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CC BY-SA 4.0
TOWARDS AN OPEN DATA EXCHANGE ECOSYSTEM: FORGING A NEW PATH FOR CELL MIGRATION DATA
ANALYSIS AND MINING
18 October 2016 public PhD defense - paola masuzzo
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
Cell migration is necessary for many physiological functions
Basementmembrane Wound
Migrating epithelial cells
CC BY-SA 4.0
Cell migration is necessary for many physiological functions
Blood vessel
Site of tissue injury
Migrating neutrophil
Basementmembrane Wound
Migrating epithelial cells
CC BY-SA 4.0
The cytoskeleton is the key structural framework responsible for cell migration
Adapted from Herzog et al., Cell Bio Lab Handbook, 1994
CC BY-SA 4.0
The cytoskeleton is the key structural framework responsible for cell migration
Adapted from Herzog et al., Cell Bio Lab Handbook, 1994
CC BY-SA 4.0
Different actin filament structures are essential for cell migration
Actin network
Filopodia
Lamellipodium
movementLeading edge
2D migration
CC BY-SA 4.0
Different actin filament structures are essential for cell migration
Actin network
Filopodia
Lamellipodium
movementLeading edge
2D migration 3D invasion
Basementmembrane
Epithelial cell
Tumor cell
Extracellular matrix
Invadopodia
Protruding bleb
Lamellipodia or pseudopodia
CC BY-SA 4.0
A typical experimental workflow for a cell migration study is composed of diverse steps
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
A typical experimental workflow for a cell migration study is composed of diverse steps
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
Several assays are available for in vitroassessment of cell migration
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
sample preparation
image acquisition
image processing
data analysis
Wound-healing assay
pipette tip
scratch
Cell-exclusion zone assay
cell-free zone
siliconestopper
Spheroid assay
multicellular spheroid
CC BY-SA 4.0
Live-cell phase-contrast and fluorescence microscopy generates quantifiable data
Servier Medical Art, CC-BY 3.0; Cell Image Library, Public Domain; Mierke et al., 2011
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
Image processing is a multi-step operation comprising segmentation and tracking
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0, Harder et al., 2015
imagepre-processing
celltracking
cellsegmentation
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
Quantitative parameters are then extracted for cell sheet and single-cell trajectories
Image processed with CELLMIA, UGent (Van Troys M, Ampe C) and DciLabs
area in timeµm²/min
coordinates (x, y, t)µm/min
CC BY-SA 4.0
Ultimately, data analysis enables interpretation of the experiment
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0; O’ Brien et al., 2014
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
The Ghent platform enables automation of high-throughput cell migration experiments
Phase-contrastlive-cell imaging
time-lapse: 16-48 hinterval: 15-20 min
Adapted from Lynn Huyck, PhD thesis, 2012 (promoter Van Troys M)
CC BY-SA 4.0
Images are automatically processed
Adapted from Lynn Huyck, PhD thesis, 2012 (promoter Van Troys M); images processed with CELLMIA, UGent and DciLabs
t = 0h t = 24h
t = 0h t = 36h
CC BY-SA 4.0
Such high-throughput experiments produce complex and rich data sets
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
sample preparation
image acquisition
image processing
data analysis
• paper laboratory notebooks
• electronic laboratory notebooks
• spreadsheets• text files• protocols• papers...
• raw files• XML files• proprietary
microscope or acquisition software files ND2 for Nikon, LIF for Leica, OIB or OIF for Olympus, LSM or ZVI for Zeiss
• image files with pixel values and metadata
• png, jpeg, tiff, avi• text files
describing processing algorithms
• text files describing extracted features
• graphs, plots• analysis pipelines• text files
describing computational algorithms...
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
The overall objective of this PhD is to advance bioinformatics for cell migration
Cell migration experiments have become de factohigh-throughput, but bioinformatics has lagged behind
Due to lack of automated systems and appropriate algorithms, a big proportion of cell migration data is still not exploited
The heterogeneity of the field hampers open data exchange, impeding advanced data analysis and mining
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
CellMissy is our open-source tool for cell migration data management and analysis
0 3h 6h
wound
cells
Experiment
Data Analyzer
Data Loader
Collective cell migration Single-cell migration
Experiment Manager
Masuzzo et al., Bioinformatics, 2013; https://github.com/compomics/cellmissy
CC BY-SA 4.0
CellMissy enables efficient data exploration and analysis
time (min)
Area
()
wound areacell-covered area
CC BY-SA 4.0
A primary focus of data analysis is statistical comparison of samples
analysis report with graphs,tables and results
cell sheet velocity (µm²/min)
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-
cell analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
Cell migration can occur in both collective and individual fashion
Collective migration
Multicellular streaming
Mesenchymal
Amoeboid (blebs)
Amoeboid (pseudopodia, filopodia)
INDIVIDUAL MIGRATION
COLLECTIVE MIGRATION
Adapted from Friedl et al., J. Exp. Med., 2010
CC BY-SA 4.0
Many informative parameters can be derived from single-cell trajectories
Masuzzo et al., under review, 2016
x
ysingle cell
CC BY-SA 4.0
Many informative parameters can be derived from single-cell trajectories
Masuzzo et al., under review, 2016
ࢻ
Euclideandistance
Cumulativedistance
x
ysingle cell
CC BY-SA 4.0
Many informative parameters can be derived from single-cell trajectories
Masuzzo et al., under review, 2016
ࢻ
Euclideandistance
Cumulativedistance
x
ysingle cell parameter mathematical description
di: instantaneous displacement of the cell centroid between adjacent time points
si: instantaneous speed between adjacent time points
αi: turning angle between consecutive steps
dtot: cumulative distance, total distance travelled
dnet: Euclidean distance, net distance travelled
ep_dr: end-point directionality ratio (confinement ratio, meandering index)
MD: median displacement
MS: median speed
MTA: median turning angle
CC BY-SA 4.0
Trajectory-centric parameters are instead computed on each cell and then averaged for the cell population
...
