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OPEN
Citation: Cell Death and Disease (2014) 5, e1342; doi:10.1038/cddis.2014.310
& 2014 Macmillan Publishers Limited All rights reserved 2041-4889/14
www.nature.com/cddis
Functional and molecular defects of hiPSC-derived
neurons from patients with ATM deficiency
L Carlessi1, E Fusar Poli1, G Bechi2, M Mantegazza2,3, B Pascucci4, L Narciso5, E Dogliotti6, C Sala7, C Verpelli7, D Lecis1 and
D Delia*,1
Loss of ataxia telangiectasia mutated (ATM) kinase, a key factor of the DNA damage response (DDR) pathway, causes the
cancer predisposing and neurodegenerative syndrome ataxia-telangiectasia (A-T). To investigate the mechanisms of
neurodegeneration, we have reprogrammed fibroblasts from ATM-null A-T patients and normal controls to pluripotency
(human-induced pluripotent stem cells), and derived from these neural precursor cells able to terminally differentiate into
post-mitotic neurons positive to 490% for b-tubulin III þ /microtubule-associated protein 2 þ . We show that A-T neurons
display similar voltage-gated potassium and sodium currents and discharges of action potentials as control neurons, but
defective expression of the maturation and synaptic markers SCG10, SYP and PSD95 (postsynaptic density protein 95).
A-T neurons exhibited defective repair of DNA double-strand breaks (DSBs) and repressed phosphorylation of ATM substrates
(e.g., cH2AX, Smc1-S966, Kap1-S824, Chk2-T68, p53-S15), but normal repair of single-strand breaks, and normal
short- and long-patch base excision repair activities. Moreover, A-T neurons were resistant to apoptosis induced by the
genotoxic agents camptothecin and trabectedin, but as sensitive as controls to the oxidative agents. Most notably, A-T neurons
exhibited abnormal accumulation of topoisomerase 1-DNA covalent complexes (Top1-ccs). These findings reveal that ATM
deficiency impairs neuronal maturation, suppresses the response and repair of DNA DSBs, and enhances Top1-cc accumulation.
Top1-cc could be a risk factor for neurodegeneration as they may interfere with transcription elongation and promote
transcriptional decline.
Cell Death and Disease (2014) 5, e1342; doi:10.1038/cddis.2014.310; published online 17 July 2014
Ataxia-telangiectasia (A-T) is a pleiotropic disorder with
predisposition to cancer and early onset neurodegeneration
as key features.1–3 The neuropathological abnormalities in
A-T include progressive loss of cerebellar Purkinje and
granule neurons, less pronounced degeneration of the bulbar
olivae in the brainstem and mild loss of myelinated fibers in
corticospinal and spinocerebellar tracts.4 A-T is caused by
germline mutations inactivating the ataxia telangiectasia
mutated (ATM) protein kinase, which has an apical role in
the DNA damage response (DDR) to double-strand breaks
(DSBs). Upon activation by DSBs, ATM phosphorylates a
plethora of substrates implicated in cell cycle arrest, DNA
processing and repair, chromatin remodeling, transcription
and apoptosis.1 Concordant with the role of ATM in the DDR,
the neurodegenerative phenotype in A-T has been attributed
to a defective DDR in pre- and post-mitotic neurons and
ensuing accumulation of genotoxic lesions. However, the fact
that cells from A-T patients and specimens from ATM knock-
out mice exhibit increased signatures of oxidative stress,5,6
together with the discovery that ATM senses and responds
to reactive oxygen species (ROS) through formation of
active, disulfide-cross-linked ATM dimers7 suggest that the
loss of redox balance may contribute to neurodegeneration
in A-T.
In neurons, a fraction of ATM is localized in the cytoplasm
where it phosphorylates the synaptic proteins VAMP2 and
synapsin-1.8 Recently, ATM has been detected in dendrites
and dendritic spines, and its activation by neuronal firing and
synaptic activity induces the phosphorylation of proteins
essential for neuronal function.9
Neurodegeneration in A-T has additionally been linked to
epigenetic modifications associated with deregulation of class
II histone deacetylase HDAC410 and hyperexpression of the
histone-lysine N-methyltransferase EZH2,11 altogether inducing transcriptional repression of multiple neuronal genes and
cell death.
