Altered thymic niche synergistically drives the massive proliferation of malignant thymocytes
- Computational Developmental Biology Group, Institute of Biodynamics and Biocomplexity, Utrecht University, Netherlands
- Department of Hematology, Oncology, Immunology, and Rheumatology, University, Hospital of Tübingen, Germany
Figures
Figure 1 with 3 supplements
The virtual thymus model enables spatiotemporally resolved clonal analysis.
(A) Schematic overview highlighting six key steps during T-cell development, which are integrated into the virtual thymus model: (1) ETPs enter the thymus niche; (2) they receive Dll4 and IL-7 signals from the thymic epithelial cells (TECs). Triggered by these signals, (3) thymocytes undergo proliferation and (4) differentiation into two distinct T-cell sublineages (5). Finally, thymocytes undergo selection, either leaving the organ or undergoing cell death (6). (B–C) Experimentally measured (‘medaka’) and computationally modeled (‘virtual’) cell speed (B) and cell directionality (C) for ETPs and thymocytes. Bars are mean values, and error bars standard deviation. (D) Timeline of medaka embryonic development (top) compared to simulated time (bottom). As indicated by the cartoon at the bottom, the first ETP enters the thymus roughly at 2.5 days post-fertilization (dpf) (t=0 hr in the simulation). At roughly 60 hr (roughly 5 dpf), the thymus reaches its homeostatic cell population, with both cell entry and exit. (E) Representative snapshots of the simulation at homeostasis showing spatial expression patterns and signaling activity of components of IL7R and Notch1 signaling pathways in TECs (top two panels) and thymocytes (bottom four panels). Data are shown in arbitrary units normalized to a scale from 0 to 1. (F) Left: Cartoon explaining the asynchronous arrival (homing) of new cells into the organ, their clonal expansion, and asynchronous cell death or exit. Right: Visualization of clonal diversity in a typical simulation; each color shade uniquely indicates a clonal lineage. The height of each colored patch indicates the number of cells in that clone, the length indicates simulation time. For illustrative purposes, a black arrow indicates the homing of a sample of lineages. (G) Data from the right panel in (F) was normalized to time of homing. This visualization highlights developmental phases of thymocyte lineages. Gray arrowheads indicate rounds of cell division. Scale bar: 50 cells. Abbreviations: ETP = early thymic progenitor, T=thymocyte, N=number of replicates (biological or computational).
Figure 1—figure supplement 1
The virtual thymus represents a slice of the organ.
Three-dimensional renders of the simulation. (A) Showing only thymic epithelial cells (TECs) in cyan. (B) Showing both thymocytes (bright green) and TECs (cyan). (C) Detail showing clonal thymocyte lineages. Each lineage was assigned a randomly selected color, TECs in dark gray. In homeostasis, most clones consist of 1–8 cells.
Figure 1—video 1
Simulation time-lapse.
Three-dimensional renders of a typical simulation where each thymocyte lineage was assigned a randomly selected color. Thymic epithelial cells (TECs) are shown in dark gray. Simulation runs for 48,000 steps, where 1 step is 15 s. Note how thymocytes can crawl over and under TECs.
Figure 1—video 2
Simulation time-lapse with fewer cells to highlight clonal dynamics.
In this simulation, a total of eight early T-cell progenitors (ETPs) were introduced into the simulation at the same time to highlight clonal expansion and motility within the organ (00:10–02:00 s), and later cell exit and cell death (starting at 02:08 s). Three-dimensional renders of a simulation where each thymocyte lineage was assigned a randomly selected color. Thymic epithelial cells (TECs) are shown in dark gray. Each simulation step is 15 s.
Figure 2 with 2 supplements
Thymic epithelial cell (TEC) density influences thymocyte proliferation via interleukin-7 receptor (IL7R) signaling.
