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Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
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Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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2
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Gierten J, Welz B, Fitzgerald T, Thumberger T, Hummel O, Leger A, Weber P, Hassel D, Hübner N, Birney E, Wittbrodt J. Natural genetic variation quantitatively regulates heart rate and dimension. bioRxiv 2023:2023.09.01.555906. [PMID: 37693611 PMCID: PMC10491305 DOI: 10.1101/2023.09.01.555906] [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] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The polygenic contribution to heart development and function along the health-disease continuum remains unresolved. To gain insight into the genetic basis of quantitative cardiac phenotypes, we utilize highly inbred Japanese rice fish models, Oryzias latipes, and Oryzias sakaizumii. Employing automated quantification of embryonic heart rates as core metric, we profiled phenotype variability across five inbred strains. We observed maximal phenotypic contrast between individuals of the HO5 and the HdrR strain. HO5 showed elevated heart rates associated with embryonic ventricular hypoplasia and impaired adult cardiac function. This contrast served as the basis for genome-wide mapping. In a segregation population of 1192 HO5 x HdrR F2 embryos, we mapped 59 loci (173 genes) associated with heart rate. Experimental validation of the top 12 candidate genes in loss-of-function models revealed their causal and distinct impact on heart rate, development, ventricle size, and arrhythmia. Our study uncovers new diagnostic and therapeutic targets for developmental and electrophysiological cardiac diseases and provides a novel scalable approach to investigate the intricate genetic architecture of the vertebrate heart.
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Affiliation(s)
- Jakob Gierten
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
- Department of Pediatric Cardiology, Heidelberg University Hospital; Heidelberg, 69120, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
| | - Bettina Welz
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University; Heidelberg, 69120, Germany
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Cambridge, CB10 1SD, UK
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
| | - Oliver Hummel
- Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC); Berlin, 13125, Germany
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Cambridge, CB10 1SD, UK
| | - Philipp Weber
- Department of Cardiology, Heidelberg University Hospital; Heidelberg, 69120, Germany
| | - David Hassel
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
- Department of Cardiology, Heidelberg University Hospital; Heidelberg, 69120, Germany
| | - Norbert Hübner
- Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC); Berlin, 13125, Germany
- Charité-Universitätsmedizin Berlin; Berlin, 10117, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Berlin, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI); Cambridge, CB10 1SD, UK
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University; Heidelberg, 69120, Germany
- German Centre for Cardiovascular Research (DZHK); Partner Site Heidelberg/Mannheim, Germany
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3
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Doering L, Cornean A, Thumberger T, Benjaminsen J, Wittbrodt B, Kellner T, Hammouda OT, Gorenflo M, Wittbrodt J, Gierten J. CRISPR-based knockout and base editing confirm the role of MYRF in heart development and congenital heart disease. Dis Model Mech 2023; 16:dmm049811. [PMID: 37584388 PMCID: PMC10445736 DOI: 10.1242/dmm.049811] [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: 08/01/2022] [Accepted: 07/21/2023] [Indexed: 08/17/2023] Open
Abstract
High-throughput DNA sequencing studies increasingly associate DNA variants with congenital heart disease (CHD). However, functional modeling is a crucial prerequisite for translating genomic data into clinical care. We used CRISPR-Cas9-mediated targeting of 12 candidate genes in the vertebrate model medaka (Oryzias latipes), five of which displayed a novel cardiovascular phenotype spectrum in F0 (crispants): mapre2, smg7, cdc42bpab, ankrd11 and myrf, encoding a transcription factor recently linked to cardiac-urogenital syndrome. Our myrf mutant line showed particularly prominent embryonic cardiac defects recapitulating phenotypes of pediatric patients, including hypoplastic ventricle. Mimicking human mutations, we edited three sites to generate specific myrf single-nucleotide variants via cytosine and adenine base editors. The Glu749Lys missense mutation in the conserved intramolecular chaperon autocleavage domain fully recapitulated the characteristic myrf mutant phenotype with high penetrance, underlining the crucial function of this protein domain. The efficiency and scalability of base editing to model specific point mutations accelerate gene validation studies and the generation of human-relevant disease models.
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Affiliation(s)
- Lino Doering
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Alex Cornean
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Joergen Benjaminsen
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Omar T. Hammouda
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Matthias Gorenflo
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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4
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Sokolova N, Zilova L, Wittbrodt J. Unravelling the link between embryogenesis and adult stem cell potential in the ciliary marginal zone: A comparative study between mammals and teleost fish. Cells Dev 2023; 174:203848. [PMID: 37172718 DOI: 10.1016/j.cdev.2023.203848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The discovery and study of adult stem cells have revolutionized regenerative medicine by offering new opportunities for treating various medical conditions. Anamniote stem cells, which retain their full proliferative capacity and full differentiation range throughout their lifetime, harbour a greater potential compared to mammalian adult stem cells, which only exhibit limited stem cell potential. Therefore, understanding the mechanisms underlying these differences is of significant interest. In this review, we examine the similarities and differences of adult retinal stem cells in anamniotes and mammals, from their embryonic stages in the optic vesicle to their residence in the postembryonic retinal stem cell niche, the ciliary marginal zone located in the retinal periphery. In anamniotes, developing precursors of retinal stem cells are exposed to various environmental cues during their migration in the complex morphogenetic remodelling of the optic vesicle to the optic cup. In contrast, their mammalian counterparts in the retinal periphery are primarily instructed by neighbouring tissues once they are in place. We explore the distinct modes of optic cup morphogenesis in mammals and teleost fish and highlight molecular mechanisms governing morphogenesis and stem cells instruction. The review concludes with the molecular mechanisms of ciliary marginal zone formation and offers a perspective on the impact of comparative single cell transcriptomic studies to reveal the evolutionary similarities and differences.
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Affiliation(s)
- Natalia Sokolova
- Centre for Organismal Studies Heidelberg, Germany; Heidelberg Biosciences International Graduate School, Germany
| | - Lucie Zilova
- Centre for Organismal Studies Heidelberg, Germany.
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5
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Medert R, Thumberger T, Tavhelidse-Suck T, Hub T, Kellner T, Oguchi Y, Dlugosz S, Zimmermann F, Wittbrodt J, Freichel M. Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice. Nucleic Acids Res 2023; 51:e14. [PMID: 36533445 PMCID: PMC10021492 DOI: 10.1093/nar/gkac1150] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 09/22/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based approaches have largely replaced conventional gene targeting strategies. However, homology-directed repair (HDR) in the mouse genome is not very efficient, and precisely inserting longer sequences using HDR remains challenging given that donor constructs preferentially integrate as concatemers. Here, we showed that injecting 5' biotinylated donor DNA into mouse embryos at the two-cell stage led to efficient single-copy HDR (scHDR) allele generation. Our dedicated genotyping strategy showed that these alleles occurred with frequencies of 19%, 20%, and 26% at three independent gene loci, indicating that scHDR was dramatically increased by 5' biotinylation. Thus, we suggest that the combination of a 5' biotinylated donor and diligent analysis of concatemer integration are prerequisites for efficiently and reliably generating conditional alleles or other large fragment knock-ins in the mouse genome.
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Affiliation(s)
- Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Tobias Hub
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yoko Oguchi
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Sascha Dlugosz
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Frank Zimmermann
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
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6
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Pakari K, Wittbrodt J, Thumberger T. De novo PAM generation to reach initially inaccessible target sites for base editing. Development 2023; 150:286701. [PMID: 36683434 PMCID: PMC10110497 DOI: 10.1242/dev.201115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023]
Abstract
Base editing by CRISPR crucially depends on the presence of a protospacer adjacent motif (PAM) at the correct distance from the editing site. Here, we present and validate an efficient one-shot approach termed 'inception' that expands the editing range. This is achieved by sequential, combinatorial base editing: de novo generated synonymous, non-synonymous or intronic PAM sites facilitate subsequent base editing at nucleotide positions that were initially inaccessible, further opening the targeting range of highly precise editing approaches. We demonstrate the applicability of the inception concept in medaka (Oryzias latipes) in three settings: loss of function, by introducing a pre-termination STOP codon in the open reading frame of oca2; locally confined multi-codon changes to generate allelic variants with different phenotypic severity in kcnh6a; and the removal of a splice acceptor site by targeting intronic sequences of rx3. Using sequentially acting base editors in the described combinatorial approach expands the number of accessible target sites by 65% on average. This allows the use of well-established tools with NGG PAM recognition for the establishment of thus far unreachable disease models, for hypomorphic allele studies and for efficient targeted mechanistic investigations in a precise and predictable manner.
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Affiliation(s)
- Kaisa Pakari
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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7
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Heilig AK, Nakamura R, Shimada A, Hashimoto Y, Nakamura Y, Wittbrodt J, Takeda H, Kawanishi T. Wnt11 acts on dermomyotome cells to guide epaxial myotome morphogenesis. eLife 2022; 11:71845. [PMID: 35522214 PMCID: PMC9075960 DOI: 10.7554/elife.71845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/19/2022] [Indexed: 12/30/2022] Open
Abstract
The dorsal axial muscles, or epaxial muscles, are a fundamental structure covering the spinal cord and vertebrae, as well as mobilizing the vertebrate trunk. To date, mechanisms underlying the morphogenetic process shaping the epaxial myotome are largely unknown. To address this, we used the medaka zic1/zic4-enhancer mutant Double anal fin (Da), which exhibits ventralized dorsal trunk structures resulting in impaired epaxial myotome morphology and incomplete coverage over the neural tube. In wild type, dorsal dermomyotome (DM) cells reduce their proliferative activity after somitogenesis. Subsequently, a subset of DM cells, which does not differentiate into the myotome population, begins to form unique large protrusions extending dorsally to guide the epaxial myotome dorsally. In Da, by contrast, DM cells maintain the high proliferative activity and mainly form small protrusions. By combining RNA- and ChIP-sequencing analyses, we revealed direct targets of Zic1, which are specifically expressed in dorsal somites and involved in various aspects of development, such as cell migration, extracellular matrix organization, and cell-cell communication. Among these, we identified wnt11 as a crucial factor regulating both cell proliferation and protrusive activity of DM cells. We propose that dorsal extension of the epaxial myotome is guided by a non-myogenic subpopulation of DM cells and that wnt11 empowers the DM cells to drive the coverage of the neural tube by the epaxial myotome.