1
Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy; 2Department of Neurophysiopathology,
Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Amadeo 42, 20133 Milano, Italy; 3Institute of Molecular and Cellular Pharmacology (IPMC) CNRS UMR7275
and University of Nice-Sophia Antipolis, 660 Route des Lucioles, 06560 Valbonne, France; 4CNR Institute of Crystallography, Via Salaria, Km. 29.300, 00016
Monterotondo Scalo, Roma, Italy; 5Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy;
6
Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy and 7CNR Institute of Neuroscience and
Department of Biotechnology and Translational Medicine, Via Vanvitelli 32, 20129 Milano, Italy
*Corresponding author: D Delia, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, Milano 20133, Italy.
Tel: +39 02 23902641; Fax: +39 02 23902764; E-mail: [email protected]
Abbreviations: ATM, ataxia telangiectasia mutated; Chk2, checkpoint kinase 2; SSEA4, stage-specific embryonic antigen 4; a-SMA, a-smooth muscle actin; MAP2,
microtubule-associated protein 2; PARP, poly (ADP ribose) polymerase; GABA, g-aminobutyric acid; PSD95, discs large homolog 4; VGAT, vesicular GABA transporter;
KChIP, Kv channel-interacting protein 1; GFAP, glial fibrillary acidic protein; XRCC1, X-ray repair cross-complementing 1; CPT, camptothecin; DAPI, 40 ,6-diamidin-2fenilindolo; APE1, apurinic/apyridinic endonuclease 1; Pol-b, DNA polymerase b; bFGF, basic fibroblast growth factor; EGF, epidermal growth factor; NPCs, neural
precursor cells; hiPSCs, human-induced pluripotent stem cells; DDR, DNA damage response; DSBs, double-strand breaks; Top1-cc, topoisomerase 1-DNA covalent
complexes; IR, ionizing radiation
Received 24.3.14; revised 30.5.14; accepted 16.6.14; Edited by A Verkhratsky
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It should be noted that germline mutations in ATM severely
impair glial cell functionality and vascular integrity, suggesting
that Purkinje cell death and cerebellar degeneration in A-T
may result from a dysfunctional neuro-astro-vascular unit.12
In summary, several factors are implicated in the neurodegenerative phenotype of A-T, but which of them has the most
crucial role is still unresolved, primarily because of the
unavailability of model systems able to recapitulate the
neurological disease. In this regard, ATM knockout mice do
not manifest the progressive ataxia seen in A-T nor the loss of
cerebellar Purkinje cells.13
The reprogramming of human somatic cells into induced
pluripotent stem cells (human-induced pluripotent stem cell
(hiPSCs)) by the introduction of pluripotency factors (Oct4/
Klf4/Sox2/cMyc) represents a prominent advance in stem cell
biology, owing to the capacity of these cells to differentiate to
virtually any cell type of the human body, and the possibility to
model patient- and allele-specific genetic diseases.14 In the
case of A-T, the establishment of hiPSCs and conversion to
functional neurons has been recently reported.15–17
In this study, we performed a previously undocumented
functional and molecular analysis of hiPSC-derived A-T
neuronal cells harboring patient-specific mutations, in order
to shed light on the causes of the neuropathology in A-T.
Results
Generation and characterization of hiPSCs derived from
A-T and Ctrl fibroblasts. The hiPSC lines were established
from primary fibroblasts of two unrelated A-T patients and a
healthy control (Ctrl), as detailed in Materials and methods
section. Colonies with embryonic stem cell-like morphology
were expanded on a mouse embryonic fibroblast (MEF)
feeder layer (Figure 1a, left). Western blot analysis revealed,
as expected, a positive signal for ATM in fibroblasts and
hiPSCs from Ctrl but not from A-T cases (Figure 1a, right).