(A) Left: Detail of confocal section highlighting the tight spatial interaction between TECs and thymocytes (T). Scale bar: 5 µm. Right: Detail from a three-dimensional render of a simulation snapshot; TECs cyan, thymocytes green. (B) Parameter permutations tested. (C) Impact of parameter permutations on average homeostatic cell population. Bars indicate means, error bars standard deviation. The abbreviations ‘S’, ‘P’, and ‘D’ correspond to parameters ‘Size’, ‘Number of Protrusions’, and ‘Density’, respectively, as in panel (B). (D) Clonal lineages normalized to time of thymic entry for reference (left), a scenario with low average population (middle) and a scenario with high average population (right). Scale bar: 100 cells. (E) Extracellular IL-7 gradient in simulations; sum projection of all z-planes of a simulated confocal stack. Units are arbitrary. (F) Mean extracellular IL-7 concentration in the entire simulated volume. Note that these values are lower than in (E) because of averaging over the volume, including empty space (black areas in (E)). (G) Thymocyte population size over time averaged over several simulation runs. Shaded area indicates standard deviation. (H) Illustration of experimental setup for IL-7KO and TEC:IL-7HI. At least three technical replicates were done for the injection of each construct. (I) Representative images of embryos stained with green fluorescent protein (GFP) (green) and phospho-histone 3 (pH3) (red) of wild-type (WT), IL-7KO, and TEC:IL-7HI. Scale bar: 20 µm. (J) Numbers of pH3 positive cells per thymus normalized to mean of WT. N represents the number of individual fish. Data show means ± standard deviation.
Figure 2—figure supplement 1
Statistical analysis of simulated data.
(A) Three-dimensional rendering of thymic epithelial cells (TECs) in the simulation with the indicated parameter alterations. Orange: IL-7-secreting TECs. Cyan: non-secreting TECs. Dotted outline indicates thymus outline in the simulation. (B) Partial residual effect plot showing linear model fit on log2-transformed thymic population size. Shaded area is 95% confidence interval. (C) Estimated coefficients and p-values of the linear model. Significance codes: <0.001 ‘***’;<0.01 ‘**’; <0.05 ‘*’. All parameters have a statistically significant effect on cell number. Parameter interactions are also statistically significant, which indicates that changing combinations has a greater effect than the sum of individual changes.
Figure 2—figure supplement 2
Reduced thymus volume upon IL-7KO.
(A) Experimental design: gRNA targeting the signal peptide of il-7 was co-injected with Cas9 into the one-cell-stage blastomere of Tg(lck:gfp) medaka. The embryo was raised until 8 days post-fertilization (dpf). Whole-mount immunostaining was performed using anti-green fluorescent protein (GFP) and M phase marker phospho-histone 3 (pH3). The thymus was imaged using confocal microscopy, and embryos were genotyped by sequencing. (B) Schematic of the il-7 gene structure and binding site for the crRNA for CRISPR-Cas9 gene editing in the signal peptide region of exon 2. Zoom in: Representative sequencing data analyzed with decodr.org (Bloh et al., 2021) software. (C) Representative image of immunostaining of Tg(lck:gfp) in wild-type (WT) and IL-7KO and evaluation of the thymus size using the area measurement tool in Imaris software (yellow). Scale bar: 20 µm. (D) Quantification of thymus size: Thymus area in µm2 in WT and IL-7KO. N represents the number of biological samples. For statistics, unpaired t-test with Welch’s correction was used. Data show means ± standard deviation. Significance threshold was set to p=0.05. ** means p<0.01. Panels A and B were created with BioRender.
Figure 3 with 1 supplement
High interleukin-7 receptor (IL7R) signaling promotes proliferation.
(A) Illustration of scenarios without extracellular IL-7 depletion (left) and with extracellular IL-7 depletion (right). (B) Ordinary differential equation used to model the IL7R signaling activity. Parameters that were modified are highlighted. (C) Effect of IL7R signaling-related parameter permutation. Bars indicate means and error bars standard deviation. The abbreviations ‘D’, ‘SD’, and ‘SA’ correspond to ‘Depletion’, ‘Signaling Deactivation Rate’, and ‘Signaling Activation Rate’, respectively, as indicated in panels (A) and (B). (D) Left: Mean extracellular IL-7 concentration in the entire simulated volume. Right: Extracellular IL-7 gradient in simulations; sum projection of all z-planes of a simulated confocal stack. Units are arbitrary. The introduction of IL-7 depletion by thymocytes leads to a slight reduction in extracellular IL-7 availability.
Figure 3—figure supplement 1
Statistical analysis of simulated data.
