruses have remained largely unknown. We show that MCMV can be adapted stepwise to replicate in cultured human retinal pigment epithelial (RPE-1) cells and human fibroblasts. The human RPE-1 cells used for the initial adaptation step showed a pronounced contact inhibition and produced very low level of interferon-β transcripts upon cytomegalovirus infection, suggesting that these cells provide a particularly favorable environment for adaptation. By whole genome sequencing of the 230 kbp viral genomes of several adapted mutants, a limited number of mutations were detected. Comparison of several human cell-adapted MCMV clones and introduction of specific mutations into the wild-type MCMV genome by site-directed mutagenesis allows for the identification of viral host range determinants and provides the basis for elucidating the molecular basis of the cytomegalovirus host species specificity.
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Affiliation(s)
- Eleonore Ostermann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 22455, Hamburg, Germany
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Kati S, Hage E, Mynarek M, Ganzenmueller T, Indenbirken D, Grundhoff A, Schulz TF. Generation of high-titre virus stocks using BrK.219, a B-cell line infected stably with recombinant Kaposi's sarcoma-associated herpesvirus. J Virol Methods 2015; 217:79-86. [PMID: 25736227 DOI: 10.1016/j.jviromet.2015.02.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 08/19/2014] [Revised: 01/13/2015] [Accepted: 02/23/2015] [Indexed: 11/15/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-2-lymphotropic human oncogenic herpesvirus associated with Kaposi's sarcoma (KS) and two B-cell lymphoproliferative diseases, primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). KSHV establishes latency soon after infection in vivo and in vitro. Consequently, it is technically difficult to generate high-titre virus stocks required for infection experiments in tissue culture. Currently used methods of KSHV stock production involve induction of the lytic/productive cycle in PEL cell lines or in adherent cell lines harbouring recombinant KSHV genomes. In this study, the BJAB-derived B-cell line BrK.219, which is infected latently with a recombinant KSHV (rKSHV.219), is used to produce high-titre virus stocks. BrK.219 cells enter the lytic KSHV replication cycle upon cross-linking of B-cell receptors (BCRs) with anti-IgM antibodies without the need for additional, potentially toxic chemical inducers. High cell concentrations can be cultured and induced easily in spinner flasks, saving time and resources. The established protocol allows the generation of KSHV virus stocks with titres of up to 10(6) IU/ml in unconcentrated culture supernatants, representing a 10(3)-10(4)-fold improvement compared to conventional methods.
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Affiliation(s)
- Semra Kati
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover D-30625, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Elias Hage
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover D-30625, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Tina Ganzenmueller
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover D-30625, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover D-30625, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany.
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Hirt MN, Werner T, Indenbirken D, Alawi M, Demin P, Kunze AC, Stenzig J, Starbatty J, Hansen A, Fiedler J, Thum T, Eschenhagen T. Deciphering the microRNA signature of pathological cardiac hypertrophy by engineered heart tissue- and sequencing-technology. J Mol Cell Cardiol 2015; 81:1-9. [PMID: 25633833 DOI: 10.1016/j.yjmcc.2015.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/24/2014] [Accepted: 01/14/2015] [Indexed: 01/27/2023]
Abstract
Pathological cardiac hypertrophy and fibrosis are modulated by a set of microRNAs, most of which have been detected in biologically complex animal models of hypertrophy by arrays with moderate sensitivity and disregard of passenger strand (previously "star") microRNAs. Here, we aimed at precisely analyzing the microRNA signature of cardiac hypertrophy and fibrosis by RNA sequencing in a standardized in vitro hypertrophy model based on engineered heart tissue (EHT). Spontaneously beating, force-generating fibrin EHTs from neonatal rat heart cells were subjected to afterload enhancement for 7days (AE-EHT), and EHTs without intervention served as controls. AE resulted in reduced contractile force and relaxation velocity, fibrotic changes and reactivation of the fetal gene program. Small RNAs were extracted from control and AE-EHTs and sequencing yielded almost 750 different mature microRNAs, many of which have never been described before in rats. The detection of both arms of the precursor stem-loop (pre-miRNA), namely -3p and -5p miRs, was frequent. 22 abundantly sequenced microRNAs were >1.3× upregulated and 15 abundantly sequenced microRNAs downregulated to <0.77×. Among the upregulated microRNAs were 3 pairs of guide and passenger strand microRNAs (miR-21-5p/-3p, miR-322-5p/-3p, miR-210-3p/-5p) and one single passenger strand microRNA (miR-140-3p). Among downregulated microRNAs were 3 pairs (miR-133a-3p/-5p, miR-30e-5p/3p, miR-30c-5p/-3p). Preincubating EHTs with anti-miR-21-5p markedly attenuated the AE-induced contractile failure, cardiomyocyte hypertrophy and fibrotic response, recapitulating prior results in whole animals. Taken together, AE-induced pathological hypertrophy in EHTs is associated with 37 differentially regulated microRNAs, including many passenger strands. Antagonizing miR-21-5p ameliorates dysfunction in this model.
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Affiliation(s)
- Marc N Hirt
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Tessa Werner
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Malik Alawi
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Demin
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ann-Cathrin Kunze
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Justus Stenzig
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Jutta Starbatty
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Arne Hansen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Thomas Eschenhagen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany.
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