151
|
Demirdizen E, Al-Ali R, Narayanan A, Sun X, Varga JP, Steffl B, Brom M, Krunic D, Schmidt C, Schmidt G, Bestvater F, Taranda J, Turcan Ş. TRIM67 drives tumorigenesis in oligodendrogliomas through Rho GTPase-dependent membrane blebbing. Neuro Oncol 2023; 25:1031-1043. [PMID: 36215168 PMCID: PMC10237422 DOI: 10.1093/neuonc/noac233] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND IDH mutant gliomas are grouped into astrocytomas or oligodendrogliomas depending on the codeletion of chromosome arms 1p and 19q. Although the genomic alterations of IDH mutant gliomas have been well described, transcriptional changes unique to either tumor type have not been fully understood. Here, we identify Tripartite Motif Containing 67 (TRIM67), an E3 ubiquitin ligase with essential roles during neuronal development, as an oncogene distinctly upregulated in oligodendrogliomas. METHODS We used several cell lines, including patient-derived oligodendroglioma tumorspheres, to knock down or overexpress TRIM67. We coupled high-throughput assays, including RNA sequencing, total lysate-mass spectrometry (MS), and coimmunoprecipitation (co-IP)-MS with functional assays including immunofluorescence (IF) staining, co-IP, and western blotting (WB) to assess the in vitro phenotype associated with TRIM67. Patient-derived oligodendroglioma tumorspheres were orthotopically implanted in mice to determine the effect of TRIM67 on tumor growth and survival. RESULTS TRIM67 overexpression alters the abundance of cytoskeletal proteins and induces membrane bleb formation. TRIM67-associated blebbing was reverted with the nonmuscle class II myosin inhibitor blebbistatin and selective ROCK inhibitor fasudil. NOGO-A/Rho GTPase/ROCK2 signaling is altered upon TRIM67 ectopic expression, pointing to the underlying mechanism for TRIM67-induced blebbing. Phenotypically, TRIM67 expression resulted in higher cell motility and reduced cell adherence. In orthotopic implantation models of patient-derived oligodendrogliomas, TRIM67 accelerated tumor growth, reduced overall survival, and led to increased vimentin expression at the tumor margin. CONCLUSIONS Taken together, our results demonstrate that upregulated TRIM67 induces blebbing-based rounded cell morphology through Rho GTPase/ROCK-mediated signaling thereby contributing to glioma pathogenesis.
Collapse
Affiliation(s)
- Engin Demirdizen
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
| | - Ruslan Al-Ali
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
| | - Ashwin Narayanan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
| | - Xueyuan Sun
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julianna Patricia Varga
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
| | - Bianca Steffl
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Brom
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Damir Krunic
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Claudia Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Gabriele Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Felix Bestvater
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Julian Taranda
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
| | - Şevin Turcan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany
| |
Collapse
|
152
|
Koops TU, Klein V, Bei der Kellen R, Hoyer J, Löwe B, Briken P. Association of sexual dysfunction according to DSM-5 diagnostic criteria with avoidance of and discomfort during sex in a population-based sample. Sex Med 2023; 11:qfad037. [PMID: 37465531 PMCID: PMC10350482 DOI: 10.1093/sexmed/qfad037] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/20/2023] Open
Abstract
Background Sexual dysfunction frequencies and diagnostic indicators among older populations are relevant for public health measures, but evidence from large population-based studies is still scarce. Aim To determine sexual dysfunction frequencies for women and men according to the Diagnostic and Statistical Manual of Mental Disorders (fifth edition; DSM-5) among 45- to 74-year-old participants of the population-based Hamburg City Health Study and the factors associated with sexual dysfunction diagnoses. Methods We determined sexual dysfunction frequencies according to the DSM-5 and the factors associated with sexual dysfunction diagnoses (quality/avoidance of and discomfort during sex) among 45- to 74-year-olds from 7786 participants of the population-based Hamburg City Health Study. We analyzed cross-sectional self-report questionnaire data collected between 2016 and 2019 using descriptive statistics, comparative tests (Fisher test, Mann-Whitney U test), and logistic regression. Outcomes Outcomes included sexual dysfunction frequencies - specifically, sexual difficulties experienced frequently or more often, over at least six months in the last year, causing severe or very severe distress, and not associated with physical health or relationship problems - and items on quality/avoidance of and discomfort during sex. Results Participants' median age was 62.0 years (IQR, 14) and 51.1% were women. The frequency of sexual dysfunction according to the DSM-5 was 9.3% (95% CI, 8.3%-10.4%) in women and 6.2% (95% CI, 5.4%-7.1%) in men, with women's sexual interest/arousal and men's erectile disorder being most common. Sexual dysfunction rates increased with age: whereas complaints were more frequent among women than men in the younger groups, participants aged ≥65 years with a sexual dysfunction were more often men. Quality/avoidance of and discomfort during sex were significantly associated with a diagnosis of sexual dysfunction. Clinical Implications Results suggest that sexual dysfunction caused by other than physical health or relationship factors is important to consider in this population. In addition, the avoidance of, perceived quality of, and discomfort during sex serve as valuable diagnostic indicators for the presence of sexual dysfunction. Strengths and Limitations This study draws on robust data from a large sample to give valuable insight on the frequency of sexual difficulties and dysfunctions as defined by DSM-5 criteria. Limitations represent the restriction to self-report questionnaire data, the focus on participants living in a metropolitan area, and the lack of experience of sexual difficulties due to a lack of sexual activity not being taken into account. Conclusion The study provides estimates for DSM-5 sexual dysfunction frequencies among Germans from a metropolitan area and points to the diagnostic value of age-related changes as well as the quality/avoidance of and discomfort during sex.
Collapse
Affiliation(s)
- Thula U Koops
- Corresponding author: Institute for Sex Research, Sexual Medicine, and Forensic Psychiatry, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany.
| | - Verena Klein
- Institute for Sex Research, Sexual Medicine, and Forensic Psychiatry, University Medical Centre Hamburg-Eppendorf, Hamburg 20246, Germany
- Department of Psychology, University of Southampton, Southampton, United Kingdom
| | - Ramona Bei der Kellen
- Epidemiological Study Center, University Medical Centre Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Jürgen Hoyer
- Institute for Clinical Psychology and Psychotherapy, Dresden University of Technology, Dresden 01062, Germany
| | - Bernd Löwe
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Centre Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Peer Briken
- Institute for Sex Research, Sexual Medicine, and Forensic Psychiatry, University Medical Centre Hamburg-Eppendorf, Hamburg 20246, Germany
| |
Collapse
|
153
|
Jung P. The right way for cyanobacteria: The metabarcoding database CyanoSeq. J Phycol 2023; 59:467-469. [PMID: 37313840 DOI: 10.1111/jpy.13338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Patrick Jung
- Department Integrative Biotechnology, University of Applied Sciences, Pirmasens, Germany
| |
Collapse
|
154
|
von Bibra C, Shibamiya A, Bähr A, Geertz B, Köhne M, Stuedemann T, Starbatty J, Horneffer-van der Sluis V, Klostermeier UC, Hornaschewitz N, Li X, Wolf E, Klymiuk N, Krane M, Kupatt C, Hiebl B, Eschenhagen T, Weinberger F. Immature human engineered heart tissues engraft in a guinea pig chronic injury model. Dis Model Mech 2023:312546. [PMID: 37259958 DOI: 10.1242/dmm.049834] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Engineered heart tissue (EHT) transplantation represents an innovative, regenerative approach for heart failure patients. Late preclinical trials are underway, and a first clinical trial has started recently. Preceding studies revealed functional recovery after implantation of in vitro-matured EHT in the subacute stage while transplantation in a chronic injury setting was less efficient. When transplanting matured EHTs we noticed that cardiomyocytes (CM) undergo a de-differentiation step before eventually forming structured grafts. Therefore, we wanted to evaluate whether immature EHT patches (EHTIm) can be used for transplantation. Chronic myocardial injury was induced in a guinea pig model. EHTIm (15x106 cells) were transplanted within hours after casting. Cryo-injury lead to large transmural scars amounting to 26% of the left ventricle. Grafts remuscularized 9% of the scar area on average. Echocardiographic analysis showed some evidence for an improvement of left ventricular function after EHTIm transplantation. In a small translational proof-of-concept study human scale EHTIm patches (4.5x108 cells) were epicardially implanted on healthy pig hearts (n=2). In summary, we provide evidence that transplantation of EHTIm patches, i.e. without pre-cultivation, is feasible with similar engraftment results.
Collapse
Affiliation(s)
- Constantin von Bibra
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | - Aya Shibamiya
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | - Andrea Bähr
- Medizinische Klinik & Poliklinik, University Clinic Rechts der Isar, Technical University Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Birgit Geertz
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
| | - Maria Köhne
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | - Tim Stuedemann
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | - Jutta Starbatty
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Ulrich C Klostermeier
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Germany
| | - Nadja Hornaschewitz
- Medizinische Klinik & Poliklinik, University Clinic Rechts der Isar, Technical University Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Xinghai Li
- Department of Cardiovascular Surgery, German Heart Centre Munich, Technical University Munich, Germany
| | - Eckhard Wolf
- Gene Center and Center for Innovative Medical Models (CiMM), LMU Munich, Germany
| | - Nikolai Klymiuk
- Medizinische Klinik & Poliklinik, University Clinic Rechts der Isar, Technical University Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Centre Munich, Technical University Munich, Germany
- Division of Cardiac Surgery, Yale School of Medicine, New Haven, USA
| | - Christian Kupatt
- Medizinische Klinik & Poliklinik, University Clinic Rechts der Isar, Technical University Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich, Germany
| | - Bernhard Hiebl
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Thomas Eschenhagen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| | - Florian Weinberger
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Germany
| |
Collapse
|
155
|
Gehlert FO, Nickel L, Vakirlis N, Hammerschmidt K, Vargas Gebauer HI, Kießling C, Kupczok A, Schmitz RA. Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon. Nucleic Acids Res 2023:7186994. [PMID: 37254817 PMCID: PMC10359463 DOI: 10.1093/nar/gkad474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023] Open
Abstract
Casposons are transposable elements containing the CRISPR associated gene Cas1solo. Identified in many archaeal genomes, casposons are discussed as the origin of CRISPR-Cas systems due to their proposed Cas1solo-dependent translocation. However, apart from bioinformatic approaches and the demonstration of Cas1solo integrase and endonuclease activity in vitro, casposon transposition has not yet been shown in vivo. Here, we report on active casposon translocations in Methanosarcina mazei Gö1 using two independent experimental approaches. First, mini-casposons, consisting of a R6Kγ origin and two antibiotic resistance cassettes, flanked by target site duplications (TSDs) and terminal inverted repeats (TIRs), were generated, and shown to actively translocate from a suicide plasmid and integrate into the chromosomal MetMaz-C1 TSD IS1a. Second, casposon excision activity was confirmed in a long-term evolution experiment using a Cas1solo overexpression strain in comparison to an empty vector control under four different treatments (native, high temperature, high salt, mitomycin C) to study stress-induced translocation. Analysis of genomic DNA using a nested qPCR approach provided clear evidence of casposon activity in single cells and revealed significantly different casposon excision frequencies between treatments and strains. Our results, providing the first experimental evidence for in vivo casposon activity are summarized in a modified hypothetical translocation model.
Collapse
Affiliation(s)
- Finn O Gehlert
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
| | - Lisa Nickel
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
| | - Nikolaos Vakirlis
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center ''Alexander Fleming'', Vari, Greece
| | - Katrin Hammerschmidt
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
| | | | - Claudia Kießling
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
| | - Anne Kupczok
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
- Bioinformatics Group, Wageningen University & Research, 6708PBWageningen, Netherlands
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University, 24118Kiel, Germany
| |
Collapse
|
156
|
Woelfle S, Deshpande D, Feldengut S, Braak H, Del Tredici K, Roselli F, Deisseroth K, Michaelis J, Boeckers TM, Schön M. CLARITY increases sensitivity and specificity of fluorescence immunostaining in long-term archived human brain tissue. BMC Biol 2023; 21:113. [PMID: 37221592 PMCID: PMC10207789 DOI: 10.1186/s12915-023-01582-6] [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: 09/15/2022] [Accepted: 03/29/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Post mortem human brain tissue is an essential resource to study cell types, connectivity as well as subcellular structures down to the molecular setup of the central nervous system especially with respect to the plethora of brain diseases. A key method is immunostaining with fluorescent dyes, which allows high-resolution imaging in three dimensions of multiple structures simultaneously. Although there are large collections of formalin-fixed brains, research is often limited because several conditions arise that complicate the use of human brain tissue for high-resolution fluorescence microscopy. RESULTS In this study, we developed a clearing approach for immunofluorescence-based analysis of perfusion- and immersion-fixed post mortem human brain tissue, termed human Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging / Immunostaining / In situ hybridization-compatible Tissue-hYdrogel (hCLARITY). hCLARITY is optimized for specificity by reducing off-target labeling and yields very sensitive stainings in human brain sections allowing for super-resolution microscopy with unprecedented imaging of pre- and postsynaptic compartments. Moreover, hallmarks of Alzheimer's disease were preserved with hCLARITY, and importantly classical 3,3'-diaminobenzidine (DAB) or Nissl stainings are compatible with this protocol. hCLARITY is very versatile as demonstrated by the use of more than 30 well performing antibodies and allows for de- and subsequent re-staining of the same tissue section, which is important for multi-labeling approaches, e.g., in super-resolution microscopy. CONCLUSIONS Taken together, hCLARITY enables research of the human brain with high sensitivity and down to sub-diffraction resolution. It therefore has enormous potential for the investigation of local morphological changes, e.g., in neurodegenerative diseases.
