Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivo
- Department of Applied Physics, Stanford University, United States
- Department of Bioengineering, Stanford University, United States
- Chan Zuckerberg Biohub, United States
Figures
Figure 1 with 3 supplements
Cell motility behavior is inconsistent with Levy flight.
(A) Maximum Z projection of a Tg(lck:GFP, nacre-/-) zebrafish at 12 dpf. This projection represents the first frame of a timecourse; see Figure 1—video 1. (B) Brightfield of the region of tissue …
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Figure 1—source data 1
Source data for Figure 1C.
MSD values and error bar bounds.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig1-data1-v1.txt
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Figure 1—source data 2
Source data for Figure 1D.
PSD values.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig1-data2-v1.txt
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Figure 1—source data 3
Source data for Figure 1E.
Bout distribution histogram values.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig1-data3-v1.txt
Figure 1—figure supplement 1
As in Figure 1B, with annotations.
Stitched brightfield image of the zebrafish tail, (same as Figure 1B), with the fin fold and tail fin regions indicated. Lines were added at the border between the fin fold and muscle regions of the …
Figure 1—figure supplement 2
MSD for all trajectories tracked through 15 min.
MSD for all trajectories tracked through 15 min, including all measured time intervals (n = 612). As with the subset of longer trajectories, we observe a curved MSD consistent with a persistent …
Figure 1—video 1
T cell dynamics in the larval zebrafish tail and fin fold.
Maximum Z projection of the tail of a Tg(lck:GFP, nacre-/-) at 12 dpf (GFP channel). Tiled Z stacks were recorded every 45 s for 2.5 hr (50 3 slices per stack). Tiles were assembled based on …
Figure 2 with 2 supplements
Cell speed and turning behavior are heterogeneous.
(A) Example of trajectories recorded over 3 hr at a 12 s interval (Tg(lck:GFP, nacre-/-) zebrafish; 10 dpf). Here we show a maximum Z projection of the 900th frame with trajectories overlaid; see Fig…
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Figure 2—source data 1
Source data for Figure 2B.
Correlation values and error bar bounds.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig2-data1-v1.txt
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Figure 2—source data 2
Source data for Figure 2C.
vx values for trajectories.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig2-data2-v1.txt
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Figure 2—source data 3
Source data for Figure 2D.
Speed histogram values.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig2-data3-v1.txt
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Figure 2—source data 4
Source data for Figure 2E.
Angle histogram values.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig2-data4-v1.txt
Figure 2—figure supplement 1
Range of speeds by sample.
Best linear predictor of speed based on sample identity (i.e. mean speed within the sample) vs. trajectory speeds. There is both variation in speeds from sample to sample and also a broad …
Figure 2—video 1
Heterogeneity of T cell migration.
Maximum Z projection of the tail of a Tg(lck:GFP, nacre-/-) at 10 dpf (GFP channel), with cell trajectories overlaid. A Z stack was recorded every 12 s for 3 hr (62 2 slices per stack). A maximum …
Figure 3 with 1 supplement
Heterogeneous cell migration statistics fall on a behavioral manifold.
(A) Distribution of turn angles amongst cells grouped by speed class. The distribution varies smoothly from faster cells, which tend to go straighter, to slower cells, which tend to turn around more …
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Figure 3—source data 1
Source data for Figure 3A.
Angle histogram values and error bounds by speed class.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig3-data1-v1.txt
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Figure 3—source data 2
Source data for Figure 3B.
Cosine statistic by speed class.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig3-data2-v1.txt
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Figure 3—source data 3
Source data for Figure 3C.
MSD by speed class and error bounds.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig3-data3-v1.txt
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Figure 3—source data 4
Source data for Figure 3D.
Speeds, turn angle cosines, and correlations by trajectory.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig3-data4-v1.txt
Figure 3—figure supplement 1
Variance explained by speed-turn relationship.
(A) Spline fit to speed-turn angle relationship. (B) The fraction of the variance in the turn angle summary statistic explained by speed (estimated based on the spline fit in A.), by stochasticity, …
Figure 4 with 2 supplements
Model predicts wide variation in length scales of exploration across the population.
(A) Mean persistence time as a function of cell speed, measured along trajectories (n = 710). Error bars represent 95% confidence intervals from a bootstrap over trajectories. UPT: Uniform …
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Figure 4—source data 1
Source data for Figure 4A.
Average persistence time measurement and error bounds.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig4-data1-v1.txt
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Figure 4—source data 2
Source data for Figure 4B.
MSD by speed for each time interval, and error bounds.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig4-data2-v1.txt
Figure 4—figure supplement 1
Statistics from Figures 3 and 4, with timepoints subsampled.
Panels A,B,D,E as in Figure 3A–D; Panels C,F as in Figure 4A–B; with all statistics re-calculated based on sub-sampling timepoints by a factor of 2. .
Figure 4—figure supplement 2
Speed-persistence relationship with shallower cut-off angle.
As in Figure 4A, where the persistence time is defined to be the average time before the angle deviates by .
Figure 5 with 1 supplement
Manifold is preserved under a drug perturbation to cell speeds, and in other species.
(A) Correlation between the average cosine of the turn angles along the trajectory and cell speed, for cells in control and Rockout-treatment conditions. Data for all cells is shown as well as a …
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Figure 5—source data 1
Source data for Figure 5A.
Speeds and turn angle cosines for each trajectory in each treatment (fish).
