www.sciencemag.org/cgi/content/full/science.aad7611/DC1
Supplementary Materials for ESCRT III repairs nuclear envelope ruptures during cell migration to
limit DNA damage and cell death
M. Raab, M. Gentili, H. de Belly, H. R. Thiam, P. Vargas, A. J. Jimenez, F. Lautenschlaeger, Raphaël Voituriez, A. M. Lennon-Duménil, N. Manel, M. Piel
*Corresponding author. E-mail: [email protected]
Published 24 March 2016 on Science First Release DOI: 10.1126/science.aad7611
This PDF file includes
Materials and Methods Figs. S1 to S13 Full References Movies S1 to S10
Other Supplementary Materials for this manuscript include the following: (available at www.sciencemag.org/cgi/content/full/science.aad7611/DC1)
Movies S1 to S10
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Materials and Methods
Channels preparation and cell loading
Micro-channels were prepared as previously described (10). Briefly,
polydimethylsiloxane (PDMS, 10/1 w/w PDMS A / crosslinker B) (GE Silicones) was
used to prepare 7µm wide and 5µm high micro-channels with constrictions of varying
lengths and widths from a self-made mold. For HeLa and U2OS cells, larger channels of
12 µm width and 5 µm height were used because of their larger nuclei. Channels with
constrictions were incubated with 15 µg/mL of fibronectin for 30 min then washed with
PBS at least 3 times and finally incubated with medium (containing drugs if necessary)
for at least 5 hours before adding cells. Note that the height inside constriction varied
depending on the width: height was 2 µm for 1.5 µm wide constrictions, 3.5 µm for 2 µm
wide constrictions, 4µm for both 3 µm and 4 µm wide constrictions, and 5 µm for 5 µm
wide constrictions. 100,000 cells in 5 uL of medium was added to each reservoir, and
after 30 min of incubation, medium was added to above the PDMS construct.
Cell Confinement
For confined migration in Fig. 1, LifeAct mDCs were plated on glass bottom 6 well
plates either with or without 1.6 mg/ml bovine collagen (Advanced BioMatrix) (Filling or
No Filling) and then a 5 µm roof of PDMS was placed on top, as previously described
(12, 30). Briefly, silicon wafers were coated with SU8 2005 photoresist (Microchem) 5
µm in height and holes were made in lithography. To make the PDMS pillars as the 5 µm
height spacers, 10 mm glass coverslips were plasma treated and then placed on top of
PDMS mixture (10/1 w/w PDMS A / crosslinker B) on the wafer with the holes. After
baking at 95°C for 10 min, coverslips with PDMS pillars were carefully removed from
the wafers under isopropanol. They were then cleaned with isopropanol, well-dried,
treated with plasma for 1 min, and treated with 0.5 mg/mL pLL-PEG in 10 mM pH 7.4
HEPES buffer for 1h at room temperature. Coverslips with PDMS pillars were rinsed and
incubated in medium for at least 5 hours before confining the cells. The modified cover
lid of a multi-well plate was used to apply confining slides to cells. In this case, large
PDMS pillars were stuck on the cover lid of the multi-well plate to hold confining slides.
There are pillars that push the confining slides from the top of the plastic 6 well plate lid
to confine the cells in 6 well glass bottom plates. The process of fabrication for these
large pillars attached to the 6 well plate lid is as follows: the large PDMS pillars were
fabricated by pouring a PDMS mixture (A:B = 35:1) into a custom-made metallic mold,
removing bubbles under vacuum, then baking overnight at 80°C, and getting the pillars
out of the mold with the help of small amount of isopropanol.
For compression to break the nucleus, cells on FluoroDishes (WPI) were squeezed
with confining structures of PDMS on glass slides as previously mentioned above except
the height for HeLa cell confinement to break the nucleus was 3 µm. A suction cup was
used to press the confining PDMS pillar coverslip onto the FluoroDish. The suction cup
device was molded in PDMS by pouring the crosslinker/polymer mix (1/10 w/w) into a
3
custom-made mold and baked at 80°C for 30 min before unmolding. Applying a vacuum
causing the confining coverslip to press down onto the cells (30).
Mice
Bone marrow was taken from C57BL/6 mice, to differentiate immature mouse
dendritic cells (mDCs), described in (31). LifeAct-GFP mice were a kind gift from
Michael Sixt lab (IST, Austria), and generated as described (32). Mice were taken care of
by the guidance of the Animal Welfare Body, Research Centre, Institut Curie.
Cells
Human monocytes were isolated from peripheral adult human blood as previously
described (38). Monocytes were cultured and differentiated into dendritic cells (hDCs) in
RPMI medium with Glutamax, 10% FBS, PenStrep, Gentamicin (50 μg/ml, GIBCO), and
HEPES (GIBCO) in the presence of recombinant human GM-CSF (Miltenyi) at 10 ng/ml
and IL-4 (Miltenyi) at 50 ng/ml. For experiments involving hDCs, 3 separate human
donors were used.