trajectory 1
trajectory 2
trajectory 3
trajectory 4
trajectory 5
CC BY-SA 4.0
The new single-cell module allows for both these computations to take place
Masuzzo et al., under review, 2016
...
trajectory 1
trajectory 2
trajectory 3
trajectory 4
trajectory 5
trajectory-centric parameters
trajectory displacement (µm)
dens
ity
step displacement (µm)
dens
ity
pool of migration steps
step-centric parameters
CC BY-SA 4.0
A flexible two-step filtering criterion is implemented for data quality control
Masuzzo et al., under review, 2016
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
More advanced features are needed to describe the complexity of the phenomenon
Masuzzo et al., in preparation, 2016
CC BY-SA 4.0
The enclosing circle set is a new way to describe local structure of trajectories
Masuzzo et al., in preparation, 2016
radius: 6 µmnr_circles: 14
directionof motion
CC BY-SA 4.0
The enclosing circle set is a new way to describe local structure of trajectories
Masuzzo et al., in preparation, 2016
radius: 6 µmnr_circles: 14
directionof motion
radius: 3 µmnr_circles: 22
directionof motion
CC BY-SA 4.0
The fractal dimension is derived from the enclosing circle set
𝐹𝐷 (𝑆 )=lim𝑟→0
¿¿
Masuzzo et al., in preparation, 2016
FD=0.35 FD=0.83
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
Data and metadata exchange options are already available in CellMissy
lab B
This is one file in CellMissy! (≈10 MB)
lab A
CC BY-SA 4.0
It only needed some water to grow
Cell migration workshop, Ghent, March 2014; Masuzzo et al., Trends in Cell Biology, 2015
CC BY-SA 4.0
An open data exchange ecosystem for cell migration research is now on its way
Masuzzo et al., Trends in Cell Biology, 2015
CC BY-SA 4.0
An open data exchange ecosystem for cell migration research is now on its way
Masuzzo et al., Trends in Cell Biology, 2015
CC BY-SA 4.0
An open data exchange ecosystem for cell migration research is now on its way
Masuzzo et al., Trends in Cell Biology, 2015
CC BY-SA 4.0
This open data ecosystem falls into the broader context of open science
Knoth and Pontika, Open Science Taxonomy, figshare, 2015
CC BY-SA 4.0
Open access is another key factor in the open science equation
Knoth and Pontika, Open Science Taxonomy, figshare, 2015
CC BY-SA 4.0
The impacts of open access are very broad and affect many areas
Tennant, Masuzzo et al., F1000Research, 2016; Wikimedia Commons, Public Domain
CC BY-SA 4.0
Publish your work open access can bring you enormous benefits
CC-BY Danny Kingsley & Sarah Brown
CC BY-SA 4.0
Publish your work open access can bring you enormous benefits
CC-BY Danny Kingsley & Sarah Brown
CC BY-SA 4.0
Publish your work open access can bring you enormous benefits
CC-BY Danny Kingsley & Sarah Brown
CC BY-SA 4.0
Open access also allows automatic knowledge extraction through text mining
automatically detect a set of core information reported when describing cell migration experiments
check for nomenclature consistency, the use of common terms or ontologies to describe the same concept
construct a knowledge map to describe the state-of-the-art, especially in terms of cell motility-related compounds and cancer cell lines
CC BY-SA 4.0
Introduction to cell migration
Research problems
ResultsCellMissy: an automated tool for cell
migrationA new CellMissy module for single-cell
analysisEngineering features to describe
stochasticityTowards an open data exchange
ecosystem
Conclusions and future perspectives
CC BY-SA 4.0
This PhD has tackled key bioinformatics challenges in cell migration research
CellMissy is the first free and open-source tool for the management, annotation and storage of cell migration experiments
A new dedicated module, together with novel features, enable detailed and more complex quantification ofsingle-cell migration experiments
International research efforts are currently spent towards the establishment of an open data exchange ecosystem, opening the way to more advanced data analysis and mining strategies
CC BY-SA 4.0
These results have paved the way to even more exciting opportunities
CellMissy has already been extended with dose-response analysis capabilities, and more development is planned to allow meta-analyses to take place
Further engineering, validation, and selection of single-cell migration features is planned; these features will then be used to automatically detect and classify migratory phenotypes
Joined efforts of MULTIMOT and the CMSO will ultimately enable global data dissemination in the field, allowing data re-use, re-discovery and re-purpose