Main

In different morphogenetic contexts, apoptosis has been shown to have an essential role in tissue folding; however, the cellular mechanisms involved remain mostly unknown10,11,12. To characterize apoptosis-dependent folding, we focused on Drosophila leg epithelium morphogenesis, a process that has been shown to rely on local apoptosis11 (Extended Data Fig. 1a, Supplementary Video 1). Interestingly, we discovered that leg disc folding follows a stereotypical sequence, with fold progression following the spreading of cell death, beginning in the most ventral part, then progressing laterally to end in the most dorsal region of the developing leg (Fig. 1a, b, Extended Data Fig. 1b). To unravel the link between apoptotic cells and fold formation, we first focused on apoptotic cell behaviour using live imaging. In the leg epithelium, apoptosis follows the classical morphological steps including cell shrinkage, membrane blebbing and fragmentation into apoptotic bodies (Extended Data Fig. 1c). Initially, apoptotic cells remain columnar and attached to their neighbours, as described previously13 (Extended Data Fig. 2a). Indeed, we noticed that adherens junction components (E-cadherin, α-catenin and β-catenin) accumulate below the apical surface of dying cells, forming an adhesion peak which coincides with local deformation of the apical surface of the surrounding epithelial cells (Fig. 1c, Supplementary Video 2). These observations prompted us to hypothesize either the presence of an apico-basal pulling force generated by the dying cells or, alternatively, a pushing force generated by the dying cell’s neighbours. Therefore, we analysed myosin II dynamics. Interestingly, we detected an apico-basal acto-myosin cable-like structure (hereafter named ‘cable’) inside each dying cell (Extended Data Fig. 2b) that is formed just before the local deformation of the epithelium surface (Fig. 1d, Supplementary Video 3). This myosin II cable is attached to the junctional structure described above (Fig. 1e). Remarkably, apical surface release coincides with myosin II cable and adhesion peak detachment from the apical surface as the dying cell fragments (Fig. 1c, d, Extended Data Fig. 2c, d). Furthermore, when apoptosis is inhibited, neither the myosin II cable nor the apical deformation are observed (Extended Data Fig. 2e), suggesting that the myosin II cable constitutes the cellular apoptotic machinery responsible for the transient deformation of the epithelium.

Figure 1: Apoptotic cells exert a transient apico-basal force upon adjacent cells.
figure 1

a, Pupal leg disc from pre-fold stage (white pupae, WP) to late-fold stage (WP + 3 h). Arrowhead colours indicate fold progression (n = 10, 7, 10 and 10, respectively). b, Average number of dying cells in the fold domain (n = 10, 6, 10 and 7, respectively). A, anterior; P, posterior. c, d, E-cadherin–green fluorescent protein (E-Cad::GFP) (c, n = 24) and MRLC::GFP (d, n = 21) dynamics in apoptotic cells (in red in c) from pre-fold stage leg discs. Time 0 = collapse of apoptotic cell apical surface; the dotted line and arrowhead colour codes indicate equivalent stages of the apoptotic process. e, Co-localization of the apoptotic myosin II cable (green arrowhead) with adherens junctions (n = 19, white arrowhead) stained with anti-E-Cad. f, g, Ectopic apoptotic cells with (f) or without (g) myosin II activity generated in the wing disc. DN, dominant negative form. Red and open arrowheads point at presence or absence of apical deformation, respectively (see quantification and genotypes in Extended Data Fig. 2g). h, Schematics of apoptotic cell dynamics.

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We then asked whether the apico-basal myosin II cable is a general characteristic of apoptotic epithelial cells. By analysing myosin II distribution in different Drosophila epithelial tissues, we revealed that an apico-basal myosin II cable also forms in apoptotic cells in other epithelia (Extended Data Fig. 2h).We further asked if this general property of apoptotic cells to generate an apico-basal myosin II cable is responsible for the local apical deformation observed around apoptotic cells. To test this, we induced ectopic apoptosis in the Drosophila wing which can be regarded as a naive tissue (as apoptosis normally occurs sporadically) and blocked myosin II function specifically in dying cells. While an apico-basal myosin II cable is formed in ectopic dying cells (Extended Data Fig. 2f), the local apical deformation around apoptotic cells is no longer visible when myosin II is inhibited (compare Fig. 1f to Fig. 1g, Extended Data Fig. 2g), indicating that the deformation strictly results from the myosin II dependent apoptotic force and is not generated by neighbouring cells. Together, these experiments demonstrate a fundamental intrinsic in vivo property of yet non-fragmented apoptotic cells, namely their ability to produce a myosin II dependent apico-basal pulling force capable of transiently deforming adjacent cells (Fig. 1h).