Immature mouse bone-marrow derived dendritic cells (mDCs) were cultured 10-12
days in IMDM supplemented with 10% FBS, Glutamine (20mM), pen-strep (100U/mL)
and 2-mercaptonethanol (50µM), and granulocyte-macrophage colony stimulating factor
(50 ng/mL)-containing supernatant obtained from transfected J558 cells, as previously
described (31). After 4 days of differentiation, all cells are passed to a density of 10-20
million per 120 cm² and repeated again at day 7. Dendritic cells were then used for
experiments between days 10 and 12. To activate and mature mDCs to express CCR7
(C-C chemokine receptor type 7) and chemotax against gradients of chemokine CCL21,
(C-C motif) ligand 21, in collagen, immature mDCs were treated with LPS (100 ng ml−1)
for 30 min and washing 3 times with complete medium and then the experiment was
performed the next day.
HeLa cells were cultured in DMEM Glutamax (Gibco) supplemented with 10% FBS
(GE Healthcare) and 1% penicillin and streptavidin (Lonza). The HeLa cells expressing
CHMP4B-EGFP at endogenous levels were a kind gift from Antony Hymann’s lab (16).
RPE-1 cells were grown in DMEM-F12 Glutamax medium (Gibco), supplemented with
10% FBS and 1% penicillin and streptavidin (Lonza). RPE-1 cells expressing 53BP1-
GFP were obtained from the lab of René Medema (21). RPE-1 cells expressing NLS-GFP
were obtained from the lab of Martin Hetzer (28). Stable cell line of HeLa expressing
MS2-mCherry-NLS was kindly made in the Buzz Baum lab. HeLa cell line expressing
LAP2β-GFP and H2B-mCherry were a kind gift from Mark Petronczki lab (33). U2OS
cells expressing LaminA-GFP were a kind gift from the lab of Harold Hermann.
Constructs
The plasmids pSIV3+, psPAX2, pCMV-VSV-G and pTRIP-CMV were previously
described (34, 35). Human cGAS WT open reading frame was amplified by PCR from
4
cDNA prepared from monocyte-derived dendritic cells. Human cGAS E225A/D227A
mutant was obtained by overlapping PCR mutagenesis. The mutation E225A/D227A
inactivates the catalytic site of cGAS impeding cGAMP production with consequent IFN
production, but leaves intact the protein ability to bind DNA.FLAG-cGAS and FLAG-
cGAS E225A/D227 were cloned in pTRIP-CMV in frame with GFP to obtain pTRIP-
CMV-GFP-FLAG-cGAS and pTRIP-CMV-GFP-FLAG-cGAS E225A/D227A. pTRIP-
CMV-tagRFP was generated by substituting the tagRFP sequence (RFP hereafter;
Evrogen) to the EGFP sequence of pTRIP-CMV. pTRIP-CMV-tagRFP-FLAG-cGAS
was generated by cloning FLAG-cGAS in frame. pTRIP-SFFV was generated by
substitution of the CMV promoter with the SFFV promoter from GAE-SFFV-GFP-
WPRE (36). pTRIP-SFFV-EGFP-NLS (NLS-GFP hereafter) was generated introducing
the SV40 NLS sequence (PKKKRKVEDP) by overlapping PCR at the C-terminal of
GFP in pTRIP-SFFV.
Plasmids and transfections
Transfections on HeLa cells were done using Lipofectamine 2000 (Thermo Fisher)
with a ratio of 1 ug DNA per 1 uL lipofectamine reagent. RPE-1 cells were transfected
with LTX (Thermo Fisher) according to the manufacturer’s instructions. NES-2xGFP
was provided by the Hetzer lab (28) and the NLS-MS2-mCherry was a gift from the lab
of Alessandro Marcello. MS2 signifies coat protein of phage.
Collagen gel with CCL21 gradient
Adapted from (37): mDCs transduced with NLS-GFP were mixed at 4 °C with 1.6%
bovine collagen type I (Advanced BioMatrix) at basic pH. Forty microliters of the mix
was deposited on a 35 mm glass -bottom dish and the drop was homogenized while
covered with a 12 mm glass slide. The sample was incubated at 37 °C for 20 min to allow
collagen polymerization. To generate the CCL21 gradient, 2 ml of BMDC medium
containing 200 ng ml−1 of CCL21 (R&D systems) was added to the plate. Cells were
imaged at a frequency of 1 image per 30 sec using a 20x objective using a spinning disk
microscope, with a z stack of 50 µm total height and 5 µm step size.
mDC Migration in Mouse Ear Explants
Ears from C57BL/6 mice were excised and a pair of forceps was used to create a
hole on the skin. The ventral and dorsal sides of the explant were separated by peeling.
The ventral sheet was kept and immunostained with anti-LYVE-1 (R&D Systems)
primary antibody to mark the lymphatic vessels. After washing with media, a secondary
antibody against rat (Jackson Immunoresearch) was used. The ear sheet was then spread
flat in a 6 well plate and a PDMS block with a central hole of diameter 8 mm was placed
on top of each explant with the ventral side up. 200,000 DCs expressing NLS-GFP (see
below) were added in 100 µL of culture medium inside the hole. After 1 h of incubation,
the ear sheet was washed with culture medium and then placed with the face on which
cells were incubating against the bottom glass slide in a FluoroDish. Ear explants were
nailed to a block of PDMS to prevent the explant from moving during imaging and also
5
to allow flow of fresh medium. Imaging was performed on an inverted spinning disk
confocal microscope, at 37°C and with 5 % CO2, taking z-stacks 50 µm in total height
using a 5 µm step size with a 20x objective.