(A) Partial residual effect plot showing linear model fit on log2-transformed thymic population size. Shaded area is 95% confidence interval. (B) Estimated coefficients and p-values of the linear model. Significance codes: <0.001 ‘***’; <0.01 ‘**’; <0.05 ‘*’. Although the population size is slightly reduced for IL-7 depletion, the effect is not statistically significant. In contrast, IL7R signaling activation and deactivation have a statistically significant effect. None of the interactions have statistically significant effects.
Figure 4 with 8 supplements
Systematic screen shows that lower thymic epithelial cell (TEC) density promotes malignant expansion.
(A) Schematic representation of the major lesions to interleukin-7 receptor (IL7R) that were implemented in the model. (B) Representative clonal plot highlighting in black the lesioned clone. (C) We defined clone size as the maximum number of terminal leaves of a lineage, regardless of eventual fate of each cell. Clone size distribution in the reference simulation (REF), compared to IL7RDA and IL7RHI. REF: N=20 simulations, with 2088 clones total: IL7RDA: N=13 simulations with 1330 non-lesioned clones and 13 lesioned clones. IL7RHI: N=13 simulations with 1336 non-lesioned clones and 13 lesioned clones. (D) Schematic of tested scenarios shown in (E). (E) Simulated permutations ordered along increasing mean lesioned clone size for the IL7RHI condition. The expected effect on proliferation is a qualitative estimate based on preliminary simulations. A total of 1580 permutations were tested with a varying amount of replicates per permutation. Error bars indicate standard deviation. Note that in (C) and (E) the axis is in base-2 logarithmic scale to better illustrate rounds of cell division.
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Figure 4—source data 1
Source data file for visualization in Figure 4E and Figure 4—figure supplement 1B.
In the data file, each row corresponds to the log2-transformed average clone size for one-cell genotype (normal or lesioned) from one single independent replicate simulation. Additionally, the parameter values used in that run are listed in separate columns. The ‘grouping’ column corresponds to the simulated scenarios (parameter permutation). The ‘simulation_datafile’ column is the unique identifier of a given simulation run.
- https://cdn.elifesciences.org/articles/101137/elife-101137-fig4-data1-v1.csv
Figure 4—figure supplement 1
Clones in control simulations show similar sensitivity to parameter alterations as non-lesioned clones.
(A) Schematic of tested scenarios shown in (B). (B) Simulated permutations ordered along increasing mean lesioned clone size for the IL7RHI condition compared to control simulations without a lesioned clone. The top panel is identical to the top panel in Figure 4E and is replicated here for easier visual comparison. The expected effect on proliferation is a qualitative estimate based on preliminary simulations. A total of 1580 permutations were tested with a varying amount of replicates per permutation. Note that control simulations were run only for a subset of parameter configurations. Error bars indicate standard deviation. Note that in (B) the axis is in base-2 logarithmic scale to better illustrate rounds of cell division.
Figure 4—figure supplement 2
Modulation of proliferation-related parameters affects lesioned thymocytes more strongly.
(A) Clones with IL7RHI lesion. (B) Clones with IL7RDA lesion. (C) Control simulations without lesioned clones. Note that the y-axis of all plots is base-2 logarithmic to better illustrate rounds of cell division. Error bars indicate standard deviation. By modulating proliferation parameters, lesioned clones gain up to 6 rounds of division, while non-lesioned clones gain only 2 rounds of division. The expected effect on proliferation is a qualitative estimate based on preliminary simulations.
Figure 4—figure supplement 3
Modulation of parameters affecting IL7-signaling has almost no effect on lesioned clones.
(A) Clones with IL7RHI lesion. (B) Clones with IL7RDA lesion. (C) Control simulations without lesioned clones. Note that the y-axis of all plots is base-2 logarithmic to better illustrate rounds of cell division. Error bars indicate standard deviation. By modulating IL-7 signaling parameters, lesioned clones do not gain extra rounds of division, while non-lesioned clones gain up to 3 rounds of division. The expected effect on proliferation is a qualitative estimate based on preliminary simulations.
Figure 4—figure supplement 4
A secondary lesion delaying differentiation doubles proliferative potential.