To determine how apoptotic cells control the reorganization of the remaining tissue, we characterized myosin II distribution and cell shape changes in the vicinity of apoptotic cells. Myosin II in this tissue is localized at the level of adherens junctions (Extended Data Fig. 3a, b). Interestingly, we observed that myosin II levels are increased along the apical membrane of apoptotic cell neighbours (Fig. 2a). Eventually, myosin II and F-actin apical stabilization is found throughout the whole fold domain where apoptosis takes place compared to the segment domain (Fig. 2b, Extended Data Fig. 3c, d) and is lost in absence of apoptosis (Fig. 2c and Extended Data Fig. 3e–g). Moreover, we observed that cells neighbouring apoptotic cells become progressively elongated and reduce their apical surface (Fig. 2d, Supplementary Video 4). Elongation then propagates from cell to cell, gradually spreading to the whole fold domain, thus generating a ring of stretched cells in which apoptosis occurs specifically (Extended Data Fig. 4a, b, Supplementary Video 5). These observations suggest that cell death is responsible for cell shape modification in the whole fold domain. We therefore compared cell shape dynamics of developing legs with or without apoptosis. In the control fold domain, cells elongate, decrease their apical surface and adopt a preferential orientation along the future fold (Fig. 2e). However, all these characteristics are lost when cell death is inhibited, demonstrating the essential role of apoptosis in determining cell morphology during folding (Fig. 2e and Extended Data Fig. 4c–e). Using laser ablation, we tested whether cell elongation and myosin II stabilization at the level of adherens junctions reveal an increase in tissue tension in the fold domain, as previously described in other tissues14. We found that the release of tension between vertices was indeed much higher in the fold domain where apoptosis takes place than in the segment domain (Extended Data Fig. 3h). In addition, when cell death was inhibited, tension in the fold domain was significantly lower than in the control situation (Extended Data Fig. 3i). Altogether these results demonstrate that, during leg folding, apoptosis induces a non-autonomous effect throughout the fold domain leading to acto-myosin apical stabilization, a global enhancement of tissue tension and cell shape changes (Fig. 2f).

Figure 2: The apoptotic force propagates to the neighbouring tissue.
figure 2

a, Leg disc three-dimensional reconstruction and schematics showing apical myosin II stabilization (arrowheads) in cells adjacent to a dead cell (n = 11). b, Leg discs from pre-fold stage (n = 9) and late-fold stage (n = 7). c, Leg discs incubated from pre-fold to mid-fold stages with DMSO (control, n = 13) or Q-VD-OPh (cell death inhibition, n = 13). Red and open arrowheads point to the presence or absence, respectively, of F-actin or myosin II stabilization in b and c. d, Leg disc time-lapse images and quantification of cell shape change parameters at the vicinity of an apoptotic cell (red arrowheads, n = 18). e, Quantification of cell shape change parameters of leg discs incubated with DMSO (n = 7) or Q-VD-OPh (n = 8) from pre-fold to mid-fold stages. f, Schematics of apoptotic force propagation.