Collapse
Affiliation(s)
- Sarah Woelfle
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- International Graduate School in Molecular Medicine Ulm, IGradU, 89081, Ulm, Germany
| | - Dhruva Deshpande
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Chemical and Systems Biology Department, Stanford School of Medicine, 269 Campus Drive, Stanford, CA, 94305, USA
| | - Simone Feldengut
- Clinical Neuroanatomy Section/Department of Neurology, Center for Biomedical Research, Ulm University, Helmholtzstraße 8/1, 89081, Ulm, Germany
| | - Heiko Braak
- Clinical Neuroanatomy Section/Department of Neurology, Center for Biomedical Research, Ulm University, Helmholtzstraße 8/1, 89081, Ulm, Germany
| | - Kelly Del Tredici
- Clinical Neuroanatomy Section/Department of Neurology, Center for Biomedical Research, Ulm University, Helmholtzstraße 8/1, 89081, Ulm, Germany
| | - Francesco Roselli
- Department of Neurology, Ulm University, 89081, Ulm, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE, Ulm Site, 89081, Ulm, Germany
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford, CA, 94305, USA
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tobias M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE, Ulm Site, 89081, Ulm, Germany
| | - Michael Schön
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| |
Collapse
|
157
|
Olejarz-Maciej A, Mogilski S, Karcz T, Werner T, Kamińska K, Kupczyk J, Honkisz-Orzechowska E, Latacz G, Stark H, Kieć-Kononowicz K, Łażewska D. Trisubstituted 1,3,5-Triazines as Histamine H 4 Receptor Antagonists with Promising Activity In Vivo. Molecules 2023; 28:molecules28104199. [PMID: 37241939 DOI: 10.3390/molecules28104199] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Pain is a very unpleasant experience that makes life extremely uncomfortable. The histamine H4 receptor (H4R) is a promising target for the treatment of inflammatory and immune diseases, as well as pain. H4R ligands have demonstrated analgesic effects in a variety of pain models, including inflammatory pain. Continuing the search for active H4R ligands among the alkyl derivatives of 1,3,5-triazine, we obtained 19 new compounds in two series: acyclic (I) and aliphatic (II). In vitro pharmacological evaluation showed their variable affinity for H4R. The majority of compounds showed a moderate affinity for this receptor (Ki > 100 nM), while all compounds tested in ß-arrestin and cAMP assays showed antagonistic activity. The most promising, compound 6, (4-(cyclopentylmethyl)-6-(4-methylpiperazin-1-yl)-1,3,5-triazin-2-amine; Ki = 63 nM) was selected for further in vitro evaluation: blood-brain barrier permeability (PAMPA assay; Pe = 12.26 × 10-6 cm/s) and toxicity tests (HepG2 and SH-5YSY cells; no toxicity up to 50 µM). Next, compound 6 tested in vivo in a carrageenan-induced inflammatory pain model showed anti-inflammatory and analgesic effects (strongest at 50 mg/kg i.p.). Furthermore, in a histamine- and chloroquine-induced pruritus model, compound 6 at a dose of 25 mg/kg i.p. and 50 mg/kg i.p., respectively, reduced the number of scratch bouts. Thus, compound 6 is a promising ligand for further studies.
Collapse
Affiliation(s)
- Agnieszka Olejarz-Maciej
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Szczepan Mogilski
- Department of Pharmacodynamics, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Tadeusz Karcz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Tobias Werner
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katarzyna Kamińska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Jarosław Kupczyk
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Ewelina Honkisz-Orzechowska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katarzyna Kieć-Kononowicz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| | - Dorota Łażewska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College in Kraków, Medyczna 9, 30-688 Kraków, Poland
| |
Collapse
|
158
|
Pettinato M, Dulja A, Colucci S, Furiosi V, Fette F, Steinbicker AU, Muckenthaler MU, Nai A, Pagani A, Silvestri L. FKBP12 inhibits hepcidin expression by modulating BMP receptors interaction and ligand responsiveness in hepatocytes. Am J Hematol 2023. [PMID: 37199280 DOI: 10.1002/ajh.26961] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/19/2023]
Abstract
The expression of the iron regulatory hormone hepcidin in hepatocytes is regulated by the BMP-SMAD pathway through the type I receptors ALK2 and ALK3, the type II receptors ACVR2A and BMPR2, and the ligands BMP2 and BMP6. We previously identified the immunophilin FKBP12 as a new hepcidin inhibitor that acts by blocking ALK2. Both the physiologic ALK2 ligand BMP6 and the immunosuppressive drug Tacrolimus (TAC) displace FKBP12 from ALK2 and activate the signaling. However, the molecular mechanism whereby FKBP12 regulates BMP-SMAD pathway activity and thus hepcidin expression remains unclear. Here, we show that FKBP12 acts by modulating BMP receptor interactions and ligand responsiveness. We first demonstrate that in primary murine hepatocytes TAC regulates hepcidin expression exclusively via FKBP12. Downregulation of the BMP receptors reveals that ALK2, to a lesser extent ALK3, and ACVR2A are required for hepcidin upregulation in response to both BMP6 and TAC. Mechanistically, TAC and BMP6 increase ALK2 homo-oligomerization and ALK2-ALK3 hetero-oligomerization and the interaction between ALK2 and the type II receptors. By acting on the same receptors, TAC and BMP6 cooperate in BMP pathway activation and hepcidin expression both in vitro and in vivo. Interestingly, the activation state of ALK3 modulates its interaction with FKBP12, which may explain the cell-specific activity of FKBP12. Overall, our results identify the mechanism whereby FKBP12 regulates the BMP-SMAD pathway and hepcidin expression in hepatocytes, and suggest that FKBP12-ALK2 interaction is a potential pharmacologic target in disorders caused by defective BMP-SMAD signaling and characterized by low hepcidin and high BMP6 expression.
Collapse
Affiliation(s)
- Mariateresa Pettinato
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Alessandro Dulja
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Silvia Colucci
- Department of Pediatric Hematology, Oncology and Immunology, Center for Translational Biomedical Iron Research - University of Heidelberg & Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Valeria Furiosi
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Franca Fette
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Johann-Wolfgang-Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andrea U Steinbicker
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Johann-Wolfgang-Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Hematology, Oncology and Immunology, Center for Translational Biomedical Iron Research - University of Heidelberg & Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Antonella Nai
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Alessia Pagani
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Laura Silvestri
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| |
Collapse
|
159
|
Aparicio-Puerta E, Hirsch P, Schmartz GP, Kern F, Fehlmann T, Keller A. miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations. Nucleic Acids Res 2023:7161530. [PMID: 37177999 DOI: 10.1093/nar/gkad392] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/.
Collapse
Affiliation(s)
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| |
Collapse
|
160
|
Chong L, Ahmadvand N, Noori A, Lv Y, Chen C, Bellusci S, Zhang JS. Injury activated alveolar progenitors (IAAPs): the underdog of lung repair. Cell Mol Life Sci 2023; 80:145. [PMID: 37166489 PMCID: PMC10173924 DOI: 10.1007/s00018-023-04789-6] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 04/24/2023] [Indexed: 05/12/2023]
Abstract
Alveolar epithelial type II cells (AT2s) together with AT1s constitute the epithelial lining of lung alveoli. In contrast to the large flat AT1s, AT2s are cuboidal and smaller. In addition to surfactant production, AT2s also serve as prime alveolar progenitors in homeostasis and play an important role during regeneration/repair. Based on different lineage tracing strategies in mice and single-cell transcriptomic analysis, recent reports highlight the heterogeneous nature of AT2s. These studies present compelling evidence for the presence of stable or transitory AT2 subpopulations with distinct marker expression, signaling pathway activation and functional properties. Despite demonstrated progenitor potentials of AT2s in maintaining homeostasis, through self-renewal and differentiation to AT1s, the exact identity, full progenitor potential and regulation of these progenitor cells, especially in the context of human diseases remain unclear. We recently identified a novel subset of AT2 progenitors named "Injury-Activated Alveolar Progenitors" (IAAPs), which express low levels of Sftpc, Sftpb, Sftpa1, Fgfr2b and Etv5, but are highly enriched for the expression of the surface receptor programmed cell death-ligand 1 (Pd-l1). IAAPs are quiescent during lung homeostasis but activated upon injury with the potential to proliferate and differentiate into AT2s. Significantly, a similar population of PD-L1 positive cells expressing intermediate levels of SFTPC are found to be expanded in human IPF lungs. We summarize here the current understanding of this newly discovered AT2 progenitor subpopulation and also try to reconcile the relationship between different AT2 stem cell subpopulations regarding their progenitor potential, regulation, and relevance to disease pathogenesis and therapeutic interventions.
Collapse
Affiliation(s)
- Lei Chong
- Department of Pediatric Respiratory Medicine, National Key Clinical Specialty of Pediatric Respiratory Medicine, Institute of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Negah Ahmadvand
- Department of Cell Biology, Duke University School of Medicine, Durham, NC27710, USA
| | - Afshin Noori
- Cardio Pulmonary Institute, Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Yuqing Lv
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Interventional Pulmonology and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Saverio Bellusci
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
- Laboratory of Extracellular Matrix Remodelling, Cardio Pulmonary Institute, Department of Pulmonary and Critical Care Medicine and Infectious Diseases, Universities of Giessen and Marburg Lung Center, Member of the German Lung Center, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Jin-San Zhang
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Interventional Pulmonology and Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| |
Collapse
|
161
|
Junkermeier EH, Hengge R. Local signaling enhances output specificity of bacterial c-di-GMP signaling networks. Microlife 2023; 4:uqad026. [PMID: 37251514 PMCID: PMC10211494 DOI: 10.1093/femsml/uqad026] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
For many years the surprising multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins has intrigued researchers studying bacterial second messengers. How can several signaling pathways act in parallel to produce specific outputs despite relying on the same diffusible second messenger maintained at a certain global cellular concentration? Such high specificity and flexibility arise from combining modes of local and global c-di-GMP signaling in complex signaling networks. Local c-di-GMP signaling can be experimentally shown by three criteria being met: (i) highly specific knockout phenotypes for particular c-di-GMP-related enzymes, (ii) actual cellular c-di-GMP levels that remain unchanged by such mutations and/or below the Kd's of the relevant c-di-GMP-binding effectors, and (iii) direct interactions between the signaling proteins involved. Here, we discuss the rationale behind these criteria and present well-studied examples of local c-di-GMP signaling in Escherichia coli and Pseudomonas. Relatively simple systems just colocalize a local source and/or a local sink for c-di-GMP, i.e. a diguanylate cyclase (DGC) and/or a specific phosphodiesterase (PDE), respectively, with a c-di-GMP-binding effector/target system. More complex systems also make use of regulatory protein interactions, e.g. when a "trigger PDE" responds to locally provided c-di-GMP, and thereby serves as a c-di-GMP-sensing effector that directly controls a target's activity, or when a c-di-GMP-binding effector recruits and directly activates its own "private" DGC. Finally, we provide an outlook into how cells can combine local and global signaling modes of c-di-GMP and possibly integrate those into other signaling nucleotides networks.
Collapse
Affiliation(s)
- Eike H Junkermeier
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany
| | - Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
| |
Collapse
|
162
|
Mügge FLB, Morlock GE. Chemical and cytotoxicity profiles of 11 pink pepper (Schinus spp.) samples via non-targeted hyphenated high-performance thin-layer chromatography. Metabolomics 2023; 19:48. [PMID: 37130976 PMCID: PMC10154279 DOI: 10.1007/s11306-023-02008-8] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 05/04/2023]
Abstract
INTRODUCTION Pink pepper is a worldwide used spice that corresponds to the berries of two species, Schinus terebinthifolia Raddi or S. molle L. (Anacardiaceae). Toxic and allergic reactions by ingestion or contact with these plants were reported, and classical in vitro studies have highlighted the cytotoxic properties of apolar extracts from the fruits. OBJECTIVES Perform a non-targeted screening of 11 pink pepper samples for the detection and identification of individual cytotoxic substances. METHODS After reversed-phase high-performance thin-layer chromatography (RP-HPTLC) separation of the extracts and multi-imaging (UV/Vis/FLD), cytotoxic compounds were detected by bioluminescence reduction from luciferase reporter cells (HEK 293 T-CMV-ELuc) applied directly on the adsorbent surface, followed by elution of detected cytotoxic substance into atmospheric-pressure chemical ionization high-resolution mass spectrometry (APCI-HRMS). RESULTS Separations for mid-polar and non-polar fruit extracts demonstrated the selectivity of the method to different substance classes. One cytotoxic substance zone was tentatively assigned as moronic acid, a pentacyclic triterpenoid acid. CONCLUSION The developed non-targeted hyphenated RP-HPTLC-UV/Vis/FLD-bioluminescent cytotoxicity bioassay-FIA-APCI-HRMS method was successfully demonstrated for cytotoxicity screening (bioprofiling) and respective cytotoxin assignment.
Collapse
Affiliation(s)
- Fernanda L B Mügge
- Chair of Food Science, Institute of Nutritional Science, and Interdisciplinary Research Center, IFZ, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Gertrud E Morlock
- Chair of Food Science, Institute of Nutritional Science, and Interdisciplinary Research Center, IFZ, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| |
Collapse
|
163
|
Liu Q, Lu X, Liu Y, Li Z, Yan P, Chen W, Meng Q, Zhang Y, Yam C, He L, Yan Y, Zhang Y, Wu J, Frauenheim T, Zhang R, Xu Y. Carrier Relaxation and Multiplication in Bi Doped Graphene. Small 2023; 19:e2206218. [PMID: 36670078 DOI: 10.1002/smll.202206218] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/09/2023] [Indexed: 05/04/2023]
Abstract
By introducing different contents of Bi adatoms to the surface of monolayer graphene, the carrier concentration and their dynamics have been effectively modulated as probed directly by the time- and angle-resolved photoemission spectroscopy technique. The Bi adatoms are found to assist acoustic phonon scattering events mediated by supercollisions as the disorder effectively relaxes the momentum conservation constraint. A reduced carrier multiplication has been observed, which is related to the shrinking Fermi sea for scattering, as confirmed by time-dependent density functional theory simulation. This work gives insight into hot carrier dynamics in graphene, which is crucial for promoting the application of photoelectric devices.
Collapse
Affiliation(s)
- Qi Liu
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Xianyang Lu
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Yuxiang Liu
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359, Bremen, Germany
| | - Zhihao Li
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Pengfei Yan
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Wang Chen
- National Laboratory of Solid State Microstructure, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
| | - Qinghao Meng
- National Laboratory of Solid State Microstructure, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
| | - Yongheng Zhang
- National Laboratory of Solid State Microstructure, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
| | - ChiYung Yam
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, 518000, China
- Hong Kong Quantum AI Lab Limited, Hong Kong, 00000, China
| | - Liang He
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Yu Yan
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Yi Zhang
- National Laboratory of Solid State Microstructure, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
| | - Jing Wu
- York-Nanjing Joint Center (YNJC) for Spintronics and Nano-engineering, Department of Electronics and Physics, University of York, York, YO10 5DD, UK
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359, Bremen, Germany
- Beijing Computational Science Research Center, Haidian District, Beijing, 100193, China
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, 518109, China
| | - Rong Zhang
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
| | - Yongbing Xu
- Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials, School of Electronic Science and Engineering, Nanjing University, Nanjing, 210093, China
- York-Nanjing Joint Center (YNJC) for Spintronics and Nano-engineering, Department of Electronics and Physics, University of York, York, YO10 5DD, UK
| |
Collapse
|
164
|
Yu Y, Zhou C, Ghosh T, Schön CF, Zhou Y, Wahl S, Raghuwanshi M, Kerres P, Bellin C, Shukla A, Cojocaru-Mirédin O, Wuttig M. Doping by Design: Enhanced Thermoelectric Performance of GeSe Alloys Through Metavalent Bonding. Adv Mater 2023; 35:e2300893. [PMID: 36920476 DOI: 10.1002/adma.202300893] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/25/2023] [Indexed: 05/12/2023]
Abstract
Doping is usually the first step to tailor thermoelectrics. It enables precise control of the charge-carrier concentration and concomitant transport properties. Doping should also turn GeSe, which features an intrinsically a low carrier concentration, into a competitive thermoelectric. Yet, elemental doping fails to improve the carrier concentration. In contrast, alloying with Ag-V-VI2 compounds causes a remarkable enhancement of thermoelectric performance. This advance is closely related to a transition in the bonding mechanism, as evidenced by sudden changes in the optical dielectric constant ε∞ , the Born effective charge, the maximum of the optical absorption ε2 (ω), and the bond-breaking behavior. These property changes are indicative of the formation of metavalent bonding (MVB), leading to an octahedral-like atomic arrangement. MVB is accompanied by a thermoelectric-favorable band structure featuring anisotropic bands with small effective masses and a large degeneracy. A quantum-mechanical map, which distinguishes different types of chemical bonding, reveals that orthorhombic GeSe employs covalent bonding, while rhombohedral and cubic GeSe utilize MVB. The transition from covalent to MVB goes along with a pronounced improvement in thermoelectric performance. The failure or success of different dopants can be explained by this concept, which redefines doping rules and provides a "treasure map" to tailor p-bonded chalcogenides.
