Spontaneous Cell Competition in Immortalized Mammalian Cell Lines

<div><p>Cell competition is a form of cell-cell interaction by which cells compare relative levels of fitness, resulting in the active elimination of less-fit cells, “losers,” by more-fit cells, “winners.” Here, we show that in three routinely-used mammalian cell lines – U2OS, 3T3, and MDCK cells – sub-clones arise stochastically that exhibit context-dependent competitive behavior. Specifically, cell death is elicited when winner and loser sub-clones are cultured together but not alone. Cell competition and elimination in these cell lines is caspase-dependent and requires cell-cell contact but does not require <i>de novo</i> RNA synthesis. Moreover, we show that the phenomenon involves differences in cellular metabolism. Hence, our study demonstrates that cell competition is a common feature of immortalized mammalian cells in vitro and implicates cellular metabolism as a mechanism by which cells sense relative levels of “fitness.”</p></div

Cell competition in U2OS cells is mediated by post-transcriptional mechanism.

<p>(A) Microarray RNA analysis experimental design. Cells were grown in mono- or co-cultures for 48h as indicated and sorted by flow cytometry before RNA extraction. (B) Venn diagram distribution of RNAs displaying >2-fold expression change across indicated sample groups. Only six transcripts were found to be differentially expressed in mono-cultured and competing YFP cells, while no transcription changes were observed in response to competition in Wt and R1 cells. (C) Immuno-staining of metabolite-labeled nascent RNA and protein chains in Wt U2OS cells treated with actinomycin D or cycloheximide for 24 hours. Ethynil-uridine (EU) and homopropargyl-glycin (HGP) were added to label nascent RNA and peptide chains 2 h before staining. Complete inhibition of transcription and translation was obtained with actinomycin D and cycloheximide, respectively. (D) Cp3-IF of Wt:YFP 72-hour cultures grown in presence or absence of actinomycin D- and cycloheximide. Cycloheximide completely abolished Wt-induced YFP apoptosis. Actinomycin D treatment resulted in a partial rescue to a degree consistent with its inhibition of cell division (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132437#pone.0132437.s010" target="_blank">S10 Fig</a>). *”p<0.05, **: p<0.01 by Student’s <i>t</i>-test.</p

Differences in energy metabolism drive cell competition in mammalian cells.

<p>(A) Quantification of apoptosis (Cp3 immunofluorescence) in U2OS cultures grown for 72 hours under normoxic (21% O₂) or hypoxic (1.5% O₂) conditions. Hypoxia inhibits cell competition-induced elimination of YFP and R1 cells in Wt:YFP and Wt:R1 co-cultures. (B) Quantification of Cp3 immunofluorescence in U2OS R1 cells expressing a nonsense (NSC, non-silencing control) shRNA or shRNAs directed against the Hif1a transcription factor. Hif1a knockdown in loser cells does not affect cell competition. qPCR analysis of Hif1a in shRNA-expressing YFP cells is shown on the right. (C) Quantification of Cp3 immunofluorescence in U2OS cultures grown for 72 hours in medium containing standard (4 mM) and reduced (0.4 mM) Glutamin (Gln) concentrations. Withholding Gln arrests cell competition in U2OS cells. (D) Quantification of Cp3 immunofluorescence in U2OS cultures treated with a mitochondrial uncoupling agent (carbonyl cyanide m-chlorophenyl hydrazine, CCCP). Uncoupling respiration from oxidative phosphorylation blocks competition-induced elimination of R1 and YFP cells, indicating that competition is driven by differences in the activity of ATP-generating pathways. (E) Luciferase analysis of intracellular ATP levels in monocultured U2OS cell. YFP, but not R1 cells, display reduced ATP levels in when compared to Wt cells. Hypoxia increases ATP levels YFP cells, suggesting that reduced ATP levels may reflect or underlie YFP cell fitness.*: p<0.001, by one-way ANOVA.</p

U2OS cell competition interactions are short-ranged.