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To test the role of apoptotic forces in folding, we constructed a physical model based on the two-dimensional vertex model15. In this model, three interactions are considered: cell elasticity dependent on the cell apical area, a contractility term dependent on the cell perimeter, and line tension dependent on apical junction length. To take into account all three dimensions of the leg epithelium, we have added an apico-basal tension to those interactions (Extended Data Fig. 5a), and have considered cell elasticity as a function of cell volume rather than cell area while retaining the main characteristics of the original model (Extended Data Fig. 5b–e). Based on our observation of the developing leg disc, the leg tissue in our model is represented by a 50-cell circumferential cylinder, with the fold domain representing three rings of cells in which 30 cells are programmed to die following the pattern of apoptosis in the leg (compare the cell death pattern in Fig. 1b and Extended Data Fig. 6a). In the absence of the apoptotic-dependent forces, the model indicates that the simple disappearance of 30 cells from a continuous ring-like domain is not sufficient to induce cell shape reorganization and to create an invagination at the tissue level (compare Fig. 3a and b). However, if a transient apico-basal force is applied in each dying cell, an invagination response is observed all around the cylindrical tissue, albeit irregular (Extended Data Fig. 8a). Now, if an increase of apical contractility is applied in two rows of apoptotic neighbours (representing the non-autonomous increase in tissue tension), a cell shape reorganization is observed, although moderate (Extended Data Fig. 7a). Finally, if the transient pulling forces generated at a cellular scale are translated as increased contractility at the tissue scale we observe cell shape reorganization similar to that observed in the leg fold, along with regular and deeper folding (Fig. 3c). This shows that the added effect of both apoptotic forces is necessary and sufficient to induce folding in silico. Importantly, rising apoptotic cell number (Extended Data Fig. 6), apico-basal force strength (Extended Data Fig. 7) or the increase in apical contractility in apoptotic cells neighbours (Extended Data Fig. 8) leads to a gradation in cell and tissue shape changes and demonstrates the robustness of the model.

Figure 3: Biophysical model of epithelium folding.
figure 3

ac, In silico models showing apoptotic pattern (insets), whole tissue (left) and cell shape (right, including normalized area) in the absence of apoptosis (a) and after removing apoptotic cells from the fold domain without (b) and with (c) an apico-basal force generated by each dying cell and transmitted apically to neighbours (noted ‘apoptotic forces’).

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Furthermore, our model predicts that an apico-basal pulling force generated by sporadic apoptosis is not sufficient to modify tissue shape (Extended Data Fig. 6c, d). Moreover, the synergy of forces arising from several apoptotic cells concentrated in a restricted region appears necessary to generate a force strong enough to produce a fold (compare Extended Data Fig. 6f with Extended Data Fig. 6g). To test this in vivo we induced apoptosis ectopically in the wing pouch (that is, a flat tissue) and observed that a high concentration of apoptotic cells in a restricted region is indeed sufficient to drastically modify the shape of the epithelium through the creation of an ectopic fold (Fig. 4a, b, left and middle panels, and Extended Data Fig. 9a–b′). Consistently, no folding was observed in regions where only sporadic apoptotic cells were generated (Extended Data Fig. 9b′′′). Importantly, this tissue bending coincides with an apical stabilization of myosin II (Fig. 4c, middle panel, Extended Data Fig. 9d–e′) and F-actin (Extended Data Fig. 9c′). It also strictly relies on apoptotic myosin II since the expression of a dominant negative form of myosin II specifically in dying cells at the onset of apoptosis induction suppresses folding (Fig. 4a, b, right panels, and Extended Data Fig. 9a′′, b′′), whereas apoptotic cell extrusion from the epithelium remains normal (Fig. 4b, middle and right panels). Interestingly, the absence of fold in this context is concomitant with an absence of myosin II apical stabilization in the whole domain of ectopic apoptosis (although the myosin II contractile ring involved in dying cell extrusion16 is still present, see right panel in Fig. 4c and Extended Data Fig. 9e′′), showing that this accumulation strictly depends on apoptotic myosin II (compare Fig. 4c middle panel with right panel, quantifications are in Extended Data Fig. 9d). Altogether, these data strongly suggest that the apoptotic force resulting from the synergy of numerous and patterned apoptotic events constitutes the primary signal leading to epithelium folding.

Figure 4: Ectopic fold formation.
figure 4

a, Schematics of wing discs depicting the genetic contexts analysed in b and c. b, c, Wing discs in the absence (left panels) or presence (middle and right panels) of ectopic apoptosis in the ptc domain (pink), with (middle panels) or without (right panels) myosin II activity in dying cells, showing wing disc morphogenesis (large panels in b) and dying cell extrusion (close ups in b, white arrowheads) and myosin II distribution (stained by an anti-Sqh/MRLC, c; in sagittal sections, red and black arrowheads point to the presence or absence, respectively, of myosin II apical stabilization). Close-up three-dimensional reconstructions are presented in c to visualize the different pools of apical myosin II and apoptotic cells; red and open arrowheads denote ‘fold domain apical myosin II’ and ‘contractile ring of myosin II’, respectively (see also Extended Data Fig. 9e-e′′). b, n = 8, 13 and 10; c, n = 6, 7 and 8 in left, middle and right panels, respectively.