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Affiliation(s)
- Ann Kathrin Heilig
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.,Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yuka Hashimoto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yuta Nakamura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Toru Kawanishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
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Cornean A, Gierten J, Welz B, Mateo JL, Thumberger T, Wittbrodt J. Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. eLife 2022; 11:72124. [PMID: 35373735 PMCID: PMC9033269 DOI: 10.7554/elife.72124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide variants (SNVs) are prevalent genetic factors shaping individual trait profiles and disease susceptibility. The recent development and optimizations of base editors, rubber and pencil genome editing tools now promise to enable direct functional assessment of SNVs in model organisms. However, the lack of bioinformatic tools aiding target prediction limits the application of base editing in vivo. Here, we provide a framework for adenine and cytosine base editing in medaka (Oryzias latipes) and zebrafish (Danio rerio), ideal for scalable validation studies. We developed an online base editing tool ACEofBASEs (a careful evaluation of base-edits), to facilitate decision-making by streamlining sgRNA design and performing off-target evaluation. We used state-of-the-art adenine (ABE) and cytosine base editors (CBE) in medaka and zebrafish to edit eye pigmentation genes and transgenic GFP function with high efficiencies. Base editing in the genes encoding troponin T and the potassium channel ERG faithfully recreated known cardiac phenotypes. Deep-sequencing of alleles revealed the abundance of intended edits in comparison to low levels of insertion or deletion (indel) events for ABE8e and evoBE4max. We finally validated missense mutations in novel candidate genes of congenital heart disease (CHD) dapk3, ube2b, usp44, and ptpn11 in F0 and F1 for a subset of these target genes with genotype-phenotype correlation. This base editing framework applies to a wide range of SNV-susceptible traits accessible in fish, facilitating straight-forward candidate validation and prioritization for detailed mechanistic downstream studies. DNA contains sequences of four different molecules known as bases that represent our genetic code. In a mutation called a single nucleotide variant (or SNV for short), a single base in the sequence is swapped for another base. This can lead the individual carrying this SNV to produce a slightly different version of a protein to that found in other people. This slightly different protein may not work properly, or may perform a different task. In recent years, researchers have identified thousands of SNVs in humans linked with congenital heart diseases, but the roles of many of these SNVs remain unclear. Tools known as base editors allow researchers to efficiently modify single bases in DNA. Base editors use molecules known as short guide RNAs (or sgRNAs for short) to direct enzymes to specific positions in the DNA to swap, delete or insert a base. The sgRNAs need to be carefully designed to target the correct bases, however, which is a time consuming process. Furthermore, base editors were developed in cells grown in laboratories and so far only a few studies have demonstrated how they could be used in living animals. To overcome these limitations, Cornean, Gierten, Welz et al. developed a framework for base editing in two species of fish that are often used as models in research, namely medaka and zebrafish. The framework uses existing base editors that swap individual target bases and a new online tool – referred to as ACEofBASEs – to help design the required sgRNAs. The team were able to use the framework to characterize the medaka equivalents of four SNVs that have been previously associated with congenital heart disease in humans. The new framework developed here will help researchers to investigate the roles of SNVs in fish and other animals and validate human disease candidates. This approach could also be used to study the various ways that cells modify proteins by changing the specific bases involved in such modifications.
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Affiliation(s)
- Alex Cornean
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Juan Luis Mateo
- Deparment of Computer Science, University of Oviedo, Oviedo, Spain
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Aghaallaei N, Agarwal R, Benjaminsen J, Lust K, Bajoghli B, Wittbrodt J, Feijoo CG. Antigen-Presenting Cells and T Cells Interact in a Specific Area of the Intestinal Mucosa Defined by the Ccl25-Ccr9 Axis in Medaka. Front Immunol 2022; 13:812899. [PMID: 35185906 PMCID: PMC8853713 DOI: 10.3389/fimmu.2022.812899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/10/2022] [Indexed: 11/21/2022] Open
Abstract
Organized intestinal mucosal immune response appears to be restricted to tetrapods. In teleost fish, there is no evidence for the existence of a particular intestinal region that facilitates the interaction of antigen-presenting cells (APCs) and T cells, such as secondary lymphoid organs. Indeed, despite their importance in the defense against pathogens, the location and manner of APC-T cell interaction within the fish gut is unknown. Here, using non-invasive live imaging of newly developed transgenic reporter lines, we addressed the spatial organization and behavior of APCs and T cells in the intestine of medaka fish both during homeostasis and inflammation. We report that Ccr9a+ T cells are recruited to a band in the lamina propria next to the muscularis mucosa in which Ccl25-expressing cells are present. Ccr9a+ T cells contact APCs for several minutes, in a process mediated by connexin 43. This type of interaction was observed in homeostasis and inflammation, with the interaction being longer and more frequent during inflammation. Thus, our results demonstrate that the mucosal immune response in the intestine of medaka is organized and endowed with a specific region with specialized microenvironment and function.
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Affiliation(s)
- Narges Aghaallaei
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Rashi Agarwal
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Joergen Benjaminsen
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Katharina Lust
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Baubak Bajoghli
- Directors' Research Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Carmen G Feijoo
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.,Departamento de Ciencias Biologicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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10
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Thumberger T, Tavhelidse-Suck T, Gutierrez-Triana JA, Cornean A, Medert R, Welz B, Freichel M, Wittbrodt J. Boosting targeted genome editing using the hei-tag. eLife 2022; 11:70558. [PMID: 35333175 PMCID: PMC9068219 DOI: 10.7554/elife.70558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Precise, targeted genome editing by CRISPR/Cas9 is key for basic research and translational approaches in model and non-model systems. While active in all species tested so far, editing efficiencies still leave room for improvement. The bacterial Cas9 needs to be efficiently shuttled into the nucleus as attempted by fusion with nuclear localization signals (NLSs). Additional peptide tags such as FLAG- or myc-tags are usually added for immediate detection or straightforward purification. Immediate activity is usually granted by administration of preassembled protein/RNA complexes. We present the ‘hei-tag (high efficiency-tag)’ which boosts the activity of CRISPR/Cas genome editing tools already when supplied as mRNA. The addition of the hei-tag, a myc-tag coupled to an optimized NLS via a flexible linker, to Cas9 or a C-to-T (cytosine-to-thymine) base editor dramatically enhances the respective targeting efficiency. This results in an increase in bi-allelic editing, yet reduction of allele variance, indicating an immediate activity even at early developmental stages. The hei-tag boost is active in model systems ranging from fish to mammals, including tissue culture applications. The simple addition of the hei-tag allows to instantly upgrade existing and potentially highly adapted systems as well as to establish novel highly efficient tools immediately applicable at the mRNA level. The genetic code stored within DNA provides cells with the instructions they need to carry out their role in the body. Any changes to these genes, or the DNA sequence around them, has the potential to completely alter how a cell behaves. Scientists have developed various tools that allow them to experimentally modify the genome of cells or even entire living organisms. This includes the popular Cas9 enzyme which cuts DNA at specific sites, and base editors which can precisely change bits of genetic code without cutting DNA. While there are lots of Cas9 enzymes and base editors currently available, these often differ greatly in their activity depending on which cell type or organism they are applied to. Finding a tool that can effectively modify the genome of an organism at the right time during development also poses a challenge. All the cells in an organism arise from a single fertilized cell. If this cell is genetically edited, all its subsequent daughter cells (which make up the entire organism) will contain the genetic modification. However, most genome editing tools only work efficiently later in development, resulting in an undesirable mosaic organism composed of both edited and non-edited cells. Here, Thumberger et al. have developed a new ‘high efficiency-tag’ (also known as hei-tag for short) that can enhance the activity of gene editing tools and overcome this barrier. The tag improves the efficiency of gene editing by immediately shuttling a Cas9 enzyme to the nucleus, the cellular compartment that stores DNA. In all cases, gene editing tools with hei-tag worked better than those without in fish embryos and mouse cells grown in the laboratory. When Cas9 enzymes connected to a hei-tag were injected into the first fertilized cell of a fish embryo, this resulted in an even distribution of edited genes spread throughout the whole organism. To understand how a gene affects an organism, researchers need to be able to edit it as early in development as possible. Attaching the ‘hei-tag’ to already available tools could help boost their activity and make them more efficient. It could also allow advances in medical research aimed at replacing faulty genes with fully functioning ones.
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Affiliation(s)
- Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | | | - Alex Cornean
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Rebekka Medert
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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11
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Leger A, Brettell I, Monahan J, Barton C, Wolf N, Kusminski N, Herder C, Aadepu N, Becker C, Gierten J, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tavhelidse T, Thumberger T, Tsingos E, Watson P, Welz B, Naruse K, Loosli F, Wittbrodt J, Birney E, Fitzgerald T. Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 2022; 23:58. [PMID: 35189951 PMCID: PMC8862245 DOI: 10.1186/s13059-022-02602-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals. RESULTS We exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines. CONCLUSIONS We present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches.