<p>(A) Schematic representation of U2OS transwell cultures, Cells shared culture medium but were separated by a 0.8 μm Durapore membrane. (B) Cp3-IF analysis of apoptosis in transwell cultures. Wt cells induce apoptosis in YFP cells in the insert but not in YFP cells separated by the transwell. (C) Spot-seeding of YFP and H2B-mCherry expressing clone R1. Mixed YFP:R1 spots surrounded by pure YFP cell populations were divided in “inner” (I), “border” (B), and “outer” (O) zones as represented. (D) Time-lapse microscopy tracking of YFP cell fates during 72-hour spot cultures. The number of cell layers separating each YFP cell from its nearest R1 neighbor was recorded, and YFP “B” cells were grouped accordingly: for instance, a YFP cell is labeled “B3” if it comes within 3 cell layers of the nearest R1 cell, while a”B0” YFP cell comes to lie adjacent to an R1 cell at any time during the observation period. The data summarizes the fate of cells present at the beginning of each experiment and their immediate progeny, followed over 72 hours. The percentage of followed cells that underwent cell division is shown at the top; cell death is shown at the middle, and net population size change at the bottom. Increased apoptosis is observed only in inner YFP cells and “B0” border cells that come in direct contact with R1 cells. Data in panel D was derived from 3 independent experiments (Supplemental Movie S1-3), comprising over 5,000 cells counted. *: p<0.05, **: p<0.01 by Student’s <i>t</i>-test; #:p<0.05, ##:p<0.01 by paired <i>t</i>-test.</p

Cell death is triggered by a cell competition-like interaction in clonally-derived mammalian cell lines.

<p>(A) Cell counts showing YFP (“loser” cells) cells first expand, then decline, in the presence of Wt (“winner”) cells but grow unimpeded when cultured alone. Time is measured from cell seeding (t = 0). (B) Cleaved caspase-3 (Cp3) immuno-fluorescence (IF) (red) of U2OS cultures showing increased apoptosis in co-cultured YFP cells (green). Arrows indicate Cp3+ apoptotic YFP cells. Wt cells are counterstained with Hoescht 33342 (blue). (C) Quantification of apoptosis on immune-stained cultures; x-axis, time in days (d) Note that the baseline level of apoptosis increases with cell density by day 6 under all culture conditions. (D) Quantification of cell proliferation in 72-hour U2Os cultures by phospho-histone H3 (PH3) immunofluorescence. (E) Cp3 IF of 72-hour U2OS cultures treated with the caspase-3 inhibitor Z-VAD-FMK. YFP cell counts per microscope field are shown at the bottom. Inhibition of apoptosis by Z-VAD-FM K prevents YFP elimination from Wt:YFP co-cultures. (F) P-H3 IF of U2OS cells cultured for 72 hours in presence of the Cyclin D1 inhibitor purvalanol A as indicated. Quantification of apoptosis is shown below. Purvalanol A treatment inhibits proliferation (top) and rescues YFP elimination (bottom). Images were taken at 100X magnification. Error bars in this and all subsequent figures reflect mean ± SD. *: p<0.05, **: p<0.01 and ***: p<0.001 by Student’s <i>t</i>-test.</p

U2OS cell “fitness” is context-dependent.

<p>(A) Aspect of U2OS G1, R1, and YFP co-cultures in fluorescence microscopy. Cells were plated at a 1:1 ratio as indicated (R1:G1 or R1:YFP) and allowed to grow for 1, 3 or 6 days. (B) Cp3-IF apoptosis quantification. R1 cells behave as “winners” in R1:YFP cultures but as “losers” in the presence of G1 cells, indicating that R1 cells assume “winner” or “loser” status depending on the properties of their co-culture partners. *: p<0.001 by Student’s <i>t</i>-test.</p

Qualitative and quantitative migration for HT-1080s and hDFs.