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In this study, we elucidated a novel cellular mechanism of epithelial folding that relies on apoptosis. In Drosophila epithelia, cells are extremely columnar and apoptotic cells, in addition to the force generated by their extrusion from the epithelium as previously described in squamous epithelium17, create a myosin-II-dependent apico-basal intracellular pulling force. Based on previous publications showing that transient mechanical forces are sufficient to induce myosin II recruitment at the apical surface of an epithelium8,14, we propose that apoptotic cells send a biomechanical signal to their neighbours, although we cannot exclude the myosin-II-dependent release of a molecular signal. The apoptotic signal triggers non-autonomous myosin II recruitment at the level of adherens junctions of neighbouring cells. The synergy of several apoptotic cells leads to a redistribution of myosin II, increased tension, apical constriction in the entire fold domain and subsequent tissue folding (Extended Data Fig. 10). Taken together, these results reveal that through the regulation of tissue tension, apoptotic cells can actively control tissue remodelling.

Interestingly, apoptosis-dependent folding has also been described in vertebrates during neural tube bending. This bending is an important step in neural tube closure and its failure can lead to spina bifida phenotypes12,18. Therefore, it would be interesting to test if the cellular mechanisms described here are conserved in vertebrates, thus generalizing the mechanism of apoptosis-dependent epithelium folding.

Methods

Fly stocks and genetics

The fluorescent reporters used are the following: E-Cad-KI(GFP)19, ubi::E-Cad::GFP20, uas::alpha-catenin-TagRFP21, uas::SCAT3 (FRET reporter of caspases activity22), sqh[AX3];;sqh::sqhGFP[40] and sqh[AX3];sqh::sqhGFP[42] (MRLC::GFP)23, w;ap::Gal4,arm::arm-GFP;uas::mCD8-Cherry (generated using Bloomington stocks), w,Dlg1-GFP (CC01936, from Flytrap), Dll::Gal4 MD23, zfh2 LP30::Gal4 and UAS::Diap1 are described in Flybase, UAS::p35 (insertions in chromosome II and III) come from Bloomington.

Stocks for ectopic cell death induction are y,w,HS::flp;act>y+>Gal4,uas::GFP and w;ptc::Gal4, uas::GFP; tub::Gal80ts (gifts from C. Benassayag), y,w,HS::flp;;act5C>CD2> Gal4 (generated using Bloomington stocks), w;uas::lifeactGFP;uas::reaper (gifts from X. Wang and from Flybase),w; uas::hid(4),uas::DN-zip::GFP (gifts from H. Steller and D. Kiehart), w; uas::DN-zip::GFP; uas::rpr. Briefly, the progeny of crosses of interest were grown on standard medium at 25 °C. Third instar larvae were heat shocked for 15–20 min at 38 °C and transferred to 29 °C for 5.5 h–6 h before dissection. Following this treatment, a reproducible bias was observed, with clones essentially following the dorsal-ventral boundary in half of the wing pouch. When using ptc::Gal4 to induce cell death, crosses were performed at 18 °C, the progeny was transferred at least 5.5 h to 30 °C before dissection.