No ATM protein was detectable in MEFs as the antibody
used was human specific. Furthermore, only Ctrl and A-T
hiPSC lines expressed the pluripotency marker Oct3/4, but
not fibroblasts or MEFs (Figure 1a, right). Immunofluorescence analysis attested the pluripotency of the hiPSCs, being
positive for Oct3/4, stage-specific embryonic antigen 4
(SSEA4) and Tra-1-81 (Figure 1b). Moreover, the hiPSCs
gave rise to the embryonic derivatives ectoderm, endoderm
and mesoderm, labeled positive for b-tubulin III, Sox17
and alpha-smooth muscle actin (a-SMA), respectively
(Figure 1c). Also, through embryoid body (EB) and neural
rosette formation and subsequent culture in a mitogen-free
medium, hiPSCs differentiated into b-tubulin III þ and
Figure 1 Generation, characterization, pluripotency validation and neuronal differentiation of hiPSC colonies from Ctrl and A-T patients. Representative images of newly
formed hiPSC colonies before picking (a, upper panel) and after picking (a, bottom panel). The hiPSC colonies were characterized by western blot (a, right) to evaluate the
expression of ATM protein and the pluripotency marker Oct 3/4 and were compared with primary fibroblasts and MEF feeders. Vinculin was used as a loading control. In b,
hiPSC colonies were labeled to visualize the expression of the pluripotency markers Oct 3/4, SSEA4 and TRA-1-81. Nuclei were counterstained with DAPI (blue). In c, Ctrl and
A-T hiPSCs were differentiated in vitro into the three germ layers. After 20 days of differentiation, cells were labeled with antibodies specific for a-SMA (mesoderm marker),
Sox17 (endoderm marker) and b-tubulin III (ectoderm marker). Nuclei were counterstained with DAPI (blue). The ability of hiPSCs to generate neuronal cells was confirmed
through the formation of floating EBs and rosette formation. Representative images for each differentiation step are shown in d
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microtubule-associated protein 2 þ (MAP2 þ ) neurons
(Figure 1d and Supplementary Figure 1).
Generation of hNPCs and neurons from A-T and Ctrl
hiPSCs. Proliferating human neural precursor cells (hNPCs)
were generated as depicted in Figure 2a. Both Ctrl and A-T
hNPCs were negative for the pluripotency markers Tra-1-81
and Oct3/4 (Figure 2b, left) but positive for the neural
precursor markers Sox2, Nestin and Vimentin, and for the
proliferation marker Ki67 (Figure 2b, right). On western blots,
hNPCs showed lower expression of Tra-1-81 and Oct3/4
than hiPSCs, and higher levels of Sox2 and Nestin, which
then decreased during neuronal differentiation (Figure 2b,
bottom left).
The capacity of hNPCs to activate the DDR was investigated in response to ionizing radiation (IR), which induces
DSBs and ATM signalling.1 Using phospho-specific antibodies for the indicated substrates of ATM and checkpoint
kinase 2 (Chk2; KAP1-pS473), we found that after 15–30 min
of IR these molecules were strongly phosphorylated in Ctrl but
not in A-T hNPCs (Figure 2c). Interestingly, after IR an
accumulation of cleaved poly (ADP ribose) polymerase
Figure 2 Generation of hNPCs from Ctrl and A-T hiPSCs. To obtain stable and proliferating hNPCs, we followed the protocol depicted in a and a representative image of
the cell culture obtained is shown. In b, the characterization of the hNPCs by immunofluorescence demonstrates the loss of the pluripotency markers Tra-1-81 and Oct3/4, the
expression of neural markers (Sox2, Nestin and Vimentin) and the proliferation ability (Ki67). A comparative analysis between hiPSCs and proliferating (hNPCs) and
differentiated (D15) hNPCs was performed by western blot. In c, proliferating hNPCs were exposed to IR (5 Gy), and the time-dependent DDR activation was evaluated by
analyzing the phosphorylation of the indicated ATM substrates, and of cleaved PARP. b-Actin was used as a loading control. The real capacity of hNPCs to differentiate into
neurons is shown in d, where a high number of MAP2 þ , b-tubulin III þ and GABA þ cells are detected at D15 and D50 (e). hNPCs and neurons at 15–30 or 50 days of
differentiation were collected and analyzed by western blot for the expression of differentiation and maturation markers (f) or for the indicated proteins (g and h)
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(PARP), a marker of apoptosis, was detected in Ctrl but not in
A-T hNPCs, suggesting that ATM deficiency confers radioresistance in proliferative cells (Figure 2c). When hNPCs
were induced to differentiate, they acquired a neuronal-like
morphology and at day 15 of differentiation (D15) were
positive for b-tubulin III or MAP2, with a fraction of cells also
expressing the marker of inhibitory neurons g-aminobutyric
acid (GABA; Figure 2d), which we were no longer able to
detect at D50 in mature neuronal cells18 expressing b-tubulin
III or MAP2 (Figure 2e). Western blot analysis confirmed the
downregulation of the stem cell marker Nestin, the upregulation of the neuronal marker b-tubulin III at D30 (Figure 2f, left)
and at D15 and D50 (Figure 2f, right), and the expression of
the postsynaptic marker PSD95 postsynaptic density
protein 95, the inhibitory synapse marker vesicular GABA
transporter (VGAT), the neuronal growth-associated protein
SCG10 and the potassium channel-interacting proteins
(KChIPs). At D30 and D50, but not D15, cells also expressed
the pre-synaptic marker Synaptophysin (SYP). We detected
no obvious differences between Ctrl and A-T hNPCs
concerning the generation of neuronal cells, but A-T neurons
displayed deficits in the expression of SYP and PSD95 as well
as of SCG10 and KChIP, and higher amounts of glial fibrillary
acidic protein (GFAP; Figure 2f).