For quantification of nuclear deformation in ear explants in Fig. 1, dendritic cells
were prelabeled with CFSE (Carboxyfluorescein succinimidyl ester) (ThermoScientific)
according the manufacturer’s instructions and then allowed to migrate in the ear explants
for 5 hours before fixation with paraformaldehyde.
Quantifications
In Fig. 1D,E, nuclear circularity was quantified by thresholding the Hoechst signal,
as = 4π(area/perimeter²), and the minimum diameter was taken as the minimum diameter
of the pinched shaped nucleus.
For nuclear leakage quantification, nuclear circularity was quantified by
thresholding the Hoechst or NLS-GFP signal and taking circularity=4π*(area/perimeter²).
To quantify nuclear leakage of NLS-GFP, a small ROI was put in front of the nucleus at
each time frame. For measuring leakage in channels as ‘NLS-GFP Intensity
Cytoplasm/Nucleoplasm’, the average intensity of the ROI of the cytoplasm in front of
the nucleus was divided by the average intensity of the nuclear NLS-GFP signal before
the nucleus entered the constriction. This takes into account differences in expression
levels of NLS-GFP for each cell. For quantifying leaking of NLS-MS2-mCherry after
photoablation, a small ROI next to the nucleus near the site of wounding was measured
for average intensity for each time frame after background subtraction.
To quantify the ‘survival after one constriction’ a cell death was counted if the
nucleus apoptosed after passing a constriction during the rest of overnight imaging
movie. If a cell moved through another constriction during the movie, then the cell was
counted as surviving another constriction. The ‘frequency of nuclear opening’ was
quantified by assessment of entry of tagged cGAS or exit of NLS during nuclear
engagement with the constriction.
To quantify ‘NLS signal recovery’ in comparing the NLS-GFP leakage with the
knockdowns of LMNA and CHMP3, the time was measured from after the nucleus exits
the constriction until full recovery of NLS-GFP back into the nucleus as observed with
20x microscopy. An empty circle indicates that full recovery of NLS-GFP occurred
before the nucleus has completely exited the constriction.
For laser wounding experiments, the ‘Timing for first appearance’ was measured as
the time after photoablation until the time of a fluorescent signal appeared above the
background intensity.
siRNA
siRNA 5’-AAA GCA UGG ACG AUC AGG AAG-3’ was used to deplete CHMP3
(13), , both 5’-GGUGGUGACGAUCUGGGCU-3’; and 5’-
6
AACUGGACUUCCAGAAGAACAUC-3’to target LMNA (4). Non-targeting siRNA
(Dharmacon, GE Life Technologies) was used as the control. siRNA was transfected with
Lipofectamine RNAiMAX (Invitrogen). Cells were transfected with 120nM siRNA 48 h
and again 24 h before the experiment.
Lentivector transductions
Transduced hDCs were obtained by infecting monocytes purified from blood with
pTRIP-CMV-GFP-FLAG-cGASE225A/D227A lentiviral vectors. Transduction of
freshly isolated monocytes from blood has been adapted from (35). 2 million monocytes
were seeded in a 6 well plate in 2 ml of medium. 2ml of fresh virus and 2 ml of SIV-VLP
were added to each well in presence of GM-CSF, IL-4 and 8µg/ml of Protamine
(SIGMA). At day 4 or 5 of differentiated cells were resuspended in fresh medium with
fresh cytokines and used in assays.
Transduced mDCs were obtained by transduction of murine bone marrow from
C57BL/6 mice. 1.8 million bone marrow cells were plated in a 6 well plate at day of
purification (day 0) in 2 ml of medium. At day 1, 40ml of fresh pTRIP-SFFV-GFP-NLS
lentivector supernatant were loaded in Ultra-Clear Centrifuge tubes (Beckman Coulter)
and ultracentrifuged at 100,000g in a SW32 rotor (Beckman coulter) for 90 minutes at
4°C and resuspended in 400µl of in RPMI medium with Glutamax, 10% FBS, PenStrep,
Gentamicin (50 μg/ml, GIBCO). 200µl of ultracentrifuged virus were used to infect one
well of cells in presence of 8µg/ml of Protamine. Cells were then differentiated for 11
days and split as described above.
For HeLa and RPE-1 cells transduction of XFP-cGAS, 0.5 million cells were plated
in a 6 well plate in 1ml and infected with 2ml of fresh lentivector, pTRIP-CMV-GFP-
FLAG-cGAS for HeLa H2B-mCherry cells and pTRIP-CMV-tagRFP-FLAG-cGAS for
RPE-1 53BP1-GFP cells in presence of 8µg/ml of Protamine. The cells were then FACS-
sorted by gating on the brightest GFP/RFP-positive cells.
Lentiviral particles production in 293FT cells
Lentiviral particles were produced as previously described from 293FT cells (38).
Lentiviral viral particles and viral-like particles were produced by transfecting 1μg of
psPAX2 and 0.4μg of pCMV-VSV-G together with 1.6μg of a lentiviral vector plasmid
per well of a 6-well plate.
Antibodies and Reagents
For imaging the nucleus, cells were incubated with 200 ng/mL of Hoechst 33342
(Life Technologies) or 34580 (Thermo Fisher) for confocal imaging with 405 nm lasers
for 30 minutes at 37 °C and 5% CO2 before washing with fresh medium. The following
primary antibodies were used for immunoblotting: LmnA/C (H110, Santa Cruz), anti-
actin (Millipore), anti-CHMP3 (Santa Cruz), and for immunofluorescence; monoclonal
mouse Anti-phospho-Histone H2A.X (Ser139) (Millipore), anti-Lamin-B1 Nuclear
7
Envelope marker (Abcam), Anti-Nuclear Pore Complex Proteins antibody [Mab414]
(Abcam), anti-CHMP2B (Abcam).
