DEPDC1B coordinates de-adhesion events and cell-cycle progression at mitosis

Abstract

Cells entering mitosis become rounded, lose attachment to the substrate, and increase their cortical rigidity. Pivotal to these events is the dismantling of focal adhesions (FAs). How mitotic reshaping is linked to commitment to divide is unclear. Here, we show that DEPDC1B, a protein that accumulates in G2, coordinates de-adhesion events and cell-cycle progression at mitosis. DEPDC1B functions as an inhibitor of a RhoA-based signaling complex, which assembles on the FA-associated protein tyrosine phosphatase, receptor type, F (PTPRF) and mediates the integrity of FAs. By competing with RhoA for the interaction with PTPRF, DEPDC1B promotes the dismantling of FAs, which is necessary for the morphological changes preceding mitosis. The circuitry is relevant in whole organisms, as shown by the control exerted by the DEPDC1B/RhoA/PTPRF axis on mitotic dynamics during zebrafish development. Our results uncover an adhesion-dependent signaling mechanism that coordinates adhesion events with the control of cell-cycle progression.

Graphical abstract

Figure 1

DEPDC1B Silencing Delays Mitotic Entry in Human Cells (A and B) HeLa cells were synchronized in S phase by D-THY and released in fresh medium with nocodazole (100 nM) to follow cell-cycle progression from S phase to mitosis. During synchronization, endogenous DEPDC1B was silenced using different siRNA oligos (1B-KD1, 1B-KD2, or 1B-KD3). A custom non-targeting oligo was used as a control. Mitotic cells were monitored using mitotic-specific phosphorylation of histone H3 (Ser-10) as a marker (mean ± SEM of three experiments). (B) Cells were transduced with an inducible EGFP-DEPDC1B transgene (EGFP-1B) and synchronized as in (A). Endogenous DEPDC1B was silenced using a 3′UTR-targeting oligo (1B-KD3). Upon release, siRNA-resistant EGFP-1B was induced by doxycycline (100 ng/ml), and mitotic cells were counted. Western blot shows levels of endogenous and exogenous DEPDC1B. Vinculin was used as loading control. (C) Mitotic events were directly measured by time-lapse microscopy. The percentage of cells entering mitosis upon silencing of DEPDC1B, DEPDC1A, or both genes (KD-1A/KD-1B) is shown. (D) Cell-cycle transitions were monitored by flow cytometry. DNA content (propidium iodide staining) of control (Ctrl) and DEPDC1B-silenced cells (1B-KD1) are shown. The percentage (mean ± SEM of two experiments) of cells in G2 phase (cyclin B positive) and M phase (pH3/cyclin B double positive) were determined. (E and F) Lamin B/cyclin B staining and distribution (mean ± SEM of three experiments) were analyzed to monitor mitotic entry dynamics. The distribution of lamin B (membrane versus diffuse [E]) and cyclin B (nucleus versus cytosol, see F) of cells in G2 phase is shown. Asterisks mark nuclear cyclin B or membrane lamin B. Arrows mark cytosolic cyclin B. (G) Western blot analysis of cyclin B and total/phospho-Cdk1 (Tyr14/15). Vinculin was used as loading control. The densitometry analysis is also reported (mean ± SEM of two experiments). Asterisks in graphs mark significant values (p < 0.05, Student’s t test). Representative images are shown. Scale bars represent 20 μm.

