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Vishal K, Bawa S, Brooks D, Bauman K, Geisbrecht ER. Thin is required for cell death in the Drosophila abdominal muscles by targeting DIAP1. Cell Death Dis 2018; 9:740. [PMID: 29970915 PMCID: PMC6030163 DOI: 10.1038/s41419-018-0756-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 12/23/2022]
Abstract
In holometabolous insects, developmentally controlled programmed cell death (PCD) is a conserved process that destroys a subset of larval tissues for the eventual creation of new adult structures. This process of histolysis is relatively well studied in salivary gland and midgut tissues, while knowledge concerning larval muscle destruction is limited. Here, we have examined the histolysis of a group of Drosophila larval abdominal muscles called the dorsal external oblique muscles (DEOMs). Previous studies have defined apoptosis as the primary mediator of DEOM breakdown, whose timing is controlled by ecdysone signaling. However, very little is known about other factors that contribute to DEOM destruction. In this paper, we examine the role of thin (tn), which encodes for the Drosophila homolog of mammalian TRIM32, in the regulation of DEOM histolysis. We find that loss of Tn blocks DEOM degradation independent of ecdysone signaling. Instead, tn genetically functions in a pathway with the death-associated inhibitor of apoptosis (DIAP1), Dronc, and death-associated APAF1-related killer (Dark) to regulate apoptosis. Importantly, blocking Tn results in the absence of active Caspase-3 immunostaining, upregulation of DIAP1 protein levels, and inhibition of Dronc activation. DIAP1 and Dronc mRNA levels are not altered in tn mutants, showing that Tn acts post-transcriptionally on DIAP1 to regulate apoptosis. Herein, we also find that the RING domain of Tn is required for DEOM histolysis as loss of this domain results in higher DIAP1 levels. Together, our results suggest that the direct control of DIAP1 levels, likely through the E3 ubiquitin ligase activity of Tn, provides a mechanism to regulate caspase activity and to facilitate muscle cell death.
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Affiliation(s)
- Kumar Vishal
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Simranjot Bawa
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - David Brooks
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Kenneth Bauman
- Department of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas, Kansas City, MO, 64110, USA
| | - Erika R Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
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Kuleesha, Feng L, Wasser M. Spatial pattern analysis of nuclear migration in remodelled muscles during Drosophila metamorphosis. BMC Bioinformatics 2017; 18:329. [PMID: 28693471 PMCID: PMC5504860 DOI: 10.1186/s12859-017-1739-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many human muscle wasting diseases are associated with abnormal nuclear localization. During metamorphosis in Drosophila melanogaster, multi-nucleated larval dorsal abdominal muscles either undergo cell death or are remodeled to temporary adult muscles. Muscle remodeling is associated with anti-polar nuclear migration and atrophy during early pupation followed by polar migration and muscle growth during late pupation. Muscle remodeling is a useful model to study genes involved in myonuclear migration. Previously, we showed that loss of Cathepsin-L inhibited anti-polar movements, while knockdown of autophagy-related genes affected nuclear positioning along the medial axis in late metamorphosis. RESULTS To compare the phenotypic effects of gene perturbations on nuclear migration more objectively, we developed new descriptors of myonuclear distribution. To obtain nuclear pattern features, we designed an algorithm to detect and track nuclear regions inside live muscles. Nuclear tracks were used to distinguish between fast moving nuclei associated with fragments of dead muscles (sarcolytes) and slow-moving nuclei inside remodelled muscles. Nuclear spatial pattern features, such as longitudinal (lonNS) and lateral nuclear spread (latNS), allowed us to compare nuclear migration during muscle remodelling in different genetic backgrounds. Anti-polar migration leads to a lonNS decrease. As expected, lack of myonuclear migration caused by the loss of Cp1 was correlated with a significantly lower lonNS decrease. Unexpectedly, the decrease in lonNS was significantly enhanced by Atg9, Atg5 and Atg18 silencing, indicating that the loss of autophagy promotes the migration and clustering of nuclei. Loss of autophagy also caused a scattering of nuclei along the lateral axis, leading to a two-row as opposed to single row distribution in control muscles. Increased latNS resulting from knockdown of Atg9 and Atg18 was correlated with increased muscle diameter, suggesting that the wider muscle fibre promotes lateral displacement of nuclei from the medial axis during polar migration. CONCLUSIONS We developed new nuclear features to characterize the dynamics of nuclear distribution in time-lapse images of Drosophila metamorphosis. Image quantification improved our understanding of phenotypic abnormalities in nuclear distribution resulting from gene perturbations. Therefore, in vivo imaging and quantitative image analysis of Drosophila metamorphosis promise to provide novel insights into the relationship between muscle wasting and myonuclear positioning.