For immunofluorescence, secondary antibodies anti-mouse-Alexa488, rabbit-Cy5,
and anti-Goat-Alexa488 (Jackson ImmunoResearch Laboratories) were used. ATMi
(KU-55933, TOCRIS) was used at 10 µM to inhibit DNA repair.
Immunoblotting
Cells were lysed on ice for 45 – 60 minutes in a buffer containing 100 mM Tris, 150
mM NaCl, 0.5% NP-40, and 1:25 of protease inhibitor cocktail (Roche). Thirty
micrograms of soluble extracts were loaded onto a 4-20% TGX gradient gel (BioRad)
and transferred onto a Trans-Blot Turbo PVDF/Nitrocellulose membrane (BioRad). The
membrane was blocked, incubated with the appropriate antibodies and revealed with
SuperSignal West Dura substrate (Thermo Scientific).
Photodamage and Time-Lapse imaging
Cells were cultured in Leibovitz’s L-15 CO2-independent medium (GIBCO) with
10% FBS during the wounding and acquisition. Spinning-disc confocal microscopy was
carried out with a Yokogawa CSU-X1 spinning-disc head on a Nikon Eclipse Ti inverted
microscope equipped with an EMCCD camera (Evolve, Photometrics), a NanoScanZ
piezo focusing stage (Prior Scientific) and a motorized scanning stage (Marzhauser) and a
Nikon S Fluor 100X/1.3 NA objective. The UV-laser damage experiments were
performed with a pulsed 355nm ultraviolet laser (Roper Scientific) driven by iLas
software. This microscope was operated with Metamorph and images were processed
with FIJI.
8
9
Fig. S1.
Dendritic cells deform their nucleus when migrating through collagen and tissue and
NLS-GFP leaks from nucleus to cytoplasm. (A) Large field view of the image of mouse
dendritic cells (mDCs) expressing LifeAct (green) and DNA labeled with Hoechst (blue).
White box indicates cell magnified in Figure1A. Cylindrical pillars of PDMS maintain
10
the 5µm height of 2D confinement. mDCs were free to migrate around the empty space
which was filled with collagen for the ‘collagen filling’ condition. (B) Large field view of
the image of mDCs shown in Figure1C (white box), labeled with CFSE (green) and
added to ear explant. LYVE1 antibody staining (red) shows location of lymphatic
vessels. Hoechst staining of entire ear explant shows the crowded environment of
endogenous cells. (C) Large field view of the image of mDCs in collagen moving across
a gradient of CCL21. Box indicates magnified cell, shown as raw images before
conversion to false colors. (D) Large field view of the image of mDCs expressing NLS-
GFP (green) added to ear explant. Lymphatic vessels indicated with LYVE1 staining
(red). White box depicts magnified cell, shown as raw images before conversion to false
colors. (E) Another example of mDCs migrating in an ear explant expressing NLS-GFP
but with an additional stain of Hoechst to stain the nuclei. Scale bars for large fields view
are 50 µm. Other scale bars are 10 µm.
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Fig. S2
HeLa and RPE-1 cells slowly migrating in microchannels with constrictions also show
NLS-GFP leakage from nucleus to cytoplasm when the nucleus passes through the
constriction. (A) Large field of view image of the reservoir where cells were added and
allowed to migrate spontaneously into channels. The channel contains successive
constrictions. Scale bar is 100 µm. (B) Higher magnification image of channels with
constrictions. Below: Phase contrast image of a mDC migrating through a constriction 15
µm length and 2 µm width. Scale bar 20 µm. (C) HeLa cell expressing NLS-MS2-
mCherry slowly passing a constriction 15 µm length and 2 µm width. False color was
applied to better show the increase in NLS-MS2-mCherry in the cytoplasm. (D) RPE-1
cell expressing NLS-GFP migrating through a constriction of 15 µm length and 1.5 µm
width. Scale bars 10 µm.
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Fig. S3
Nucleoplasm leaks out of the nucleus as bursts of varying size from nuclear constriction.
(A) Quantification of cytoplasmic NLS-GFP for the hDC shown in (Fig. 2A) with the
nuclear circularity determined from Hoechst labeling. (B) Quantification of NLS leakage
into the cytoplasm for the HeLa cell shown in Fig. 2B. 4 burst events are indicated on the
13
graph, with events 2 and 4 depicted in the images to the right of the graph with colored
dots to indicate location in time on the graph. The size of the blebs vary during nuclear
passage, and so an example of a HeLa nucleus passing with very small blebs which
constantly form and burst is shown in (C). The increase in NLS-MS2-mCherry in the
cytoplasm is quantified in the graph and appears to continuously increase because there
are many small blebs rupturing. Constriction L=15 µm w=2µm. (D) Example of a
nucleus passing that forms larger blebs. Rupture of these blebs cause dramatic increases
in the NLS-MS2-mCherry in the cytoplasm, with one example shown in the graph. Also
to note, when the nucleus is becoming deformed when first entering the constriction, the
NLS-MS2-mCherry in the cytoplasm can increase very slightly, pointed out during the
early phase of the graph before plateauing, which could be attributed to an increase in
nuclear pressure. Constriction L=15 µm w=4µm. (E) During the formation of blebs,
there was no increase in NLS-MS2-mCherry in the cytoplasm, only after rupture. The
time between the formation of blebs and their rupture was measured as ‘Lifetime of bleb’
in the histogram plot. Most blebs rupture in less than 10 min. n=43, N=2. (F) Viability of
cells after passing a constriction for constrictions of 15 µm in length and 4 µm in width
(less nuclear constriction than Fig. 2E of constriction width=2 µm). n=10 for HeLa, n>20
for hDCs and RPE-1, N=2. Scale bars are 10 µm.