The post-mitotic status of the differentiated cells was
confirmed by the downregulation in D15–D50 (Figure 2h)
and D30 samples (Figure 2g) of Cdc2 and cyclin B1.
Concordant with our previous results,19 cleaved poly (ADP
ribose) polymerase (PARP) was higher in Ctrl than in A-T
neuronal cells. To note, gH2AX (pS139) was also highly
expressed at D50, and its levels were lower in A-T than in Ctrl
cells (Figure 2g).
Electrophysiological characterization. Ctrl and A-T neurons at D53±6 were analyzed by whole-cell patch clamp
recordings in order to verify their functional maturation.
Voltage clamp experiments showed similar voltage-gated
potassium currents (Figure 3a) and, most importantly,
voltage-gated sodium currents, selectively blocked by
tetrodotoxin (TTX), which is a specific feature of mature
neurons (Figure 3a, left panel). Transient peak sodium
inward currents had similar amplitude in Ctrl and A-T
neurons: maximal peak current density was 84.9±19.6 pA/pF,
n ¼ 10 in Ctrl neurons, 82.7±13.5 pA/pF, n ¼ 13 in A-T
neurons (Figure 3b). Moreover, current clamp experiments
showed that both Ctrl and A-T neurons could generate
discharges of action potentials in response to injection of
depolarizing current steps (Figure 3c). Finally, to determine
whether neurons developed functional synapses, we performed voltage clamp experiments for recording spontaneous excitatory and inhibitory postsynaptic currents
(sEPSCs and sIPSCs). Both Ctrl and A-T neurons exhibited
sEPSCs (Figure 3d) with similar frequencies (0.02±0.01 Hz,
n ¼ 4 cells and 0.03±0.02 Hz, n ¼ 4 cells, respectively),
which were blocked by application of kynurenic acid (3 mM;
data not shown), but no sIPSCs (Figure 3e).
DNA damage-induced G1/S checkpoint in relation to
development stage. In somatic cells, ATM mediates the
G1/S checkpoint but is inactive in ESCs and iPSCs.20,21
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To further delineate this activity in relation to the developmental stage, we analyzed the cell cycle profile of primary
fibroblast, hiPSCs, hNPCs and terminally differentiated
neurons by flow cytometry before and 24 h after IR treatment
(Supplementary Figure 2). Primary Ctrl fibroblasts displayed a
normal G1/S checkpoint arrest, in contrast to A-T fibroblasts in
which this checkpoint defect resulted in a significant increase
in the percentage of G2 phase cells (Figure 4a). Notably, not
only A-T hiPSCs, but also Ctrl hiPSCs lacked the G1/S
checkpoint although, interestingly, Ctrl hNPCs regained it,
whereas A-T hNPCs maintained this defect. The analysis of
neurons at D30 revealed that all cells were in the G0/G1
phase and this condition was not perturbed 24 h after IR.
To better understand the implication of DDR proteins in the
regulation of cell cycle arrest in fibroblasts, hiPSCs and
hNPCs, Ctrl cells were harvested at the indicated time points
after treatment with 5 Gy IR (Figure 4b) and the expression
of ATM-pS1981, p53-pS15, CDC25A and p21waf1 was
analyzed. Interestingly, although all cell types proficiently
activated ATM and induced the accumulation of p53, hiPSCs
were unable to induce p21waf1, and did not express CDC25A.