Collapse
Affiliation(s)
- Yuan Yu
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Chongjian Zhou
- State Key Laboratory of Solidification Processing, and Key Laboratory of Radiation Detection Materials and Devices, Ministry of Industry and Information Technology, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Tanmoy Ghosh
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Carl-Friedrich Schön
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Yiming Zhou
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Sophia Wahl
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Mohit Raghuwanshi
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Peter Kerres
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
- PGI 10 (Green IT), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Christophe Bellin
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 4 Place Jussieu, Paris, F-75005, France
| | - Abhay Shukla
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 4 Place Jussieu, Paris, F-75005, France
| | - Oana Cojocaru-Mirédin
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
| | - Matthias Wuttig
- Institute of Physics (IA), RWTH Aachen University, Sommerfeldstraße 14, 52074, Aachen, Germany
- PGI 10 (Green IT), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
- Jülich - Aachen Research Alliance (JARA-FIT and JARA-HPC), RWTH Aachen University, 52056, Aachen, Germany
| |
Collapse
|
165
|
Koehnsen A, Gorb SN, Büsse S. A switchable joint in the head of dragonfly larvae (Insecta: Odonata) as key to the multifunctionality of the prehensile labial mask. J Exp Zool A Ecol Integr Physiol 2023. [PMID: 37186461 DOI: 10.1002/jez.2706] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Dragonfly and damselfly larvae (Insecta: Odonata) capture prey by rapid protraction of a raptorial mouthpart, based on a modified labium. Yet, in insects with biting-chewing mouthparts, the labium has an essential role in food handling. These two distinct functions -prey capturing and handling-lead to a mechanical problem in Odonata larvae: while the labium is always protracted in a straight line during prey capture, food handling requires more dexterity. In this study, we investigate the role of the labium in the feeding process and analyse the mechanics of the labial joints in the dragonfly larva Anax imperator. Our results show that the labium features a multiaxial joint connecting the basal segment (postmentum) and the head. During feeding, a combination of rotations around different axes is used to handle and orient prey, which is unique among biting-chewing mouthparts. Furthermore, we identified structures at the joint which likely restrict lateral motion during the predatory strike. Our results provide a further understanding of the unique prey-capturing apparatus of odonate larvae capable of controlling a 'switchable' multiaxial to a restricted monoaxial joint. This concept highlights the evolution of a highly modified raptorial mouthpart appendage where the degrees of freedom can be actively restricted to allow for the respectively needed functionality.
Collapse
Affiliation(s)
- Alexander Koehnsen
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Kiel, Germany
| | - Stanislav N Gorb
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Kiel, Germany
| | - Sebastian Büsse
- Department of Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Kiel, Germany
| |
Collapse
|
166
|
Sandt R, Spatschek R. Efficient low temperature Monte Carlo sampling using quantum annealing. Sci Rep 2023; 13:6754. [PMID: 37185931 PMCID: PMC10130176 DOI: 10.1038/s41598-023-33828-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Quantum annealing is an efficient technology to determine ground state configurations of discrete binary optimization problems, described through Ising Hamiltonians. Here we show that-at very low computational cost-finite temperature properties can be calculated. The approach is most efficient at low temperatures, where conventional approaches like Metropolis Monte Carlo sampling suffer from high rejection rates and therefore large statistical noise. To demonstrate the general approach, we apply it to spin glasses and Ising chains.
Collapse
Affiliation(s)
- Roland Sandt
- Structure and Function of Materials, Institute of Energy and Climate Research, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
| | - Robert Spatschek
- Structure and Function of Materials, Institute of Energy and Climate Research, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- JARA-ENERGY, 52425, Jülich, Germany
| |
Collapse
|
167
|
Bott FS, Nickel MM, Hohn VD, May ES, Gil Ávila C, Tiemann L, Gross J, Ploner M. Local brain oscillations and interregional connectivity differentially serve sensory and expectation effects on pain. Sci Adv 2023; 9:eadd7572. [PMID: 37075123 PMCID: PMC10115421 DOI: 10.1126/sciadv.add7572] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pain emerges from the integration of sensory information about threats and contextual information such as an individual's expectations. However, how sensory and contextual effects on pain are served by the brain is not fully understood so far. To address this question, we applied brief painful stimuli to 40 healthy human participants and independently varied stimulus intensity and expectations. Concurrently, we recorded electroencephalography. We assessed local oscillatory brain activity and interregional functional connectivity in a network of six brain regions playing key roles in the processing of pain. We found that sensory information predominantly influenced local brain oscillations. In contrast, expectations exclusively influenced interregional connectivity. Specifically, expectations altered connectivity at alpha (8 to 12 hertz) frequencies from prefrontal to somatosensory cortex. Moreover, discrepancies between sensory information and expectations, i.e., prediction errors, influenced connectivity at gamma (60 to 100 hertz) frequencies. These findings reveal how fundamentally different brain mechanisms serve sensory and contextual effects on pain.
Collapse
Affiliation(s)
- Felix S. Bott
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Moritz M. Nickel
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Vanessa D. Hohn
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Elisabeth S. May
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Cristina Gil Ávila
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Laura Tiemann
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Joachim Gross
- Institute for Biomagnetism and Biosignalanalysis, University of Münster, Münster, Germany
| | - Markus Ploner
- Department of Neurology and TUM-Neuroimaging Center (TUM-NIC), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Corresponding author.
| |
Collapse
|
168
|
Enomoto G, Wallner T, Wilde A. Control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP. Microlife 2023; 4:uqad019. [PMID: 37223735 PMCID: PMC10124867 DOI: 10.1093/femsml/uqad019] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/01/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide-derived signalling molecules control a wide range of cellular processes in all organisms. The bacteria-specific cyclic dinucleotide c-di-GMP plays a crucial role in regulating motility-to-sessility transitions, cell cycle progression, and virulence. Cyanobacteria are phototrophic prokaryotes that perform oxygenic photosynthesis and are widespread microorganisms that colonize almost all habitats on Earth. In contrast to photosynthetic processes that are well understood, the behavioural responses of cyanobacteria have rarely been studied in detail. Analyses of cyanobacterial genomes have revealed that they encode a large number of proteins that are potentially involved in the synthesis and degradation of c-di-GMP. Recent studies have demonstrated that c-di-GMP coordinates many different aspects of the cyanobacterial lifestyle, mostly in a light-dependent manner. In this review, we focus on the current knowledge of light-regulated c-di-GMP signalling systems in cyanobacteria. Specifically, we highlight the progress made in understanding the most prominent behavioural responses of the model cyanobacterial strains Thermosynechococcus vulcanus and Synechocystis sp. PCC 6803. We discuss why and how cyanobacteria extract crucial information from their light environment to regulate ecophysiologically important cellular responses. Finally, we emphasize the questions that remain to be addressed.
Collapse
Affiliation(s)
- Gen Enomoto
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Wallner
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
169
|
Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. Microlife 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
Collapse
Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
| |
Collapse
|
170
|
Martins Nascentes Melo L, Herrera-Rios D, Hinze D, Löffek S, Oezel I, Turiello R, Klein J, Leonardelli S, Westedt IV, Al-Matary Y, Egea-Rodriguez S, Brenzel A, Bau M, Sucker A, Hadaschik E, Wirsdörfer F, Hanenberg H, Uhlenbrock N, Rauh D, Poźniak J, Rambow F, Marine JC, Effern M, Glodde N, Schadendorf D, Jablonska J, Hölzel M, Helfrich I. Glucocorticoid activation by HSD11B1 limits T cell-driven interferon signaling and response to PD-1 blockade in melanoma. J Immunother Cancer 2023; 11:e004150. [PMID: 37028818 PMCID: PMC10083881 DOI: 10.1136/jitc-2021-004150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Accepted: 03/14/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Immune responses against tumors are subject to negative feedback regulation. Immune checkpoint inhibitors (ICIs) blocking Programmed cell death protein 1 (PD-1), a receptor expressed on T cells, or its ligand PD-L1 have significantly improved the treatment of cancer, in particular malignant melanoma. Nevertheless, responses and durability are variables, suggesting that additional critical negative feedback mechanisms exist and need to be targeted to improve therapeutic efficacy. METHODS We used different syngeneic melanoma mouse models and performed PD-1 blockade to identify novel mechanisms of negative immune regulation. Genetic gain-of-function and loss-of-function approaches as well as small molecule inhibitor applications were used for target validation in our melanoma models. We analyzed mouse melanoma tissues from treated and untreated mice by RNA-seq, immunofluorescence and flow cytometry to detect changes in pathway activities and immune cell composition of the tumor microenvironment. We analyzed tissue sections of patients with melanoma by immunohistochemistry as well as publicly available single-cell RNA-seq data and correlated target expression with clinical responses to ICIs. RESULTS Here, we identified 11-beta-hydroxysteroid dehydrogenase-1 (HSD11B1), an enzyme that converts inert glucocorticoids into active forms in tissues, as negative feedback mechanism in response to T cell immunotherapies. Glucocorticoids are potent suppressors of immune responses. HSD11B1 was expressed in different cellular compartments of melanomas, most notably myeloid cells but also T cells and melanoma cells. Enforced expression of HSD11B1 in mouse melanomas limited the efficacy of PD-1 blockade, whereas small molecule HSD11B1 inhibitors improved responses in a CD8+ T cell-dependent manner. Mechanistically, HSD11B1 inhibition in combination with PD-1 blockade augmented the production of interferon-γ by T cells. Interferon pathway activation correlated with sensitivity to PD-1 blockade linked to anti-proliferative effects on melanoma cells. Furthermore, high levels of HSD11B1, predominantly expressed by tumor-associated macrophages, were associated with poor responses to ICI therapy in two independent cohorts of patients with advanced melanomas analyzed by different methods (scRNA-seq, immunohistochemistry). CONCLUSION As HSD11B1 inhibitors are in the focus of drug development for metabolic diseases, our data suggest a drug repurposing strategy combining HSD11B1 inhibitors with ICIs to improve melanoma immunotherapy. Furthermore, our work also delineated potential caveats emphasizing the need for careful patient stratification.
Collapse
Affiliation(s)
- Luiza Martins Nascentes Melo
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Dayana Herrera-Rios
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Daniel Hinze
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Stefanie Löffek
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Irem Oezel
- Department of Otorhinolaryngology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Roberta Turiello
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Juliane Klein
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Sonia Leonardelli
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Isa-Vanessa Westedt
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Yahya Al-Matary
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Sara Egea-Rodriguez
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Alexandra Brenzel
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Maja Bau
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Antje Sucker
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Eva Hadaschik
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
| | - Florian Wirsdörfer
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Niklas Uhlenbrock
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Dortmund, Belgium
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Daniel Rauh
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Dortmund, Belgium
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Joanna Poźniak
- Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Florian Rambow
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
- Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Maike Effern
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nicole Glodde
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Dirk Schadendorf
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Jadwiga Jablonska
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
- Department of Otorhinolaryngology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Hölzel
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Iris Helfrich
- Skin Cancer Unit of the Dermatology Department, Medical Faculty, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilian University (LMU) Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| |
Collapse
|
171
|
Yamoah A, Tripathi P, Guo H, Scheve L, Walter P, Johnen S, Müller F, Weis J, Goswami A. Early Alterations of RNA Binding Protein (RBP) Homeostasis and ER Stress-Mediated Autophagy Contributes to Progressive Retinal Degeneration in the rd10 Mouse Model of Retinitis Pigmentosa (RP). Cells 2023; 12:cells12071094. [PMID: 37048167 PMCID: PMC10092976 DOI: 10.3390/cells12071094] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
The retinal degeneration 10 (rd10) mouse model is widely used to study retinitis pigmentosa (RP) pathomechanisms. It offers a rather unique opportunity to study trans-neuronal degeneration because the cell populations in question are separated anatomically and the mutated Pde6b gene is selectively expressed in rod photoreceptors. We hypothesized that RNA binding protein (RBP) aggregation and abnormal autophagy might serve as early pathogenic events, damaging non-photoreceptor retinal cell types that are not primarily targeted by the Pde6b gene defect. We used a combination of immunohistochemistry (DAB, immunofluorescence), electron microscopy (EM), subcellular fractionation, and Western blot analysis on the retinal preparations obtained from both rd10 and wild-type mice. We found early, robust increases in levels of the protective endoplasmic reticulum (ER) calcium (Ca2+) buffering chaperone Sigma receptor 1 (SigR1) together with other ER-Ca2+ buffering proteins in both photoreceptors and non-photoreceptor neuronal cells before any noticeable photoreceptor degeneration. In line with this, we found markedly altered expression of the autophagy proteins p62 and LC3, together with abnormal ER widening and large autophagic vacuoles as detected by EM. Interestingly, these changes were accompanied by early, prominent cytoplasmic and nuclear aggregation of the key RBPs including pTDP-43 and FET family RBPs and stress granule formation. We conclude that progressive neurodegeneration in the rd10 mouse retina is associated with early disturbances of proteostasis and autophagy, along with abnormal cytoplasmic RBP aggregation.