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig5-data1-v1.txt
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Figure 5—source data 2
Source data for Figure 5B.
Speed histogram values for each treatment (fish).
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig5-data2-v1.txt
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Figure 5—source data 3
Source data for Figure 5C.
Speeds and turn angle cosines for each trajectory in each treatment (mouse).
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig5-data3-v1.txt
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Figure 5—source data 4
Source data for Figure 5D.
Speed histogram values for each treatment (mouse).
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig5-data4-v1.txt
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Figure 5—source data 5
Source data for Figure 5E.
Speeds and turn angle cosines for each trajectory in each treatment (Dictyostelium).
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig5-data5-v1.txt
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Figure 5—source data 6
Source data for Figure 5F.
Speed histogram values for each treatment (Dictyostelium).
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig5-data6-v1.txt
Figure 5—figure supplement 1
Figure 5A,B, including only paired control-Rockout treatment samples.
As in Figure 5A,B, but including only those control samples with a paired Rockout treatment sample (n = 6 fish). Fish were imaged for 2.5 hr, and imaging media was replaced with media containing …
Figure 6 with 3 supplements
Single cell RNA sequencing shows moderate covariation in actin nucleation across T cells.
(A) UMAP dimensional reduction of single-cell RNA sequencing profiles of zebrafish T cells (Materials and methods) shows two main subtypes. Cluster colors are shared across panels A, B, D, and E. …
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Figure 6—source data 1
Source data for Figure 6A.
UMAP coordinates for cells.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig6-data1-v1.txt
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Figure 6—source data 2
Source data for Figure 6B.
Expression (Log10(CPM+1)) for marker genes for cells, and cluster labels.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig6-data2-v1.txt
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Figure 6—source data 3
Source data for Figure 6C.
Histogram values for correlation statistic, as well as values for the four significant genes.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig6-data3-v1.txt
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Figure 6—source data 4
Source data for Figure 6D.
Expression (counts + 1) for actb2 and arpc1b, and cluster labels.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig6-data4-v1.txt
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Figure 6—source data 5
Source data for Figure 6E.
Expression (counts + 1) for actb2 and cdc42l, and cluster labels.
- https://cdn.elifesciences.org/articles/53933/elife-53933-fig6-data5-v1.txt
Figure 6—figure supplement 1
Comparison between UMAP and index sort, over all cells.
(A) UMAP dimensional reduction of cell gene expression profiles from scRNAseq, with clusters assigned by HDBSCAN (colors). (B) Index sort data of FSC/BSC for these cells (colors correspond to …
Figure 6—figure supplement 2
Differential expression between the two main clusters.
Differential expression analysis between the two cell clusters in Figure 6—figure supplement 1. Named genes with the top 100 p values are labeled. See also Supplementary file 2.
Figure 6—figure supplement 3
Plate effect in variation within T cell cluster.
UMAP dimensional reduction of only the T cell cluster, using the self-assembling manifold algorithm, colored by sort plate. This revealed a significant plate effect involving p1. We therefore …
Appendix 1—figure 1
Comparisons between speed-persistence time relationship in simulations and data.
(A) Data (as in Figure 4A). (B) Simulation of the SPC model with empirical parameters (see Appendix 1 for details). (C) Simulation of uniform persistence time (UPT) model, with speeds and …
Appendix 1—figure 2
MSD measured on all control trajectories except those from the sample shown in Figure 2, compared with MSD measured on the trajectories from the held-out sample.
All trajectories for this sample were measured in the tail fin area, and so are not subject to potential effects due to a boundary between the fin fold and muscle region of the tail (Figure 1—figure …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Danio rerio) | Tg(lck:GFP) | Gift from Aya Ludin-Tal and Leonard Zon Langenau et al., 2004 | ||
| Chemical compound, drug | Tricaine-S, MS-222 | Pentair | ||
| Chemical compound, drug | Rockout | Sigma Aldrich | #555553 | |
| Software, algorithm | Ilastik | Sommer et al., 2011 | ||
| Software, algorithm | Custom analysis software | This paper | Available at https:// github.com/ erjerison/ TCellMigration | |
| Software, algorithm | STAR | Dobin et al., 2013 | ||
| Software, algorithm | htseq | Anders et al., 2015 | ||
| Software, algorithm | SAMalg | Tarashansky et al., 2019 |
Additional files
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Supplementary file 1
Differentially-expressed genes between the two T cell sub-clusters (Figure 6A).
Log differential expression ratio (see Materials and methods) and Bonferroni-corrected Wilcoxon rank-sum p-value are listed for each gene. Genes with at least 10-fold differential expression and Bonferroni-corrected Wilcoxon rank-sum p-value are included.
- https://cdn.elifesciences.org/articles/53933/elife-53933-supp1-v1.txt
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Supplementary file 2
Differentially-expressed genes between the T cells and putative epithelial cell clusters (Figure 6—figure supplement 1, Figure 6—figure supplement 2).
Log differential expression ratio (see Materials and methods) and Bonferroni-corrected Wilcoxon rank-sum p-value are listed for each gene. Genes with at least 10-fold differential expression and Bonferroni-corrected Wilcoxon rank-sum p-value are included.
- https://cdn.elifesciences.org/articles/53933/elife-53933-supp2-v1.txt
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Transparent reporting form
- https://cdn.elifesciences.org/articles/53933/elife-53933-transrepform-v1.pages