This could explain the incapacity of hiPSCs to regulate the cell
cycle after DNA damage. We also investigated other DDR
proteins such as RAD51, the MRN complex (RAD50-MRE11NBS1) and X-ray repair cross-complementing 1 (XRCC1),
and found changes in expression during the developmental
stages, suggesting a different ability to repair DNA damage in
the different cell types (Supplementary Figure 3).
Base excision repair capacity in undifferentiated and
differentiated hNPCs. In neurons, the base excision repair
(BER) pathway is essential to remove oxidative DNA
damage and single-strand breaks (SSBs) generated by high
levels of ROS, and defects in BER contribute to neurodegeneration.22–25 To determine how BER is regulated in preand post-mitotic neurons, we analyzed the short-patch (SP)
and long-patch (LP) BER subpathways.23 Analysis of SPBER revealed no significant differences between Ctrl and
A-T both in the proliferation and post-mitotic (D15) stage
(Figure 5a). To better understand this result, we analyzed the
levels of the SP-BER proteins apurinic/apyridinic endonuclease 1 (APE1), DNA polymerase b (Pol-b) and XRCC1,
and after differentiation (D15) only the levels of XRCC1
appear reduced (Figure 5c). Similar findings were seen in
D30 neurons (data not shown).
LP-BER activity appeared markedly lower in both Ctrl and
A-T post-mitotic neurons than in their respective proliferating
hNPCs (Figure 5b). This finding is concordant with the
reduced expression of Flap endonuclease 1, a protein
involved in LP-BER in non-replicating cells (Figure 5c).
Overall, these results point out differences that depend on
different levels of expression or differential activation of BER
enzymes in undifferentiated and differentiated cells, but
appear independent of ATM.
DNA damage response and repair in post-mitotic
neurons. IR-time course analysis of Ctrl neurons at D30
showed a vigorous ATM-dependent phosphorylation of
SMC1-S966, KAP1-S824, Chk2-T68, p53-S15 and
g-H2AX, while this response was repressed in A-T neurons
Defects of ATM-deficient neural-specified hiPSCs
L Carlessi et al
5
Figure 3 Functional characterization of Ctrl and A-T neurons after 50 days of differentiation. In a, left, patch clamp whole-cell recordings of representative total ionic
currents elicited with depolarizing voltage steps between –70 and þ 10 mV (10 mV increments from a holding potential of –70 mV) in Ctrl and A-T hNP-derived neurons; scale
bar: 500 pA, 10 ms. In a, right, representative currents elicited with a depolarizing voltage step to ÿ 10 mV in control (black), during perfusion with TTX 3 mM (red) and after
washout (blue) in Ctrl (upper panels) and A-T (lower panels) hNP-derived neurons; scale bar: 500 pA, 10 ms. In b, bar graph of maximum sodium current densities (CD) in Ctrl
and A-T hNPC-derived neurons (no statistical significant difference: unpaired T-test). In c, representative action potential discharges recorded in current clamp during
injections of 1-s long depolarizing current steps from a holding potential of ÿ 70 mV; scale bar: 10 mV, 100 ms. In d, traces showing sEPSCs, recorded at the holding potential
of ÿ 70 mV, while in e traces showing the absence of sIPSCs, recorded at the holding potential of þ 30 mV; scale bar: 10 mV, 1 s
(Figure 6a). Similarly, the phosphorylation of the Chk2
substrate KAP1-S473 was abrogated in A-T neurons.
Interestingly, as previously described for proliferating
hNPCs (Figure 2c), 24 h after IR an accumulation of
cleaved PARP was detected in Ctrl but not in A-T neurons,
indicating that ATM deficiency confers short-term radioresistance also in terminally differentiated cells (Figure 6a,
upper panel). Altogether, these results indicate that normal
post-mitotic neurons activate the DDR as efficiently as their
proliferating precursors, and that ATM deficiency ablates
this response.
The ability of post-mitotic neurons to repair SSBs and DSBs
was investigated with the alkaline and neutral comet assay,
respectively. Although the repair of SSBs, induced by
hydrogen peroxide (H2O2),26 showed no major differences
between Ctrl and A-T post-mitotic neurons (Figure 6b), the
repair of DSBs, induced by IR,26 appeared defective in A-T
neurons, which displayed 30% more unrepaired lesions than
Ctrl cells (Figure 6c). The latter finding is consistent with a
defective DDR, as shown in Figure 6a.
