Cell culture and transfections
MDCKII cells with inducible expression of JAM-A shRNAs [27] or CRISP/Cas9-mediated inactivation of the JAM-A gene [28], and HEK293T cells (ATCC #CRL-3216) were cultivated in DMEM high glucose medium (Sigma-Aldrich (SA) #D5671) containing 10% FCS, 2 mM glutamine, 100 U/ml penicillin and 100 U/ml streptomycin. For stable MDCKII cell lines with inducible expression of JAM-A shRNAs, the growth media were additionally supplemented with 500 μg/ml G418 and 5 μg/ml blasticidin [79], and shRNA expression was induced by the addition of 2 µg/ml doxycycline. Stable LifeAct-EGFP (LA-EGFP) or LifeAct-mCherry (LA-mCherry) expressing MDCKII cells were generated by lentiviral transduction and selection in growth media containing 0.1 mg/ml zeocin or 1 µg/ml puromycin, respectively. MDCKII JAM-A KO cell lines expressing murine JAM-A (mJAM-A)/WT, mJAM-A/Y281F or mJAM-A/S285A under a tetracycline-regulated promotor were generated by lentiviral transduction and maintained in DMEM media containing 1 µg/ml puromycin and 2 µg/ml doxycycline (selectively added for induction of mJAM-A expression). These cell lines were additionally transfected with LA-EGFP or LA-mCherry, as described above. Cell–cell contact integrity in JAM-A KO MDCKII cells was verified by immunofluorescence microscopy for ZO-1 (Suppl. Fig. S1B). The expression levels as well as the subcellular localization of the ectopically expressed JAM-A constructs are shown in Suppl. Fig. S1C.
Transient transfections of siRNAs were performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific). Transfections of expression vectors were performed using Lipofectamine 2000 (Thermo Fisher Scientific) or Xfect transfection reagent (TaKaRa Bio Europe SAS, Saint-Germain-en-Laye, France) according to the manufacturer's instructions. Lentiviral particles for the generation of stably transfected cell lines expressing either shRNAs or cDNAs were generated by cotransfection of the lentiviral vector and the packaging vectors psPAX2 and pMD2.G (kindly provided by Dr. Didier Trono, Addgene plasmids 12,260 and 12,259) in a ratio of 3:2:1 into HEK293T cells. Lentiviral transduction of cells was performed as described [79].
RNA interference, plasmid vectors and constructs
The following siRNAs and shRNAs directed against canine (c) genes were used: cJAM-A shRNA 5′-CCAGTAAGAAGGTGATTTA-3′ (in pLVTHM (Addgene #12247) and in pEmU6proT (provided by Dr. Karl Matter); cCD151 siRNA pool (NCBI Gene ID475992, siTOOLs Biotech, München), cCD9 siRNA (NCBI Gene ID611695, siTOOLs Biotech, München), cITGA3 (NCBI Gene ID491074, siTOOLs Biotech, München); negative control siRNA pool (neg. ctrl. siPOOL Neg D1, siTOOLs Biotech, München); negative control siRNA (Qiagen 1027280), OnTarget plus non-targeting pool (Dharmacon D-001810-10-05). Knockdown efficiencies of all shRNAs and siRNAs used in this study are depicted in Suppl. Figs S1A, S1D, S1E. The following constructs were used: LifeAct-eGFP in pFUGW, LifeAct-mCherry in pLV-PGK-Puro (provided by Dr. H. Farin); hJAM-A/WT, hJAM-A/Δ3, hJAM-A/Δ40, ΔD1-hJAM-A, hJAM-A/MC, hJAM-A/N185Q in pFLAG-CMV-1 (SA, Munich, Germany); Flag-mJAM-A/WT, Flag-mJAM-A/Y281F, Flag-mJAM-A/S285A in pInducer21-Puro (Addgene #46948) [80] (provided by Dr. T. Weide); hCD151 in pEGFP-C1 (TaKaRa Bio).