(A) Clones with IL7RHI lesion. (B) Clones with IL7RDA lesion. (C) Control simulations without lesioned clones. Note that the y-axis of all plots is base-2 logarithmic to better illustrate rounds of cell division. Error bars indicate standard deviation. Secondary clonal lesions lead to a gain of 4 rounds of division in the lesioned clones, with no effect on non-lesioned clones. Expected effect on proliferation is a qualitative estimate based on preliminary simulations. (D) Mean extracellular IL-7 concentration over time for selected simulations shown in (A–C). The increase in extracellular IL-7 by autocrine activity of lesioned clones is not enough to promote substantial proliferation of non-lesioned cells.
Figure 4—figure supplement 5
Parameters affecting thymic epithelial cell (TEC) distribution have opposing effects on lesioned and non-lesioned clones.
(A) Clones with IL7RHI lesion. (B) Clones with IL7RDA lesion. (C) Control simulations without lesioned clones. Note that the y-axis of all plots is base-2 logarithmic to better illustrate rounds of cell division. As TEC architecture is made denser, lesioned clones lose up to 2 rounds of cell division, while non-lesioned clones gain 2 rounds of cell division. The expected effect on proliferation is a qualitative estimate based on preliminary simulations.
Figure 4—figure supplement 6
Sparse thymic epithelial cell (TEC) distribution is among permutations that most enabled lesioned clone expansion.
Shown are the top 8 conditions from Figure 4E. (A) Clones with IL7RHI lesion. (B) Clones with IL7RDA lesion. (C) Control simulations without lesioned clones. Note how lesioned clones with autocrine IL-7 production favor expansion of non-lesioned clones as well. The y-axis of plots in (A–C) is base-2 logarithmic to better illustrate rounds of cell division. Points are mean values, and error bars indicate standard deviation. Expected effect on proliferation is a qualitative estimate based on preliminary simulations. (D) Volume occupied by thymocytes (1 thymocyte ≅ 33.5 μm3) of a hypothetical lesioned clone compared to the volume of the virtual thymus (≅ 7854 μm3). The y-axis is scaled in millions of cubic micrometers. The volumes strongly diverge after 12 rounds of cell division, indicating extremely dense cell packing that would result in hyperplasia or metastasis in vivo.
Figure 4—video 1
Simulation time-lapse with lesioned clone.
Two-dimensional projections of the virtual thymus volume showing time-lapse of simulations representing conditions in Figure 4B. Each thymocyte lineage was assigned a unique color; the lesioned clone was colored in black. Representative position of thymic epithelial cells (TECs) shown in light blue (non-secreting) and light orange (IL-7-secreting). Movies were synchronized to the time of entry of the first thymocyte.
Figure 4—video 2
Simulation time-lapse.
Two-dimensional projections of the virtual thymus volume showing time-lapse of simulations representing conditions in Figure 4—figure supplement 1A–C. Specifically, left column represents the condition with reduced proliferation, and the right column the condition with increased proliferation. Note how, with increased proliferation, newcomer cells struggle to enter deeper into the organ due to cell crowding. Each thymocyte lineage was assigned a unique color; the lesioned clone was colored in black. Representative position of thymic epithelial cells (TECs) shown in light blue (non-secreting) and light orange (IL-7-secreting). Movies were synchronized to the time of entry of the first thymocyte.
Figure 5 with 1 supplement
Interplay of interleukin-7 receptor (IL7R) and NOTCH1 potentiates clonal expansion in vivo.
(A) Schematic of Notch1 and IL7R signaling and their regulation of thymocyte cell cycle entry, proliferation, and differentiation as implemented in the virtual thymus model. (B) Simulated data; rounds of cell division of normal and lesioned clones with different types of lesions in NOTCH1 or IL7R signaling. Note that the y-axis is base-2 logarithmic. Green boxes: condition/lesion present. Gray boxes: condition/lesion absent. (C) Illustration of plasmids for DNA microinjection for transient overexpression of the different genes. Note that the expression of green fluorescent protein (GFP) was used to select successfully injected embryos. (D) Representative image: (left) of the WT control at 9 days post-fertilization (dpf) where thymocytes are labeled in green with normal thymus size; (middle) of a thymus hyperplasia phenotype at 7 dpf; (right) same embryo developed T-cell acute lymphoblastic leukemia (T-ALL) phenotype at 9 dpf, where infiltration in other organs was detected, namely in central nervous system (CNS) and gut. (E) Percentage of phenotypes: normal thymus, thymus hyperplasia, and T-ALL at 11 dpf. For each construct injection, we did at least three technical replicates. For detailed statistics, see Figure 5—source data 1. Statistical data rounded to 4 decimal places. (F) Number of pH3 positive cells per thymus counted during confocal imaging. (G) Representative confocal images of immunostaining against pH3 (red) and GFP (green). Scale bar: 20 µm. N represents the number of biological samples.