<div><p>Time-lapse images (10 min./frame) illustrating migration for (<b>A</b>) an hDF and (<b>B</b>) an HT-1080 in synthetic ECM (220 Pa, 1000 μM CRGDS). Image sequences in (<b>A</b>,<b>B</b>) are contrast and brightness enhanced for better display (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081689#pone.0081689.s013" target="_blank">Movies S2, S3</a> for unaltered images, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081689#pone.0081689.s015" target="_blank">Movie S4</a> for overview comparison of many cells). (<b>A</b>) Migration movement for hDF is characterized by: 1. Front end extension, 2. Attachment, 3. Cell body contraction, and 4. Rear-end release. (<b>B</b>) HT-1080 movement illustrates cell body contraction (white dashed lines and arrow) and simultaneous front end extension (red dashed lines and arrow). </p> <p>(<b>C</b>-<b>E</b>) Comparison of quantified 3D migration for HT-1080s and hDFs in synthetic ECM (220 Pa and 1000 μM CRGDS): (<b>C</b>) Cell speed (adjusted by a factor of √3/2, which was a 3D correction for analysis on 2D minimum intensity z-projections), (<b>D</b>) directionality (DTO/TD), and (<b>E</b>) fraction migrating cells. DTO/TD is a dimensionless parameter that provides a measure of directional motility analogous to persistence time (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081689#pone.0081689.s001" target="_blank">Fig. S1A</a>) that is calculated as the distance-to-origin (DTO) after 6 hours divided by the total path length (total distance, TD) (shown schematically, panel to right of C). Migration was calculated from images collected in 15 min. increments for 6 hours, with dividing or interacting cells excluded (≥200 cells, ≥ 3 separate experiments, ≥ 9 total hydrogels). <i>Box</i> and <i>whisker </i><i>plot </i><i>for </i><i>cell </i><i>speed</i>: White diamond = mean, white line = median, boxes = middle upper (top) and middle lower (bottom) quartile of the cell population, whiskers = highest (above) and lowest (below) migration speeds. Values for DTO/TD represent the mean for all cells while fraction migrating represents the mean for replicate experiments (N ≥ 3). Significance was calculated for hDF relative to HT-1080 migration for each parameter (*** = p<0.001). </p></div

Morphologies and cytoskeletal structure for HT-1080 fibrosarcoma cells (HT-1080s) and primary human dermal fibroblasts (hDFs) in synthetic extracellular matrix (ECM).

<div><p>(<b>A</b>) Schematic representation of synthetic extracellular matrix (synthetic ECM) formed through “thiol-ene” photopolymerization chemistry to couple norbornene C=C bonds on 4-arm poly(ethylene glycol) (PEG) molecules with thiol (-SH) bonds of cysteine-containing peptides. Crosslinks were formed using matrix metalloproteinase (MMP)-degradable peptides with cysteine groups on each end while adhesion was promoted using pendant RGD-containing peptides (C<b>RGDS</b>) with a single cysteine (2.5 or 3 wt% by mass PEG-NB + MMP-degradable crosslinking peptide, shear moduli = 140 Pa or 220 Pa respectively). Constant total pendant peptide was maintained using non-bioactive C<i><b>RDGS</b></i> (1500 μM active C<b>RGDS</b> + non-active C<i><b>RDGS</b></i>). </p> <p>(<b>B</b>-<b>I</b>) Projected z-stack immunofluorescence (IF) images illustrating hDFs and HT-1080s seeded in synthetic ECM (220 Pa, 1000 μM CRGDS). All overlay images are counterstained with TRITC-conjugated phalloidin (F-actin, red) and DAPI (nuclei, blue). (<b>B</b>,<b>C</b>) Overview to illustrate morphological differences (F-actin, red; Nuclei, blue) for (<b>B</b>) hDFs and (<b>C</b>) HT-1080s. (<b>D</b>-<b>F</b>) IF images illustrating myosin IIb expression for hDFs: (<b>D</b>) Overlay image (Myosin IIb, green; F-actin, red; Nuclei, blue); Single channel images (grayscale) illustrate (<b>E</b>) F-actin and (<b>F</b>) Myosin IIb. White arrows point to actomyosin filaments. (<b>G</b>-<b>I</b>) IF images illustrating myosin IIb expression for <b><i>HT-1080s</i></b>: (<b>G</b>) Overlay (Myosin IIb, green; F-actin, red; Nuclei, blue); Single channel images (grayscale) illustrate (<b>H</b>) F-actin and (<b>I</b>) Myosin IIb. </p> <p>(<b>J</b>-<b>L</b>) Comparison of quantified mean (<b>J</b>) circularity and (<b>K</b>) elongation for hDFs and HT-1080s calculated using Nikon NIS Elements software (n > 150 cells, ≥ 6 hydrogels, at least two separate experiments; *** = p<0.001). (<b>L</b>) Fraction of elongated (Elongation ≥ 3.0), middle (2.0 ≤ Elongation < 3.0), and rounded (Elongation < 2.0) cells. Differences in fraction of elongated and rounded hDFs compared to HT-1080s were each statistically significant (N ≥ 6 total gels, at least two separate experiments; *** = p<0.001). </p></div

Matrix influences on migration and morphologies for HT-1080s in synthetic ECM.