Antibodies and reagents
The following antibodies were used in this study: mouse mAb anti-α-catenin (BD TL 610194, IF 1:600), mouse mAb anti-β-catenin (BD TL 610154, IF 1:600), mouse mAb anti-p120ctn (BD TL 610134, IF 1:600), mouse mAb anti-E-cadherin (BD TL 610181, IF 1:600), mouse mAb anti-Paxillin (BD TL 610,051, WB 1:500, IF 1:600), mouse mAb anti-CD9 clone MM2-57 (Millipore CBL162, WB 1:1000), rabbit pAb anti-Flag (SA, F7425, IF 1:1000, WB 1:1000), rabbit pAb anti-GAPDH clone FL-335 (SCBT SC-25778, WB 1:3000), mouse mAb anti-Integrin α3/CD49c (BD TL 611044, WB 1:500, IF 1:500), mouse mAb anti-Integrin β1 / CD29 (BD TL 610467, WB 1:500), mouse mAb anti-α-tubulin (SA, clone B-5-1-2, T5168, WB 1:10,000), rat mAb anti-ZO-1 (kindly provided by Dr. B. Stevenson, University of Alberta, Edmonton, Canada), clone R40.76, IF 1:800). Isotype-specific control antibody: rabbit IgG (Thermo Scientific 02-6102). A polyclonal antibody against canine JAM-A (Affi831) was generated by immunizing rabbits with a fusion protein consisting of the extracellular part of canine JAM-A fused to the Fc-part of human IgG, as described previously [27]. Reagents: recombinant human vitronectin (VN, Peprotech 140-09), rat tail type I collagen (Col-I, Advanced BioMatrix #5153), laminin (LN, isolated from human fibroblasts, SA #L4544), fibronectin (FN, isolated from human plasma, SA #F2006).
Quantitative polymerase chain reaction (qPCR)
To analyze the mRNA level of CD9 and CD151, the total RNA was extracted from the cell lysate using the RNeasy Mini Kit following the instructions from Qiagen (Hilden, Germany) and transcribed in cDNA using the High-Capacity cDNA Reverse Transcription Kit from Applied Biosystems (Waltham, Massachusetts, US). The following primer pairs were used (forward; reverse): CD9_1: GCTCTTGCTGGGATTGCAG; GAAACCCACCAGCATCATG, CD9_2: CTGGGGTTGTTCTTTGGC; CGTAGTGGATGGCCTTCAG, CD9_3: GTGGAACAGTTTATCTCCGAC; GATAGCACAGCACAGGATC, CD151: GAGAAGACGACATGTGGCAC; GTAGGCTGTGGCCAGGTAG, CD151_2: GTTGTCGTCATGGTGACTG; GTTCAGCTGCTGGTAGTAG, CD151_3: CAACCTGAAGGACACCATG; CACCCTCCACCTTGTAGATG, GAPDH: TCACCACCATGGAGAAGGC; GGCTAGAGGAGCCAAGCAG, HPRT: GCTTGCTGGTGAAAAGGAC; TTATAGTCAAGGGCATATCC.
Immunoprecipitation and western blot analysis
For immunoprecipitations, cells were lysed in lysis buffer (150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, 0,02% (w/v) NaN3, 10 mM TrisHCl pH 7.4, 1% (w/v) Brij98 (Merck, Darmstadt, Germany) supplemented with protease inhibitors (Complete Protease Inhibitor Cocktail; Roche, Indianapolis, IN) and phosphatase inhibitors (PhosSTOP™, Roche, Indianapolis) for 30 min on ice and then centrifuged for 20 min at 4 °C. For one experiment (Fig. 4A), 1% (v/v) Nonidet P-40 (NP-40, AppliChem, Darmstadt, Germany) was used as an alternative for Brij98. The resulting supernatants were incubated with 2.5 µg of antibodies coupled to protein A-Sepharose beads (GE Healthcare, Solingen, Germany) for 4 h at 4 °C. Afterwards, the beads were washed five times with lysis buffer and bound proteins were eluted using SDS sample buffer. For Western blot analysis of the tetraspanin CD9 by immunoblotting, SDS sample buffer without DTT was added for elution, and 50 mM DTT was selectively added to the samples used for the detection of JAM-A. Proteins were separated by SDS-PAGE and analyzed by Western blot with near-infrared fluorescence detection (Odyssey Infrared Imaging System Application Software Version 3.0 and IRDye 800CW- or IRDye 680CW-conjugated antibodies; LI-COR Biosciences, Bad Homburg, Germany). All immunoprecipitations shown in the figures are representatives for at least three experiments. For quantification of signal intensities, the same software as for data acquisition (Odyssey application software Version 3.0) was used.