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Fig. S4
Compression of the nucleus and migration through constrictions cause entering of
cytoplasmic GFP-cGAS into the nucleus. (A) hDC expressing GFP-cGAS (green) and
15
DNA labeled with Hoechst (red). The cell was compressed with a PDMS roof until
nuclear blebs were observed (dark region between DNA and cytoplasm in green with
GFP-cGAS, noted with white arrow). The bleb then burst and –GFP-cGAS bound to
DNA along the nuclear edge locally where the bleb originated (B) Frequency of GFP-
cGAS entry in the nucleus for varying constriction dimensions for hDCs. , n>25 for each
condition, N=3 (C) Position along the constriction at which GFP-cGAS entered the
nucleus for various constriction dimensions. Dashed lines indicate the exiting end of the
constriction, thus points after the dashed line signify breaks occurring after the front
nuclear tip had passed the constriction. (D) Location of GFP-cGAS entry in the nucleus
for HeLa cells expressing GFP-cGAS migrating through constrictions, L=15 µm, w=2
µm. n=19, N=2. (E) Plot of total intensity of GFP-cGAS which has entered the nucleus
in the HeLa cell depicted in Fig. 2I. while passing the constriction. Green arrows
indicate sequential events of entry of GFP-cGAS. (F) Additional example of pronounced
rupture events. R indicates a rupture event with a sharp increase in GFP-cGAS,
quantified in (G). The gradual decrease in GFP-cGAS after the ruptures indicate the slow
export of GFP-cGAS back out of the nucleus into the cytoplasm. Step increases larger
than 2 standard deviations are colored red. Scale bars are 10 µm.
16
17
Fig. S5
Migration through constrictions causes rupturing of the lamina which is then reformed.
(A) U2OS cell expressing LaminA-GFP migrating through a constriction. The Lamina
ruptures and reforms constantly at the tip of the nucleus. (B) mDC with nuclei inside
constrictions fixed and stained for nuclear pore complex protein (NPC) (green), DNA
18
with Hoechst (blue) and LaminB (red). (C) mDC stained for NPC and DNA. The tip of
the nucleus appears devoid of nuclear pores or LaminB staining (white arrows). (D-F)
Three representative examples of HeLa BAC cells expressing LAP2β-GFP and H2B-
mCherry migrating through constrictions (L=15 µm, w=2 µm). New LAP2β-GFP
quickly reforms around DNA herniations. In some cases, threads of chromatin could
extend in front of the nucleus (E), but the nuclear envelope quickly reformed around
them. Multiple blebs on top of other blebs could also be observed (F). Scale bars are 10
µm.
19
Fig. S6
Minimal physical model for nuclear deformation during cell migration through a narrow
pore.
The cell nucleus has a complex rheology. It is often described effectively as a linear
elastomer, whose elastic component is largely due to the lamina layer (4). For slow
deformations, as involved in cell migration, a viscous behavior of the nucleoplasm is
expected. Based on these observations, we assume that the nucleus can be modeled as a
viscous fluid enclosed by the NE, a double membrane (ONE: outer nuclear membrane,
INE: inner nuclear membrane). The lamina layer is modeled as a thin elastic membrane
connected to the NE by linkers such as LAP2β and SUN proteins.
We consider a cell migrating through a narrow pore or constriction. When the nucleus is
engaged in the constriction, it induces a physical barrier between the back and the front of
the cell cytoplasm (defined by the direction of migration). This allows for a difference of
hydrostatic pressure in the cytoplasm between the back (Pb) and front (Pf) compartments.
We assume that the contractility of the actomyosin cortex at the back of the cell increases
upon engagement of the nucleus in the pore; we will therefore assume that Pb increases
over the process, and in particular Pb> Pf. Force balance at the NE is then expressed by
Laplace law, which relates the pressure in the nucleus Pn and the total surface tension
𝛾𝑛 of the NE and lamina to Pb and Pf :
𝑃𝑛 − 𝑃𝑏 = 𝛾𝑛𝐶𝑏 , 𝑃𝑛 − 𝑃𝑓 = 𝛾𝑛𝐶𝑓 (1)
20
where Cb (resp. Cf) denotes the curvature of the nucleus at the back (resp. the tip). For
very narrow pores, as in experiments, one has 𝐶𝑓 ≫ 𝐶𝑏 so that
𝑃𝑛 − 𝑃𝑓 ≈ 𝑃𝑏 − 𝑃𝑓 ≈ 𝛾𝑛𝐶𝑓. (2)
This description suggests the following mechanism. Upon the build-up of 𝑃𝑏 − 𝑃𝑓 by
tension of the actomyosin cortex, the pressure difference 𝑃𝑛 − 𝑃𝑓 at the tip of the nucleus
is increased, leading to a nuclear protrusion in the pore. This deformation eventually
increases the total area of the NE and therefore its tension.