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Affiliation(s)
- Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Brettell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jack Monahan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carl Barton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadeshda Wolf
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Natalja Kusminski
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Cathrin Herder
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Narendar Aadepu
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.,Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Clara Becker
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Omar T Hammouda
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Eva Hasel
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Colin Lischik
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Katharina Lust
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Risa Suzuki
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Philip Watson
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Kiyoshi Naruse
- National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan
| | - Felix Loosli
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, University of Heidelberg, Campus Im Neuenheimer Feld, Heidelberg, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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12
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Fitzgerald T, Brettell I, Leger A, Wolf N, Kusminski N, Monahan J, Barton C, Herder C, Aadepu N, Gierten J, Becker C, Hammouda OT, Hasel E, Lischik C, Lust K, Sokolova N, Suzuki R, Tsingos E, Tavhelidse T, Thumberger T, Watson P, Welz B, Khouja N, Naruse K, Birney E, Wittbrodt J, Loosli F. The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 2022; 23:59. [PMID: 35189950 PMCID: PMC8862526 DOI: 10.1186/s13059-022-02623-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic. To address this, we establish a vertebrate genetic resource specifically to allow for robust genotype-to-phenotype investigations. The teleost medaka (Oryzias latipes) is an established genetic model system with a long history of genetic research and a high tolerance to inbreeding from the wild. Results Here we present the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel: the first near-isogenic panel of 80 inbred lines in a vertebrate model derived from a wild founder population. Inbred lines provide fixed genomes that are a prerequisite for the replication of studies, studies which vary both the genetics and environment in a controlled manner, and functional testing. The MIKK panel will therefore enable phenotype-to-genotype association studies of complex genetic traits while allowing for careful control of interacting factors, with numerous applications in genetic research, human health, drug development, and fundamental biology. Conclusions Here we present a detailed characterization of the genetic variation across the MIKK panel, which provides a rich and unique genetic resource to the community by enabling large-scale experiments for mapping complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02623-z.
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Affiliation(s)
- Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Brettell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadeshda Wolf
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Natalja Kusminski
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Jack Monahan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carl Barton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cathrin Herder
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Narendar Aadepu
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.,Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Clara Becker
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Omar T Hammouda
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Eva Hasel
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Colin Lischik
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Risa Suzuki
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Philip Watson
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Nadia Khouja
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Kiyoshi Naruse
- National Institute for Basic Biology, Laboratory of Bioresources, Okazaki, Japan
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Campus Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Felix Loosli
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany.
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13
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Aghaallaei N, Inoue D, Hasel de Carvalho E, Dick AM, Wittbrodt J, Leptin M, Bajoghli B. Notch1 deficiency alters the migratory behavior of developing T cells and calcium signaling in the thymus of medaka. Eur J Immunol 2021; 52:261-269. [PMID: 34731490 DOI: 10.1002/eji.202149512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/13/2021] [Accepted: 10/29/2021] [Indexed: 12/18/2022]
Abstract
The differentiation of T cells from lymphoid progenitors in the thymus follows sequential developmental stages that constantly require interaction with thymic epithelial cells. Several distinct aspects of early T cell development depend on the activation of Notch receptors on thymocytes, while the selection of thymocytes at later stages are believed to be Notch independent. Using reverse genetic approaches and whole-thymus live imaging in an in vivo teleost model, the medaka, we report that Notch1 signals is required for proliferation and specification of developing T cells as well as involved in their selection in the thymus. We reveal that Notch1 controls the migratory behavior of thymocytes through controlling the chemokine receptor Ccr9b and thereby influence the T cell receptor (TCR) activation. Hence, we propose that, in lower vertebrates, the function of Notch signaling extends to all stages of T cell development, except when thymocytes undergo TCRβ rearrangement.
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Affiliation(s)
- Narges Aghaallaei
- Department of Hematology, Oncology, Immunology, and Rheumatology, University Hospital of Tübingen, Tübingen, Germany.,Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Daigo Inoue
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | | | - Advaita M Dick
- Department of Hematology, Oncology, Immunology, and Rheumatology, University Hospital of Tübingen, Tübingen, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Maria Leptin
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,EMBO, Heidelberg, Germany
| | - Baubak Bajoghli
- Department of Hematology, Oncology, Immunology, and Rheumatology, University Hospital of Tübingen, Tübingen, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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14
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Zilova L, Weinhardt V, Tavhelidse T, Schlagheck C, Thumberger T, Wittbrodt J. Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. eLife 2021; 10:e66998. [PMID: 34252023 PMCID: PMC8275126 DOI: 10.7554/elife.66998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Mammalian organoids are however limited by long developmental time, variable success, and lack of direct comparison to an in vivo reference. To overcome these limitations and address species-specific cellular organization, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic pluripotent cells from medaka and zebrafish efficiently assemble into anterior neural structures, particularly retina. Within 4 days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis, and differentiation. The number of aggregated cells and genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting the in vivo situation. High efficiency and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematic probing of impact of the physical environment on morphogenesis and differentiation.
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Affiliation(s)
- Lucie Zilova
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Venera Weinhardt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Christina Schlagheck
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
- Heidelberg International Biosciences Graduate School HBIGS and HeiKa Graduate School on “Functional Materials”HeidelbergGermany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
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15
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Aghaallaei N, Dick AM, Tsingos E, Inoue D, Hasel E, Thumberger T, Toyoda A, Leptin M, Wittbrodt J, Bajoghli B. αβ/γδ T cell lineage outcome is regulated by intrathymic cell localization and environmental signals. Sci Adv 2021; 7:7/29/eabg3613. [PMID: 34261656 PMCID: PMC8279519 DOI: 10.1126/sciadv.abg3613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/28/2021] [Indexed: 05/07/2023]
Abstract
αβ and γδ T cells are two distinct sublineages that develop in the vertebrate thymus. Thus far, their differentiation from a common progenitor is mostly understood to be regulated by intrinsic mechanisms. However, the proportion of αβ/γδ T cells varies in different vertebrate taxa. How this process is regulated in species that tend to produce a high frequency of γδ T cells is unstudied. Using an in vivo teleost model, the medaka, we report that progenitors first enter a thymic niche where their development into γδ T cells is favored. Translocation from this niche, mediated by chemokine receptor Ccr9b, is a prerequisite for their differentiation into αβ T cells. On the other hand, the thymic niche also generates opposing gradients of the cytokine interleukin-7 and chemokine Ccl25a, and, together, they influence the lineage outcome. We propose a previously unknown mechanism that determines the proportion of αβ/γδ lineages within species.
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Affiliation(s)
- Narges Aghaallaei
- Department of Hematology, Oncology, Immunology, and Rheumatology, University Hospital of Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Advaita M Dick
- Department of Hematology, Oncology, Immunology, and Rheumatology, University Hospital of Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Erika Tsingos
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Daigo Inoue
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Eva Hasel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Maria Leptin
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- EMBO, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Baubak Bajoghli
- Department of Hematology, Oncology, Immunology, and Rheumatology, University Hospital of Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany.
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
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16
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Gücüm S, Sakson R, Hoffmann M, Grote V, Becker C, Pakari K, Beedgen L, Thiel C, Rapp E, Ruppert T, Thumberger T, Wittbrodt J. A patient-based medaka alg2 mutant as a model for hypo-N-glycosylation. Development 2021; 148:269015. [PMID: 34106226 PMCID: PMC8217707 DOI: 10.1242/dev.199385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022]
Abstract
Defects in the evolutionarily conserved protein-glycosylation machinery during embryonic development are often fatal. Consequently, congenital disorders of glycosylation (CDG) in human are rare. We modelled a putative hypomorphic mutation described in an alpha-1,3/1,6-mannosyltransferase (ALG2) index patient (ALG2-CDG) to address the developmental consequences in the teleost medaka (Oryzias latipes). We observed specific, multisystemic, late-onset phenotypes, closely resembling the patient's syndrome, prominently in the facial skeleton and in neuronal tissue. Molecularly, we detected reduced levels of N-glycans in medaka and in the patient's fibroblasts. This hypo-N-glycosylation prominently affected protein abundance. Proteins of the basic glycosylation and glycoprotein-processing machinery were over-represented in a compensatory response, highlighting the regulatory topology of the network. Proteins of the retinal phototransduction machinery, conversely, were massively under-represented in the alg2 model. These deficiencies relate to a specific failure to maintain rod photoreceptors, resulting in retinitis pigmentosa characterized by the progressive loss of these photoreceptors. Our work has explored only the tip of the iceberg of N-glycosylation-sensitive proteins, the function of which specifically impacts on cells, tissues and organs. Taking advantage of the well-described human mutation has allowed the complex interplay of N-glycosylated proteins and their contribution to development and disease to be addressed.