Immunoprecipitation of GFP fusion proteins
GFP fusion proteins were precipitated by using the GFP Selector (NanoTag Biotechnologies, Göttingen, Germany). After cell lysis, the postnuclear supernatant was added to 20 µl of GFP Selector slurry. After incubation for 1 h at 4 °C, the GFP Selector beads were washed five times with lysis buffer. Bound proteins were eluted by boiling in SDS sample buffer analyzed by Western blotting as described above.
Immunofluorescence microscopy
For immunofluorescence microscopy, cells were grown on collagen-I-coated glass slides for 24 h and subsequently fixed with 4% paraformaldehyde (PFA, Sigma-Aldrich) for 10 min at room temperature (RT) or methanol (BioChemica, Billingham, England) for 5 min on ice. For PFA-fixed cells, permeabilization was performed by applying 0.5% Triton X-100 in PBS for 10 min at RT and the cells were washed three times with 100 mM glycine in PBS. For both fixation methods, unspecific binding sites were blocked for 1 h using blocking buffer (10% FCS, 0.2% Triton X-100, 0.05% Tween-20, 0.02% BSA in PBS) and the primary antibody was applied overnight at 4 °C. After washing three times with PBS, the cells were incubated with fluorochrome (AlexaFluor488, AlexaFluor594 or AlexaFluor647)-conjugated, highly cross-adsorbed secondary antibodies (Invitrogen) and 2,4,diamidino-2-phenylindole (DAPI, Sigma-Aldrich) for 2 h at RT. F-actin was visualized using AlexaFluor647-conjugated phalloidin. The samples were washed thoroughly with PBS and mounted in fluorescence mounting medium (Mowiol 4-88, Sigma-Aldrich). Immunofluorescence microscopy was performed using the confocal LSM800 Airyscan microscope (Carl Zeiss, Jena, Germany) equipped with a Plan-Apochromat × 63/1.4 oil differential interference contrast objective (Carl Zeiss). Image processing and quantification was performed using ZEN 2012, ImageJ (National Institutes of Health, Bethesda, MD) and Imaris (Bitplane, Version 9.1.2) software.
Single cell migration
For single cell migration assays, MDCK II cells transfected with either LA-EGFP or LA-mCherry were seeded on Col-I-, VN-, FN-, or LN-coated microscope slides (Ibidi µ-Slide 8 well glass bottom, Ibidi #80827) at a cell density of 2000 cells / cm2. After overnight incubation, the cells were analyzed using the confocal LSM780 microscope (Carl Zeiss, Jena, Germany) with a Plan-Neofluar × 20/0.5 objective for 10 h with images taken every 10 min. The velocity of single cells was determined by tracking the cells using the TrackMate Plugin from ImageJ, which tracks the cell from frame to frame and thereby determines its average velocity.