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Affiliation(s)
- Kuleesha
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore. .,Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Lin Feng
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Martin Wasser
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,BioImagingMW, Block 28D Dover Crescent #31-73, Singapore, 134028, Singapore
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Fujita N, Huang W, Lin TH, Groulx JF, Jean S, Nguyen J, Kuchitsu Y, Koyama-Honda I, Mizushima N, Fukuda M, Kiger AA. Genetic screen in Drosophila muscle identifies autophagy-mediated T-tubule remodeling and a Rab2 role in autophagy. eLife 2017; 6. [PMID: 28063257 PMCID: PMC5249261 DOI: 10.7554/elife.23367] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/17/2016] [Indexed: 01/04/2023] Open
Abstract
Transverse (T)-tubules make-up a specialized network of tubulated muscle cell membranes involved in excitation-contraction coupling for power of contraction. Little is known about how T-tubules maintain highly organized structures and contacts throughout the contractile system despite the ongoing muscle remodeling that occurs with muscle atrophy, damage and aging. We uncovered an essential role for autophagy in T-tubule remodeling with genetic screens of a developmentally regulated remodeling program in Drosophila abdominal muscles. Here, we show that autophagy is both upregulated with and required for progression through T-tubule disassembly stages. Along with known mediators of autophagosome-lysosome fusion, our screens uncovered an unexpected shared role for Rab2 with a broadly conserved function in autophagic clearance. Rab2 localizes to autophagosomes and binds to HOPS complex members, suggesting a direct role in autophagosome tethering/fusion. Together, the high membrane flux with muscle remodeling permits unprecedented analysis both of T-tubule dynamics and fundamental trafficking mechanisms. DOI:http://dx.doi.org/10.7554/eLife.23367.001
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Affiliation(s)
- Naonobu Fujita
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Wilson Huang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Tzu-Han Lin
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Jean-Francois Groulx
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Steve Jean
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Jen Nguyen
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Yoshihiko Kuchitsu
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Amy A Kiger
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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Kuleesha Y, Puah WC, Wasser M. Live imaging of muscle histolysis in Drosophila metamorphosis. BMC DEVELOPMENTAL BIOLOGY 2016; 16:12. [PMID: 27141974 PMCID: PMC4855724 DOI: 10.1186/s12861-016-0113-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/26/2016] [Indexed: 11/23/2022]
Abstract
Background The contribution of programmed cell death (PCD) to muscle wasting disorders remains a matter of debate. Drosophila melanogaster metamorphosis offers the opportunity to study muscle cell death in the context of development. Using live cell imaging of the abdomen, two groups of larval muscles can be observed, doomed muscles that undergo histolysis and persistent muscles that are remodelled and survive into adulthood. Method To identify and characterize genes that control the decision between survival and cell death of muscles, we developed a method comprising in vivo imaging, targeted gene perturbation and time-lapse image analysis. Our approach enabled us to study the cytological and temporal aspects of abnormal cell death phenotypes. Results In a previous genetic screen for genes controlling muscle size and cell death in metamorphosis, we identified gene perturbations that induced cell death of persistent or inhibit histolysis of doomed larval muscles. RNA interference (RNAi) of the genes encoding the helicase Rm62 and the lysosomal Cathepsin-L homolog Cysteine proteinase 1 (Cp1) caused premature cell death of persistent muscle in early and mid-pupation, respectively. Silencing of the transcriptional co-repressor Atrophin inhibited histolysis of doomed muscles. Overexpression of dominant-negative Target of Rapamycin (TOR) delayed the histolysis of a subset of doomed and induced ablation of all persistent muscles. RNAi of AMPKα, which encodes a subunit of the AMPK protein complex that senses AMP and promotes ATP formation, led to loss of attachment and a spherical morphology. None of the perturbations affected the survival of newly formed adult muscles, suggesting that the method is useful to find genes that are crucial for the survival of metabolically challenged muscles, like those undergoing atrophy. The ablation of persistent muscles did not affect eclosion of adult flies. Conclusions Live imaging is a versatile approach to uncover gene functions that are required for the survival of muscle undergoing remodelling, yet are dispensable for other adult muscles. Our approach promises to identify molecular mechanisms that can explain the resilience of muscles to PCD. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0113-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yadav Kuleesha
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.,School of Computer Engineering, Nanyang Technological University, N4-2A-05, Nanyang Avenue, Singapore, 639798, Republic of Singapore
| | - Wee Choo Puah
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Martin Wasser
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore. .,Present address: BioImagingMW, Block 28D Dover Crescent, #31-73, Singapore, 134028, Republic of Singapore.