Immunostainings

Primary antibodies obtained from Developmental Studies Hybridoma Bank were: rat anti-E-Cad (DCAD2, 1:50), mouse anti-Arm (N2 7A1, 1:5) and mouse anti-Dlg (4F3, 1:200). Rabbit anti-cleaved Caspase 3 (9661, 1:100) and anti-cleaved Dcp1 (9578, 1:200) were obtained from Cell Signaling Technologies and chicken anti-beta-Gal (GTX77365, 1:1,000) was obtained from GeneTex. Mouse anti-Sqh (MRLC) and Guinea pig anti-Sqh1P (1:1,000) were gifts from R. Ward. Staining of the actin cytoskeleton was achieved using phalloidin-Rhodamine (1:200, Invitrogen) or phalloidin-Alexa647 (1:100, Interchim). Secondary antibodies coupled to Alexa-488 or-555 were obtained from Fisher Scientific and diluted 1:200 while secondary antibodies coupled to Cy5 were obtained from Jackson Laboratories and diluted 1:50. Briefly, for immunostainings, imaginal tissues were fixed using paraformaldehyde (PFA) 4% diluted in PBS 1×. Samples were washed and saturated using PBS 1×, Triton X-100, 0.3% BSA 1% (BBT). Primary antibodies were diluted in BBT and incubated overnight at 4 °C. Next, samples were washed and saturated in BBT, incubated with secondary antibodies (and phalloidin if required to stain F-actin) as indicated above, and subsequently washed with PBS 1×, Triton X-100, 0.3%. Samples were mounted in Vectashield containing DAPI (Vectors laboratories) and analysed under a Zeiss LSM710 laser scanning microscope. A similar protocol was followed for immunostainings on embryos except that fixation was performed for 5 min in heptane:formaldehyde 37% (1:1). For E-cadherin and MyoII, embryos were devitellinised manually and stained immediately. Note that in order to preserve wing morphology in ectopic cell death experiments; dissections were performed in Schneider medium, followed by fixation with 4% PFA diluted in Schneider medium.

Time-lapse imaging

Leg discs were dissected in Schneider's insect medium (from Sigma Aldrich) supplemented with 2% FCS and 0.5% penicillin-streptomycin. Ecdysone (from Sigma aldrich, 20-hydroxyecdysone H5142) was stored in a stock solution of 200 μg ml−1 at −20 °C and added to meet a final concentration of 2 μg ml−1. For in vivo imaging, leg discs were transferred on a coverslip in 15 µl of the above medium complemented with methyl cellulose (from Sigma-Aldrich) at a final concentration of 2.5% to obtain a more viscous medium24. Spacers (Secure -Seal Imaging Spacers 0.12 depth from Sigma-Aldrich) were added between the coverslip and an air-permeable membrane (Lumox 25 from Sarstedt,) to avoid compression of the tissue, and halocarbon oil was added on the sides of the spacer to protect from dehydration. Note that forceps and scissors, as well as air-permeable membrane, were washed with ethanol before dissection. The membrane is rinsed with water and dried before use.

Before imaging, dissected leg discs may be incubated for 30 min with acridine orange (final concentration 0.1 µg ml−1) to reveal dying cells or with the red fluorescent lipid-binding dye FM4-64 (final concentration 36 µM). FM4-64 was also added at a concentration of 18 µM in the imaging medium.

Imaging was essentially performed under an inverted laser scanning LSM710 confocal (Zeiss). Under our conditions, ex vivo leg development reproduces morphologic stages of pupal leg development characterized on fixed tissues (including leg evagination, local folding and the pattern of cell death), albeit at a lower speed (around 2 times).

Importantly, we found that image stacks of 30–40 µm have to be taken every 3 min with optimal sectioning (0.438 µm for a 40× objective with 1.3 aperture and the pinhole set to 1 AU) in order to spot apico-basal myosin II cables and adhesion peaks as they are very dynamic structures.

Note that apoptotic cells were identified using the caspase FRET sensor (SCAT322, see section ‘Post-imaging analysis’ for details), acridine orange25 or FM4-64 that strongly labels apoptotic bodies.

Ex vivo culture and drug treatment

Q-VD-OPh is a broad spectrum caspase inhibitor which binds to the active site of activated proteases, more efficiently than the commonly used Z-VAD caspase inhibitor and is described as non-toxic even at extremely high concentrations26. Discs from white pupae (WP) were dissected in complemented Schneider medium as described above and incubated from pre-fold to mid-fold stage with either Q-VD-OPh (from R&D systems; final concentration 500 µM) or DMSO (from Sigma Aldrich, final concentration 0.5% in Fig. 2e and 0.06% in other experiments) in Fig. 2c (incubation of 6h) or Fig. 2e and Extended Data Fig. 4d (incubation of 4 h). Q-VD-OPh was stored in a stock solution of 10 mM in either DMSO 100% (Fig. 2e) or in Schneider + 1.25% DMSO (other experiments). Throughout this study, we focused on the t4-t5 fold, the only fold that is exclusively formed during the pupal stage and for which progression can be easily followed due to disc evagination. At WP stage, formation of the t4-t5 fold is not initiated yet, while other tarsal folds are partially formed. Hence, in this particular context of apoptosis inhibition, we observe, as expected, a slight perturbation of the formation of t3-t4 and strongly perturb the t4-t5 fold.