Figure 2

DEPDC1B Silencing Perturbs Adhesion and Actin Cytoskeleton Dynamics in G2 Phase (A and B) FA dynamics were observed using GFP-paxillin (A) or vinculin (B) as reporters in control (Ctrl) or DEPDC1B-silenced (1B-KD1) HeLa cells synchronized in early G2 phase (D-THY plus 4 hr release). (A) The mean number, size (area, μm²), and the duration of FAs, determined by total internal reflection fluorescence (TIRF) microscopy, in control (Ctrl, blue) and DEPDC1B-silenced cells (KD-1B, red) are shown. (B) The average number and area (μm²) of FAs per cell, determined by confocal microscopy using vinculin staining, are shown. (C) The actin cytoskeleton (FITC-phalloidin) and the activation of myosin light chain (phospho-MLC2-Ser19) were analyzed by immunofluorescence and confocal microscopy in HeLa cells synchronized in G2 phase. The percentage (mean ± SEM of three experiments) of cells with high/low phospho-MLC2 staining is reported. (D) Western blot analysis shows levels of phospho-MLC2, phospho-Cofilin (Ser3) upon DEPDC1B-KD. Vinculin, total MLC2, and Cofilin were used as loading controls. In parallel, RhoA activity was measured by GST-RBD pull-down (right panel). As positive control, the lysate was activated by GTPγS stimulation. An asterisk marks a nonspecific band detected by the anti-RhoA antibody. The densitometry analysis of active RhoA in two experiments is shown. (E) IMR90 and MCF10A cells were analyzed in G2 phase for actin cytoskeleton and FA dynamics as described in (B) and (C). Western blot analysis shows levels of phospho-MLC2 (Ser19) upon DEPDC1B silencing. (F) Cell spreading dynamics, on fibronectin substrate, of G2 synchronized HeLa cells was monitored by Real Time Cell Analyzer (Atienzar et al., 2011). Graph shows the normalized cell index, as a measure of cell-covered area after replating. Asterisks in graphs mark significant values (p < 0.05, Wilcoxon test in A and B; Student’s t test in C). Representative images are shown. Scale bars represent 10 μm.

Figure 3

DEPDC1B Controls an Adhesion-Dependent Checkpoint at the G2/M Transition (A and B) HeLa (grown in adhesion) and HeLa-S3 (grown in suspension) cells were treated with control or DEPDC1B siRNAs and synchronized (D-THY) to follow cell-cycle progression. (B) Percentage of cyclin B-positive (G2 phase) and pH3/cyclin B double-positive (mitosis) cells were determined by flow cytometry. (C and D) Control (Ctrl) or DEPDC1B-silenced (1B-KD1) HeLa cells were treated either with vinculin, FAK, or alpha-actinin siRNA oligos. (D) Mitotic events were measured using pH3 marker (mean ± SEM of three experiments). (E and F) Control (Ctrl) or DEPDC1B-silenced (1B-KD1) HeLa cells were synchronized as in (A) and treated with the ROCK kinase inhibitor (Y27632, 10 μM) upon release. Mitotic cells were measured using pH3 staining (E) or by time-lapse microscopy (F). Western blot analysis shows levels of phospho-MLC2 on DEPDC1B-KD and Y27632 treatment. Vinculin and total MLC2 were used as loading controls. (G) HeLa cells were synchronized (as in A) and treated upon release with Mn²⁺ (1 mM, upper panel). In the lower panel, HeLa cells were transfected with pEGFP-vinculin (VincT12 mutant) during synchronization. Western blot analysis shows levels of phospho-MLC2 and phospho-CDK1 upon Mn²⁺ treatment and VincT12 expression. RhoA activation by Mn²⁺ treatment was measured by RBD pull-down. An asterisk marks a nonspecific band detected by the anti-RhoA antibody. (H and I) Mitotic cells were measured using pH3 staining (H and I) or cyclin B distribution (H). Scale bar graphs report the mean ± SEM of three (C and D) or two (B, E, H, and I) experiments. Asterisks mark significant values (p < 0.05, Student’s t test).