Collapse
Affiliation(s)
- Alfred Yamoah
- Institute of Neuropathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
- EURON-European Graduate School of Neuroscience, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Priyanka Tripathi
- Institute of Neuropathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
- EURON-European Graduate School of Neuroscience, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Haihong Guo
- Institute of Neuropathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Leonie Scheve
- Institute of Neuropathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Peter Walter
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Frank Müller
- Institute of Biological Information Processing, Molecular and Cellular Physiology, IBI-1, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Joachim Weis
- Institute of Neuropathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Anand Goswami
- Institute of Neuropathology, University Hospital RWTH Aachen, 52074 Aachen, Germany
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Department of Neurology, Eleanor and Lou Gehrig ALS Center, Columbia University, New York, NY 10032, USA
| |
Collapse
|
172
|
Nuaima RH, Heuer H. Genetic Variation among Heterodera schachtii Populations Coincided with Differences in Invasion and Propagation in Roots of a Set of Cruciferous Plants. Int J Mol Sci 2023; 24:ijms24076848. [PMID: 37047819 PMCID: PMC10095055 DOI: 10.3390/ijms24076848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
Genes of host plants and parasitic nematodes govern the plant-nematode interaction. The biological receptors and parasitism effectors are variable among plant species and nematode populations, respectively. In the present study, hatch testing and bioassays on cabbage, oilseed radish, and mustard were conducted to compare the biological characteristics among six populations of the beet cyst nematode Heterodera schachtii. Genetic patterns of the vap1 gene for the studied populations were distinct as shown by denaturing the gradient gel electrophoresis of PCR-amplified gene fragments. Concurrently, significant differences in the hatching rates, number of penetrated J2 in roots, and eggs/cyst ratios among the six nematode populations for the three cruciferous species were observed. In conclusion, analyzing the population genetic structure of H. schachtii plays a pivotal role in illustrating the variability in the plant-nematode interaction among its populations and plant species, which in its role leads to developing nematode management depending on plant resistance.
Collapse
Affiliation(s)
- Rasha Haj Nuaima
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| |
Collapse
|
173
|
Leßmann V, Kartalou GI, Endres T, Pawlitzki M, Gottmann K. Repurposing drugs against Alzheimer's disease: can the anti-multiple sclerosis drug fingolimod (FTY720) effectively tackle inflammation processes in AD? J Neural Transm (Vienna) 2023:10.1007/s00702-023-02618-5. [PMID: 37014414 PMCID: PMC10374694 DOI: 10.1007/s00702-023-02618-5] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/02/2023] [Indexed: 04/05/2023]
Abstract
Therapeutic approaches providing effective medication for Alzheimer's disease (AD) patients after disease onset are urgently needed. Previous studies in AD mouse models and in humans suggested that physical exercise or changed lifestyle can delay AD-related synaptic and memory dysfunctions when treatment started in juvenile animals or in elderly humans before onset of disease symptoms. However, a pharmacological treatment that can reverse memory deficits in AD patients was thus far not identified. Importantly, AD disease-related dysfunctions have increasingly been associated with neuro-inflammatory mechanisms and searching for anti-inflammatory medication to treat AD seems promising. Like for other diseases, repurposing of FDA-approved drugs for treatment of AD is an ideally suited strategy to reduce the time to bring such medication into clinical practice. Of note, the sphingosine-1-phosphate analogue fingolimod (FTY720) was FDA-approved in 2010 for treatment of multiple sclerosis patients. It binds to the five different isoforms of Sphingosine-1-phosphate receptors (S1PRs) that are widely distributed across human organs. Interestingly, recent studies in five different mouse models of AD suggest that FTY720 treatment, even when starting after onset of AD symptoms, can reverse synaptic deficits and memory dysfunction in these AD mouse models. Furthermore, a very recent multi-omics study identified mutations in the sphingosine/ceramide pathway as a risk factor for sporadic AD, suggesting S1PRs as promising drug target in AD patients. Therefore, progressing with FDA-approved S1PR modulators into human clinical trials might pave the way for these potential disease modifying anti-AD drugs.
Collapse
Affiliation(s)
- Volkmar Leßmann
- Institute for Physiology, Medical Faculty, Otto-Von-Guericke-University, Leipziger Str. 44, 39120, Magdeburg, Germany.
- Center for Behavioral Brain Sciences, Magdeburg, Germany.
| | - Georgia-Ioanna Kartalou
- Institute for Physiology, Medical Faculty, Otto-Von-Guericke-University, Leipziger Str. 44, 39120, Magdeburg, Germany
- Institute of Neuro- and Sensory Physiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Thomas Endres
- Institute for Physiology, Medical Faculty, Otto-Von-Guericke-University, Leipziger Str. 44, 39120, Magdeburg, Germany
- Institute of Neuro- and Sensory Physiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Marc Pawlitzki
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Duesseldorf, Germany
| | - Kurt Gottmann
- Institute of Neuro- and Sensory Physiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany.
| |
Collapse
|
174
|
Labinsky H, Gupta L, Raimondo MG, Schett G, Knitza J. Real-world usage of digital health applications (DiGA) in rheumatology: results from a German patient survey. Rheumatol Int 2023; 43:713-719. [PMID: 36543961 PMCID: PMC9770561 DOI: 10.1007/s00296-022-05261-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Mobile health applications and digital therapeutics (DTx) aim to improve current patient care. Real-world data on DTx are, however, scarce. The aim of this study was to evaluate the adherence, acceptance, and efficacy of DTx in a clinical routine rheumatology setting. We conducted a prospective observational cohort study assessing the use, adherence, acceptance, and efficacy of the DTx DiGA (Digitale Gesundheitsanwendungen) by survey over 12 weeks. Patients included had to have a rheumatic disease and had been prescribed a DiGA. Acceptance was assessed using the Net promoter score (NPS). 48 patients were prescribed DiGA. Of these, 39/48 (81%) completed the follow-up survey. 21/39 (54%) patients downloaded the DTx and 20/39 (51%) used the DTx at least once. 9/39 (23%) of patients stopped quickly afterward and 5/39 (13%) reported having completed the whole DTx program. Lack of time and commitment were reported as the main reasons for non-use. Overall acceptance of DiGA was high (Net promoter score (NPS) mean (SD) 7.8/10 (2.3)). While the majority of patients (60%) reported no improvement, one subgroup of patients (7/20, 35%) who regularly used an exercise-based DTx for back pain reported symptom improvement. Acceptance of DTx in patients with rheumatic diseases is high, however onboarding to DTx use and adherence to DTx is still challenging in patients with rheumatic diseases. In a subgroup of patients with back pain, however, the use of an exercise-based DTx led to symptom improvement.
Collapse
Affiliation(s)
- Hannah Labinsky
- Department of Internal Medicine 3- Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Latika Gupta
- Department of Rheumatology, Royal Wolverhampton Hospitals NHS Trust, Wolverhampton, UK
- Department of Rheumatology, City Hospital, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
- Division of Musculoskeletal and Dermatological Sciences, Centre for Musculoskeletal Research, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Maria Gabriella Raimondo
- Department of Internal Medicine 3- Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Georg Schett
- Department of Internal Medicine 3- Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Johannes Knitza
- Department of Internal Medicine 3- Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Ulmenweg 18, 91054, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
| |
Collapse
|
175
|
Olalekan A, Bader BK, Iwalokun B, Wolf S, Lalremruata A, Dike A, Mannie-Udoh M, Lo Presti L, Liese J, Guther J, D’alvise P, Peter S. High incidence of carbapenemase-producing Pseudomonas aeruginosa clinical isolates from Lagos, Nigeria. JAC Antimicrob Resist 2023; 5:dlad038. [PMID: 37051191 PMCID: PMC10084947 DOI: 10.1093/jacamr/dlad038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/03/2022] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
Background Carbapenem-resistant Pseudomonas aeruginosa strains are on the rise worldwide. This study characterized clinical isolates of P. aeruginosa from three Nigerian hospitals for carbapenem resistance. Methods Strains isolated from wounds (n = 88), urine/catheter tips (n = 25), sputum/tracheotomy aspirates (n = 5), ear swabs (n = 4) and vaginal swabs (n = 1) were identified by MALDI-TOF and antibiotic susceptibility testing was performed using the VITEK 2 system. The genomic DNA of each isolate was subject to sequencing using Illumina and Oxford nanopore technology. Bioinformatics analyses were performed to detect antimicrobial resistance genes, clonal affiliations and phylogenetic relations of 123 non-duplicate P. aeruginosa isolates, whereas assembly of the nanopore reads using the plasmIDent pipeline enabled the identification of plasmids. Results Forty-three percent of the isolates were resistant to all antibiotic categories tested. More than 40% of the isolates were resistant to the carbapenems imipenem and/or meropenem (39% and 44%, respectively). Among the meropenem-resistant isolates, 48 (89%) carried at least one carbapenemase gene. The predominant one was bla NDM-1 (n = 34), which conferred resistance to all five antibiotic categories and highly increased the MICs of both meropenem and imipenem. The other recurrent carbapenemase genes were bla VIM-2 (n = 4), and bla VIM-5-like (n = 11), which co-existed with bla NDM-1 in two isolates. Conclusions The study revealed a high rate of carbapenem resistance and conjugative, broad host range plasmids carrying carbapenemase-encoding genes, especially the NDM-1 type, among isolates of P. aeruginosa. This may forebode the emergency of ubiquitous carbapenem resistance urging the implementation of infection control and antimicrobial stewardship strategies in Nigerian hospitals.
Collapse
Affiliation(s)
| | - Baris Kai Bader
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Bamidele Iwalokun
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Sophia Wolf
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Albert Lalremruata
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Adobi Dike
- Department of Microbiology, Lagos University Teaching Hospital, Idi-Araba, Lagos, Nigeria
| | | | - Libera Lo Presti
- Cluster of Excellence EXC2124: Controlling Microbes to Fight Infections, Tübingen University, Tübingen, Germany
| | - Jan Liese
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Julia Guther
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | | | | |
Collapse
|
176
|
Wang Y, Zhao R, Ackermann L. Electrochemical Syntheses of Polycyclic Aromatic Hydrocarbons (PAHs). Adv Mater 2023:e2300760. [PMID: 36965124 DOI: 10.1002/adma.202300760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) have surfaced as increasingly viable components in optoelectronics and material sciences. The development of highly efficient and atom-economic tools to prepare PAHs under exceedingly mild conditions constitutes a long-term goal. Traditional syntheses of PAHs have largely relied on multistep approaches or the conventional Scholl reaction. However, Scholl reactions are largely inefficient with electron-deficient substrates, require stoichiometric chemical oxidants, and typically occur in the presence of strong acid. In sharp contrast, electrochemistry has gained considerable momentum during the past decade as an alternative for the facile and straightforward PAHs assembly, generally via electro-oxidative dehydrogenative annulation, releasing molecular hydrogen as the sole stoichiometric byproduct by the hydrogen evolution reaction. This review provides an overview on the recent and significant advances in the field of electrochemical syntheses of various PAHs until January 2023.
Collapse
Affiliation(s)
- Yulei Wang
- Institut für Organische und Biomolekulare Chemie and Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, Tammanstraße 2, 37077, Göttingen, Germany
| | - Rong Zhao
- Institut für Organische und Biomolekulare Chemie and Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, Tammanstraße 2, 37077, Göttingen, Germany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie and Wöhler Research Institute for Sustainable Chemistry (WISCh), Georg-August-Universität Göttingen, Tammanstraße 2, 37077, Göttingen, Germany
| |
Collapse
|
177
|
Obana N, Takada H, Crowe-McAuliffe C, Iwamoto M, Egorov AA, Wu KJY, Chiba S, Murina V, Paternoga H, Tresco BIC, Nomura N, Myers AG, Atkinson GC, Wilson DN, Hauryliuk V. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Nucleic Acids Res 2023; 51:4536-4554. [PMID: 36951104 DOI: 10.1093/nar/gkad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.
Collapse
Affiliation(s)
- Nozomu Obana
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Mizuki Iwamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | | | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
| |
Collapse
|
178
|
Melzer MK, Schirge S, Gout J, Arnold F, Srinivasan D, Burtscher I, Allgöwer C, Mulaw M, Zengerling F, Günes C, Lickert H, Christoffels VM, Liebau S, Wagner M, Seufferlein T, Bolenz C, Moon AM, Perkhofer L, Kleger A. TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration. BMC Biol 2023; 21:55. [PMID: 36941669 PMCID: PMC10029195 DOI: 10.1186/s12915-023-01553-x] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND The reactivation of genetic programs from early development is a common mechanism for injury-induced organ regeneration. T-box 3 (TBX3) is a member of the T-box family of transcription factors previously shown to regulate pluripotency and subsequent lineage commitment in a number of tissues, including limb and lung. TBX3 is also involved in lung and heart organogenesis. Here, we provide a comprehensive and thorough characterization of TBX3 and its role during pancreatic organogenesis and regeneration. RESULTS We interrogated the level and cell specificity of TBX3 in the developing and adult pancreas at mRNA and protein levels at multiple developmental stages in mouse and human pancreas. We employed conditional mutagenesis to determine its role in murine pancreatic development and in regeneration after the induction of acute pancreatitis. We found that Tbx3 is dynamically expressed in the pancreatic mesenchyme and epithelium. While Tbx3 is expressed in the developing pancreas, its absence is likely compensated by other factors after ablation from either the mesenchymal or epithelial compartments. In an adult model of acute pancreatitis, we found that a lack of Tbx3 resulted in increased proliferation and fibrosis as well as an enhanced inflammatory gene programs, indicating that Tbx3 has a role in tissue homeostasis and regeneration. CONCLUSIONS TBX3 demonstrates dynamic expression patterns in the pancreas. Although TBX3 is dispensable for proper pancreatic development, its absence leads to altered organ regeneration after induction of acute pancreatitis.
Collapse
Affiliation(s)
- Michael Karl Melzer
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
- Clinic of Urology, Ulm University Hospital, Ulm, 89081, Germany
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany
| | - Silvia Schirge
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Johann Gout
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany
| | - Frank Arnold
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany
| | - Dharini Srinivasan
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Chantal Allgöwer
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany
| | - Medhanie Mulaw
- Unit for Single-cell Genomics, Ulm University, 89081, Ulm, Germany
| | | | - Cagatay Günes
- Clinic of Urology, Ulm University Hospital, Ulm, 89081, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
- Chair of b-Cell Biology, Technische Universität München, School of Medicine, Klinikum Rechts der Isar, 81675, München, Germany
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Meibergdreef 15, 1105AZ, Amsterdam, The Netherlands
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, Österbergstrasse 3, 72074, Tübingen, Germany
| | - Martin Wagner
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
| | - Thomas Seufferlein
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
| | | | - Anne M Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Department of Human Genetics (adjunct), University of Utah, Salt Lake City, UT, USA
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, USA
| | - Lukas Perkhofer
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany
| | - Alexander Kleger
- Clinic of Internal Medicine I, Ulm University Hospital, Ulm, 89081, Germany.
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, 89081, Germany.
- Core Facility Organoids, Ulm University, 89081, Ulm, Germany.
| |
Collapse
|
179
|
Abstract
Spin and valley indices represent the key quantum labels of quasi-particles in a wide class of two-dimensional materials and form the foundational elements of the fields of spintronics and valleytronics. Control over these degrees of freedom, therefore, remains the central challenge in these fields. Here, we show that femtosecond laser light combining optical frequency circularly polarized pulse and a terahertz (THz) frequency linearly polarized pulse, a so-called "hencomb" pulse, can generate precisely tailored and 90% pure spin currents for the dichalcogenide WSe2 and >75% pure valley currents for bilayer graphene with gaps greater than 120 millielectron volts (dephasing time, 20 femtoseconds). The frequency of the circular light component and the polarization vector of the THz light component are shown to represent the key control parameters of these pulses. Our results thus open a route toward light control over spin/valley current states at ultrafast times.