The specific rheology of the lamina layer is still to be determined; we assume here that it
can be described as a linear elastic membrane. We therefore write 𝛾𝑛 ≈ 𝛾0𝜀, where ε is
the strain of the lamina layer and 𝛾0 a constant. In the case of microfabricated pores of
small rectangular cross-section 𝑙 × ℎ, the larger strain is found in the extension of the
nuclear protrusion in the pore; it can be written 𝜀 ≈∆𝐿
𝐿0 where L0 denotes the initial length
of the nuclear protrusion length when strain starts increasing, and ∆L is the increase of
the length of the nuclear protrusion. In turn the curvature at the front nuclear interface can
be estimated as
𝐶𝑓 ≈2
𝑙+
2
ℎ. Equation (3) then related the deformation ∆L observed in response to a given
pressure difference 𝑃𝑏 − 𝑃𝑓:
𝑃𝑏 − 𝑃𝑓 ≈ 𝛾0 (2
𝑙+
2
ℎ) ∆𝐿/𝐿0 (3)
This shows in particular that for narrow pores (l,h small), a larger pressure difference is
needed to deform the nucleus through the full pore length.
Following the mechanism of formation of plasma membrane blebs, we hypothesize that
the pressure difference between the nucleoplasm and the cytoplasm, when it reaches a
threshold value Pt, leads to the breakage of the links connecting the lamina layer to the
NE, resulting in the formation of a nuclear bleb.
The above analysis then implies that: (i) nuclear blebs are formed preferentially at the
front of the nucleus, where the pressure difference is the largest (𝑃𝑛 − 𝑃𝑓 ≫ 𝑃𝑛 − 𝑃𝑏).
This is consistent with observations (Fig 2F, I). (ii) Formation of nuclear blebs are more
likely for narrower pores, for which a larger pressure increase 𝑃𝑏 − 𝑃𝑓 is needed for
nuclear translocation through the full pore length. This is consistent with observations
(Fig. 2G). (iii) The length ∆L of the nuclear protrusion when blebbing starts is larger for
larger pores (see Eq. (3)), as observed (Fig 2H).
It should be noted that the increase in tension 𝛾𝑛 could also induce the rupture of the
lamina layer, as is observed when chromatin invades the bleb (Fig S5). This is however
not the rule since a physical barrier is often preserved between small blebs and the
chromatin, when the lamina remains intact.
21
Last, when the bleb is formed, the pressure difference 𝑃𝑛 − 𝑃𝑓is supported locally by the
NE only, inducing an increase of its tension and potentially its rupture.
Overall, this simple model of nuclear passage through narrow pores and nuclear blebs
formation is therefore fully consistent with experimental observations.
22
Fig. S7
Recruitment of ESCRT-III occurs at ruptured nuclear blebs during compression and also
at sites of laser wounding at nuclear edge. (A) Images of a representative HeLa cell
expressing CHMP4B-EGFP (green) and DNA stained with Hoechst (blue) which was
23
compressed and held to 3 µm in height. This compression caused formation of nuclear
blebs which could be detected by the elevated CHMP4B-EGFP signal in the nucleus. The
blebs protruded away from the DNA and after they burst, a transient recruitment in
CHMP4B-EGFP was observed along the edge of the DNA, white arrow. Scale bar for
low magnification image 10 µm, cropped images 5 µm. (B) Representative images of a
HeLa cell expressing CHMP4B-EGFP before and after UV laser wounding at 2 spots.
One along the nuclear edge and a second one farther randomly into the cytoplasm as a
control (yellow circles). Localized enhancement in CHMP4B-EGFP was observed for the
region along the nuclear edge but not for the second ablated region in the cytoplasm. (C)
Quantification of the kinetics of the increase in CHMP4B-EGFP after photoablation, n=8
cells, N=3 (D) Images of a representative HeLa cell expressing both CHMP4B-EGFP and
NLS-MS2-mCherry before and after laser wounding. The XZ plane shows that the
CHMP4B-EGFP is recruited along the contour of the nuclear edge. (B, D) Scale bars 10
µm.
24
Fig. S8
Endogenous ESCRT-III is also recruited to sites of laser wounding at nuclear edge. (A)
Images of HeLa cell expressing CHMP4B-EGFP before laser wounding on NE. White
box shows the ROI in (B) before and time sequence after laser wounding. Site of
wounding indicated with yellow arrow. After recruitment of CHMP4B-EGFP was
25
visualized in live micrsocopy, the cell was fixed and immunostained for endogenous
CHMP2B, shown in (C). CHMP2B (red) co-localized with CHMP4B-EGFP (green) at
the nuclear edge, yellow arrow. (D) An additional example of this experiment. (E)
Enhancement of ROI. First, a laser wounding was made and confirmed with live imaging
for CHMP4B-EGFP recruitment, and then a second wounding was made after 7 min and
the cell was then fixed shortly after. The woundings are marked ‘1’ and ‘2’. (F) The same
cell was found with the cell shape from the CHMP2B immunofluorescence. Z stack was
taken in the higher region above the cell surface where the wounding took place on the
nuclear edge. The immunostain for CHMP2B reveals weak recruitment to the first site of
wounding and strong accumulation as the second wounding. This agrees well with the
concept that after wounding, ESCRT III is recruited transiently for repair and slowly
diminishes over time.