<p>(<b>A</b>) Cell speed and (<b>B</b>) directionality (DTO/TD) for HT-1080s as a function of matrix conditions (≥ 6 gels, ≥ 40 cells, at least two separate experiments; * = p<0.05; ** = p<0.01). X-axis: Modulus in Pa / RGD concentration in μM. <i>Box</i> and <i>whisker </i><i>plot </i><i>for </i><i>cell </i><i>speed</i>: White diamond = mean, white line = median, boxes = middle upper (top) and middle lower (bottom) quartile of the cell population, whiskers = highest (above) and lowest (below) migration speeds. Error bars for DTO/TD represent standard error of the mean for individual cells. There is also a statistical difference in cell speed for the 140 Pa (1500 μM RGD) and 220 Pa (250 μM RGD) conditions (p<0.05, not shown on graph for clarity). (<b>C</b>) A comparison of the fraction of rounded HT-1080s (Elongation Index < 2.0) as a function of synthetic ECM conditions (x-axis: Modulus in Pa / RGD concentration in μM; white bar = 140 Pa; black bars = 220 Pa). Error bars represent standard deviation for fraction of rounded cells per gel (≥ 6 gels, at least two separate experiments; * = p<0.05; ** = p<0.01; *** = p<0.001). </p

Comparison of adhesion properties for HT-1080s and hDFs.

<div><p>(<b>A</b>-<b>M</b>) Projected z-stack immunofluorescence (IF) images for hDFs and HT-1080s in synthetic ECM (220 Pa, 1000 μM CRGDS). All overlay images are counterstained with TRITC-conjugated phalloidin (F-actin, red) and DAPI (nuclei, blue). </p> <p>(<b>A</b>-<b>D</b>) IF images illustrating vinculin expression for <i><b>hDFs</b></i> (boxed region from A shown in B-D): (<b>A</b>) Overlay image (Vinculin, green; F-actin, red; Nuclei, blue). White arrows point to regions enriched with vinculin. (<b>B</b>) Overlay (Vinculin, green; F-actin, red); Single channel images (grayscale) illustrate (<b>C</b>) F-actin and (<b>D</b>) Vinculin. (<b>E</b>-<b>G</b>) IF images illustrating vinculin expression for <b><i>HT-1080s</i></b>: (<b>E</b>) Overlay image (Vinculin, green; F-actin, red; Nuclei, blue). Single channel images (grayscale) illustrate (<b>F</b>) F-actin and (<b>G</b>) Vinculin. </p> <p>(<b>H</b>-<b>J</b>) IF images illustrating β1-integrin expression for <i><b>hDFs</b></i>: (<b>H</b>) Overlay (β1-integrin, green; F-actin, red; Nuclei, blue); Single channel images (grayscale) illustrate (<b>I</b>) F-actin and (<b>J</b>) β1-integrin (White arrows point to punctate β1-integrin features; Also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081689#pone.0081689.s003" target="_blank">Fig. S3</a>). (<b>K</b>-<b>M</b>) IF images illustrating β1-integrin expression for <b><i>HT-1080s</i></b>: (<b>K</b>) Overlay (β1-integrin, green; F-actin, red; Nuclei, blue); Single channel images (grayscale) illustrate (<b>L</b>) F-actin and (<b>M</b>) β1-integrin. </p> <p>(<b>N</b>) Comparison of attachment for hDFs and HT-1080s on RGD-SAMs as a function of RGD density. Attachment was statistically significant (cell number > 0 RGD control spots) for HT-1080s on surfaces with ≥ 0.19% mol fraction RGD and for hDFs on surfaces ≥ 0.007% mol fraction RGD. Error bars represent standard error of the mean (SEM) for array spots at given RGD density. Significance for cell attachment on individual spots was calculated for hDFs relative to HT-1080s (* = p<0.05; ** = p<0.01; *** = p<0.001). </p></div