Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane
Preprint posted on 28 April 2020 https://www.biorxiv.org/content/10.1101/2020.04.27.064204v1
Article now published in Journal of Cell Science at http://dx.doi.org/10.1242/jcs.252254
Mitosis is a highly regulated stage of the cell cycle where multiple subcellular structures take part in a complex chain of events that culminate in chromosome segregation. This involves, among various steps, disassembly of adhesion complexes, reorganization of the cytoskeleton, and migration of duplicated centrosomes along the nuclear envelope so that a bipolar spindle can form. Players involved in this process include microtubule-associated motors kinesin 5, dynein, actin, and myosin II. How the dynamic changes in all these events are coordinated in space and time to ensure efficient centrosome separation and spindle assembly, remains unknown.
Recent advances in live-cell imaging and image analysis techniques made it possible to access the subcellular environment and quantitatively examine its underlying mechanisms. However, available tracking tools are not fine-tuned for the constrains and motion dynamics of centrosome pairs. This limits their tracking performance, and often demands for exhaustive parameter optimization. Moreover, when studying the dynamics of spindle formation, it is often necessary to analyze centrosomes movement in reference to the cellular and nuclear membrane; however, the available computational tools do not directly allow the analysis of the coordinated changes between different structures, in specific subcellular frames of reference. Driven by these computational limitations and the need to better characterize the crosstalk between subcellular structures during mitotic entry, Castro et al developed the open-source software Trackosome . This novel computational tool enables a quantitative analysis of the spatiotemporal dynamics of three cellular components: centrosomes, nuclear envelope and cellular membrane.
Key findings and developments
Trackosome is a freely available open-source computational tool to track the centrosomes and reconstruct the nuclear and cellular membranes, based on live imaging datasets, where the structures of interest are independently tagged. The toolbox runs in MATLAB and provides a graphical user interface for easy and efficient access to the tracking and analysis algorithms. The tool has two modules: “centrosome dynamics”, used for tracking centrosomes or other subcellular organelles in 3D and studying their spatiotemporal relations with the nucleus and cell membrane; and “nuclear envelope fluctuations”, used to reconstruct, measure and analyse the dynamic fluctuations of the nuclear membrane (or others) in 2D. Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Trackosome can be downloaded from https://github.com/Trackosome
Tracking and trajectory analysis of centrosomes is performed in the Trackosome toolbox through the «centrosomes dynamics»module. In a test setup, this module allowed tracking centrosomes with high fidelity even in highly noisy environments.
The authors went on to explore the potential of the tool for following dynamics of cellular organization during early spindle assembly. Trackosome allowed quantification of specific spatiotemporal relations between the centrosome pairs and nuclear and cell membranes, during mitotic entry. Trackosome was able to reconstruct the membranes’ surface, together with the centrosomes’ trajectories in 3D. Moreover it also allowed obtaining quantitative metrics of the intracellular reorganization that occurs in cells as they enter mitosis, namely the distance and angles between centrosomes, the eccentricity of the nuclear and cellular membranes, and the angles between the major axis of the nucleus, cell and centrosomes.
Using Trackosome, the authors were able to study centrosome trajectories, and show that they are not independent. The authors followed cell development in two cell lines, until nuclear breakdown. They found that during this stage, nuclear shape remained approximately constant and correlated with the label of chromatin, while the centrosomes exhibited complex trajectories resembling a search/adaptive path around the nucleus. To infer about the coordination of movement between the centrosomes, their trajectories were analyzed using the nucleus as a reference (which is made possible by Trackosome algorithms). The results indicated a considerable degree of coordination and synchrony among trajectory pairs. The authors discuss the hypothesis of synchronous variation of the forces applied to both centrosomes, probably driven by kinesin-5 or dynein.
The authors then used Trackosome to analyse the dynamic morphology of the nuclear envelope, using Trackosome’s “membrane fluctuations” module. The membrane oscillations are determined by calculating the orthogonal displacement of each point of the membrane with respect to its medial position. The authors were able to quantify and compare the nuclear deformations for cells in interphase and mitosis. They were able to confirm that in interphase, cells present subtle but measurable nuclear membrane movements. This behavior changes in prophase, where there is an increase of the fluctuations amplitude, reflecting the occurrence of nucleus-wide deformations. The authors explored whether Trackosome would be able to detect fluctuations of the nuclear envelope based on pharmacological alterations of the cytoskeleton and the microtubule networks. They found that disruption of the microtubule cytoskeleton significantly reduces the large scale deformations of the nucleus during this stage. The authors conclude that overall, Trackosome is a powerful tool to help unravel new elements in the spatiotemporal dynamics of subcellular structures.
What I like about this preprint
I like this preprint because in it the authors identified a gap in the currently available tools for image analysis of sub-cellular structures during the process of mitosis, and went on to create their own toolbox, and validate it in different settings. I think method development and validation is extremely important in science, and it helps not only the developers, but is useful to the scientific community in general. I also like that the authors made the tool freely available, in the spirit of open science.
- Castro D., et al, Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane, bioRxiv, 2020.
Posted on: 2 July 2020
doi: https://doi.org/10.1242/prelights.22554Read preprint
Also in the cell biology category:
CTCF is essential for proper mitotic spindle structure and anaphase segregation
Actin nucleators safeguard replication forks by limiting nascent strand degradation
BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote replication fork stability and continuous DNA synthesis
preListscell biology category:in the
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
|List by||Sergio Menchero et al.|
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
|List by||Nadja Hümpfer et al.|
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
|List by||Osvaldo Contreras|
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
|List by||Alex Eve|
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
|List by||Ana Dorrego-Rivas|
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
|List by||Ana Dorrego-Rivas|
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
|List by||Dey Lab, Samantha Seah|
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
|List by||Yamini Ravichandran|
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
|List by||Maiko Kitaoka et al.|
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
|List by||Paul Gerald L. Sanchez and Stefano Vianello|
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
|List by||Hiral Shah|
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
|List by||Madhuja Samaddar et al.|
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
|List by||Dey Lab|
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
|List by||Sandra Malmgren Hill|
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
|List by||Rob Hynds|
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
|List by||Pablo Ranea Robles|
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
|List by||Dey Lab|
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
|List by||Sandra Franco Iborra|
Biophysical Society Annual Meeting 2019
Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA
|List by||Joseph Jose Thottacherry|
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
|List by||Dey Lab, Amanda Haage|