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Figure 5—source data 1
Detailed statistics for phenotype comparison using Fisher’s exact test and pairwise comparisons; adjusted p-values were calculated with the Benjamini and Hochberg method.
Values reported in figures are the adjusted p-values. Significance threshold was set to 0.05. Data rounded to 4 decimal places.
- https://cdn.elifesciences.org/articles/101137/elife-101137-fig5-data1-v1.docx
Figure 5—figure supplement 1
Increased il7 expression upon NICDΔPEST-mycn overexpression.
(A) Schematic depiction of NOTCH1 signaling (left) and overexpression of notch1b intracellular domain (NICD) (right). The engagement of NOTCH1 receptor with its ligand (DLL4) leads to its cleavage, and release and translocation of the NICD in the nucleus. NICD, through its interaction with other co-factors, triggers the expression of the target genes. Overexpression of NICD leads to activation of NOTCH signaling independent of the ligand. (B) Relative expression of il7r and il7 of isolated thymocytes from wild-type (WT) compared to those expressing both NICDΔPEST and mycn. Each dot represents data from an individual sorted embryo. Data are log10 means ± standard error of the mean. Statistics: unpaired Mann-Whitney test, significance threshold was set to 0.05. (C) Whole-mount in situ hybridization (WISH) with the il7 probe of freshly hatched yolk sac WT and NICDΔPEST and mycn larvae. Scale bar: 100 µm. (D) Pairwise sequence alignment was done using EMBOSS Needle and the Needleman-Wunsch algorithm (Madeira et al., 2022), highlighting the partial medaka IL7R protein sequence and IL7RNPC insertion mutation of amino acids NPC at position 266 in the extracellular juxtamembrane-transmembrane interface. (E) Relative lck expression quantified by qPCR of sorted WT thymocytes compared to those in IL7RHI and IL7RNPC. The lck expression was normalized to the housekeeping gene ef1a. Each dot represents an individual sorted embryo. Data are log10 means ± standard error of the mean. Statistics: unpaired Mann-Whitney test. Significance threshold was set to p=0.05. * means p<0.05.
Figure 6
Interleukin-7 (IL-7) supplied by the niche can lead to thymus hyperplasia.
(A) Simulated data; rounds of cell division of normal and lesioned clones for different combinations of lesions and thymic epithelial cells (TECs) expressing IL-7 ubiquitously. Note that some conditions are reproduced from Figure 5B for easier comparison. (B) Left panel: Frequency of thymus hyperplasia and T-cell acute lymphoblastic leukemia (T-ALL) phenotype observed in the injected embryos at 11 days post-fertilization (dpf). For detailed statistics, see Figure 5—source data 1. Statistical data rounded to 4 decimal places. Note that some data from Figure 5E are repeated here to facilitate a better comparison. N represents the number of biological samples. Right panel: Representative images at 10 dpf after co-injection of lck:gfp-NICD∆PEST-mycn and ccl25a:tagRFP-il-7 constructs. Arrows indicate green fluorescent protein (GFP)-expressing malignant thymocytes in the thymus, brain, and gut. Scale bar: 400 µm. (C) We propose a hypothetical negative feedback loop from proliferation to differentiation, which could explain the discrepancy between in silico predictions and in vivo observations.
Appendix 1—figure 1
Overview of simulation components.
(A) Schematic representation of model components at the tissue, cell, and subcellular scale. (B) Flowchart illustrating the model operation with references to equations shown in the text.
Appendix 1—figure 2
Biomechanical interaction zones.
Schematic representation of the different interaction zones that are used for calculating biomechanical contact forces. The radii of the interaction zones in the image have been scaled assuming two spherical particles of identical radius.
Appendix 1—figure 3
Active motility model.
