1
|
Bialic M, Al Ahmad Nachar B, Koźlak M, Coulon V, Schwob E. Measuring S-Phase Duration from Asynchronous Cells Using Dual EdU-BrdU Pulse-Chase Labeling Flow Cytometry. Genes (Basel) 2022; 13:genes13030408. [PMID: 35327961 PMCID: PMC8951228 DOI: 10.3390/genes13030408] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 02/07/2023] Open
Abstract
Eukaryotes duplicate their chromosomes during the cell cycle S phase using thousands of initiation sites, tunable fork speed and megabase-long spatio-temporal replication programs. The duration of S phase is fairly constant within a given cell type, but remarkably plastic during development, cell differentiation or various stresses. Characterizing the dynamics of S phase is important as replication defects are associated with genome instability, cancer and ageing. Methods to measure S-phase duration are so far indirect, and rely on mathematical modelling or require cell synchronization. We describe here a simple and robust method to measure S-phase duration in cell cultures using a dual EdU-BrdU pulse-labeling regimen with incremental thymidine chases, and quantification by flow cytometry of cells entering and exiting S phase. Importantly, the method requires neither cell synchronization nor genome engineering, thus avoiding possible artifacts. It measures the duration of unperturbed S phases, but also the effect of drugs or mutations on it. We show that this method can be used for both adherent and suspension cells, cell lines and primary cells of different types from human, mouse and Drosophila. Interestingly, the method revealed that several commonly-used cancer cell lines have a longer S phase compared to untransformed cells.
Collapse
Affiliation(s)
- Marta Bialic
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
- Institut de Médecine Régénératrice et Biothérapie, INSERM, CHU, 34295 Montpellier, France
| | - Baraah Al Ahmad Nachar
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| | - Maria Koźlak
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| | - Vincent Coulon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
- Correspondence: ; Tel.: +33-43435-9679
| | - Etienne Schwob
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| |
Collapse
|
2
|
Recent advances in nucleotide analogue-based techniques for tracking dividing stem cells: An overview. J Biol Chem 2021; 297:101345. [PMID: 34717955 PMCID: PMC8592869 DOI: 10.1016/j.jbc.2021.101345] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
Detection of thymidine analogues after their incorporation into replicating DNA represents a powerful tool for the study of cellular DNA synthesis, progression through the cell cycle, cell proliferation kinetics, chronology of cell division, and cell fate determination. Recent advances in the concurrent detection of multiple such analogues offer new avenues for the investigation of unknown features of these vital cellular processes. Combined with quantitative analysis, temporal discrimination of multiple labels enables elucidation of various aspects of stem cell life cycle in situ, such as division modes, differentiation, maintenance, and elimination. Data obtained from such experiments are critically important for creating descriptive models of tissue histogenesis and renewal in embryonic development and adult life. Despite the wide use of thymidine analogues in stem cell research, there are a number of caveats to consider for obtaining valid and reliable labeling results when marking replicating DNA with nucleotide analogues. Therefore, in this review, we describe critical points regarding dosage, delivery, and detection of nucleotide analogues in the context of single and multiple labeling, outline labeling schemes based on pulse-chase, cumulative and multilabel marking of replicating DNA for revealing stem cell proliferative behaviors, and determining cell cycle parameters, and discuss preconditions and pitfalls in conducting such experiments. The information presented in our review is important for rational design of experiments on tracking dividing stem cells by marking replicating DNA with thymidine analogues.
Collapse
|
3
|
Khushi M, Napier CE, Smyth CM, Reddel RR, Arthur JW. MatCol: a tool to measure fluorescence signal colocalisation in biological systems. Sci Rep 2017; 7:8879. [PMID: 28827650 PMCID: PMC5566543 DOI: 10.1038/s41598-017-08786-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
Protein colocalisation is often studied using pixel intensity-based coefficients such as Pearson, Manders, Li or Costes. However, these methods cannot be used to study object-based colocalisations in biological systems. Therefore, a novel method is required to automatically identify regions of fluorescent signal in two channels, identify the co-located parts of these regions, and calculate the statistical significance of the colocalisation. We have developed MatCol to address these needs. MatCol can be used to visualise protein and/or DNA colocalisations and fine tune user-defined parameters for the colocalisation analysis, including the application of median or Wiener filtering to improve the signal to noise ratio. Command-line execution allows batch processing of multiple images. Users can also calculate the statistical significance of the observed object colocalisations compared to overlap by random chance using Student's t-test. We validated MatCol in a biological setting. The colocalisations of telomeric DNA and TRF2 protein or TRF2 and PML proteins in >350 nuclei derived from three different cell lines revealed a highly significant correlation between manual and MatCol identification of colocalisations (linear regression R2 = 0.81, P < 0.0001). MatCol has the ability to replace manual colocalisation counting, and the potential to be applied to a wide range of biological areas.