Collapse
|
180
|
Koeniger A, Polo P, Brichkina A, Finkernagel F, Visekruna A, Nist A, Stiewe T, Daude M, Diederich W, Gress T, Adhikary T, Lauth M. Tumor-suppressive disruption of cancer subtype-associated super enhancer circuits by small molecule treatment. NAR Cancer 2023; 5:zcad007. [PMID: 36755960 PMCID: PMC9900422 DOI: 10.1093/narcan/zcad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Transcriptional cancer subtypes which correlate with traits such as tumor growth, drug sensitivity or the chances of relapse and metastasis, have been described for several malignancies. The core regulatory circuits (CRCs) defining these subtypes are established by chromatin super enhancers (SEs) driving key transcription factors (TFs) specific for the particular cell state. In neuroblastoma (NB), one of the most frequent solid pediatric cancer entities, two major SE-directed molecular subtypes have been described: A more lineage-committed adrenergic (ADRN) and a mesenchymal (MES) subtype. Here, we found that a small isoxazole molecule (ISX), a frequently used pro-neural drug, reprogrammed SE activity and switched NB cells from an ADRN subtype towards a growth-retarded MES-like state. The MES-like state shared strong transcriptional overlap with ganglioneuroma (GN), a benign and highly differentiated tumor of the neural crest. Mechanistically, ISX suppressed chromatin binding of N-MYC, a CRC-amplifying transcription factor, resulting in loss of key ADRN subtype-enriched components such as N-MYC itself, PHOX2B and ALK, while concomitently, MES subtype markers were induced. Globally, ISX treatment installed a chromatin accessibility landscape typically associated with low risk NB. In summary, we provide evidence that CRCs and cancer subtype reprogramming might be amenable to future therapeutic targeting.
Collapse
Affiliation(s)
- Anke Koeniger
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Pierfrancesco Polo
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Anna Brichkina
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Florian Finkernagel
- Philipps University Marburg, Bioinformatics Core Facility, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Alexander Visekruna
- Philipps University Marburg, Institute for Medical Microbiology and Hygiene, 35043 Marburg, Germany
| | - Andrea Nist
- Member of the German Center for Lung Research (DZL), Center for Tumor- and Immune Biology, Genomics Core Facility, Institute of Molecular Oncology, Philipps University Marburg, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Member of the German Center for Lung Research (DZL), Center for Tumor- and Immune Biology, Genomics Core Facility, Institute of Molecular Oncology, Philipps University Marburg, 35043 Marburg, Germany
| | - Michael Daude
- Philipps University Marburg, Core Facility Medical Chemistry, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Wibke E Diederich
- Philipps University Marburg, Dept. of Medicinal Chemistry and Core Facility Medical Chemistry, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Thomas M Gress
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| | - Till Adhikary
- Philipps University Marburg, Institute for Medical Bioinformatics and Biostatistics and Institute for Molecular Biology and Tumor Research, Marburg, Germany
| | - Matthias Lauth
- Philipps University Marburg, Dept. of Gastroenterology, Endocrinology and Metabolism, Center for Tumor- and Immune Biology, 35043 Marburg, Germany
| |
Collapse
|
181
|
Pfeiffer J, Günther H, Völlinger L, Botros D, Scheibe B, Möbs M, Kraus F, Weigend F, Tambornino F. Double Addition vs. Ring Closure: Systematic Reactivity Study of CO(NCO) 2 and CO(NCS) 2 towards Hydrogen Halides. Chemistry 2023; 29:e202203983. [PMID: 36780136 DOI: 10.1002/chem.202203983] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/14/2023]
Abstract
The reactivity of carbonyl diisocyanate, CO(NCO)2 , and carbonyl diisothiocyanate, CO(NCS)2 with nucleophiles shows different patterns: Whereas carbonyl diisocyanate adds two equivalents of nucleophile forming carbonyl bis(carbamoylhalides), carbonyl diisothiocyanate only adds one equivalent and undergoes intramolecular ring closure, resulting in the formation of substituted thiadiazines. In this study we have reacted both carbonyl diisocyanate and carbonyl diisothiocyanate with the full series of hydrogen halides HF to HI, isolating carbonyl bis(carbamoylfluoride) (1), -chloride (2), -bromide (3), and -iodide (4) as well as (6-chloro-2,3-dihydro-2-thioxo-4H-1,3,5-thiadiazin-4-one (5), and 6-bromo-2,3-dihydro-2-thioxo-4H-1,3,5-thiadiazin-4-one (6). The compounds were analysed by single-crystal X-ray diffraction, NMR spectroscopy, IR and Raman spectroscopy, and elemental analysis. Quantum mechanical calculations show thermodynamic reasons for the differences in reactivity.
Collapse
Affiliation(s)
- Jonathan Pfeiffer
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Hennes Günther
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Lena Völlinger
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Demian Botros
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Benjamin Scheibe
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Martin Möbs
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Florian Kraus
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Florian Weigend
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Frank Tambornino
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| |
Collapse
|
182
|
Kohrt F, Smaldino PE, McElreath R, Schönbrodt F. Replication of the natural selection of bad science. R Soc Open Sci 2023; 10:221306. [PMID: 36844805 PMCID: PMC9943874 DOI: 10.1098/rsos.221306] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
This study reports an independent replication of the findings presented by Smaldino and McElreath (Smaldino, McElreath 2016 R. Soc. Open Sci. 3, 160384 (doi:10.1098/rsos.160384)). The replication was successful with one exception. We find that selection acting on scientist's propensity for replication frequency caused a brief period of exuberant replication not observed in the original paper due to a coding error. This difference does not, however, change the authors' original conclusions. We call for more replication studies for simulations as unique contributions to scientific quality assurance.
Collapse
Affiliation(s)
- Florian Kohrt
- Department of Psychology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul E. Smaldino
- Department of Cognitive and Information Sciences, University of California, Merced, CA 95343, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Richard McElreath
- Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felix Schönbrodt
- Department of Psychology, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
183
|
Weisser W, Blüthgen N, Staab M, Achury R, Müller J. Experiments are needed to quantify the main causes of insect decline. Biol Lett 2023; 19:20220500. [PMID: 36789531 PMCID: PMC9929502 DOI: 10.1098/rsbl.2022.0500] [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: 10/31/2022] [Accepted: 01/11/2023] [Indexed: 02/16/2023] Open
Abstract
Sparked by reports of insect declines of unexpected extent, there has been a surge in the compilation and analysis of insect time series data. While this effort has led to valuable databases, disagreement remains as to whether, where and why insects are declining. The 'why' question is particularly important because successful insect conservation will need to address the most important drivers of decline. Despite repeated calls for more long-term data, new time series will have to run for decades to quantitatively surpass those currently available. Here we argue that experimentation in addition to quantitative analysis of existing data is needed to identify the most important drivers of insect decline. While most potential drivers of insect population change are likely to have already been identified, their relative importance is largely unknown. Researchers should thus unite and use statistical insight to set up suitable experiments to be able to rank drivers by their importance. Such a coordinated effort is needed to produce the knowledge necessary for conservation action and will also result in increased monitoring and new time series.
Collapse
Affiliation(s)
- Wolfgang Weisser
- School of Life Sciences, Technical University of Munich, Terrestrial Ecology Research Group, Freising, Germany
| | - Nico Blüthgen
- Ecological Networks, Technische Universität Darmstadt, Darmstadt, Germany
| | - Michael Staab
- Ecological Networks, Technische Universität Darmstadt, Darmstadt, Germany
| | - Rafael Achury
- School of Life Sciences, Technical University of Munich, Terrestrial Ecology Research Group, Freising, Germany
| | - Jörg Müller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
- Bavarian Forest National Park, Grafenau, Germany
| |
Collapse
|
184
|
Garside GB, Sandoval M, Beronja S, Rudolph KL. Lentiviral in situ targeting of stem cells in unperturbed intestinal epithelium. BMC Biol 2023; 21:6. [PMID: 36627630 PMCID: PMC9832770 DOI: 10.1186/s12915-022-01466-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/16/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Methods for the long-term in situ transduction of the unperturbed murine intestinal epithelium have not been developed in past research. Such a method could speed up functional studies and screens to identify genetic factors influencing intestinal epithelium biology. Here, we developed an efficient method achieving this long-sought goal. RESULTS We used ultrasound-guided microinjections to transduce the embryonic endoderm at day 8 (E8.0) in utero. The injection procedure can be completed in 20 min and had a 100% survival rate. By injecting a small volume (0.1-0.2 μl) of concentrated virus, single shRNA constructs as well as lentiviral libraries can successfully be transduced. The new method stably and reproducibly targets adult intestinal epithelium, as well as other endoderm-derived organs such as the lungs, pancreas, liver, stomach, and bladder. Postnatal analysis of young adult mice indicates that single transduced cells at E8.0 gave rise to crypt fields that were comprised of 20-30 neighbouring crypts per crypt-field at 90 days after birth. Lentiviral targeting of ApcMin/+ mutant and wildtype mice revealed that heterozygous loss of Apc function suppresses the developmental normal growth pattern of intestinal crypt fields. This suppression of crypt field sizes did not involve a reduction of the crypt number per field, indicating that heterozygous Apc loss impaired the growth of individual crypts within the fields. Lentiviral-mediated shRNA knockdown of p53 led to an approximately 20% increase of individual crypts per field in both Apc+/+ and ApcMin/+ mice, associating with an increase in crypt size in ApcMin/+ mice but a slight reduction in crypt size in Apc+/+ mice. Overall, p53 knockdown rescued the reduction in crypt field size in Apc-mutant mice but had no effect on crypt field size in wildtype mice. CONCLUSIONS This study develops a novel technique enabling robust and reproducible in vivo targeting of intestinal stem cells in situ in the unperturbed intestinal epithelium across different regions of the intestine. In vivo somatic gene editing and genetic screening of lentiviral libraries has the potential to speed up discoveries and mechanistic understanding of genetic pathways controlling the biology of the intestinal epithelium during development and postnatal life. The here developed method enables such approaches.
Collapse
Affiliation(s)
- George B. Garside
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
- National Center for Tumor Diseases, 01307 Dresden, Germany
| | - Madeline Sandoval
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - Slobodan Beronja
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - K. Lenhard Rudolph
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| |
Collapse
|
185
|
Jeblick T, Leisen T, Steidele CE, Albert I, Müller J, Kaiser S, Mahler F, Sommer F, Keller S, Hückelhoven R, Hahn M, Scheuring D. Botrytis hypersensitive response inducing protein 1 triggers noncanonical PTI to induce plant cell death. Plant Physiol 2023; 191:125-141. [PMID: 36222581 PMCID: PMC9806589 DOI: 10.1093/plphys/kiac476] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/20/2022] [Indexed: 05/28/2023]
Abstract
According to their lifestyle, plant pathogens are divided into biotrophic and necrotrophic organisms. Biotrophic pathogens exclusively nourish living host cells, whereas necrotrophic pathogens rapidly kill host cells and nourish cell walls and cell contents. To this end, the necrotrophic fungus Botrytis cinerea secretes large amounts of phytotoxic proteins and cell wall-degrading enzymes. However, the precise role of these proteins during infection is unknown. Here, we report on the identification and characterization of the previously unknown toxic protein hypersensitive response-inducing protein 1 (Hip1), which induces plant cell death. We found the adoption of a structurally conserved folded Alternaria alternata Alt a 1 protein structure to be a prerequisite for Hip1 to exert its necrosis-inducing activity in a host-specific manner. Localization and the induction of typical plant defense responses by Hip1 indicate recognition as a pathogen-associated molecular pattern at the plant plasma membrane. In contrast to other secreted toxic Botrytis proteins, the activity of Hip1 does not depend on the presence of the receptor-associated kinases BRI1-associated kinase 1 and suppressor of BIR1-1. Our results demonstrate that recognition of Hip1, even in the absence of obvious enzymatic or pore-forming activity, induces strong plant defense reactions eventually leading to plant cell death. Botrytis hip1 overexpression strains generated by CRISPR/Cas9 displayed enhanced infection, indicating the virulence-promoting potential of Hip1. Taken together, Hip1 induces a noncanonical defense response which might be a common feature of structurally conserved fungal proteins from the Alt a 1 family.
Collapse
Affiliation(s)
- Tanja Jeblick
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Thomas Leisen
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Christina E Steidele
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Isabell Albert
- Molecular Plant Physiology, FAU Erlangen, Erlangen 91058, Germany
| | - Jonas Müller
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Sabrina Kaiser
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Florian Mahler
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Frederik Sommer
- Molecular Biotechnology & Systems Biology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern 67663, Germany
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Matthias Hahn
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | | |
Collapse
|
186
|
Prautsch J, Erickson JL, Özyürek S, Gormanns R, Franke L, Lu Y, Marx J, Niemeyer F, Parker JE, Stuttmann J, Schattat MH. Effector XopQ-induced stromule formation in Nicotiana benthamiana depends on ETI signaling components ADR1 and NRG1. Plant Physiol 2023; 191:161-176. [PMID: 36259930 PMCID: PMC9806647 DOI: 10.1093/plphys/kiac481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 09/22/2022] [Indexed: 05/28/2023]
Abstract
In Nicotiana benthamiana, the expression of the Xanthomonas effector XANTHOMONAS OUTER PROTEIN Q (XopQ) triggers RECOGNITION OF XOPQ1 (ROQ1)-dependent effector-triggered immunity (ETI) responses accompanied by the accumulation of plastids around the nucleus and the formation of stromules. Both plastid clustering and stromules were proposed to contribute to ETI-related hypersensitive cell death and thereby to plant immunity. Whether these reactions are directly connected to ETI signaling events has not been tested. Here, we utilized transient expression experiments to determine whether XopQ-triggered plastid reactions are a result of XopQ perception by the immune receptor ROQ1 or a consequence of XopQ virulence activity. We found that N. benthamiana mutants lacking ROQ1, ENHANCED DISEASE SUSCEPTIBILITY 1, or the helper NUCLEOTIDE-BINDING LEUCINE-RICH REPEAT IMMUNE RECEPTORS (NLRs) N-REQUIRED GENE 1 (NRG1) and ACTIVATED DISEASE RESISTANCE GENE 1 (ADR1), fail to elicit XopQ-dependent host cell death and stromule formation. Mutants lacking only NRG1 lost XopQ-dependent cell death but retained some stromule induction that was abolished in the nrg1_adr1 double mutant. This analysis aligns XopQ-triggered stromules with the ETI signaling cascade but not to host programmed cell death. Furthermore, data reveal that XopQ-triggered plastid clustering is not strictly linked to stromule formation during ETI. Our data suggest that stromule formation, in contrast to chloroplast perinuclear dynamics, is an integral part of the N. benthamiana ETI response and that both NRG1 and ADR1 hNLRs play a role in this ETI response.