Schematic flowchart illustrating how cell location and state affect cell motility. Early thymic progenitors (ETPs) entering the thymus for the first time (‘immigrating’), mature thymocytes leaving the thymus after positive selection (‘emigrating’), and thymocytes at various stages of development that accidentally exit the thymus volume (‘accidentally exit’) have a strong directed component and weak random component to their migration. Otherwise, resident thymocytes at all stages of development do a random walk if they are in the correct thymic compartment, or a biased random walk if they are not in the correct thymic compartment.
Appendix 1—figure 4
Intracellular signal transduction model.
(A) Schematic flowchart illustrating the intracellular IL-7 signal transduction model. Early thymic progenitors (ETPs) entering the thymus for the first time are labeled as ‘immigrants’ and undergo an initialization of variables. (B) Schematic flowchart illustrating the intracellular Notch signaling model.
Appendix 1—figure 5
Differentiation model.
Schematic flowchart illustrating how cell differentiation stage is updated at every simulation step. Early thymic progenitors (ETPs) entering the thymus for the first time are labeled as ‘immigrants’ and undergo an initialization of variables.
Appendix 1—figure 6
Proliferation model.
Schematic flowchart illustrating the cell proliferation model. At each simulation step, cells first check if they completed the cell cycle and divide if yes. Next, if a cell is already past the G1 phase, it is committed to finish the cell cycle. Note that this condition is checked before the cell state, hence a differentiated cell could divide once if it differentiated while already committed to the cell cycle. Only undifferentiated cells (‘pre-T’) can start a new cell cycle, which is conditional on sufficient pro-proliferative IL-7 and Notch signals.
Tables
Table 1
Clonal lesions and their effects.
| Lesion | Explanation |
|---|---|
| IL7RWT | The concentration of IL7R receptor in the lesioned clone was set to the maximum attainable in wild-type thymocytes. Thus, this lesion is representative of an extreme example among the non-lesioned population and was included as a control. |
| IL7RDA | This concentration of IL7R receptor in the lesioned clone was set to the maximum attainable in wild-type thymocytes. Moreover, the receptor was constitutively active, irrespective of the presence of IL-7 ligand. |
| IL7RHI | The concentration of IL7R receptor in the lesioned clone was set to 10-fold higher than the maximum attainable in wild-type thymocytes. |
| IL-7 autocrine | Lesioned clones secrete IL-7 at the same rate as TECs, acting as additional sources in Equation 4. |
| NOTCH1DA | Lesioned clones had constitutively active Notch signaling irrespective of the presence of Delta ligand. The levels of Notch signaling were set to the maximum attainable in non-lesioned thymocytes and could not be reduced. |
| Delayed differentiation | The lesioned clone had its rate of differentiation halved, effectively doubling the duration of the proliferative phase. |
| Slower cell speed | The lesioned clone’s maximum speed was half of the non-lesioned population’s maximum speed. |
Table 2
Parameters varied in this work.
For a full list of parameters and their values, please refer to Appendix 1 and to Aghaallaei et al., 2021.
| Symbol | Values tested(reference in bold) | Description |
|---|---|---|
| N | 2; 3; 4 | Number of concentric subdivisions in algorithm to generate TEC positions. The higher the value, the larger the number of TECs, thus the larger the TEC density. |
| pTEC | 3; 4; 5 | Number of protrusions initialized for each TEC. |
| rTEC | 2.0 μm; 2.5 μm; 3.0 μm | Radius of the main TEC body. Also scales the radius of the spheres in the TEC protrusions. |
| DEPL | True; False | Boolean flag that sets if the simulation has thymocytes that internalize IL-7 according to Equation 4 in Materials and methods (True) or if it defaults to Equation 3 in Materials and methods (False). |
| aIL-7 | 120 hr–1; 240 hr–1; 480 hr–1 | IL7R signaling activation rate |
| dIL-7 | 25 hr–1; 50 hr–1; 100 hr–1 | IL7R signaling deactivation rate |
| θprol | 1.3; 1.4; 1.5 | Threshold level of IL-7 and Notch signaling activity required to progress through G1 phase and to commit to the cell cycle. |
| μ | 5 hr; 7 hr; 9 hr | Mean cell cycle duration. |
| Tdiff | 15 hr; 24 hr; 33 hr | Minimum duration of the proliferative phase before terminal differentiation. |
Appendix 1—table 1
Parameters defining initial condition.