Collapse
Affiliation(s)
- Matloob Khushi
- Bioinformatics Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Christine M Smyth
- Gene Therapy Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| |
Collapse
|
4
|
Grudniewska M, Mouton S, Simanov D, Beltman F, Grelling M, de Mulder K, Arindrarto W, Weissert PM, van der Elst S, Berezikov E. Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano. eLife 2016; 5. [PMID: 27997336 PMCID: PMC5173321 DOI: 10.7554/elife.20607] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022] Open
Abstract
The regeneration-capable flatworm Macrostomum lignano is a powerful model organism to study the biology of stem cells in vivo. As a flatworm amenable to transgenesis, it complements the historically used planarian flatworm models, such as Schmidtea mediterranea. However, information on the transcriptome and markers of stem cells in M. lignano is limited. We generated a de novo transcriptome assembly and performed the first comprehensive characterization of gene expression in the proliferating cells of M. lignano, represented by somatic stem cells, called neoblasts, and germline cells. Knockdown of a selected set of neoblast genes, including Mlig-ddx39, Mlig-rrm1, Mlig-rpa3, Mlig-cdk1, and Mlig-h2a, confirmed their crucial role for the functionality of somatic neoblasts during homeostasis and regeneration. The generated M. lignano transcriptome assembly and gene expression signatures of somatic neoblasts and germline cells will be a valuable resource for future molecular studies in M. lignano. DOI:http://dx.doi.org/10.7554/eLife.20607.001
Collapse
Affiliation(s)
- Magda Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Daniil Simanov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Frank Beltman
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Margriet Grelling
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katrien de Mulder
- Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wibowo Arindrarto
- Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Philipp M Weissert
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan van der Elst
- Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| |
Collapse
|
5
|
Van Lent S, De Vos WH, Huot Creasy H, Marques PX, Ravel J, Vanrompay D, Bavoil P, Hsia RC. Analysis of Polymorphic Membrane Protein Expression in Cultured Cells Identifies PmpA and PmpH of Chlamydia psittaci as Candidate Factors in Pathogenesis and Immunity to Infection. PLoS One 2016; 11:e0162392. [PMID: 27631978 PMCID: PMC5025070 DOI: 10.1371/journal.pone.0162392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/22/2016] [Indexed: 12/22/2022] Open
Abstract
The polymorphic membrane protein (Pmp) paralogous families of Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia abortus are putative targets for Chlamydia vaccine development. To determine whether this is also the case for Pmp family members of C. psittaci, we analyzed transcription levels, protein production and localization of several Pmps of C. psittaci. Pmp expression profiles were characterized using quantitative real-time PCR (RT-qPCR), immunofluorescence (IF) and immuno-electron microscopy (IEM) under normal and stress conditions. We found that PmpA was highly produced in all inclusions as early as 12 hpi in all biological replicates. In addition, PmpA and PmpH appeared to be unusually accessible to antibody as determined by both immunofluorescence and immuno-electron microscopy. Our results suggest an important role for these Pmps in the pathogenesis of C. psittaci, and make them promising candidates in vaccine development.
Collapse
Affiliation(s)
- Sarah Van Lent
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- * E-mail:
| | - Winnok H. De Vos
- Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Heather Huot Creasy
- Institute for Genome Sciences and Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, Unites States of America
| | - Patricia X. Marques
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, Unites States of America
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, Unites States of America
| | - Daisy Vanrompay
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Patrik Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, Unites States of America
| | - Ru-ching Hsia
- University of Maryland, Baltimore, Electron Microscopy Core Imaging Facility, Maryland, Unites States of America
| |
Collapse
|
6
|
Adhesive organ regeneration in Macrostomum lignano. BMC DEVELOPMENTAL BIOLOGY 2016; 16:20. [PMID: 27255153 PMCID: PMC4890501 DOI: 10.1186/s12861-016-0121-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022]
Abstract
Background Flatworms possess pluripotent stem cells that can give rise to all cell types, which allows them to restore lost body parts after injury or amputation. This makes flatworms excellent model systems for studying regeneration. In this study, we present the adhesive organs of a marine flatworm as a simple model system for organ regeneration. Macrostomum lignano has approximately 130 adhesive organs at the ventral side of its tail plate. One adhesive organ consists of three interacting cells: one adhesive gland cell, one releasing gland cell, and one modified epidermal cell, called an anchor cell. However, no specific markers for these cell types were available to study the regeneration of adhesive organs. Results We tested 15 commercially available lectins for their ability to label adhesive organs and found one lectin (peanut agglutinin) to be specific to adhesive gland cells. We visualized the morphology of regenerating adhesive organs using lectin- and antibody staining as well as transmission electron microscopy. Our findings indicate that the two gland cells differentiate earlier than the connected anchor cells. Using EdU/lectin staining of partially amputated adhesive organs, we showed that their regeneration can proceed in two ways. First, adhesive gland cell bodies are able to survive partial amputation and reconnect with newly formed anchor cells. Second, adhesive gland cell bodies are cleared away, and the entire adhesive organ is build anew. Conclusion Our results provide the first insights into adhesive organ regeneration and describe ten new markers for differentiated cells and tissues in M. lignano. The position of adhesive organ cells within the blastema and their chronological differentiation have been shown for the first time. M. lignano can regenerate adhesive organs de novo but also replace individual anchor cells in an injured organ. Our findings contribute to a better understanding of organogenesis in flatworms and enable further molecular investigations of cell-fate decisions during regeneration. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0121-1) contains supplementary material, which is available to authorized users.