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Affiliation(s)
- Sevinç Gücüm
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.,HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany
| | - Roman Sakson
- HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany.,Core facility for Mass Spectrometry and Proteomics, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Valerian Grote
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Clara Becker
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Kaisa Pakari
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Lars Beedgen
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany.,glyXera GmbH, 39120 Magdeburg, Germany
| | - Thomas Ruppert
- Core facility for Mass Spectrometry and Proteomics, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- COS, Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
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17
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Cirksena K, Hütte HJ, Shcherbakova A, Thumberger T, Sakson R, Weiss S, Jensen LR, Friedrich A, Todt D, Kuss AW, Ruppert T, Wittbrodt J, Bakker H, Buettner FFR. The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development. Mol Cell Proteomics 2021; 20:100092. [PMID: 33975020 PMCID: PMC8256286 DOI: 10.1016/j.mcpro.2021.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
C-mannosylation is a modification of tryptophan residues with a single mannose and can affect protein folding, secretion, and/or function. To date, only a few proteins have been demonstrated to be C-mannosylated, and studies that globally assess protein C-mannosylation are scarce. To interrogate the C-mannosylome of human induced pluripotent stem cells, we compared the secretomes of CRISPR–Cas9 mutants lacking either the C-mannosyltransferase DPY19L1 or DPY19L3 to WT human induced pluripotent stem cells using MS-based quantitative proteomics. The secretion of numerous proteins was reduced in these mutants, including that of A Disintegrin And Metalloproteinase with ThromboSpondin Motifs 16 (ADAMTS16), an extracellular protease that was previously reported to be essential for optic fissure fusion in zebrafish eye development. To test the functional relevance of this observation, we targeted dpy19l1 or dpy19l3 in embryos of the Japanese rice fish medaka (Oryzias latipes) by CRISPR–Cas9. We observed that targeting of dpy19l3 partially caused defects in optic fissure fusion, called coloboma. We further showed in a cellular model that DPY19L1 and DPY19L3 mediate C-mannosylation of a recombinantly expressed thrombospondin type 1 repeat of ADAMTS16 and thereby support its secretion. Taken together, our findings imply that DPY19L3-mediated C-mannosylation is involved in eye development by assisting secretion of the extracellular protease ADAMTS16. TSR1 of ADAMTS16 can be C-mannosylated. Deletion of DPY19L1 or DPY19L3 in hiPSCs caused reduced secretion of ADAMTS16. Targeting of dpy19l3 in medaka occasionally led to coloboma.
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Affiliation(s)
- Karsten Cirksena
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hermann J Hütte
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | | | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Stefan Weiss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Riff Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alina Friedrich
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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18
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Wagner N, Beuttenmueller F, Norlin N, Gierten J, Boffi JC, Wittbrodt J, Weigert M, Hufnagel L, Prevedel R, Kreshuk A. Deep learning-enhanced light-field imaging with continuous validation. Nat Methods 2021; 18:557-563. [PMID: 33963344 DOI: 10.1038/s41592-021-01136-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 04/01/2021] [Indexed: 12/17/2022]
Abstract
Visualizing dynamic processes over large, three-dimensional fields of view at high speed is essential for many applications in the life sciences. Light-field microscopy (LFM) has emerged as a tool for fast volumetric image acquisition, but its effective throughput and widespread use in biology has been hampered by a computationally demanding and artifact-prone image reconstruction process. Here, we present a framework for artificial intelligence-enhanced microscopy, integrating a hybrid light-field light-sheet microscope and deep learning-based volume reconstruction. In our approach, concomitantly acquired, high-resolution two-dimensional light-sheet images continuously serve as training data and validation for the convolutional neural network reconstructing the raw LFM data during extended volumetric time-lapse imaging experiments. Our network delivers high-quality three-dimensional reconstructions at video-rate throughput, which can be further refined based on the high-resolution light-sheet images. We demonstrate the capabilities of our approach by imaging medaka heart dynamics and zebrafish neural activity with volumetric imaging rates up to 100 Hz.
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Affiliation(s)
- Nils Wagner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Informatics, Technical University of Munich, Garching, Germany.,Munich School for Data Science (MUDS), Munich, Germany
| | - Fynn Beuttenmueller
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nils Norlin
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Experimental Medical Science, Lund University, Lund, Sweden.,Lund Bioimaging Centre, Lund University, Lund, Sweden
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Juan Carlos Boffi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Martin Weigert
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy. .,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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19
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Becker C, Lust K, Wittbrodt J. Igf signaling couples retina growth with body growth by modulating progenitor cell division. Development 2021; 148:dev.199133. [PMID: 33722901 PMCID: PMC8077508 DOI: 10.1242/dev.199133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/04/2021] [Indexed: 12/19/2022]
Abstract
How the body and organs balance their relative growth is of key importance for coordinating size and function. This is of particular relevance in organisms, which continue to grow over their entire life span. We addressed this issue in the neuroretina of medaka fish (Oryzias latipes), a well-studied system with which to address vertebrate organ growth. We reveal that a central growth regulator, Igf1 receptor (Igf1r), is necessary and sufficient for proliferation control in the postembryonic retinal stem cell niche: the ciliary marginal zone (CMZ). Targeted activation of Igf1r signaling in the CMZ uncouples neuroretina growth from body size control, and we demonstrate that Igf1r operates on progenitor cells, stimulating their proliferation. Activation of Igf1r signaling increases retinal size while preserving its structural integrity, revealing a modular organization in which progenitor differentiation and neurogenesis are self-organized and highly regulated. Our findings position Igf signaling as a key module for controlling retinal size and composition, with important evolutionary implications. Highlighted Article: Targeted activation of Igf1r signaling in the retinal stem cell niche increases retina size through expanding the progenitor but not stem cell population.
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Affiliation(s)
- Clara Becker
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg 69120, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
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20
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Bosze B, Ono Y, Mattes B, Sinner C, Gourain V, Thumberger T, Tlili S, Wittbrodt J, Saunders TE, Strähle U, Schug A, Scholpp S. Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish. Histochem Cell Biol 2020; 154:463-480. [PMID: 32488346 PMCID: PMC7609436 DOI: 10.1007/s00418-020-01887-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2020] [Indexed: 01/07/2023]
Abstract
The notochord defines the axial structure of all vertebrates during development. Notogenesis is a result of major cell reorganization in the mesoderm, the convergence and the extension of the axial cells. However, it is currently not fully understood how these processes act together in a coordinated way during notochord formation. The prechordal plate is an actively migrating cell population in the central mesoderm anterior to the trailing notochordal plate cells. We show that prechordal plate cells express Protocadherin 18a (Pcdh18a), a member of the cadherin superfamily. We find that Pcdh18a-mediated recycling of E-cadherin adhesion complexes transforms prechordal plate cells into a cohesive and fast migrating cell group. In turn, the prechordal plate cells subsequently instruct the trailing mesoderm. We simulated cell migration during early mesoderm formation using a lattice-based mathematical framework and predicted that the requirement for an anterior, local motile cell cluster could guide the intercalation and extension of the posterior, axial cells. Indeed, a grafting experiment validated the prediction and local Pcdh18a expression induced an ectopic prechordal plate-like cell group migrating towards the animal pole. Our findings indicate that the Pcdh18a is important for prechordal plate formation, which influences the trailing mesodermal cell sheet by orchestrating the morphogenesis of the notochord.
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Affiliation(s)
- Bernadett Bosze
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | - Yosuke Ono
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Benjamin Mattes
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Claude Sinner
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76021, Germany.,Department of Physics, Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | - Victor Gourain
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Sham Tlili
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Timothy E Saunders
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.,Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76021, Germany
| | - Steffen Scholpp
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76021, Karlsruhe, Germany. .,Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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21
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Eckert P, Knickmeyer MD, Schütz L, Wittbrodt J, Heermann S. Morphogenesis and axis specification occur in parallel during optic cup and optic fissure formation, differentially modulated by BMP and Wnt. Open Biol 2020; 9:180179. [PMID: 30958096 PMCID: PMC6395882 DOI: 10.1098/rsob.180179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Optic cup morphogenesis is an intricate process. Especially, the formation of the optic fissure is not well understood. Persisting optic fissures, termed coloboma, are frequent causes for congenital blindness. Even though the defective fusion of the fissure margins is the most acknowledged reason for coloboma, highly variable morphologies of coloboma phenotypes argue for a diverse set of underlying pathomechanisms. Here, we investigate optic fissure morphogenesis in zebrafish to identify potential morphogenetic defects resulting in coloboma. We show that the formation of the optic fissure depends on tissue flow movements, integrated into the bilateral distal epithelial flow forming the optic cup. On the temporal side, the distal flow translates into a ventral perpendicular flow, shaping the temporal fissure margin. On the nasal side, however, the distal flow is complemented by tissue derived from the optic stalk, shaping the nasal fissure margin. Notably, a distinct population of TGFβ-signalling positive cells is translocated from the optic stalk into both fissure margins. Furthermore, we show that induced BMP signalling as well as Wnt-signalling inhibition result in morphogenetic defects of the optic fissure. Our data also indicate that morphogenesis is crucial for a proper positioning of pre-specified dorsal–ventral optic cup domains.