Collapse
Affiliation(s)
- Jennifer Prautsch
- Biology, Plant Physiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Jessica Lee Erickson
- Biology, Plant Genetics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
- Leibniz-Institut for Plant Biochemistry, Halle, Germany
| | - Sedef Özyürek
- Biology, Plant Physiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Rahel Gormanns
- Biology, Plant Physiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Lars Franke
- Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Yang Lu
- Biology, Plant Physiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Jolina Marx
- Leibniz-Institut for Plant Biochemistry, Halle, Germany
| | - Frederik Niemeyer
- Biology, Plant Physiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Johannes Stuttmann
- Biology, Plant Genetics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | | |
Collapse
|
187
|
Kumar A, Cuccuru G, Grüning B, Backofen R. An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy. Gigascience 2022; 12:7143185. [PMID: 37099385 PMCID: PMC10132306 DOI: 10.1093/gigascience/giad028] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Artificial intelligence (AI) programs that train on large datasets require powerful compute infrastructure consisting of several CPU cores and GPUs. JupyterLab provides an excellent framework for developing AI programs, but it needs to be hosted on such an infrastructure to enable faster training of AI programs using parallel computing. FINDINGS An open-source, docker-based, and GPU-enabled JupyterLab infrastructure is developed that runs on the public compute infrastructure of Galaxy Europe consisting of thousands of CPU cores, many GPUs, and several petabytes of storage to rapidly prototype and develop end-to-end AI projects. Using a JupyterLab notebook, long-running AI model training programs can also be executed remotely to create trained models, represented in open neural network exchange (ONNX) format, and other output datasets in Galaxy. Other features include Git integration for version control, the option of creating and executing pipelines of notebooks, and multiple dashboards and packages for monitoring compute resources and visualization, respectively. CONCLUSIONS These features make JupyterLab in Galaxy Europe highly suitable for creating and managing AI projects. A recent scientific publication that predicts infected regions in COVID-19 computed tomography scan images is reproduced using various features of JupyterLab on Galaxy Europe. In addition, ColabFold, a faster implementation of AlphaFold2, is accessed in JupyterLab to predict the 3-dimensional structure of protein sequences. JupyterLab is accessible in 2 ways-one as an interactive Galaxy tool and the other by running the underlying Docker container. In both ways, long-running training can be executed on Galaxy's compute infrastructure. Scripts to create the Docker container are available under MIT license at https://github.com/usegalaxy-eu/gpu-jupyterlab-docker.
Collapse
Affiliation(s)
- Anup Kumar
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Gianmauro Cuccuru
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
| |
Collapse
|
188
|
Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J. Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens. Microlife 2022; 4:uqac027. [PMID: 37223738 PMCID: PMC10117718 DOI: 10.1093/femsml/uqac027] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 05/25/2023]
Abstract
Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA-protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
Collapse
Affiliation(s)
| | | | | | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Jörg Vogel
- Corresponding author. Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany. Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany. E-mail:
| |
Collapse
|
189
|
Baumgardt M, Hülsemann M, Löwa A, Fatykhova D, Hoffmann K, Kessler M, Mieth M, Hellwig K, Frey D, Langenhagen A, Voss A, Obermayer B, Wyler E, Dökel S, Gruber AD, Tölch U, Hippenstiel S, Hocke AC, Hönzke K. State-of-the-art analytical methods of viral infections in human lung organoids. PLoS One 2022; 17:e0276115. [PMID: 36538516 PMCID: PMC9767351 DOI: 10.1371/journal.pone.0276115] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
Human-based organ models can provide strong predictive value to investigate the tropism, virulence, and replication kinetics of viral pathogens. Currently, such models have received widespread attention in the study of SARS-CoV-2 causing the COVID-19 pandemic. Applicable to a large set of organoid models and viruses, we provide a step-by-step work instruction for the infection of human alveolar-like organoids with SARS-CoV-2 in this protocol collection. We also prepared a detailed description on state-of-the-art methodologies to assess the infection impact and the analysis of relevant host factors in organoids. This protocol collection consists of five different sets of protocols. Set 1 describes the protein extraction from human alveolar-like organoids and the determination of protein expression of angiotensin-converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2) and FURIN as exemplary host factors of SARS-CoV-2. Set 2 provides detailed guidance on the extraction of RNA from human alveolar-like organoids and the subsequent qPCR to quantify the expression level of ACE2, TMPRSS2, and FURIN as host factors of SARS-CoV-2 on the mRNA level. Protocol set 3 contains an in-depth explanation on how to infect human alveolar-like organoids with SARS-CoV-2 and how to quantify the viral replication by plaque assay and viral E gene-based RT-qPCR. Set 4 provides a step-by-step protocol for the isolation of single cells from infected human alveolar-like organoids for further processing in single-cell RNA sequencing or flow cytometry. Set 5 presents a detailed protocol on how to perform the fixation of human alveolar-like organoids and guides through all steps of immunohistochemistry and in situ hybridization to visualize SARS-CoV-2 and its host factors. The infection and all subsequent analytical methods have been successfully validated by biological replications with human alveolar-like organoids based on material from different donors.
Collapse
Affiliation(s)
- Morris Baumgardt
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Maren Hülsemann
- Berlin Institute of Health at Charité (BIH), BIH QUEST Center for Responsible Research, Berlin, Germany
| | - Anna Löwa
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Diana Fatykhova
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Karen Hoffmann
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Mirjana Kessler
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Department of Gynecology and Obstetrics, University Hospital, LMU, Munich, Germany
| | - Maren Mieth
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Katharina Hellwig
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Doris Frey
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alina Langenhagen
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voss
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) and IRI Life Sciences, Institute for Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Simon Dökel
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Ulf Tölch
- Berlin Institute of Health at Charité (BIH), BIH QUEST Center for Responsible Research, Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Andreas C. Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Katja Hönzke
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| |
Collapse
|
190
|
van der Velden J, Asselbergs FW, Bakkers J, Batkai S, Bertrand L, Bezzina CR, Bot I, Brundel BJJM, Carrier L, Chamuleau S, Ciccarelli M, Dawson D, Davidson SM, Dendorfer A, Duncker DJ, Eschenhagen T, Fabritz L, Falcão-Pires I, Ferdinandy P, Giacca M, Girao H, Gollmann-Tepeköylü C, Gyongyosi M, Guzik TJ, Hamdani N, Heymans S, Hilfiker A, Hilfiker-Kleiner D, Hoekstra AG, Hulot JS, Kuster DWD, van Laake LW, Lecour S, Leiner T, Linke WA, Lumens J, Lutgens E, Madonna R, Maegdefessel L, Mayr M, van der Meer P, Passier R, Perbellini F, Perrino C, Pesce M, Priori S, Remme CA, Rosenhahn B, Schotten U, Schulz R, Sipido KR, Sluijter JPG, van Steenbeek F, Steffens S, Terracciano CM, Tocchetti CG, Vlasman P, Yeung KK, Zacchigna S, Zwaagman D, Thum T. Animal models and animal-free innovations for cardiovascular research: current status and routes to be explored. Consensus document of the ESC Working Group on Myocardial Function and the ESC Working Group on Cellular Biology of the Heart. Cardiovasc Res 2022; 118:3016-3051. [PMID: 34999816 PMCID: PMC9732557 DOI: 10.1093/cvr/cvab370] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 01/05/2022] [Indexed: 01/09/2023] Open
Abstract
Cardiovascular diseases represent a major cause of morbidity and mortality, necessitating research to improve diagnostics, and to discover and test novel preventive and curative therapies, all of which warrant experimental models that recapitulate human disease. The translation of basic science results to clinical practice is a challenging task, in particular for complex conditions such as cardiovascular diseases, which often result from multiple risk factors and comorbidities. This difficulty might lead some individuals to question the value of animal research, citing the translational 'valley of death', which largely reflects the fact that studies in rodents are difficult to translate to humans. This is also influenced by the fact that new, human-derived in vitro models can recapitulate aspects of disease processes. However, it would be a mistake to think that animal models do not represent a vital step in the translational pathway as they do provide important pathophysiological insights into disease mechanisms particularly on an organ and systemic level. While stem cell-derived human models have the potential to become key in testing toxicity and effectiveness of new drugs, we need to be realistic, and carefully validate all new human-like disease models. In this position paper, we highlight recent advances in trying to reduce the number of animals for cardiovascular research ranging from stem cell-derived models to in situ modelling of heart properties, bioinformatic models based on large datasets, and state-of-the-art animal models, which show clinically relevant characteristics observed in patients with a cardiovascular disease. We aim to provide a guide to help researchers in their experimental design to translate bench findings to clinical routine taking the replacement, reduction, and refinement (3R) as a guiding concept.
Collapse
Grants
- R01 HL150359 NHLBI NIH HHS
- RG/16/14/32397 British Heart Foundation
- FS/18/37/33642 British Heart Foundation
- PG/17/64/33205 British Heart Foundation
- PG/15/88/31780 British Heart Foundation
- FS/RTF/20/30009, NH/19/1/34595, PG/18/35/33786, CS/17/4/32960, PG/15/88/31780, and PG/17/64/33205 British Heart Foundation
- NC/T001488/1 National Centre for the Replacement, Refinement and Reduction of Animals in Research
- PG/18/44/33790 British Heart Foundation
- CH/16/3/32406 British Heart Foundation
- FS/RTF/20/30009 British Heart Foundation
- NWO-ZonMW
- ZonMW and Heart Foundation for the translational research program
- Dutch Cardiovascular Alliance (DCVA)
- Leducq Foundation
- Dutch Research Council
- Association of Collaborating Health Foundations (SGF)
- UCL Hospitals NIHR Biomedical Research Centre, and the DCVA
- Netherlands CardioVascular Research Initiative CVON
- Stichting Hartekind and the Dutch Research Counsel (NWO) (OCENW.GROOT.2019.029)
- National Fund for Scientific Research, Belgium and Action de Recherche Concertée de la Communauté Wallonie-Bruxelles, Belgium
- Netherlands CardioVascular Research Initiative CVON (PREDICT2 and CONCOR-genes projects), the Leducq Foundation
- ERA PerMed (PROCEED study)
- Netherlands Cardiovascular Research Initiative
- Dutch Heart Foundation
- German Centre of Cardiovascular Research (DZHH)
- Chest Heart and Stroke Scotland
- Tenovus Scotland
- Friends of Anchor and Grampian NHS-Endowments
- National Institute for Health Research University College London Hospitals Biomedical Research Centre
- German Centre for Cardiovascular Research
- European Research Council (ERC-AG IndivuHeart), the Deutsche Forschungsgemeinschaft
- European Union Horizon 2020 (REANIMA and TRAINHEART)
- German Ministry of Education and Research (BMBF)
- Centre for Cardiovascular Research (DZHK)
- European Union Horizon 2020
- DFG
- National Research, Development and Innovation Office of Hungary
- Research Excellence Program—TKP; National Heart Program
- Austrian Science Fund
- European Union Commission’s Seventh Framework programme
- CVON2016-Early HFPEF
- CVON She-PREDICTS
- CVON Arena-PRIME
- European Union’s Horizon 2020 research and innovation programme
- Deutsche Forschungsgemeinschaft
- Volkswagenstiftung
- French National Research Agency
- ERA-Net-CVD
- Fédération Française de Cardiologie, the Fondation pour la Recherche Médicale
- French PIA Project
- University Research Federation against heart failure
- Netherlands Heart Foundation
- Dekker Senior Clinical Scientist
- Health Holland TKI-LSH
- TUe/UMCU/UU Alliance Fund
- south African National Foundation
- Cancer Association of South Africa and Winetech
- Netherlands Heart Foundation/Applied & Engineering Sciences
- Dutch Technology Foundation
- Pie Medical Imaging
- Netherlands Organisation for Scientific Research
- Dr. Dekker Program
- Netherlands CardioVascular Research Initiative: the Dutch Heart Foundation
- Dutch Federation of University Medical Centres
- Netherlands Organization for Health Research and Development and the Royal Netherlands Academy of Sciences for the GENIUS-II project
- Netherlands Organization for Scientific Research (NWO) (VICI grant); the European Research Council
- Incyte s.r.l. and from Ministero dell’Istruzione, Università e Ricerca Scientifica
- German Center for Cardiovascular Research (Junior Research Group & Translational Research Project), the European Research Council (ERC Starting Grant NORVAS),
- Swedish Heart-Lung-Foundation
- Swedish Research Council
- National Institutes of Health
- Bavarian State Ministry of Health and Care through the research project DigiMed Bayern
- ERC
- ERA-CVD
- Dutch Heart Foundation, ZonMw
- the NWO Gravitation project
- Ministero dell'Istruzione, Università e Ricerca Scientifica
- Regione Lombardia
- Netherlands Organisation for Health Research and Development
- ITN Network Personalize AF: Personalized Therapies for Atrial Fibrillation: a translational network
- MAESTRIA: Machine Learning Artificial Intelligence Early Detection Stroke Atrial Fibrillation
- REPAIR: Restoring cardiac mechanical function by polymeric artificial muscular tissue
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
- European Union H2020 program to the project TECHNOBEAT
- EVICARE
- BRAV3
- ZonMw
- German Centre for Cardiovascular Research (DZHK)
- British Heart Foundation Centre for Cardiac Regeneration
- British Heart Foundation studentship
- NC3Rs
- Interreg ITA-AUS project InCARDIO
- Italian Association for Cancer Research
Collapse
Affiliation(s)
- Jolanda van der Velden
- Amsterdam UMC, Vrije Universiteit, Physiology, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Faculty of Population Health Sciences, Institute of Cardiovascular Science and Institute of Health Informatics, University College London, London, UK
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Sandor Batkai
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hannover, Germany
| | - Luc Bertrand
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hannover, Germany
| | - Connie R Bezzina
- Université catholique de Louvain, Institut de Recherche Expérimentale et Clinique, Pole of Cardiovascular Research, Brussels, Belgium
| | - Ilze Bot
- Heart Center, Department of Experimental Cardiology, Amsterdam UMC, Location Academic Medical Center, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bianca J J M Brundel
- Amsterdam UMC, Vrije Universiteit, Physiology, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - Lucie Carrier
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Steven Chamuleau
- Amsterdam UMC, Heart Center, Cardiology, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Odontology, University of Salerno, Fisciano (SA), Italy
| | - Dana Dawson
- Department of Cardiology, Aberdeen Cardiovascular and Diabetes Centre, Aberdeen Royal Infirmary and University of Aberdeen, Aberdeen, UK
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London WC1E 6HX, UK
| | - Andreas Dendorfer
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Dirk J Duncker
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Larissa Fabritz
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
- University Center of Cardiovascular Sciences and Department of Cardiology, University Heart Center Hamburg, Germany and Institute of Cardiovascular Sciences, University of Birmingham, UK
| | - Ines Falcão-Pires
- UnIC - Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, Portugal
| | - Péter Ferdinandy
- Cardiometabolic Research Group and MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Mauro Giacca
- Department of Medicine, Surgery and Health Sciences and Cardiovascular Department, Centre for Translational Cardiology, Azienda Sanitaria Universitaria Integrata Trieste, Trieste, Italy
- International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- King’s British Heart Foundation Centre, King’s College London, London, UK
| | - Henrique Girao
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology, Faculty of Medicine, Coimbra, Portugal