Figure 4

DEPDC1B Controls RhoA-Dependent Cell Adhesion at the G2/M Transition (A and B) Control (Ctrl) or DEPDC1B-silenced (1B-KD1) D-THY synchronized HeLa cells were treated with RhoA, Rac1, or Cdc42 siRNA oligos. Mitotic cells were measured using pH3 staining (A) or by time-lapse microscopy (B). (C–E) HeLa cells were treated with control, DEPDC1B and RhoA siRNA oligos as indicated and synchronized in G2 phase. Staining for pH3 was used to distinguish G2 from mitotic cells. G2 cells were examined for FAs (using vinculin as marker) and actin cytoskeleton (Phalloidin). (D and E) The distribution of FA mean area per cell (D) or percentage of cells displaying enlarged FAs and actin stress fibers (E) are shown. (F–H) HeLa cells were transfected with RhoA-myc and synchronized in G2 (F and G) or M phase (H). (F) Western blot analysis shows levels of RhoA-myc and phospho-MLC2. Total MLC2 was used as loading control. In parallel, FA dynamics were analyzed by vinculin staining. (G and H) Bar graphs show the percentage of cells with normal/enlarged FAs and actin stress fibers (G) and the percentage of pH3-positive cells (H). Scale bar graphs report the mean ± SEM of three (A, D, and E) or two (F and H) experiments. Asterisks mark significant values (p < 0.05, Student’s t test). Representative images are shown. Scale bars represent 10 μm.

Figure 5

The Membrane Receptor PTPRF Interacts Biochemically and Genetically with DEPDC1B and RhoA (A) An Y2H screen was employed to search for DEPDC1B interactors. The chart shows the distribution of positive clones. (B and C) GST-PTPRF-c (cytoplasmic fragment, 1 μM) was incubated with total lysates (2 mg) from HeLa cells overexpressing EGFP-1B (B) or from control HeLa cells (C). Western blot analysis was performed using anti-GFP or anti-DEPDC1B antibodies. Asterisk marks a non-specific band detected by the anti-GFP. Ponceau staining is shown. (D) GST-PTPRF-c (1 μM) was incubated with the purified GAP domain of DEPDC1B (1B-GAP, 3 μM). Proteins were resolved by SDS-PAGE and detected by Coomassie staining to reveal the amount of 1B-GAP pulled down by PTPRF-c. (E and F) Control (Ctrl) or DEPDC1B-silenced (1B-KD1) HeLa cells were synchronized and treated or not with PTPRF siRNA. (E) Mitotic cells were measured using pH3-staining (mean ± SEM of three experiments). Asterisks mark significant values (p < 0.05, Student’s t test). (F) Western blot analysis shows levels of DEPDC1B, PTPRF, and phospho-MLC2. Vinculin and total MLC2 were used as loading controls. (G) Mass spectrometry analysis of proteins pulled down using GST or GST-PTPRF-c identified several members of RhoA signaling pathway (listed in the table) as PTPRF interactors. (H) Coomassie Staining of GST-PTPRF-c pull-down assay (1 μM), using purified RhoA (3 μM). (I and J) HeLa cells were transfected with RhoA-myc, treated with control or PTPRF-targeting siRNA oligo, and synchronized in S phase to follow mitotic entry. (I) Western blot analysis shows levels of RhoA-myc, PTPRF, and vinculin (loading control). (J) Scale bar graphs report the percentage of cells entering mitosis (mean ± SEM of two experiments) using pH3 staining as a mitotic marker. Asterisks mark significant values (p < 0.05, Student’s t test).