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Affiliation(s)
- Priska Eckert
- 1 Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg , 79104 Freiburg , Germany.,2 Faculty of Biology, University of Freiburg , Schaenzlestrasse 1, 79104 Freiburg , Germany
| | - Max D Knickmeyer
- 1 Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg , 79104 Freiburg , Germany.,2 Faculty of Biology, University of Freiburg , Schaenzlestrasse 1, 79104 Freiburg , Germany
| | - Lucas Schütz
- 3 Centre for Organismal Studies, Heidelberg University , 69120 Heidelberg , Germany
| | - Joachim Wittbrodt
- 3 Centre for Organismal Studies, Heidelberg University , 69120 Heidelberg , Germany
| | - Stephan Heermann
- 1 Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg , 79104 Freiburg , Germany
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22
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Gierten J, Fitzgerald T, Loosli F, Gorenflo M, Birney E, Wittbrodt J. Genome-Wide Analysis of Polygenic Cardiac Traits in Medaka Inbred Strains. Thorac Cardiovasc Surg 2020. [DOI: 10.1055/s-0040-1705539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Dasyani M, Tan WH, Sundaram S, Imangali N, Centanin L, Wittbrodt J, Winkler C. Lineage tracing of col10a1 cells identifies distinct progenitor populations for osteoblasts and joint cells in the regenerating fin of medaka (Oryzias latipes). Dev Biol 2019; 455:85-99. [DOI: 10.1016/j.ydbio.2019.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 06/30/2019] [Accepted: 07/16/2019] [Indexed: 01/24/2023]
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24
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Vázquez-Marín J, Gutiérrez-Triana JA, Almuedo-Castillo M, Buono L, Gómez-Skarmeta JL, Mateo JL, Wittbrodt J, Martínez-Morales JR. yap1b, a divergent Yap/Taz family member, cooperates with yap1 in survival and morphogenesis via common transcriptional targets. Development 2019; 146:dev.173286. [PMID: 31142542 DOI: 10.1242/dev.173286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/17/2019] [Indexed: 11/20/2022]
Abstract
Yap1/Taz are well-known Hippo effectors triggering complex transcriptional programs controlling growth, survival and cancer progression. Here, we describe yap1b, a new Yap1/Taz family member with a unique transcriptional activation domain that cannot be phosphorylated by Src/Yes kinases. We show that yap1b evolved specifically in euteleosts (i.e. including medaka but not zebrafish) by duplication and adaptation of yap1. Using DamID-seq, we generated maps of chromatin occupancy for Yap1, Taz (Wwtr1) and Yap1b in gastrulating zebrafish and medaka embryos. Our comparative analyses uncover the genetic programs controlled by Yap family proteins during early embryogenesis, and show largely overlapping targets for Yap1 and Yap1b. CRISPR/Cas9-induced mutation of yap1b in medaka does not result in an overt phenotype during embryogenesis or adulthood. However, yap1b mutation strongly enhances the embryonic malformations observed in yap1 mutants. Thus yap1 -/-; yap1b -/- double mutants display more severe body flattening, eye misshaping and increased apoptosis than yap1 -/- single mutants, thus revealing overlapping gene functions. Our results indicate that, despite its divergent transactivation domain, Yap1b cooperates with Yap1 to regulate cell survival and tissue morphogenesis during early development.
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Affiliation(s)
| | - José Arturo Gutiérrez-Triana
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.,Escuela de Microbiología, Facultad de la Salud, Universidad Industrial de Santander, Bucaramanga, 680002, Colombia
| | | | - Lorena Buono
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), 41013 Seville, Spain
| | | | - Juan Luis Mateo
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.,Departamento de Informática, Universidad de Oviedo, Oviedo 33005, Spain
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
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25
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Wagner N, Norlin N, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R. Instantaneous isotropic volumetric imaging of fast biological processes. Nat Methods 2019; 16:497-500. [PMID: 31036959 DOI: 10.1038/s41592-019-0393-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/05/2019] [Indexed: 11/09/2022]
Abstract
To capture highly dynamic biological processes at cellular resolution is a recurring challenge in biology. Here we show that combining selective-volume illumination with simultaneous acquisition of orthogonal light fields yields three-dimensional images with high, isotropic spatial resolution and a significant reduction of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate medaka heart and blood flow imaging at single-cell resolution and free of motion artefacts at volume rates of up to 200 Hz.
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Affiliation(s)
- Nils Wagner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nils Norlin
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Gustavo de Medeiros
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Bálint Balázs
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy.
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26
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Knickmeyer MD, Mateo JL, Eckert P, Roussa E, Rahhal B, Zuniga A, Krieglstein K, Wittbrodt J, Heermann S. TGFβ-facilitated optic fissure fusion and the role of bone morphogenetic protein antagonism. Open Biol 2019; 8:rsob.170134. [PMID: 29593116 PMCID: PMC5881030 DOI: 10.1098/rsob.170134] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/02/2018] [Indexed: 12/25/2022] Open
Abstract
The optic fissure is a transient gap in the developing vertebrate eye, which must be closed as development proceeds. A persisting optic fissure, coloboma, is a major cause for blindness in children. Although many genes have been linked to coloboma, the process of optic fissure fusion is still little appreciated, especially on a molecular level. We identified a coloboma in mice with a targeted inactivation of transforming growth factor β2 (TGFβ2). Notably, here the optic fissure margins must have touched, however failed to fuse. Transcriptomic analyses indicated an effect on remodelling of the extracellular matrix (ECM) as an underlying mechanism. TGFβ signalling is well known for its effect on ECM remodelling, but it is at the same time often inhibited by bone morphogenetic protein (BMP) signalling. Notably, we also identified two BMP antagonists among the downregulated genes. For further functional analyses we made use of zebrafish, in which we found TGFβ ligands expressed in the developing eye, and the ligand binding receptor in the optic fissure margins where we also found active TGFβ signalling and, notably, also gremlin 2b (grem2b) and follistatin a (fsta), homologues of the regulated BMP antagonists. We hypothesized that TGFβ is locally inducing expression of BMP antagonists within the margins to relieve the inhibition from its regulatory capacity regarding ECM remodelling. We tested our hypothesis and found that induced BMP expression is sufficient to inhibit optic fissure fusion, resulting in coloboma. Our findings can likely be applied also to other fusion processes, especially when TGFβ signalling or BMP antagonism is involved, as in fusion processes during orofacial development.
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Affiliation(s)
- Max D Knickmeyer
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, Freiburg D-79104, Germany
| | - Juan L Mateo
- Departamento de Informática, Universidad de Oviedo, Jesús Arias de Velasco, Oviedo 33005, Spain
| | - Priska Eckert
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany.,Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, Freiburg D-79104, Germany
| | - Eleni Roussa
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | - Belal Rahhal
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | - Aimee Zuniga
- Developmental Genetics, University of Basel Medical School, Basel CH-4058, Switzerland
| | - Kerstin Krieglstein
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
| | | | - Stephan Heermann
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg D-79104, Germany
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27
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Tsingos E, Höckendorf B, Sütterlin T, Kirchmaier S, Grabe N, Centanin L, Wittbrodt J. Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish. eLife 2019; 8:42646. [PMID: 30910010 PMCID: PMC6486154 DOI: 10.7554/elife.42646] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
Combining clonal analysis with a computational agent based model, we investigate how tissue-specific stem cells for neural retina (NR) and retinal pigmented epithelium (RPE) of the teleost medaka (Oryzias latipes) coordinate their growth rates. NR cell division timing is less variable, consistent with an upstream role as growth inducer. RPE cells divide with greater variability, consistent with a downstream role responding to inductive signals. Strikingly, the arrangement of the retinal ciliary marginal zone niche results in a spatially biased random lineage loss, where stem- and progenitor cell domains emerge spontaneously. Further, our data indicate that NR cells orient division axes to regulate organ shape and retinal topology. We highlight an unappreciated mechanism for growth coordination, where one tissue integrates cues to synchronize growth of nearby tissues. This strategy may enable evolution to modulate cell proliferation parameters in one tissue to adapt whole-organ morphogenesis in a complex vertebrate organ. By the time babies reach adulthood, they have grown many times larger than they were at birth. This development is driven by an increase in the number and size of cells in the body. In particular, special types of cells, called stem cells, act as a reservoir for tissues: they divide to create new cells that will mature into various specialized structures. The retina is the light-sensitive part of the eye. It consists of the neural retina, a tissue that contains light-detecting cells, which is supported by the retinal pigment epithelium or RPE. In fish, the RPE and neural retina are replenished by distinct groups of stem cells that do not mix, despite the tissues being close together. Unlike humans, fish grow throughout adulthood, and their eyes must then keep pace with the body. This means that the different tissues in the retina must somehow coordinate to expand at the same rate: otherwise, the retina would get wrinkled and not work properly. Tsingos et al. therefore wanted to determine how stem cells in the neural retina and RPE co-operated to produce the right number of new cells at the right time. First, stem cells in the eyes of newly hatched fish were labelled with a visible marker so that their divisions could be tracked over time to build cell family trees. This showed that stem cells behaved differently in the neural retina and the RPE. Computer simulations of the growing retina explained this behavior: stem cells in the neural retina were telling the RPE stem cells when it was time to divide. Combining results from the simulations with data from the experiments revealed that a stem cell decided to keep up dividing partly because of its position in the tissue, and partly because of random chance. To be healthy, the body needs to fine-tune the number of cells it produces: creating too few cells may make it difficult to heal after injury, but making too many could lead to diseases such as cancer. Understanding how tissues normally agree to grow together could therefore open new avenues of treatment for these conditions.
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Affiliation(s)
- Erika Tsingos
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Burkhard Höckendorf
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas Sütterlin
- National Center for Tumor Diseases, Hamamatsu TIGA Center, Bioquant, Heidelberg University, Heidelberg, Germany
| | - Stephan Kirchmaier
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Niels Grabe
- National Center for Tumor Diseases, Hamamatsu TIGA Center, Bioquant, Heidelberg University, Heidelberg, Germany
| | - Lazaro Centanin
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
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Lischik CQ, Adelmann L, Wittbrodt J. Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One 2019; 14:e0212956. [PMID: 30845151 PMCID: PMC6405165 DOI: 10.1371/journal.pone.0212956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
Fish are ideally suited for in vivo-imaging due to their transparency at early stages combined with a large genetic toolbox. Key challenges to further advance imaging are fluorophore selection, immobilization of the specimen and approaches to eliminate pigmentation. We addressed all three and identified the fluorophores and anaesthesia of choice by high throughput time-lapse imaging. Our results indicate that eGFP and mCherry are the best conservative choices for in vivo-fluorescence experiments, when availability of well-established antibodies and nanobodies matters. Still, mVenusNB and mGFPmut2 delivered highest absolute fluorescence intensities in vivo. Immobilization is of key importance during extended in vivo imaging. Here, traditional approaches are outperformed by mRNA injection of α-Bungarotoxin which allows a complete and reversible, transient immobilization. In combination with fully transparent juvenile and adult fish established by the targeted inactivation of both, oca2 and pnp4a via CRISPR/Cas9-mediated gene editing in medaka we could dramatically improve the state-of-the art imaging conditions in post-embryonic fish, now enabling light-sheet microscopy of the growing retina, brain, gills and inner organs in the absence of side effects caused by anaesthetic drugs or pigmentation.