Collective cell migration
For the analysis of collective cell migration in epithelial monolayers, a monolayer expansion assay was used in which collective cell migration is triggered by a free surface [13, 32]. MDCK cells were seeded in different compartments of Col-I-, VN-, FN-, or LN-coated microscope slides (Ibidi µ-Slide 2 well glass bottom, Ibidi #80287) separated by a removable silicone stamp (Ibidi Culture-Inserts 2 Well for self-insertion, Ibidi #80209). Cells were grown for 72 h to confluency before removal of the stamp to trigger sheet migration. Pictures were taken directly after removal of the stamp and 8 h later using an EVOS digital inverted microscope. The collective cell migration speed was calculated as the mean distance of the front of the cell sheet from the initial position of the cell sheet’s front at the end of the observation time using ImageJ. Briefly, the cell-free area measured at the end of the observation period (t1 = 8 h) was subtracted from the cell-free area at the beginning (t0) resulting in the total area covered by migrated cells. This area was divided by the height of the gap resulting in the total distance that the cells had migrated. To take into account that the cells close the gap from both sides, the total distance was divided by two resulting in the distance migrated by a single sheet. The migration speed of the cellular collective was calculated by dividing the distance of a single sheet by the observation time and is given in µm/min. Experiments were performed at least three times with at least three separate migration chambers (biological replicates) per experiment.
Analysis of single cell motility within cell collectives
Cell motility of single cells embedded in migrating cell collectives was analyzed by seeding co-cultures of LA-mCherry- and LA-EGFP-transfected MDCK cells (mixed at ratios of 1:5) on Col-I-coated microscope slides used for collective cell migration (see above). After cells had reached full confluency (72 h after seeding) stamps were removed to induce collective cell migration. 6 h after removal of the stamps, cell behavior was recorded for 10 h with images taken every 3 min using the confocal LSM780 microscope (Carl Zeiss, Jena, Germany) with a Plan-Apochromat × 63/1.4 oil objective. For analysis, the LA-mCherry and LA-EGFP channels, a median filter was applied and cells from one channel were segmented as binary (black and white) images (BW) by manual thresholding.
For single cells movies, cell segmentation was performed according to [81]. Briefly, the center of the segmented cell was determined for each frame to calculate the average velocity and directionality using the TrackMate Plugin for ImageJ. To access the dynamic changes of the cell outline, the segmentations of a cell at two different time points was compared using the Jaccard index J according to the following formula:
$$J\left(t\right)=\frac{\left|A\cap B\right|}{\left|A\cup B\right|},$$
where A and B are the segmented cells at time point \((t-\Delta t)\) and \((t+\Delta t)\), respectively:
$$A=BW\left(t-\Delta t\right),$$
$$B=BW\left(t+\Delta t\right).$$
The Jaccard index is equal to 1 if the cell outline is not changed between the two time points and tends to zero for higher differences, indicating higher protrusion/retraction activity at the cell border. Note, that this index can change, even if the center of the segmented cell does not move at all.
For movies with one or more cells, the protrusion and retraction activity along the segmented region was quantified. To estimate the protrusion activity, the area that was exclusively occupied by the segmented cells at the time point \((t+\Delta t)\) but not at time point \((t-\Delta t)\) was determined and normalized to the perimeter of the segmented area at time point t:
$$Area increase\left(t\right)=\frac{|B\backslash A|}{perimeter(BW\left(t\right))}.$$
In analogy, the retraction activity was calculated:
$$Area decrease\left(t\right)=\frac{|A\backslash B|}{perimeter(BW\left(t\right))}.$$
For these calculations, \(\Delta t\) was set to 3 min.
All parameters are represented as mean values over the entire duration of the experiment. The scripts to calculate the Area Increase, the Area Decrease and the Jaccard indices are freely available by the authors upon request.
Statistics
Results are expressed as arithmetic means ± SD as indicated. To test the normality of data, D’Agostino–Pearson normality test was used. Data with normal distributions were statistically compared by using unpaired, two-tailed Student’s t test, whereas Mann–Whitney U test was applied for data without normal distribution. Statistical analyses were performed using GraphPad Prism version 6 (GraphPad Software, San Diego, CA). P values are indicated as follows: *P < 0.05, **P < 0.01, ***P < 0.001 and ****P < 0.0001.