Post imaging analysis

SCAT3 FRET probe was previously described22. It is an indicator of caspase-3 activation using fluorescence resonance energy transfer (FRET) between an enhanced cyan fluorescent protein (the donor) and an enhanced yellow fluorescent protein (the acceptor) separated by a caspase cleavage site. FRET images of live leg discs were acquired with a Zeiss LSM710 microscope. A 458 nm laser was used to excite the sample. Cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) emission signals were collected through channel I (470–510 nm) and channel II (525–600 nm), respectively. CFP and YFP images were acquired simultaneously. Sequential acquisition of CFP and YFP channels in alternative orders were tested and gave the same result as simultaneous acquisition. CFP and YFP images were processed by ImageJ software. A background region of interest was subtracted from the original image. Gaussian smooth filter was then applied to both channels. The final ratio image (YFP/CFP signal) was generated in ImageJ program.

Zen software (Zeiss) was used to generate three-dimensional reconstruction and sagittal views of tissues. Images were processed in Adobe Photoshop CS5 or ImageJ.

Automated image analysis and quantifications of cell shape changes

Matlab, DipImage, Cell profiler and ICY were used to make automatic segmentation for quantification of cell shape in Fig. 2e and Extended Data Fig. 4d). Three-dimensional median filter was performed from confocal images before segmentation. A Z projection based on the maximum intensity from each Z stack was applied. An adaptive threshold was made to the Z projection images to define the outline of cells based on the Otsu method. The local maximum of the “distance” function was used to find the centre of each cell to produce a resulting binary image. The distance transform is then used on the binary image to calculate the distance from cell membrane. The local maxima of the distance transform was calculated and were selected as seeds. For cells with high anisotropy the calculation of local maximum induced some errors and was manually corrected. The coordinate of each local maximum was used like seed to use a watershed algorithm function in Matlab and obtain a label matrix allowing the quantification of each cell object. The cells situated out of the domain of interest were rejected. To perform statistics we calculated the maximum and the minimum vertical coordinates based on the coordinates of the centre of outlined cells. Then 12 domains were defined based on this coordinate. The calculation of anisotropy was defined as the ratio between the lengths of the principal axes of an ellipsis fitting the cell contour.

Measurements of actomyosin levels

To quantify junctional acto-myosin (Extended Data Fig. 3c). For each leg disc, acto-myosin intensity was measured using ImageJ by drawing a circular region of interest of 1 μm2 in 8 individual junctions in the fold domain (t4-t5) and in 8 individual junctions in the segment domain (t4). The measurements done in the fold were then normalized with the mean value of acto-myosin intensity in the segment domain independently in each leg disc (to insure the presence of an internal control). As a consequence, the values represent the differential accumulation of junctional acto-myosin in the fold compared to the segment domain.

To quantify acto-myosin per surface unit (Extended Data Fig. 3d, e, g). For each leg disc, acto-myosin intensity was measured using ImageJ by drawing a segmented line either in the fold (t4-t5) or in the segment (t4) domain. These values were divided by the length of the line and each measure in the fold was then normalized by the corresponding segment domain value (to insure the presence of an internal control). As a consequence, the values represent the differential accumulation per surface unit of acto-myosin in the fold compared to the segment.

Statistics

To calculate P-values, we used the non-parametric Wilcoxon rank sum test (also called Mann and Whitney test) since samples do not follow a normal distribution and do not have equal variances in Extended Data Fig. 3c–e, g, Extended Data Fig. 4d and Extended Data Fig. 9d. The null hypothesis is that the measures are samples from continuous distributions with equal medians. The test considers that the samples are independent and in Extended Data Fig. 4d, it takes into account that the control and Q-VD-OPh can have different lengths. For cell shape characteristics (anisotropy, area and orientation), values are represented by box plot (the red line represent the median). For acto-myosin level quantifications, values are represented as mean values with standard error bars.