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Affiliation(s)
- Colin Q Lischik
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany
| | - Leonie Adelmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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29
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Abstract
In the era of CRISPR gene editing and genetic screening, there is an increasing demand for quick and reliable nucleic acid extraction pipelines for rapid genotyping of large and diverse sample sets. Despite continuous improvements of current workflows, the handling-time and material costs per sample remain major limiting factors. Here we present a robust method for low-cost DIY-pipet tips addressing these needs; i.e. using a cellulose filter disc inserted into a regular pipet tip. These filter-in-tips allow for a rapid, stand-alone four-step genotyping workflow by simply binding the DNA contained in the primary lysate to the cellulose filter, washing it in water and eluting it directly into the buffer for the downstream application (e.g. PCR). This drastically cuts down processing time to maximum 30 seconds per sample, with the potential for parallelizing and automation. We show the ease and sensitivity of our procedure by genotyping genetically modified medaka (Oryzias latipes) and zebrafish (Danio rerio) embryos (targeted by CRISPR/Cas9 knock-out and knock-in) in a 96-well plate format. The robust isolation and detection of multiple alleles of various abundancies in a mosaic genetic background allows phenotype-genotype correlation already in the injected generation, demonstrating the reliability and sensitivity of the protocol. Our method is applicable across kingdoms to samples ranging from cells to tissues i. e. plant seedlings, adult flies, mouse cell culture and tissue as well as adult fish fin-clips.
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Affiliation(s)
- Omar T. Hammouda
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
- Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany
| | - Frank Böttger
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
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30
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Pérez Saturnino A, Lust K, Wittbrodt J. Notch signalling patterns retinal composition by regulating atoh7 during post-embryonic growth. Development 2018; 145:dev.169698. [PMID: 30337377 PMCID: PMC6240314 DOI: 10.1242/dev.169698] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023]
Abstract
Patterning of a continuously growing naive field in the context of a life-long growing organ such as the teleost eye is of high functional relevance. Intrinsic and extrinsic signals have been proposed to regulate lineage specification in progenitors that exit the stem cell niche in the ciliary marginal zone (CMZ). The proper cell-type composition arising from those progenitors is a prerequisite for retinal function. Our findings in the teleost medaka (Oryzias latipes) uncover that the Notch-Atoh7 axis continuously patterns the CMZ. The complement of cell types originating from the two juxtaposed progenitors marked by Notch or Atoh7 activity contains all constituents of a retinal column. Modulation of Notch signalling specifically in Atoh7-expressing cells demonstrates the crucial role of this axis in generating the correct cell-type proportions. After transiently blocking Notch signalling, retinal patterning and differentiation is re-initiated de novo. Taken together, our data show that Notch activity in the CMZ continuously structures the growing retina by juxtaposing Notch and Atoh7 progenitors that give rise to distinct complementary lineages, revealing coupling of de novo patterning and cell-type specification in the respective lineages. Summary: Mutually exclusive activity of Notch and Atoh7 in the ciliary marginal zone gives rise to two distinct lineages resulting in specification of the full complement of cell types in medaka retina.
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Affiliation(s)
- Alicia Pérez Saturnino
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg 69120, Germany
| | - Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
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31
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Gutierrez-Triana JA, Tavhelidse T, Thumberger T, Thomas I, Wittbrodt B, Kellner T, Anlas K, Tsingos E, Wittbrodt J. Efficient single-copy HDR by 5' modified long dsDNA donors. eLife 2018; 7:39468. [PMID: 30156184 PMCID: PMC6125127 DOI: 10.7554/elife.39468] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/14/2018] [Indexed: 12/03/2022] Open
Abstract
CRISPR/Cas9 efficiently induces targeted mutations via non-homologous-end-joining but for genome editing, precise, homology-directed repair (HDR) of endogenous DNA stretches is a prerequisite. To favor HDR, many approaches interfere with the repair machinery or manipulate Cas9 itself. Using Medaka we show that the modification of 5’ ends of long dsDNA donors strongly enhances HDR, favors efficient single-copy integration by retaining a monomeric donor conformation thus facilitating successful gene replacement or tagging. CRISPR/Cas9 technology has revolutionized the ability of researchers to edit the DNA of any organism whose genome has already been sequenced. In the editing process, a section of RNA acts as a guide to match up to the location of the target DNA. The enzyme Cas9 then makes a cut in both strands of the DNA at this specific location. New segments of DNA can be introduced to the cell, incorporated into DNA ‘templates’. The cell uses the template to help it to heal the double-strand break, and in doing so adds the new DNA segment into the organism’s genome. A drawback of CRISPR/Cas9 is that it often introduces multiple copies of the new DNA segment into the genome because the templates can bind to each other before being pasted into place. In addition, some parts of the new DNA segment can be missed off during the editing process. However, most applications of CRISPR/Cas9 – for example, to replace a defective gene with a working version – require exactly one whole copy of the desired DNA to be inserted into the genome. In order to achieve more accurate CRISPR/Cas9 genome editing, Gutierrez-Triana, Tavhelidse, Thumberger et al. attached additional molecules to the end of the DNA template to shield the DNA from mistakes during editing. The modified template was used to couple a stem cell gene to a reporter that produces a green fluorescent protein into the genome of fish embryos. The fluorescent proteins made it easy to identify when the coupling was successful. Gutierrez-Triana et al. found that the additional molecules prevented multiple templates from joining together end to end, and ensured the full DNA segment was inserted into the genome. Furthermore, the results of the experiments showed that only one copy of the template was inserted into the DNA of the fish. In the future, the new template will allow DNA to be edited in a more controlled way both in basic research and in therapeutic applications.
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Affiliation(s)
| | | | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Isabelle Thomas
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Kerim Anlas
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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32
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Inoue D, Wittbrodt J, Gruss OJ. Loss and Rebirth of the Animal Microtubule Organizing Center: How Maternal Expression of Centrosomal Proteins Cooperates with the Sperm Centriole in Zygotic Centrosome Reformation. Bioessays 2018. [PMID: 29522658 DOI: 10.1002/bies.201700135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Centrosomes are the main microtubule organizing centers in animal cells. In particular during embryogenesis, they ensure faithful spindle formation and proper cell divisions. As metazoan centrosomes are eliminated during oogenesis, they have to be reassembled upon fertilization. Most metazoans use the sperm centrioles as templates for new centrosome biogenesis while the egg's cytoplasm re-prepares all components for on-going centrosome duplication in rapidly dividing embryonic cells. We discuss our knowledge and the experimental challenges to analyze zygotic centrosome reformation, which requires genetic experiments to enable scrutinizing respective male and female contributions. Male and female knockout animals and mRNA injection to mimic maternal expression of centrosomal proteins could point a way to the systematic molecular dissection of the process. The most recent data suggest that timely expression of centrosome components in oocytes is the key to zygotic centrosome reformation that uses male sperm as coordinators for de novo centrosome production.
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Affiliation(s)
- Daigo Inoue
- Dr. D. Inoue, Prof. Dr. J. Wittbrodt, Centre of Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Dr. D. Inoue, Prof. Dr. J. Wittbrodt, Centre of Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Oliver J Gruss
- Prof. Dr. O. J. Gruss, Institute of Genetics, University of Bonn, Karlrobert-Kreiten-Str.13, 53115 Bonn, Germany
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33
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Lust K, Wittbrodt J. Activating the regenerative potential of Müller glia cells in a regeneration-deficient retina. eLife 2018; 7:32319. [PMID: 29376827 PMCID: PMC5815849 DOI: 10.7554/elife.32319] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022] Open
Abstract
Regeneration responses in animals are widespread across phyla. To identify molecular players that confer regenerative capacities to non-regenerative species is of key relevance for basic research and translational approaches. Here, we report a differential response in retinal regeneration between medaka (Oryzias latipes) and zebrafish (Danio rerio). In contrast to zebrafish, medaka Müller glia (olMG) cells behave like progenitors and exhibit a restricted capacity to regenerate the retina. After injury, olMG cells proliferate but fail to self-renew and ultimately only restore photoreceptors. In our injury paradigm, we observed that in contrast to zebrafish, proliferating olMG cells do not maintain sox2 expression. Sustained sox2 expression in olMG cells confers regenerative responses similar to those of zebrafish MG (drMG) cells. We show that a single, cell-autonomous factor reprograms olMG cells and establishes a regeneration-like mode. Our results position medaka as an attractive model to delineate key regeneration factors with translational potential. All animals have at least some ability to repair their bodies after injury. But certain species can regenerate entire body parts and even internal organs. Salamanders, for example, can regrow their tail and limbs, as well as their eyes and heart. Many species of fish can also regenerate organs and tissues. In comparison, mammals have only limited regenerative capacity. Why does regeneration vary between species, and is it possible to convert a non-regenerating system into a regenerating one? Laboratory studies of regeneration often use the model organism, zebrafish. Zebrafish can restore their sight after an eye injury by regenerating the retina, the light-sensitive tissue at the back of the eye. They are able to do this thanks to cells in the retina called Müller glial cells. These behave like stem cells. They divide to produce identical copies of themselves, which then transform into all of the different cell types necessary to produce a new retina. Lust and Wittbrodt now show that a distant relative of the zebrafish, the Japanese ricefish ‘medaka’, lacks these regenerative skills. Although Müller glial cells in medaka also divide after injury, they give rise to only a single type of retinal cell. This means that these fish cannot regenerate an entire retina. Lust and Wittbrodt demonstrate that in medaka, but not zebrafish, levels of a protein called Sox2 fall after eye injury. As Sox2 has been shown to be important for regeneration in zebrafish Müller glial cells, the loss of Sox2 may be preventing regeneration in medaka. Consistent with this, restoring Sox2 levels in medaka Müller glial cells enabled them to turn into several different types of retinal cell. Sox2 is also present in the Müller glial cells of other species with backbones, including chickens, mice, and humans. Future experiments should test whether loss of Sox2 after injury contributes to the lack of regeneration in these species. If it does, the next question will be whether restoring Sox2 can drive a regenerative response.