Collapse
|
7
|
Shang C, Chen Q, Dell A, Haslam SM, De Vos WH, Van Damme EJM. The Cytotoxicity of Elderberry Ribosome-Inactivating Proteins Is Not Solely Determined by Their Protein Translation Inhibition Activity. PLoS One 2015; 10:e0132389. [PMID: 26148207 PMCID: PMC4493096 DOI: 10.1371/journal.pone.0132389] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/13/2015] [Indexed: 11/18/2022] Open
Abstract
Although the protein translation inhibition activity of ribosome inactivating proteins (RIPs) is well documented, little is known about the contribution of the lectin chain to the biological activity of these proteins. In this study, we compared the in vitro and intracellular activity of several S. nigra (elderberry) RIPs and non-RIP lectins. Our data demonstrate that RIPs from elderberry are much more toxic to HeLa cells than to primary fibroblasts. Differences in the cytotoxicity between the elderberry proteins correlated with differences in glycan specificity of their lectin domain, cellular uptake efficiency and intracellular destination. Despite the fact that the bulk of the RIPs accumulated in the lysosomes and partly in the Golgi apparatus, we could demonstrate effective inhibition of protein synthesis in cellula. As we also observed cytotoxicity for non-RIP lectins, it is clear that the lectin chain triggers additional pathways heralding cell death. Our data suggest that one of these pathways involves the induction of autophagy.
Collapse
Affiliation(s)
- Chenjing Shang
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Qiushi Chen
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Anne Dell
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Stuart M. Haslam
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Winnok H. De Vos
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Antwerp, Belgium
| | - Els J. M. Van Damme
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| |
Collapse
|
8
|
Lengerer B, Pjeta R, Wunderer J, Rodrigues M, Arbore R, Schärer L, Berezikov E, Hess MW, Pfaller K, Egger B, Obwegeser S, Salvenmoser W, Ladurner P. Biological adhesion of the flatworm Macrostomum lignano relies on a duo-gland system and is mediated by a cell type-specific intermediate filament protein. Front Zool 2014; 11:12. [PMID: 24520881 PMCID: PMC4016567 DOI: 10.1186/1742-9994-11-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/20/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Free-living flatworms, in both marine and freshwater environments, are able to adhere to and release from a substrate several times within a second. This reversible adhesion relies on adhesive organs comprised of three cell types: an adhesive gland cell, a releasing gland cell, and an anchor cell, which is a modified epidermal cell responsible for structural support. However, nothing is currently known about the molecules that are involved in this adhesion process. RESULTS In this study we present the detailed morphology of the adhesive organs of the free-living marine flatworm Macrostomum lignano. About 130 adhesive organs are located in a horse-shoe-shaped arc along the ventral side of the tail plate. Each organ consists of exactly three cells, an adhesive gland cell, a releasing gland cell, and an anchor cell. The necks of the two gland cells penetrate the anchor cell through a common pore. Modified microvilli of the anchor cell form a collar surrounding the necks of the adhesive- and releasing glands, jointly forming the papilla, the outer visible part of the adhesive organs. Next, we identified an intermediate filament (IF) gene, macif1, which is expressed in the anchor cells. RNA interference mediated knock-down resulted in the first experimentally induced non-adhesion phenotype in any marine animal. Specifically, the absence of intermediate filaments in the anchor cells led to papillae with open tips, a reduction of the cytoskeleton network, a decline in hemidesmosomal connections, and to shortened microvilli containing less actin. CONCLUSION Our findings reveal an elaborate biological adhesion system in a free-living flatworm, which permits impressively rapid temporary adhesion-release performance in the marine environment. We demonstrate that the structural integrity of the supportive cell, the anchor cell, is essential for this adhesion process: the knock-down of the anchor cell-specific intermediate filament gene resulted in the inability of the animals to adhere. The RNAi mediated changes of the anchor cell morphology are comparable to situations observed in human gut epithelia. Therefore, our current findings and future investigations using this powerful flatworm model system might contribute to a better understanding of the function of intermediate filaments and their associated human diseases.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr, 25, Innsbruck A-6020, Austria.
| |
Collapse
|