To investigate the role of ATM in the resolution of IR-induced
DSBs in D30 neurons, we scored the time-dependent
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Figure 4 Cell cycle phase distribution changes after IR treatment. Ctrl and A-T cells at various developmental stages (primary fibroblasts, hiPSCs, hNPCs, D30 postmitotic neurons) were treated with 5 Gy IR, collected after 24 h, and analyzed for DNA content by flow cytometry (a). In b, Ctrl fibroblasts, hiPSCs and hNPCs were treated with
5 Gy IR, collected at the indicated times and analyzed by western blot. b-Actin was used as a loading control
formation and clearance of g-H2AX and 53BP1 nuclear foci by
immunofluorescence, as described.27,28 Unirradiated Ctrl
D30 neurons showed a basal number of g-H2AX and 53BP1
foci per cell (1.4±1.2 and 0.9±1), which increased to
13.3±3.3 and 10.1±2.4, respectively, after IR, to decline
after 6 h and even further after 24 h (Figures 6d and e).
Untreated A-T cells showed a number of foci per cell
comparable to Ctrl cells, which increased more modestly,
5.6±2.6 for g-H2AX and 5.6±2.1 for 53BP1 after 15 min, and
persisted after 24 h (Figures 6d and e graphs). These findings
Cell Death and Disease
indicate that A-T post-mitotic neurons show slower kinetics of
DSBs repair than Ctrl, concordant with previous findings in
other ATM-deficient cells.19
The apoptotic effect of radiation on Ctrl and A-T neurons
24 h after 5 Gy IR was assessed by flow cytometry analysis of
the subdiploid DNA peak (Supplementary Figure 4). Fewer
apoptotic cells were detected in IR-treated A-T cells (22.2%)
than in Ctrl cells (32.3%), suggesting that ATM deficiency
attenuates short-term apoptosis, concordant with the findings
on cleaved PARP (Figure 6a) and our previous findings.19,29
Defects of ATM-deficient neural-specified hiPSCs
L Carlessi et al
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Figure 5 BER activities in proliferating and post-mitotic Ctrl and A-T neuronal cells. In vitro repair reactions were performed by using whole-cell extracts and as substrate a
32P-labeled circular plasmid containing a single AP site (pGEM-AP) to measure SP-BER (a) or a THF residue (pGEM-THF) for LP-BER (b). The correct insertion of a single
lesion in the plasmid molecules was checked by digestion with uracil DNA glycosylase (UDG) followed by endonuclease III (NTH) for pGEM-AP (a), and by AP endonuclease
(HAP1) for pGEM-THF (b). Repair kinetics of the AP site (a) or THF residue (b) by proliferating hNPCs and post-mitotic neurons (D15) were measured following incubation of
the single lesion-containing plasmids with extracts from Ctrl or A-T defective neuronal cells for increasing periods of time. Repair products were analyzed by agarose gel
electrophoresis and the radioactivity of the bands corresponding to nicked (form II) and supercoiled (form I) plasmids was quantified. Repair efficiency is expressed as relative
amount of Form I over total radioactivity in each lane. Blue bar, Ctrl cell extracts; red bar, A-T cell extracts. The expression level of SP-BER and LP-BER proteins was
evaluated by western blot in proliferating and post-mitotic neuronal cells (c). b-Actin was used as a loading control
Treatment of A-T and Ctrl neuronal cells with genotoxic
and oxidative agents. As genotoxic agents and oxidative
stress may similarly affect ATM-deficient neurons, we
investigated the viability of Ctrl and A-T post-mitotic neurons
(D30) upon treatment with compounds that work through
different mechanisms: camptothecin (CPT), which inhibits
Topoisomerase I (Top1) and traps Top1-DNA covalent
complexes (Top1-ccs);30 trabectedin, which blocks transcription factor activity;31 Paraquat, which induces ROS through
depolarization of the inner mitochondrial membrane,32 and
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Defects of ATM-deficient neural-specified hiPSCs
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Figure 6 A-T post-mitotic neurons are defective in DDR. In a, D30 post-mitotic neurons (D30) were tested by western blot with antibodies specific for the various ATM
phosphosubstrates and cleaved PARP at various times after treatment with 5 Gy IR. b-Actin was used as a loading control. DNA SSBs (b) and DSBs (c) were analyzed in
neurons (D30) by alkaline and neutral comet assay, respectively, at two different times after treatment. 20 min after H2O2 or IR treatment was considered the time point with the
maximum DNA damage. In b and c, representative photos of comets from untreated cells and at different time points following treatment. The ratio between treated and
untreated tail moments of at least 50–70 cells per experimental point is shown in the graphs (values in %). One representative experiment out of three is shown. In d and e,
formation and resolution of IR-induced nuclear foci. Neurons (D30) were irradiated with 0.5 Gy, collected at the indicated times and labeled for g-H2AX (d) and 53BP1 (e). For
each treatment, the number of foci was scored from 100 cell nuclei per duplicate preparations and from three independent experiments (mean±S.D.) (d and e, bottom) For
each time point, the difference between Ctrl and A-T was statistically significant (#Po0.01) (analysis performed by the Student’s t-test)
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H2O2. Ctrl and A-T post-mitotic neurons were equally
sensitive to H2O2 and Paraquat (Figures 7a and b), a finding
concordant with previous data33 and with the results in
Figure 6b showing that these cells have the same ability to
resolve SSBs. By contrast, A-T neurons were significantly
more resistant than Ctrl neurons to CPT and trabectedin by
about 40% and 30%, respectively (Figures 7c and d).