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Affiliation(s)
- Katharina Lust
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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34
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Gierten J, Loosli F, Gehrig J, Pylatiuk C, Fitzgerald T, Birney E, Wittbrodt J, Gorenflo M. Systems Genetics Approach to Study Congenital Heart Disease in a Fish Model. Thorac Cardiovasc Surg 2018. [DOI: 10.1055/s-0038-1628326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- J. Gierten
- Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - F. Loosli
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Eggenstein-Leopoldshafen, Germany
| | - J. Gehrig
- ACQUIFER is a division of DITABIS, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
| | - C. Pylatiuk
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science (IAI), Eggenstein-Leopoldshafen, Germany
| | - T. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - E. Birney
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - J. Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - M. Gorenflo
- Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
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35
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Mateo JL, van den Berg DLC, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res 2017; 27:2129. [PMID: 29196563 DOI: 10.1101/gr.231845.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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37
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Kuri P, Schieber NL, Thumberger T, Wittbrodt J, Schwab Y, Leptin M. Dynamics of in vivo ASC speck formation. J Cell Biol 2017; 216:2891-2909. [PMID: 28701426 PMCID: PMC5584180 DOI: 10.1083/jcb.201703103] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/31/2017] [Accepted: 06/13/2017] [Indexed: 12/18/2022] Open
Abstract
The inflammasome adaptor ASC forms enormous intracellular complexes called specks. Live imaging of endogenous ASC in keratinocytes reveals speck formation dynamics and their lethal effects, as well as macrophages’ engulfment and digestion of the specks left behind by dead cells. Activated danger or pathogen sensors trigger assembly of the inflammasome adaptor ASC into specks, large signaling platforms considered hallmarks of inflammasome activation. Because a lack of in vivo tools has prevented the study of endogenous ASC dynamics, we generated a live ASC reporter through CRISPR/Cas9 tagging of the endogenous gene in zebrafish. We see strong ASC expression in the skin and other epithelia that act as barriers to insult. A toxic stimulus triggered speck formation and rapid pyroptosis in keratinocytes in vivo. Macrophages engulfed and digested that speck-containing, pyroptotic debris. A three-dimensional, ultrastructural reconstruction, based on correlative light and electron microscopy of the in vivo assembled specks revealed a compact network of highly intercrossed filaments, whereas pyrin domain (PYD) or caspase activation and recruitment domain alone formed filamentous aggregates. The effector caspase is recruited through PYD, whose overexpression induced pyroptosis but only after substantial delay. Therefore, formation of a single, compact speck and rapid cell-death induction in vivo requires a full-length ASC.
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Affiliation(s)
- Paola Kuri
- Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maria Leptin
- Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Institute of Genetics, University of Cologne, Cologne, Germany.,European Molecular Biology Organization, Heidelberg, Germany
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38
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Tan WH, Dasyani M, Centanin L, Wittbrodt J, Winkler C. col10a1 + osteoblast progenitors contribute to bone formation during lineage-restricted fin regeneration in Medaka. Mech Dev 2017. [DOI: 10.1016/j.mod.2017.04.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. Correction: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS One 2017; 12:e0176619. [PMID: 28426791 PMCID: PMC5398662 DOI: 10.1371/journal.pone.0176619] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0124633.].
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Pereiro L, Loosli F, Fernández J, Härtel S, Wittbrodt J, Concha ML. Gastrulation in an annual killifish: Molecular and cellular events during germ layer formation in Austrolebias. Dev Dyn 2017; 246:812-826. [DOI: 10.1002/dvdy.24496] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 01/27/2017] [Accepted: 01/28/2017] [Indexed: 12/18/2022] Open
Affiliation(s)
- Luisa Pereiro
- Anatomy and Developmental Biology; Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile; Santiago Chile
| | - Felix Loosli
- Karlsruhe Institute of Technology; Institute of Toxicology and Genetics; Karlsruhe Germany
| | - Juan Fernández
- Department of Biology; Faculty of Sciences, Universidad de Chile; Santiago Chile
| | - Steffen Härtel
- Anatomy and Developmental Biology; Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile; Santiago Chile
- Biomedical Neuroscience Institute; Santiago Chile
- National Center for Health Information Systems CENS; Santiago Chile
| | - Joachim Wittbrodt
- Center for Organismal Studies; Heidelberg University; Heidelberg Germany
| | - Miguel L. Concha
- Anatomy and Developmental Biology; Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile; Santiago Chile
- Biomedical Neuroscience Institute; Santiago Chile
- Center for Geroscience, Brain Health and Metabolism; Santiago Chile
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41
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Shi D, Tavhelidse T, Thumberger T, Wittbrodt J, Greb T. Bifacial stem cell niches in fish and plants. Curr Opin Genet Dev 2017; 45:28-33. [PMID: 28242480 DOI: 10.1016/j.gde.2017.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/01/2017] [Accepted: 02/07/2017] [Indexed: 12/20/2022]
Abstract
Embryonic development is key for determining the architecture and shape of multicellular bodies. However, most cells are produced postembryonically in, at least partly, differentiated organs. In this regard, organismal growth faces common challenges in coordinating expansion and function of body structures. Here we compare two examples for postembryonic growth processes from two different kingdoms of life to reveal common regulatory principles: lateral growth of plants and the enlargement of the fish retina. In both cases, growth is based on stem cell systems mediating radial growth by a bifacial mode of tissue production. Surprisingly, although being evolutionary distinct, we find similar patterns in regulatory circuits suggesting the existence of preferable solutions to a common developmental problem.
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Affiliation(s)
- Dongbo Shi
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.
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42
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Inoue D, Stemmer M, Thumberger T, Ruppert T, Bärenz F, Wittbrodt J, Gruss OJ. Expression of the novel maternal centrosome assembly factor Wdr8 is required for vertebrate embryonic mitoses. Nat Commun 2017; 8:14090. [PMID: 28098238 PMCID: PMC5253655 DOI: 10.1038/ncomms14090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
The assembly of the first centrosome occurs upon fertilisation when male centrioles recruit pericentriolar material (PCM) from the egg cytoplasm. The mechanisms underlying the proper assembly of centrosomes during early embryogenesis remain obscure. We identify Wdr8 as a novel maternally essential protein that is required for centrosome assembly during embryonic mitoses of medaka (Oryzias latipes). By CRISPR-Cas9-mediated knockout, maternal/zygotic Wdr8-null (m/zWdr8-/-) blastomeres exhibit severe defects in centrosome structure that lead to asymmetric division, multipolar mitotic spindles and chromosome alignment errors. Via its WD40 domains, Wdr8 interacts with the centriolar satellite protein SSX2IP. Combining targeted gene knockout and in vivo reconstitution of the maternally essential Wdr8-SSX2IP complex reveals an essential link between maternal centrosome proteins and the stability of the zygotic genome for accurate vertebrate embryogenesis. Our approach provides a way of distinguishing maternal from paternal effects in early embryos and should contribute to understanding molecular defects in human infertility.
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Affiliation(s)
- Daigo Inoue
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Manuel Stemmer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Felix Bärenz
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Oliver J Gruss
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,Institute of Genetics, University of Bonn, Karlrobert-Kreiten-Straße 13, Bonn 53115, Germany
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43
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Mateo JL, van den Berg DLC, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res 2016; 26:1626. [PMID: 27803196 DOI: 10.1101/gr.216044.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gutierrez-Triana JA, Mateo JL, Ibberson D, Ryu S, Wittbrodt J. iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. Development 2016; 143:4272-4278. [PMID: 27707796 PMCID: PMC5117216 DOI: 10.1242/dev.139261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/26/2016] [Indexed: 02/02/2023]
Abstract
DNA adenine methyltransferase identification (DamID) has emerged as an alternative method to profile protein-DNA interactions; however, critical issues limit its widespread applicability. Here, we present iDamIDseq, a protocol that improves specificity and sensitivity by inverting the steps DpnI-DpnII and adding steps that involve a phosphatase and exonuclease. To determine genome-wide protein-DNA interactions efficiently, we present the analysis tool iDEAR (iDamIDseq Enrichment Analysis with R). The combination of DamID and iDEAR permits the establishment of consistent profiles for transcription factors, even in transient assays, as we exemplify using the small teleost medaka (Oryzias latipes). We report that the bacterial Dam-coding sequence induces aberrant splicing when it is used with different promoters to drive tissue-specific expression. Here, we present an optimization of the sequence to avoid this problem. This and our other improvements will allow researchers to use DamID effectively in any organism, in a general or targeted manner. Summary: Critical improvements to the DamID protocol improve specificity and sensitivity in determining genome-wide protein-DNA interactions in transient or stable transgenic animal lines.