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Kuleesha Y, Puah WC, Wasser M. A model of muscle atrophy based on live microscopy of muscle remodelling in Drosophila metamorphosis. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150517. [PMID: 26998322 PMCID: PMC4785973 DOI: 10.1098/rsos.150517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
Genes controlling muscle size and survival play important roles in muscle wasting diseases. In Drosophila melanogaster metamorphosis, larval abdominal muscles undergo two developmental fates. While a doomed population is eliminated by cell death, another persistent group is remodelled and survives into adulthood. To identify and characterize genes involved in the development of remodelled muscles, we devised a workflow consisting of in vivo imaging, targeted gene perturbation and quantitative image analysis. We show that inhibition of TOR signalling and activation of autophagy promote developmental muscle atrophy in early, while TOR and yorkie activation are required for muscle growth in late pupation. We discovered changes in the localization of myonuclei during remodelling that involve anti-polar migration leading to central clustering followed by polar migration resulting in localization along the midline. We demonstrate that the Cathepsin L orthologue Cp1 is required for myonuclear clustering in mid, while autophagy contributes to central positioning of nuclei in late metamorphosis. In conclusion, studying muscle remodelling in metamorphosis can provide new insights into the cell biology of muscle wasting.
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Affiliation(s)
- Yadav Kuleesha
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, no. 07-01 Matrix, Singapore 138671, Republic of Singapore
- School of Computer Engineering, Nanyang Technological University, N4-2A-05, Nanyang Avenue, Singapore 639798, Republic of Singapore
| | - Wee Choo Puah
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, no. 07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Martin Wasser
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, no. 07-01 Matrix, Singapore 138671, Republic of Singapore
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Puah WC, Wasser M. Live imaging of muscles in Drosophila metamorphosis: Towards high-throughput gene identification and function analysis. Methods 2015; 96:103-117. [PMID: 26431669 DOI: 10.1016/j.ymeth.2015.09.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/16/2022] Open
Abstract
Time-lapse microscopy in developmental biology is an emerging tool for functional genomics. Phenotypic effects of gene perturbations can be studied non-invasively at multiple time points in chronological order. During metamorphosis of Drosophila melanogaster, time-lapse microscopy using fluorescent reporters allows visualization of alternative fates of larval muscles, which are a model for the study of genes related to muscle wasting. While doomed muscles enter hormone-induced programmed cell death, a smaller population of persistent muscles survives to adulthood and undergoes morphological remodeling that involves atrophy in early, and hypertrophy in late pupation. We developed a method that combines in vivo imaging, targeted gene perturbation and image analysis to identify and characterize genes involved in muscle development. Macrozoom microscopy helps to screen for interesting muscle phenotypes, while confocal microscopy in multiple locations over 4-5 days produces time-lapse images that are used to quantify changes in cell morphology. Performing a similar investigation using fixed pupal tissues would be too time-consuming and therefore impractical. We describe three applications of our pipeline. First, we show how quantitative microscopy can track and measure morphological changes of muscle throughout metamorphosis and analyze genes involved in atrophy. Second, our assay can help to identify genes that either promote or prevent histolysis of abdominal muscles. Third, we apply our approach to test new fluorescent proteins as live markers for muscle development. We describe mKO2 tagged Cysteine proteinase 1 (Cp1) and Troponin-I (TnI) as examples of proteins showing developmental changes in subcellular localization. Finally, we discuss strategies to improve throughput of our pipeline to permit genome-wide screens in the future.
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Affiliation(s)
- Wee Choo Puah
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore.
| | - Martin Wasser
- Imaging Informatics Division, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore.
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Yadav K, Lin F, Wasser M. Muscle segmentation in time series images of Drosophila metamorphosis. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2015:3085-3088. [PMID: 26736944 DOI: 10.1109/embc.2015.7319044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In order to study genes associated with muscular disorders, we characterize the phenotypic changes in Drosophila muscle cells during metamorphosis caused by genetic perturbations. We collect in vivo images of muscle fibers during remodeling of larval to adult muscles. In this paper, we focus on the new image processing pipeline designed to quantify the changes in shape and size of muscles. We propose a new two-step approach to muscle segmentation in time series images. First, we implement a watershed algorithm to divide the image into edge-preserving regions, and then, we classify these regions into muscle and non-muscle classes on the basis of shape and intensity. The advantage of our method is two-fold: First, better results are obtained because classification of regions is constrained by the shape of muscle cell from previous time point; and secondly, minimal user intervention results in faster processing time. The segmentation results are used to compare the changes in cell size between controls and reduction of the autophagy related gene Atg 9 during Drosophila metamorphosis.
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Ranganathan S, Tan TW, Schönbach C. InCoB2014: bioinformatics to tackle the data to knowledge challenge. Introduction. BMC Bioinformatics 2014; 15 Suppl 16:I1. [PMID: 25521055 PMCID: PMC4290632 DOI: 10.1186/1471-2105-15-s16-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Since 2006, the International Conference on Bioinformatics (InCoB) has been publishing selected papers in BMC Bioinformatics. Papers within the scope of the journal from the 13th InCoB July 31-2 August, 2014 in Sydney, Australia have been compiled in this supplement. These span protein and proteome informatics, structural bioinformatics, software development and bioimaging to pharmacoinformatics and disease informatics, representing the breadth of bioinformatics research in the Asia-Pacific.
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Affiliation(s)
- Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney NSW 2109, Australia
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Christian Schönbach
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana 010000, Republic of Kazakhstan
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
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