- Clinical Academic Centre of Coimbra, Coimbra, Portugal
| | | | - Mariann Gyongyosi
- Division of Cardiology, Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Tomasz J Guzik
- Instutute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
- Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Nazha Hamdani
- Division Cardiology, Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany
- Institute of Physiology, Ruhr University Bochum, Bochum, Germany
| | - Stephane Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht University, Maastricht, The Netherlands
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Andres Hilfiker
- Department for Cardiothoracic, Transplant, and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Denise Hilfiker-Kleiner
- Department for Cardiology and Angiology, Hannover Medical School, Hannover, Germany
- Department of Cardiovascular Complications in Pregnancy and in Oncologic Therapies, Comprehensive Cancer Centre, Philipps-Universität Marburg, Germany
| | - Alfons G Hoekstra
- Computational Science Lab, Informatics Institute, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Jean-Sébastien Hulot
- Université de Paris, INSERM, PARCC, F-75015 Paris, France
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, F-75015 Paris, France
| | - Diederik W D Kuster
- Amsterdam UMC, Vrije Universiteit, Physiology, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - Linda W van Laake
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sandrine Lecour
- Department of Medicine, Hatter Institute for Cardiovascular Research in Africa and Cape Heart Institute, University of Cape Town, Cape Town, South Africa
| | - Tim Leiner
- Department of Radiology, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Wolfgang A Linke
- Institute of Physiology II, University of Muenster, Robert-Koch-Str. 27B, 48149 Muenster, Germany
| | - Joost Lumens
- Department of Biomedical Engineering, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Esther Lutgens
- Experimental Vascular Biology Division, Department of Medical Biochemistry, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-Universität München (LMU), Munich, Germany
- DZHK, Partner Site Munich Heart Alliance, Munich, Germany
| | - Rosalinda Madonna
- Department of Pathology, Cardiology Division, University of Pisa, 56124 Pisa, Italy
- Department of Internal Medicine, Cardiology Division, University of Texas Medical School in Houston, Houston, TX, USA
| | - Lars Maegdefessel
- DZHK, Partner Site Munich Heart Alliance, Munich, Germany
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Manuel Mayr
- King’s British Heart Foundation Centre, King’s College London, London, UK
| | - Peter van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Robert Passier
- Department of Applied Stem Cell Technologies, TechMed Centre, University of Twente, 7500AE Enschede, The Netherlands
- Department of Anatomy and Embryology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Filippo Perbellini
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hannover, Germany
| | - Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Maurizio Pesce
- Unità di Ingegneria Tissutale Cardiovascolare, Centro cardiologico Monzino, IRCCS, Milan, Italy
| | - Silvia Priori
- Molecular Cardiology, Istituti Clinici Scientifici Maugeri, Pavia, Italy
- University of Pavia, Pavia, Italy
| | - Carol Ann Remme
- Université catholique de Louvain, Institut de Recherche Expérimentale et Clinique, Pole of Cardiovascular Research, Brussels, Belgium
| | - Bodo Rosenhahn
- Institute for information Processing, Leibniz University of Hanover, 30167 Hannover, Germany
| | - Ulrich Schotten
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Rainer Schulz
- Institute of Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - Karin R Sipido
- Department of Cardiovascular Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Joost P G Sluijter
- Experimental Cardiology Laboratory, Department of Cardiology, Regenerative Medicine Center Utrecht, Circulatory Health Laboratory, Utrecht University, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Frank van Steenbeek
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Sabine Steffens
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-Universität München (LMU), Munich, Germany
- DZHK, Partner Site Munich Heart Alliance, Munich, Germany
| | | | - Carlo Gabriele Tocchetti
- Cardio-Oncology Unit, Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI), Interdepartmental Center for Clinical and Translational Research (CIRCET), Interdepartmental Hypertension Research Center (CIRIAPA), Federico II University, Naples, Italy
| | - Patricia Vlasman
- Amsterdam UMC, Vrije Universiteit, Physiology, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - Kak Khee Yeung
- Amsterdam UMC, Vrije Universiteit, Surgery, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - Serena Zacchigna
- Department of Medicine, Surgery and Health Sciences and Cardiovascular Department, Centre for Translational Cardiology, Azienda Sanitaria Universitaria Integrata Trieste, Trieste, Italy
- International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Dayenne Zwaagman
- Amsterdam UMC, Heart Center, Cardiology, Amsterdam Cardiovascular Science, Amsterdam, The Netherlands
| | - Thomas Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| |
Collapse
|
191
|
Fache E, Piovano S, Soderberg A, Tuiono M, Riera L, David G, Kowasch M, Pauwels S, Breckwoldt A, Carrière SM, Sabinot C. "Draw the sea…": Children's representations of ocean connectivity in Fiji and New Caledonia. Ambio 2022; 51:2445-2458. [PMID: 36149595 PMCID: PMC9584002 DOI: 10.1007/s13280-022-01777-1] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
In the South Pacific region, marine territories and resources play a crucial role for local communities. Children engage with these territories and resources from an early age onwards. As the next ocean stewards, they are a stakeholder group whose understandings of ocean connectivity and fisheries should be given serious consideration in decision-making processes towards the sustainable use and management of coastal seas. This paper analyses 290 children's drawings from Fiji and New Caledonia, created in 2019 in spontaneous response to the instruction: "Draw the sea and what you and others do in the sea". Exploring the webs of connections with and within the sea revealed by these children's drawings and their own interpretations leads us to discuss children's representations of the sea: (1) beyond a land-sea compartmentation, (2) as a locus of both exploitation and conservation of marine life, and (3) as a 'place-full' space connecting human and more-than-human realms.
Collapse
Affiliation(s)
- Elodie Fache
- SENS, IRD, CIRAD, Univ Paul Valery Montpellier 3, Univ Montpellier, Montpellier, France
| | - Susanna Piovano
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Bay Road, Private Mail Bag, Suva, Fiji
| | - Alisi Soderberg
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Bay Road, Private Mail Bag, Suva, Fiji
| | - Malakai Tuiono
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Bay Road, Private Mail Bag, Suva, Fiji
| | - Léa Riera
- SENS, IRD, CIRAD, Univ Paul Valery Montpellier 3, Univ Montpellier, Montpellier, France
- Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen, Germany
| | - Gilbert David
- UMR ESPACE-DEV, Univ Montpellier, IRD, Univ Antilles, Univ Avignon-Pays de Vaucluse, Univ Guyane, Univ La Réunion, Univ Nouvelle-Calédonie, Montpellier, France
| | - Matthias Kowasch
- Institute of Secondary Teacher Education, University College of Teacher Education Styria, Hasnerplatz 12, 8010 Graz, Austria
- Inland Norway University of Applied Sciences, Hamar, Norway
- UMR ESPACE-DEV, Univ Montpellier, IRD, Univ Antilles, Univ Avignon-Pays de Vaucluse, Univ Guyane, Univ La Réunion, Univ Nouvelle-Calédonie, Montpellier, France
- Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simonne Pauwels
- Aix-Marseille Université, CNRS, EHESS, CREDO (UMR 7308), Labex Corail, Marseille, France
| | - Annette Breckwoldt
- Leibniz Centre for Tropical Marine Research (ZMT), Fahrenheitstraße 6, 28359 Bremen, Germany
| | - Stéphanie M. Carrière
- SENS, IRD, CIRAD, Univ Paul Valery Montpellier 3, Univ Montpellier, Montpellier, France
| | - Catherine Sabinot
- UMR ESPACE-DEV, Univ Montpellier, IRD, Univ Antilles, Univ Avignon-Pays de Vaucluse, Univ Guyane, Univ La Réunion, Univ Nouvelle-Calédonie, Montpellier, France
- Centre IRD Anse Vata, BPA5, 98848 Nouméa Cedex, Nouvelle-Calédonie
| |
Collapse
|
192
|
He J, Yang B, Hause G, Rössner N, Peiter-Volk T, Schattat MH, Voiniciuc C, Peiter E. The trans-Golgi-localized protein BICAT3 regulates manganese allocation and matrix polysaccharide biosynthesis. Plant Physiol 2022; 190:2579-2600. [PMID: 35993897 PMCID: PMC9706472 DOI: 10.1093/plphys/kiac387] [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] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2022] [Indexed: 05/11/2023]
Abstract
Manganese (Mn2+) is essential for a diversity of processes, including photosynthetic water splitting and the transfer of glycosyl moieties. Various Golgi-localized glycosyltransferases that mediate cell wall matrix polysaccharide biosynthesis are Mn2+ dependent, but the supply of these enzymes with Mn2+ is not well understood. Here, we show that the BIVALENT CATION TRANSPORTER 3 (BICAT3) localizes specifically to trans-cisternae of the Golgi. In agreement with a role in Mn2+ and Ca2+ homeostasis, BICAT3 rescued yeast (Saccharomyces cerevisiae) mutants defective in their translocation. Arabidopsis (Arabidopsis thaliana) knockout mutants of BICAT3 were sensitive to low Mn2+ and high Ca2+ availability and showed altered accumulation of these cations. Despite reduced cell expansion and leaf size in Mn2+-deficient bicat3 mutants, their photosynthesis was improved, accompanied by an increased Mn content of chloroplasts. Growth defects of bicat3 corresponded with an impaired glycosidic composition of matrix polysaccharides synthesized in the trans-Golgi. In addition to the vegetative growth defects, pollen tube growth of bicat3 was heterogeneously aberrant. This was associated with a severely reduced and similarly heterogeneous pectin deposition and caused diminished seed set and silique length. Double mutant analyses demonstrated that the physiological relevance of BICAT3 is distinct from that of ER-TYPE CA2+-ATPASE 3, a Golgi-localized Mn2+/Ca2+-ATPase. Collectively, BICAT3 is a principal Mn2+ transporter in the trans-Golgi whose activity is critical for specific glycosylation reactions in this organelle and for the allocation of Mn2+ between Golgi apparatus and chloroplasts.
Collapse
Affiliation(s)
- Jie He
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Bo Yang
- Independent Junior Research Group—Designer Glycans, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Gerd Hause
- Biocentre, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Nico Rössner
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Tina Peiter-Volk
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Martin H Schattat
- Plant Physiology, Institute of Biology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Cătălin Voiniciuc
- Independent Junior Research Group—Designer Glycans, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
| | | |
Collapse
|
193
|
Abstract
Molecular targeted therapy plays an increasingly important role in the treatment of metastatic pheochromocytomas and paragangliomas (PPGLs), which are rare tumors but remain difficult to treat. This mini-review provides an overview of established molecular targeted therapies in present use, and perspectives on those currently under development and evaluation in clinical trials. Recently published research articles, guidelines, and expert views on molecular targeted therapies in PPGLs are systematically reviewed and summarized. Some tyrosine kinase inhibitors (sunitinib, cabozantinib) are already in clinical use with some promising results, but without formal approval for the treatment of PPGLs. Sunitinib is the only therapeutic option which has been investigated in a randomized placebo-controlled clinical trial. It is clinically used as a first-, second-, or third-line therapeutic option for the treatment of progressive metastatic PPGLs. Some other promising molecular targeted therapies (hypoxia-inducible factor 2 alpha [HIF2α] inhibitors, tumor vaccination together with checkpoint inhibitors, antiangiogenic therapies, kinase signaling inhibitors) are under evaluation in clinical trials. The HIF2α inhibitor belzutifan may prove to be particularly interesting for cluster 1B-/VHL/EPAS1-related PPGLs, whereas antiangiogenic therapies seem to be primarily effective in cluster 1A-/SDHx-related PPGLs. Some combination therapies currently being evaluated in clinical trials, such as temozolomide/olaparib, temozolomide/talazoparib, or cabozantinib/atezolizumab, will provide data for novel therapy for metastatic PPGLs. It is likely that advances in such molecular targeted therapies will play an essential role in the future treatment of these tumors, with more personalized therapy options paving the way towards improved therapeutic outcomes.
Collapse
Affiliation(s)
- Katharina Wang
- Department of Internal Medicine IV, University Hospital, LMU Klinikum, Ludwig Maximilian University of Munich, 80336 Munich, Germany
| | - Joakim Crona
- Department of Medical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Felix Beuschlein
- Department of Internal Medicine IV, University Hospital, LMU Klinikum, Ludwig Maximilian University of Munich, 80336 Munich, Germany
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), 8091 Zurich, Switzerland
| | - Ashley B Grossman
- Green Templeton College, University of Oxford, Oxford OX2 6HG, United Kingdom
- NET Unit, ENETS Centre of Excellence, Royal Free Hospital, London NW3 2QG, United Kingdom
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-1109, USA
| | - Svenja Nölting
- Department of Internal Medicine IV, University Hospital, LMU Klinikum, Ludwig Maximilian University of Munich, 80336 Munich, Germany
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), 8091 Zurich, Switzerland
| |
Collapse
|
194
|
Niemeyer D, Stenzel S, Veith T, Schroeder S, Friedmann K, Weege F, Trimpert J, Heinze J, Richter A, Jansen J, Emanuel J, Kazmierski J, Pott F, Jeworowski LM, Olmer R, Jaboreck MC, Tenner B, Papies J, Walper F, Schmidt ML, Heinemann N, Möncke-Buchner E, Baumgardt M, Hoffmann K, Widera M, Thao TTN, Balázs A, Schulze J, Mache C, Jones TC, Morkel M, Ciesek S, Hanitsch LG, Mall MA, Hocke AC, Thiel V, Osterrieder K, Wolff T, Martin U, Corman VM, Müller MA, Goffinet C, Drosten C. SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression. PLoS Biol 2022; 20:e3001871. [PMID: 36383605 PMCID: PMC9710838 DOI: 10.1371/journal.pbio.3001871] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/30/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Epidemiological data demonstrate that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) Alpha and Delta are more transmissible, infectious, and pathogenic than previous variants. Phenotypic properties of VOC remain understudied. Here, we provide an extensive functional study of VOC Alpha replication and cell entry phenotypes assisted by reverse genetics, mutational mapping of spike in lentiviral pseudotypes, viral and cellular gene expression studies, and infectivity stability assays in an enhanced range of cell and epithelial culture models. In almost all models, VOC Alpha spread less or equally efficiently as ancestral (B.1) SARS-CoV-2. B.1. and VOC Alpha shared similar susceptibility to serum neutralization. Despite increased relative abundance of specific sgRNAs in the context of VOC Alpha infection, immune gene expression in infected cells did not differ between VOC Alpha and B.1. However, inferior spreading and entry efficiencies of VOC Alpha corresponded to lower abundance of proteolytically cleaved spike products presumably linked to the T716I mutation. In addition, we identified a bronchial cell line, NCI-H1299, which supported 24-fold increased growth of VOC Alpha and is to our knowledge the only cell line to recapitulate the fitness advantage of VOC Alpha compared to B.1. Interestingly, also VOC Delta showed a strong (595-fold) fitness advantage over B.1 in these cells. Comparative analysis of chimeric viruses expressing VOC Alpha spike in the backbone of B.1, and vice versa, showed that the specific replication phenotype of VOC Alpha in NCI-H1299 cells is largely determined by its spike protein. Despite undetectable ACE2 protein expression in NCI-H1299 cells, CRISPR/Cas9 knock-out and antibody-mediated blocking experiments revealed that multicycle spread of B.1 and VOC Alpha required ACE2 expression. Interestingly, entry of VOC Alpha, as opposed to B.1 virions, was largely unaffected by treatment with exogenous trypsin or saliva prior to infection, suggesting enhanced resistance of VOC Alpha spike to premature proteolytic cleavage in the extracellular environment of the human respiratory tract. This property may result in delayed degradation of VOC Alpha particle infectivity in conditions typical of mucosal fluids of the upper respiratory tract that may be recapitulated in NCI-H1299 cells closer than in highly ACE2-expressing cell lines and models. Our study highlights the importance of cell model evaluation and comparison for in-depth characterization of virus variant-specific phenotypes and uncovers a fine-tuned interrelationship between VOC Alpha- and host cell-specific determinants that may underlie the increased and prolonged virus shedding detected in patients infected with VOC Alpha.