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Affiliation(s)
- Jose Arturo Gutierrez-Triana
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg D-69120, Germany
| | - Juan L Mateo
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg D-69120, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Cell Networks, University of Heidelberg, Im Neuenheimer 267, Heidelberg D-69120, Germany
| | - Soojin Ryu
- Developmental Genetics of the Nervous System, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg D-69120, Germany.,Focus Program Translational Neuroscience, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstr. 1, Mainz D-55131, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg D-69120, Germany
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Aghaallaei N, Gruhl F, Schaefer CQ, Wernet T, Weinhardt V, Centanin L, Loosli F, Baumbach T, Wittbrodt J. Identification, visualization and clonal analysis of intestinal stem cells in fish. Development 2016; 143:3470-3480. [PMID: 27578784 PMCID: PMC5087619 DOI: 10.1242/dev.134098] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 08/08/2016] [Indexed: 01/09/2023]
Abstract
Recently, a stochastic model of symmetrical stem cell division followed by neutral drift has been proposed for intestinal stem cells (ISCs), which has been suggested to represent the predominant mode of stem cell progression in mammals. In contrast, stem cells in the retina of teleost fish show an asymmetric division mode. To address whether the mode of stem cell division follows phylogenetic or ontogenetic routes, we analysed the entire gastrointestinal tract of the teleost medaka (Oryzias latipes). X-ray microcomputed tomography shows a correlation of 3D topography with the functional domains. Analysis of ISCs in proliferation assays and via genetically encoded lineage tracing highlights a stem cell niche in the furrow between the long intestinal folds that is functionally equivalent to mammalian intestinal crypts. Stem cells in this compartment are characterized by the expression of homologs of mammalian ISC markers – sox9, axin2 and lgr5 – emphasizing the evolutionary conservation of the Wnt pathway components in the stem cell niche of the intestine. The stochastic, sparse initial labelling of ISCs ultimately resulted in extended labelled or unlabelled domains originating from single stem cells in the furrow niche, contributing to both homeostasis and growth. Thus, different modes of stem cell division co-evolved within one organism, and in the absence of physical isolation in crypts, ISCs contribute to homeostatic growth. Summary: Adult medaka intestinal stem cells (ISCs) proliferate within a niche functionally equivalent to that in the mammal. Like mammalian ISCs, but unlike medaka retinal stem cells, their mode of division is largely symmetric.
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Affiliation(s)
- Narges Aghaallaei
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Franziska Gruhl
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Colin Q Schaefer
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Tobias Wernet
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany Laboratory for applications of synchrotron radiation, Karslruhe Institute for Technology (KIT), 76131 Karlsruhe, Germany
| | - Venera Weinhardt
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany Laboratory for applications of synchrotron radiation, Karslruhe Institute for Technology (KIT), 76131 Karlsruhe, Germany
| | - Lázaro Centanin
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Felix Loosli
- Laboratory for applications of synchrotron radiation, Karslruhe Institute for Technology (KIT), 76131 Karlsruhe, Germany
| | - Tilo Baumbach
- Laboratory for applications of synchrotron radiation, Karslruhe Institute for Technology (KIT), 76131 Karlsruhe, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
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Lust K, Sinn R, Pérez Saturnino A, Centanin L, Wittbrodt J. De novo neurogenesis by targeted expression of atoh7 to Müller glia cells. Development 2016; 143:1874-83. [PMID: 27068106 PMCID: PMC4920165 DOI: 10.1242/dev.135905] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/05/2016] [Indexed: 01/11/2023]
Abstract
Regenerative responses in the vertebrate CNS depend on quiescent radial glia stem cells, which re-enter the cell cycle and eventually differentiate into neurons. The entry into the cell cycle and the differentiation into neurons are events of opposite nature, and therefore efforts to force quiescent radial glia into neurons require different factors. Here, we use fish to show that a single neurogenic factor, Atoh7, directs retinal radial glia (Müller glia, MG) into proliferation. The resulting neurogenic clusters differentiate in vivo into various retinal neurons. We use signaling reporters to demonstrate that the Atoh7-induced regeneration-like response of MG cells is mimicked by Notch, resembling the behavior of early progenitors during retinogenesis. Activation of Notch signaling in MG cells is sufficient to trigger proliferation and differentiation. Our results uncover a new role for Atoh7 as a universal neurogenic factor, and illustrate how signaling modules are re-employed in diverse contexts to trigger different biological responses. Highlighted article: Induced activation of atoh7 in Müller glia cells in vivo is sufficient to drive cell cycle re-entry and proliferation, followed by the formation of neurogenic clusters and de novo neurogenesis.
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Affiliation(s)
- Katharina Lust
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg, Germany
| | - Rebecca Sinn
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg, Germany
| | - Alicia Pérez Saturnino
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg, Germany
| | - Lázaro Centanin
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
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Abstract
This chapter introduces the principles and advantages of selective plane illumination microscopy (SPIM) and compares it to commonly used epifluorescence or confocal setups. Due to the low phototoxicity, speed of imaging, high penetration depth, and spatiotemporal resolution, SPIM is predestined for in vivo imaging but can as well be used for in toto analysis of large fixed samples. Key points of light-sheet microscopy are highlighted and discussed priming the investigator to choose the best suitable system from the large collection of possible SPIM setups. Mounting of samples is shown and the demands for data acquisition, processing, handling, and visualization are discussed.
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Affiliation(s)
- D Kromm
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - T Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - J Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Lust K, Wittbrodt J. Hold your breath! eLife 2015; 4:e12523. [PMID: 26671521 PMCID: PMC4744187 DOI: 10.7554/elife.12523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 11/13/2022] Open
Abstract
Reactive oxygen species produced in response to changes in the level of oxygen in water can promote the regeneration of brain tissue in newts.
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Affiliation(s)
- Katharina Lust
- Centre for Organismal Studies Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
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Dolle D, Mateo JL, Eichenlaub MP, Sinn R, Reinhardt R, Höckendorf B, Inoue D, Centanin L, Ettwiller L, Wittbrodt J. Correction: Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PLoS One 2015; 10:e0143989. [PMID: 26599359 PMCID: PMC4658166 DOI: 10.1371/journal.pone.0143989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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50
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Zhang P, Kratz AS, Salama M, Elabd S, Heinrich T, Wittbrodt J, Blattner C, Davidson G. Expression screening using a Medaka cDNA library identifies evolutionarily conserved regulators of the p53/Mdm2 pathway. BMC Biotechnol 2015; 15:92. [PMID: 26450685 PMCID: PMC4599741 DOI: 10.1186/s12896-015-0208-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/30/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The p53 tumor suppressor protein is mainly regulated by alterations in the half-life of the protein, resulting in significant differences in p53 protein levels in cells. The major regulator of this process is Mdm2, which ubiquitinates p53 and targets it for proteasomal degradation. This process can be enhanced or reduced by proteins that associate with p53 or Mdm2 and several proteins have been identified with such an activity. Furthermore, additional ubiquitin ligases for p53 have been identified in recent years. Nevertheless, our understanding of how p53 abundance and Mdm2 activity are regulated remains incomplete. Here we describe a cell culture based overexpression screen to identify evolutionarily conserved regulators of the p53/Mdm2 circuit. The results from this large-scale screening method will contribute to a better understanding of the regulation of these important proteins. METHODS Expression screening was based on co-transfection of H1299 cells with pools of cDNA's from a Medaka library together with p53, Mdm2 and, as internal control, Ror2. After cell lysis, SDS-PAGE/WB analysis was used to detect alterations in these proteins. RESULTS More than one hundred hits that altered the abundance of either p53, Mdm2, or both were identified in the primary screen. Subscreening of the library pools that were identified in the primary screen identified several potential novel regulators of p53 and/or Mdm2. We also tested whether the human orthologues of the Medaka genes regulate p53 and/or Mdm2 abundance. All human orthologues regulated p53 and/or Mdm2 abundance in the same manner as the proteins from Medaka, which underscores the suitability of this screening methodology for the identification of new modifiers of p53 and Mdm2. CONCLUSIONS Despite enormous efforts in the last two decades, many unknown regulators for p53 and Mdm2 abundance are predicted to exist. This cross-species approach to identify evolutionarily conserved regulators demonstrates that our Medaka unigene cDNA library represents a powerful tool to screen for these novel regulators of the p53/Mdm2 pathway.
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Affiliation(s)
- Ping Zhang
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany. .,Faculty of Biosciences, University of Heidelberg, 69120, Heidelberg, Germany. .,Present address: Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
| | - Anne Sophie Kratz
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany. .,Present address: Cell Cycle Control and Carcinogenesis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.
| | - Mohammed Salama
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany.
| | - Seham Elabd
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany.
| | - Thorsten Heinrich
- Department of Anti-Aging Medicine, University of Tokyo, Tokyo, 113-8865, Japan.
| | - Joachim Wittbrodt
- Department of Developmental Biology and Physiology, University of Heidelberg, 69120, Heidelberg, Germany.
| | - Christine Blattner
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany.
| | - Gary Davidson
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021, Karlsruhe, Germany.
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