26
Fig. S9
Laser wounding at nuclear edge causes leakage of NLS-MS-mCherry out of the nucleus.
(A) Images of HeLa cell expressing CHMP4B-EGFP before and after laser wounding on
NE. ROI denotes the recruitment of CHMP4B-EGFP. (B) NLS-MS2-mCherry images
27
before and after laser wounding and their corresponding false color images in (C). Both
images where montaged together as one image to keep the same brightness and contrast
settings. (D) Quantification of NLS-MS2-mCherry of a small ROI of cytoplasm adjacent
to the nucleus after laserablation of the nuclear edge. n=4, N=2. Scale bar is 10 µm.
28
Fig. S10
ESCRT-III is involved in resealing the NE. (A) Quantification of subsequent opening
events as the nucleus continued to pass through the constriction for the cell shown in Fig.
3A. (B) Time for rise to maximum intensity for RFP-cGAS and CHMP4B-EGFP for
several break and resealing events (n=7, N=2). (C) Time delay between laser wounding
and first appearance of CHMP4B-EGFP at the nuclear edge for HeLa cells treated with a
29
control SiRNA or a CHMP3 SiRNA. n≥6 for each condition, N=2. (D) Images of a
representative RPE1 cell expressing NLS-GFP, after SiRNA against LMNA/C, migrating
in a channel without constrictions, showing spontaneous leakage events without nuclear
constriction. (E-G) RPE-1 cells expressing NLS-GFP passing through constrictions
(L=20µm, w=3µm), after various treatments with siRNA. Less nuclear constriction with
constriction width=3µm was chosen to more clearly detect more NLS-GFP leakage, refer
to Fig. 2C.
30
Fig. S11
Controls for siRNA knockdowns and efficacy of ATMi drug. (A-B) Quantification of
efficiency for siRNA knockdown of RPE-1 cells for CHMP3 (A) and LMNA/C (B),
normalized to β-actin, quantified in bar plots underneath. Non-targeting siRNA was used
as siCTL. (C) Control for efficacy of ATMi (KU-55933) treatment. mDCs in culture
were irradiated (IR) with 10 Gγ with or without 10 µM of ATMi. ATMi reduced the total
intensity of γH2AX immunostaining by nearly 50% in cells fixed 30 min after irradiation.
N>30 for each condition, N=2. Scale bar is 10 µm.
31
32
Fig. S12
Deciphering the precise mechanism by which nuclear deformation in migrating cells lead
to NE opening would require further investigation, but our observations suggest the
following model (see also Fig S6). Migrating cells, when facing a constriction, exert a
force on their nucleus to deform it; this produces an increase in nuclear surface tension
and in intra-nuclear pressure (as seen in experiments in which the nucleus is deformed by
application of an external compression, 12); increased intra-nuclear pressure would lead
to formation of nuclear envelope blebs (separation of the inner and outer NE membranes
from the underlying nuclear lamina), which would eventually rupture, inducing a
transient leakage of nuclear proteins in the cytoplasm and likewise allow cytoplasmic
proteins to enter the nucleus. The rupture of the double membrane would spontaneously
lead to the formation of pores, to which ESCRT complex components would be recruited,
leading to rapid sealing, similar to what happens at the end of mitosis during NE
reformation (14, 15) or plasma membrane repair (13). The fact that similar mechanisms
underlie membrane repair in these different contexts is consistent with the similar kinetics
observed.
Schematic of the process: as the nucleus flows through the constriction, the NE (blue
lines) dissociates from the lamina layer (red line), and forms a nuclear bleb containing
nucleoplasm (light blue) but not chromatin (not depicted here). The NE bleb then
collapses as the NE breaks and opens. This is because NE rupture releases the NE surface
tension. While the NE remains open, nuclear proteins (light blue) can diffuse in the
cytoplasm (the whole cell is now light blue). Similarly, cytoplasmic proteins (not
depicted here) can enter the nucleus. This is visualized by the binding of the cytoplasmic
DNA binding protein (cGAS, green) at the tip of the nucleus.
After the rupture of the two nuclear membranes occurred, likely due to increased tension
following the bleb formation, blunt lipid membrane edges are formed; this is a highly
unstable state, which would rapidly result in the fusion of the inner and outer membranes,
to minimize lipid-water free energy.
This would result in the formation of a pore in the double membrane. Such a topology is
highly favorable for recruitment of the ESCRT III complex (dark blue helix). The
ESCRT III complex would allow fusion of the membranes in the pore, thus closing it.
33
Fig. S13
Influx of NES-GFP from cytoplasm to nucleus during nuclear constriction. (A) RPE-1
cell expressing NES-GFP migrating through a constriction L=15µm, w=3µm. Brightfield
image and confocal plane through the nucleus inside the constriction. The nucleus
normally is dark when the NES-GFP is exported out of the nucleus. (B) R1 and R2 note
34
the times when NES-GFP fluxes into the nuclear tip, as 2 separate rupture events. Line
scans of the average intensity of the NES-GFP were taken from the cytoplasm on the left
side of the nucleus, through the nucleus, and until the cytoplasm on the right side of the
nucleus, and plotted to the right of each picture. During rupture events, line scans show a
gradient in NES-GFP concentration along the nucleus. (C) Quantification of the average
cytoplasmic NES-GFP on the left of the nucleus for each time normalized to the initial
average intensity, black curve. The A similar quantification was made for the NES-GFP
intensity inside the nucleus, again normalized to the initial time before rupture. Average
intensity of NES-GFP in the nucleus increases 3-fold for R1 and R2. As expected,
cytoplasmic NES-GFP does not deviate much from 1. Scale bar is 10 µm.