Figure 6

PTPRF as a Hub for the Activation of the RhoA Signaling Complex, which Is Dependent on DEPDC1B Protein Levels (A) GST-PTPRF-c pull-down assay with total lysates (1 mg) from HeLa control cells or cells overexpressing 1B-GFP. Western blot analysis shows levels of GEF-H1 and 1B-GFP. (B and C) The effects of silencing or overexpression of GEF-H1 has been analyzed on HeLa cells. Bar graphs report the percentage of cells entering mitosis (mean ± SEM of two experiments) using pH3 staining as mitotic marker. Asterisks mark significant values (p < 0.05, Student’s t test). (B) A bar graph on the right shows the relative mRNA expression of another RhoA GEF, PDZ-GEF, upon silencing. (C, below) Western blot shows levels of GEF-H1 upon silencing or overexpression and vinculin (loading control). (Above) Representative images of FAs (vinculin) and actin cytoskeleton (phalloidin) of control HeLa cells or cells overexpressing GEF-H1. Scale bars represent 10 μm. (D–G) GST-PTPRF-c pull-down assays were performed with total lysates (1 mg) from control cells, cells overexpressing both 1B-GFP and RhoA-GFP (D), cells overexpressing just 1B-GFP (E and F), cells overexpressing RhoA-myc and silenced for endogenous DEPDC1B (G). Western blot analysis was performed using the anti-GFP antibody for both 1B-GFP and RhoA-GFP, the anti-myc antibody for RhoA-myc, the anti-mDIA1 or anti-ROCK2 antibodies (RhoA downstream effectors), or anti-DEPDC1B antibody. The asterisk marks a nonspecific band detected by the anti-GFP antibody (D and F). In (E), protein bound to PTPRF-c were identified and quantified by SILAC in presence or not of DEPDC1B-GFP overexpression (two independent experiments, forward and reverse, with swapping of isotope-encoded amino acid among the two channels). Among PTPRF interactors, 39 proteins were found with binding consistently upmodulated or downmodulated by DEPDC1B overexpression (>1 log₂ fold), such as DEPDC1B itself and RhoA. (H) Western blot analysis shows levels of ROCK2 (RhoA effector) bound to active RhoA (RBD-pull-down) upon DEPDC1B silencing or Mn²⁺ treatment. As positive control, the lysate was activated by GTPγS stimulation. (I) GST-PTPRF-c (1 μM) was incubated with purified RhoA (3 μM) and/or 1B-GAP (3 μM). Proteins were resolved by SDS-PAGE and detected by Coomassie staining to reveal the amount of protein pulled down by PTPRF-c. The densitometry analysis of the PTPRF-c/RhoA (and 1B-GAP) interaction in three experiments is shown. (J) The scheme depicts the working model for DEPDC1B as a competitive inhibitor of the RhoA/PTPRF interaction resulting in inhibition of RhoA-dependent signaling that regulates the adhesion dynamics of G2 cells and mitotic entry. Positive (left) and negative (right) inducers of the G2/M adhesion checkpoint are also reported, according to the findings of this study.

Figure 7

DEPDC1B Controls Mitotic Events in Zebrafish Embryo (A) Zebrafish (ZF) embryos were collected at different times from fertilization (hpf) and levels of depdc1b or depdc1a mRNA expression measured by RT-qPCR. Actin B (Actb) was used as a normalizer. (B) ZF embryos were injected with control or depdc1b splice-blocking morpholino (MOSB) at the one-cell stage. Pictures show representative images of the resulting morphological defects observed at the late gastrula (10 hpf, left) or late segmentation (24 hpf, right) stages. Scale bars represent 125 μm (left) and 500 μm (right). (C–I) Zebrafish embryos were treated as in (B), and mitotic figures were monitored in the embryonic dorsal region of the Tg(h2afva:GFP)kca6 zebrafish transgenic line using confocal microscopy. Representative images are shown in (C).The scale bar represents 10 μm. (D) The graphs show the number of mitotic events (mean ± SD of two experiments) occurring from 4 to 6 hpf. DEPDC1B human mRNA was microinjected together with depdc1b MOSB to rescue embryo defects. (E) Duration of mitotic phases (mean ± SEM) was measured by confocal time-lapse microscopy, after MBT. (F) The graphs show the number of mitotic cells at 10 hpf determined by immunofluorescence upon various treatments (mean ± SEM of two experiments). (G) Cortical actin cytoskeleton was analyzed in the anterodorsal region of embryos treated as in (D), at 10 hpf by FITC-phalloidin staining. Representative images are shown. Red arrows mark thickening and actin protrusions on cell edges. hs-1B, human DEPDC1B mRNA. The scale bar represents 10 μm. (H) Bar graphs show the number of cell contacts (left panel) and actin protrusions observed in two independent experiments (mean ± SEM). Asterisk marks significant values (p < 0.05). (I) Embryos were treated as in (D), with different splice-blocking morpholinos (MOSBs for depdc1b, rhoab, or ptprf) at the one-cell stage. The graphs show the number of mitotic events (mean ± SD of two experiments) occurring from 4 to 6 hpf.