Collapse
Affiliation(s)
- Daniela Niemeyer
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Saskia Stenzel
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Talitha Veith
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Simon Schroeder
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Kirstin Friedmann
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Friderike Weege
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Julian Heinze
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Jackson Emanuel
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Kazmierski
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Fabian Pott
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Mark-Christian Jaboreck
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Beate Tenner
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Papies
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Walper
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Marie L. Schmidt
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Nicolas Heinemann
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Elisabeth Möncke-Buchner
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Morris Baumgardt
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Karen Hoffmann
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | | | - Anita Balázs
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jessica Schulze
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Christin Mache
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Terry C. Jones
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Morkel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, Berlin, Germany
- BIH Bioportal Single Cells, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Center for Infection Research, DZIF, Braunschweig, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt am Main, Germany
| | - Leif G. Hanitsch
- Institute of Medical Immunology, Charité — Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Marcus A. Mall
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Lung Research (DZL), associated partner Charité, Berlin, Germany
| | - Andreas C. Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern, Switzerland
| | - Klaus Osterrieder
- Berlin Institute of Health, Berlin, Germany
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Thorsten Wolff
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Victor M. Corman
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| |
Collapse
|
195
|
Vogt S, Feijs K, Hosch S, De Masi R, Lintermann R, Loll B, Wirthmueller L. The superior salinity tolerance of bread wheat cultivar Shanrong No. 3 is unlikely to be caused by elevated Ta-sro1 poly-(ADP-ribose) polymerase activity. Plant Cell 2022; 34:4130-4137. [PMID: 35980152 PMCID: PMC9614482 DOI: 10.1093/plcell/koac261] [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] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/16/2022] [Indexed: 05/02/2023]
Abstract
Structural and biochemical analyses demonstrate that the elevated salinity tolerance of bread wheat cultivar Shanrong No. 3 is unlikely to be caused by elevated Ta-sro1 poly(ADP-ribose) polymerase activity.
Collapse
Affiliation(s)
- Sarah Vogt
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Karla Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, 52074, Germany
| | - Sebastian Hosch
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Department of Plant Biochemistry, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin, 14195, Germany
| | - Raffaella De Masi
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Department of Plant Biochemistry, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin, 14195, Germany
| | - Ruth Lintermann
- Department of Plant Biochemistry, Freie Universität Berlin, Dahlem Centre of Plant Sciences, Berlin, 14195, Germany
| | - Bernhard Loll
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, 14195, Germany
| | | |
Collapse
|
196
|
Fischer S, Flis P, Zhao FJ, Salt DE. Transcriptional network underpinning ploidy-related elevated leaf potassium in neo-tetraploids. Plant Physiol 2022; 190:1715-1730. [PMID: 35929797 PMCID: PMC9614460 DOI: 10.1093/plphys/kiac360] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome duplication generates a tetraploid from a diploid. Newly created tetraploids (neo-tetraploids) of Arabidopsis (Arabidopsis thaliana) have elevated leaf potassium (K), compared to their diploid progenitor. Micro-grafting has previously established that this elevated leaf K is driven by processes within the root. Here, mutational analysis revealed that the K+-uptake transporters K+ TRANSPORTER 1 (AKT1) and HIGH AFFINITY K+ TRANSPORTER 5 (HAK5) are not necessary for the difference in leaf K caused by whole-genome duplication. However, the endodermis and salt overly sensitive and abscisic acid-related signaling were necessary for the elevated leaf K in neo-tetraploids. Contrasting the root transcriptomes of neo-tetraploid and diploid wild-type and mutants that suppress the neo-tetraploid elevated leaf K phenotype allowed us to identify a core set of 92 differentially expressed genes associated with the difference in leaf K between neo-tetraploids and their diploid progenitor. This core set of genes connected whole-genome duplication with the difference in leaf K between neo-tetraploids and their diploid progenitors. The set of genes is enriched in functions such as cell wall and Casparian strip development and ion transport in the endodermis, root hairs, and procambium. This gene set provides tools to test the intriguing idea of recreating the physiological effects of whole-genome duplication within a diploid genome.
Collapse
Affiliation(s)
- Sina Fischer
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | | |
Collapse
|
197
|
Demir S, Wolff G, Wieder A, Maida A, Bühler L, Brune M, Hautzinger O, Feuchtinger A, Poth T, Szendroedi J, Herzig S, Ekim Üstünel B. TSC22D4 interacts with Akt1 to regulate glucose metabolism. Sci Adv 2022; 8:eabo5555. [PMID: 36269831 PMCID: PMC9586482 DOI: 10.1126/sciadv.abo5555] [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] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 08/31/2022] [Indexed: 06/13/2023]
Abstract
Maladaptive insulin signaling is a key feature in the pathogenesis of severe metabolic disorders, including obesity and diabetes. Enhancing insulin sensitivity represents a major goal in the treatment of patients affected by diabetes. Here, we identify transforming growth factor-β1 stimulated clone 22 D4 (TSC22D4) as a novel interaction partner for protein kinase B/Akt1, a critical mediator of insulin/phosphatidylinositol 3-kinase signaling pathway. While energy deprivation and oxidative stress promote the TSC22D4-Akt1 interaction, refeeding mice or exposing cells to glucose and insulin impairs this interaction, which relies on an intrinsically disordered region (D2 domain) within TSC22D4. Functionally, the interaction with TSC22D4 reduces basal phosphorylation of Akt and its downstream targets during starvation, thereby promoting insulin sensitivity. Genetic, liver-specific reconstitution experiments in mice demonstrate that the interaction between TSC22D4 and Akt1 improves glucose handling and insulin sensitivity. Overall, our findings postulate a model whereby TSC22D4 acts as an environmental sensor and interacts with Akt1 to regulate insulin signaling and glucose metabolism.
Collapse
Affiliation(s)
- Sevgican Demir
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Gretchen Wolff
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Annika Wieder
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Adriano Maida
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Lea Bühler
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Maik Brune
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Oksana Hautzinger
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, German Research Center for Environmental Health, Institute of Pathology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Tanja Poth
- Center for Model System and Comparative Pathology (CMCP), Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Julia Szendroedi
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Stephan Herzig
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Bilgen Ekim Üstünel
- Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Diabetes Center, Helmholtz Center, Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| |
Collapse
|
198
|
Pérez Arévalo A, Lutz AK, Atanasova E, Boeckers TM. Trans-cardiac perfusion of neonatal mice and immunofluorescence of the whole body as a method to study nervous system development. PLoS One 2022; 17:e0275780. [PMID: 36227942 PMCID: PMC9560478 DOI: 10.1371/journal.pone.0275780] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
Whole animal perfusion is a well-established method that has been used for the past decades in multiple research fields. Particularly, it has been very important for the study of the brain. The rapid and uniform fixation of tissue is essential for the preservation of its integrity and the study of complex structures. For small tissue pieces submerging in formaldehyde solution oftentimes is sufficient to get a good fixation, larger tissues or organs with a more complicated structure present a greater difficulty. Here, we report the precise parameters to successfully perform trans-cardiac perfusion of neonatal mouse pups that allows a uniform fixation of the whole body for subsequent structural analysis and immunohistochemistry. In comparison to standard perfusion procedures of adult mice, changes in the pump velocity, the buffer volume and in the needle size lead to high quality fixation of neonatal mice pups. Further, we present a whole-body section staining, which results in a highly specific immunofluorescence signal suited for detailed analysis of multiple tissues or systems at the same time. Thus, our protocol provides a reproducible and reliable method for neonatal perfusion and staining that can rapidly be applied in any laboratory. It allows a high quality analysis of cellular structures and expression profiles at early developmental stages.
Collapse
Affiliation(s)
| | - Anne-Kathrin Lutz
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- * E-mail:
| | | | - Tobias M. Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ulm Site, Ulm, Germany
| |
Collapse
|
199
|
Marquet C, Heinzinger M, Olenyi T, Dallago C, Erckert K, Bernhofer M, Nechaev D, Rost B. Embeddings from protein language models predict conservation and variant effects. Hum Genet 2022; 141:1629-1647. [PMID: 34967936 PMCID: PMC8716573 DOI: 10.1007/s00439-021-02411-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 06/01/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
The emergence of SARS-CoV-2 variants stressed the demand for tools allowing to interpret the effect of single amino acid variants (SAVs) on protein function. While Deep Mutational Scanning (DMS) sets continue to expand our understanding of the mutational landscape of single proteins, the results continue to challenge analyses. Protein Language Models (pLMs) use the latest deep learning (DL) algorithms to leverage growing databases of protein sequences. These methods learn to predict missing or masked amino acids from the context of entire sequence regions. Here, we used pLM representations (embeddings) to predict sequence conservation and SAV effects without multiple sequence alignments (MSAs). Embeddings alone predicted residue conservation almost as accurately from single sequences as ConSeq using MSAs (two-state Matthews Correlation Coefficient-MCC-for ProtT5 embeddings of 0.596 ± 0.006 vs. 0.608 ± 0.006 for ConSeq). Inputting the conservation prediction along with BLOSUM62 substitution scores and pLM mask reconstruction probabilities into a simplistic logistic regression (LR) ensemble for Variant Effect Score Prediction without Alignments (VESPA) predicted SAV effect magnitude without any optimization on DMS data. Comparing predictions for a standard set of 39 DMS experiments to other methods (incl. ESM-1v, DeepSequence, and GEMME) revealed our approach as competitive with the state-of-the-art (SOTA) methods using MSA input. No method outperformed all others, neither consistently nor statistically significantly, independently of the performance measure applied (Spearman and Pearson correlation). Finally, we investigated binary effect predictions on DMS experiments for four human proteins. Overall, embedding-based methods have become competitive with methods relying on MSAs for SAV effect prediction at a fraction of the costs in computing/energy. Our method predicted SAV effects for the entire human proteome (~ 20 k proteins) within 40 min on one Nvidia Quadro RTX 8000. All methods and data sets are freely available for local and online execution through bioembeddings.com, https://github.com/Rostlab/VESPA , and PredictProtein.
Collapse
Affiliation(s)
- Céline Marquet
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany.
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany.
| | - Michael Heinzinger
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany
| | - Tobias Olenyi
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany
| | - Christian Dallago
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany
| | - Kyra Erckert
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany
| | - Michael Bernhofer
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany
| | - Dmitrii Nechaev
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology - i12, TUM-Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, Garching, 85748, Munich, Germany
- TUM School of Life Sciences Weihenstephan (TUM-WZW), Alte Akademie 8, Freising, Germany
| |
Collapse
|
200
|
Blankenagel S, Eggels S, Frey M, Grill E, Bauer E, Dawid C, Fernie AR, Haberer G, Hammerl R, Barbosa Medeiros D, Ouzunova M, Presterl T, Ruß V, Schäufele R, Schlüter U, Tardieu F, Urbany C, Urzinger S, Weber APM, Schön CC, Avramova V. Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize. Plant Cell 2022; 34:3860-3872. [PMID: 35792867 PMCID: PMC9520448 DOI: 10.1093/plcell/koac200] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Altering plant water use efficiency (WUE) is a promising approach for achieving sustainable crop production in changing climate scenarios. Here, we show that WUE can be tuned by alleles of a single gene discovered in elite maize (Zea mays) breeding material. Genetic dissection of a genomic region affecting WUE led to the identification of the gene ZmAbh4 as causative for the effect. CRISPR/Cas9-mediated ZmAbh4 inactivation increased WUE without growth reductions in well-watered conditions. ZmAbh4 encodes an enzyme that hydroxylates the phytohormone abscisic acid (ABA) and initiates its catabolism. Stomatal conductance is regulated by ABA and emerged as a major link between variation in WUE and discrimination against the heavy carbon isotope (Δ13C) during photosynthesis in the C4 crop maize. Changes in Δ13C persisted in kernel material, which offers an easy-to-screen proxy for WUE. Our results establish a direct physiological and genetic link between WUE and Δ13C through a single gene with potential applications in maize breeding.
Collapse
Affiliation(s)
| | | | - Monika Frey
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 2, 85354 Freising, Germany
| | - Erwin Grill
- Botany, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany
| | - Eva Bauer
- Campus Office, TUM School of Life Sciences, Technical University of Munich, Weihenstephaner Steig 22, 85354 Freising, Germany
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Alisdair R Fernie
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Richard Hammerl
- Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - David Barbosa Medeiros
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | | | | | - Victoria Ruß
- Botany, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany
| | - Rudi Schäufele
- Grassland, TUM School of Life Sciences, Technical University of Munich, Alte Akademie 12, 85654 Freising, Germany
| | - Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Francois Tardieu
- Université de Montpellier, INRAE, Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), Place Viala, F-34060, Montpellier, France
| | - Claude Urbany
- KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Sebastian Urzinger
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 2, 85354 Freising, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Chris-Carolin Schön
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 2, 85354 Freising, Germany
| | | |
Collapse
|