How would NE opening lead to DNA damage? The cell cytoplasm contains several
enzymes that degrade DNA, some of which are involved in protection against
cytoplasmic DNA (23), others in mitotic processing of chromatin (24). Mitotic control of
the activity of these enzymes has been reported; this control prevents chromosomal
damage after nuclear envelope breakdown at mitotic entry (25). But when such proteins
are artificially engineered to accumulate in the nucleus in interphase cells, they induce a
large number of DNA breaks (26). Upon opening of the nuclear envelope during cell
migration through constrictions in interphase cells, such proteins could diffuse inside the
nucleus and damage it. Alternatively, cytoplasmic ROS (27) could have a similar effect.
Support for this hypothesis comes from reports of massive DNA damage in micronuclei
after nuclear envelope rupture, although the precise factors inducing this damage have
not been identified (28). This makes DNA repair an essential process for the survival of
cells migrating through dense environments, as they are constantly opening their NE.
Consistent with this observation, nuclear rupture induced by compression was shown to
induce expression of genes associated with DNA repair (12).
35
Movie legends
Movie S1. Two successive image sequences—fig. S1, C and D. The sequences correspond to images shown in fig. S1C, mDC expressing NLS-GFP migrating in a collagen gel, and fig. S1D, mDC expressing NLSGFP migrating in an ear explant. Time is hours:minutes. Scale bars, 20 μm.
Movie S2. Three successive image sequences—Fig. 2, A and B, and figs. S3B and S2D. The sequences correspond to images shown in Fig. 2A, hDC expressing NLS-GFP migrating in a microchannel with a constriction of length L = 15 μm and width W = 2 μm; Fig. 2B, HeLa cell expressing NLS-GFP migrating in a microchannel with a constriction (L = 15 μm, W = 2 μm); fig. S3B, same cell with slow motion on nuclear blebs; and fig. S2D, RPE1 cell expressing NLS-GFP migrating in a microchannel with a constriction (L = 15 μm W = 1.5 μm). Time is hours:minutes. Scale bars, 10 μm.
Movie S3. A sequence corresponding to images in fig. S4A. An hDC cell expressing GFP-cGAS (green, labeled DNA_BP in the movie, for DNA binding protein) and stained with Hoechst (red), is first uncompressed then compressed, which forms a nuclear bleb that bursts. Scale bar, 10 μm.
Movie S4. Two successive image sequences— from Fig. 2, F and I. The sequences correspond to images shown in Fig. 2F, hDC expressing GFP-cGAS (green, labeled DNA_BP in the movie) stained with Hoechst (red) migrating through a constriction (L = 15 μm W = 2 μm), and Fig. 2I, HeLa cell expressing DNA_BP-GFP (green) and H2B-mCherry (red) migrating through a constriction (L = 15 μm W = 2 μm). Time is hours:minutes. Scale bars, 10 μm.
Movie S5. Three successive image sequences—fig. S5, D to F. The sequences correspond to images shown in fig. S5, D, E, and F, three examples of HeLa cells expressing Lap2β-GFP (green) and H2B-mCherry (red) migrating through a constriction (L = 15 μm W = 2 μm). Time is hours:minutes. Scale bars, 10 μm.
Movie S6. A sequence corresponding to image in fig. S7A .HeLa cell expressing CHMP4B-EGFP (green) stained with Hoechst (blue) first not compressed and then compressed, with nuclear blebs that burst. Time is minutes:seconds. Scale bar, 5 μm.
Movie S7. A sequence corresponding to images in fig. S7B. HeLa cell expressing CHMP4B-EGFP laser wounded at two spots (arrows). Time is minutes:seconds. Scale bar, 10 μm.
Movie S8. A sequence corresponding to images shown in Fig. 3A. HeLa cell expressing RFP-cGAS (green, labeled DNA_BP in the movie) and CHMP4B-EGFP (red) migrating through a constriction (L = 15 μm, W = 2 μm). Time is hours:minutes:seconds. Scale bar, 20 μm.
Movie S9. Four successive image sequences—fig. S11C and fig. S10, C, E, and F. Sequences of RPE1 cells expressing NLS-GFP corresponding to images shown in fig. S11C. SiLMNA/C in a straight channel showing spontaneous nuclear leakage; fig. S10C, SiCTRL through a constriction (L = 15 μm W = 3 μm) showing transient partial nuclear leakage; fig. S10E, SiLMNA/C through a constriction (L = 15 μm W = 3 μm) showing repeated total nuclear leakage and cell death; and fig. S10F, SiCHMP3 through a constriction (L = 1 μm W = 3 μm) showing total nuclear leakage and delayed recovery but no death. Time is hours:minutes. Scale bars, 20 μm.
Movie S10. A sequence corresponding to images shown in Fig. 4B. RPE1 cell expressing 53BP1-GFP (gray) and RFP-cGAS (red, labeled DNA_BP in the movie) migrating through a constriction (L = 15 μm W = 2 μm). Time is hours:minutes. Scale bars, 20 μm.
36
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