All parameters were adapted from Aghaallaei et al., 2021, unless noted.
| Symbol | Reference value | Description |
|---|---|---|
| a | 50 μm | Long hemi-axis of thymus cylindrical ellipse. |
| b | 25 μm | Short hemi-axis of thymus cylindrical ellipse. |
| hc | 5 μm | Height of thymus cylindrical ellipse. |
| g | 2 μm | Spatial discretization for solving IL-7 reaction-diffusion equation. |
| t | 15 s | Duration of one simulation step. |
| rTEC | 2.5 μm | Radius of the main TEC body. Also scales the radius of the spheres in the TEC protrusions. |
| rC | 2 μm | Radius of thymocytes. |
| N | 3 | Number of concentric subdivisions in algorithm to generate TEC positions. The higher the value, the larger the number of TECs, thus the larger the TEC density. |
| pTEC | 4 | Number of protrusions initialized for each TEC. |
| DEPL | False | New parameter introduced in this work. Boolean flag that sets if the simulation operates with thymocytes as IL-7 sinks according to Equations 10 and 12 (True) or if it defaults to having no sink terms (False). |
Appendix 1—table 2
Simulation parameters.
All parameters were adapted from Aghaallaei et al., 2021, unless noted.
| Symbol | Reference value | Description |
|---|---|---|
| γ | 4·10–7 N·s·μm–1 | Friction of the environment. |
| kspawn | 0.45 hr–1 | Rate of thymocyte entry into the simulation from two separate positions in the simulation box, resulting in a net influx of 0.9 thymocytes per hour. |
| δadh | 1.3 | Scaling factor to define neighborhood and adhesive interaction distances. |
| δol_max | 0.5 | Scaling factor to define the inner repulsive interaction zone. |
| δol | 0.85 | Scaling factor to define the outer repulsive interaction zone. |
| dol_min | 0.1 μm | Defines a neutral zone of no adhesive or repulsive forces. |
| μS, imm | 720 μm·hr–1 | Mean speed of cells immigrating into or emigrating out of the thymus. |
| μS, res | 150 μm·hr–1 | Mean speed of cells resident in the thymus |
| σS | 0.5 | Scaling factor for cell speed variance. |
| τ | 1 (wild-type, non-resident) τdiff (wild-type, resident) 0.5 (speed lesion) | Scales the cell speed. In this work, the possibility of including a speed lesion was introduced by setting the parameter to 0.5 for lesioned clones only. |
| DIL-7 | 1·10–12 m2·s–1 | Extracellular IL-7 diffusion coefficient. |
| kIL-7 | 0.0167 hr–1 | Extracellular IL-7 degradation rate. |
| aIL-7 | 240 hr–1 | New parameter introduced in this work. IL7R signaling activation rate (reference value equivalent to previous work). |
| dIL-7 | 50 hr–1 | IL7R signaling deactivation rate. |
| kσNotch | 0.029 hr–1 | Notch signaling deactivation rate. |
| κ | 0.3 | Notch-independent differentiation rate. |
| Tdiff | 24 hr | Minimum duration of the proliferative phase before terminal differentiation. |
| ddiff_lesion | 1 (wild-type) 0.5 (differentiation lesion) | New parameter introduced in this work. Scales the rate of differentiation. |
| θdiff | 0.4 | Threshold level of IL-7 signaling activity required to differentiate into γδ+ T-cell subtype. |
| Tmat | 24 hr | Duration of the maturation phase before thymic selection |
| μ | 7 hr | Mean cell cycle duration. |
| k | 50 | Shape parameter scaling the variance of the cell cycle distribution function. |
| tM | 0.5 hr | Duration of the M phase of the cell cycle. |
| κS | 0.5 | Fraction of the cell cycle duration allocated to the S phase. |
| θprol | 1.4 | Threshold level of IL-7 and Notch signaling activity required to progress in G1 phase and to commit to the cell cycle. |
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Altered thymic niche synergistically drives the massive proliferation of malignant thymocytes
eLife 13:RP101137.
https://doi.org/10.7554/eLife.101137.3