Photo-ablation experiments

Laser-ablation experiments in prepupal leg imaginal discs were performed with a pulsed Q-switched microchip double-frequency Nd:YAGlaser (λ = 532 nm, 550 ps, 7 kHz, 3.5 μJ per pulse). The laser beam was focused through a high numerical aperture oil-immersion lens (×60 C-Apochromat NA 1.4, Leica) to produce an experimental beam waist around 600 nm in the focal plane. Photo-disruption was produced in the focal plane due to the plasma generation in the middle of the adherens junctions after a total of 21 laser pulses of 3 kHz. A pair of Galvanometric mirrors were conjugated to the black focal plane of the microscope objective lens to stir the ablation beam and allow simultaneous ablation of two junctions. We used an inverted microscope (Leica DMI6000B) with wide field illumination to produce fluorescent live imaging of adherens junctions labelled with arm::GFP fusion protein. Adherens junctions were placed in the centre of the field to produce a better reproducibility. METAMORPH coupled to ILAS software controlled the laser and the microscope (RopperScientifiC SA). The Images were taken every second over a period of 30 s. Note that for laser ablations, in absence of cell death (incubation with Q-VD-OPh, Extended Data Fig. 3i), expression of a membrane-bound cherry protein under the control of the apterous driver (w;ap::Gal4,arm::arm-GFP;uas::mCD8-Cherry; for expression pattern, see Extended Data Fig. 4c) was used to visualize the fold domain since cell shape changes do not occur in these conditions.

Modelling

Our apical junction network model is a generalization to three-dimensional of the Farhadifar et al. model15. In order to allow non-planar interactions, the surface elasticity is replaced by a volume elasticity. The apico-basal interaction is modelled as an energy proportional to cell height, with the same linear form as the apical line tension. The initial epithelium is represented as an hexagonal lattice of cells over a cylinder. Next, each cell follows a division process with a random division plane orientation. The order of cell divisions on the epithelium is chosen randomly, uniformly across the epithelium. Division is modelled by first increasing the cell equilibrium volume, finding the local energy minimum and second by dividing the cell and finding the new local energy minimum. Then, apoptotic cells are chosen randomly in a region around the centre of the epithelium, with a biased distribution reproducing the in vivo cell death pattern. Apoptosis is performed by gradually diminishing the cell preferred volume, increasing its contractility and rising the apico-basal tension term (ten steps are performed). At each step, the local energy is minimised by a gradient descent strategy. After the first step of the first apoptotic cell is performed, the second cell starts its apoptosis, and so on. Once ten steps are performed for one cell, it is removed from the tissue, such that no centripetal force remains at that point. When removing the apoptotic cell, its neighbours are rearranged through a series of type 1 intercalations (see Faradifar et al.15). To model acto-myosin activity increase in the neighbouring cells, contractility is increased in the neighbouring cells by a factor the amplitude of which decreases exponentially with the distance to the apoptotic cells. After a cell has been eliminated and its neighbours rearranged, the whole tissue is brought back to equilibrium by successively computing the local energy minimum for all the cells of the tissue in a random order. Technically, the epithelium is described as an oriented graph in the graph-tool library28 (http://graph-tool.skewed.de) in the Python programming language. Energy minimisation is performed with the scipy library29 (http://scipy.org), using the Broyden, Fletcher, Goldfarb, and Shanno bound constrained minimisation algorithm provided by this library. The source code for the model is released under the GNU General Public Licence and is available on github at https://github.com/glyg/leg-joint and http://dx.doi.org/10.5281/zenodo.13386. Extensive details on the numerical method as well as a complete derivation of the gradient can be found at this address.

The apical contractility and linear tension parameters Γ and Λ where chosen so that the relation between cell apical area and number of neighbours follows the same linear increase as observed by Farhadifar et al.15 in the wing disc (compare Fig. 2g of Farhadifar et al.15 with Extended Data Fig. 5b of the present work). We explored a range of apoptotic cell number, apico-basal force amplitude and contractility increase values (Extended Data Figs 6, 7, 8) and observed that cell morphology in the fold is best reproduced with amplitudes of 1 Γ and 1 Λ. The fact that they are in the same order of magnitude as the apical interactions gives us confidence that the chosen parameters are realistic. Furthermore, our tissue has a consistent morphology with or without apoptosis, increased apical contractility or apico-basal force, meaning that the balance of forces is coherent and equilibrated.

For cell shape analysis, a sector centred 30° above the ventral most part of the cylindrical epithelium was extracted. Radius and area were normalized with respect to their average values on the simulated epithelium in the absence of apoptosis.