Accumulation of Top1-ccs in A-T post-mitotic neurons.
As in murine neural cells ATM deficiency results in
accumulation of Top1-ccs and failure to recover global
transcription after Top1-cc trapping,34 we used a modified
alkaline comet assay (MACA),34 which indirectly quantifies
Top1-ccs, to analyze hNPC-derived neurons (D30) untreated
or treated for 45 min with 30 mM CPT (Figure 8a, left).
As shown in the graph, the accumulation of Top1-ccs was
much greater in A-T than in Ctrl neurons, both before and
after CPT treatment. Of note, the overall levels of Top1 in
proliferating and post-mitotic neurons (D30) were similar
(Figure 8a, right).
To further confirm these findings, we applied the rapid
approach to DNA adduct recovery (RADAR) assay that allows
to directly detect Top1-ccs bound to genomic DNA.35 D30
neurons, incubated for 1 h with 30 mM CPT, were harvested
immediately or 3 h after washout of the drug to analyze the
recovery of the damage. DNA was isolated, dot blotted and
Top1-ccs were revealed with an anti-Top1 antibody and ECL.
The levels of Top1-ccs (Figure 8b, left) were then normalized
with the total amount of DNA, revealed by 40 ,6-diamidin2-fenilindolo (DAPI; Figure 8b, middle). b-Actin was used to
verify that the DNA samples were free of non-covalently
bound contaminating proteins (Figure 8b, right). The graph
shows Top1 protein levels after normalization with DNA, and,
as expected, untreated A-T neurons displayed higher
accumulation of Top1-ccs than Ctrl cells, and also appeared
defective in Top1-cc recovery after CPT removal.
Discussion
The mechanisms underlying neurodegeneration in A-T still
remain elusive. Up to the present, ATM knockout and knockin
mice36,37 and in vitro ATM-deficient human neural stem cell
(hNSC) models19,38 have been useful for elucidating many
aspects of the neuropathology, but animal models do not
recapitulate the CNS disease,39 while hNSCs have been
argued to be very heterogeneous.40 To obtain a more reliable
in vitro model of neurodegeneration in A-T, two novel
approaches have recently been described: the establishment
of patient olfactory mucosa-derived neurospheres, which give
rise to neurons,41 and the reprogramming of patient fibroblasts to a pluripotent stage.15,17
As a functional analysis of the neuronal cells harboring
patient-specific mutations in ATM has not yet been reported,
in this study we examined hiPSC-derived A-T hNPCs and
terminally differentiated neurons in culture. We found that A-T
hNPCs displayed a strongly attenuated response to DSBs
with respect to Ctrl hNPCs, which is concordant with our
previous study on hNSCs.19
Moreover, terminally differentiated A-T neurons exhibited
decreased expression of SYP and PSD95, which is
Figure 7 A-T post-mitotic cells are resistant to CPT and trabectedin treatment. Neurons at D30 grown in 96-well plates were assessed for cell viability by CellTiter-Glo 72 h
after exposure to H2O2 for 20 min (a), or continuously with Paraquat (b), CPT (c) and trabectedin (d) at the indicated doses. All treatments were performed in triplicate wells.
The graphs show mean±S.D. and, where indicated, the difference between Ctrl and A-T was statistically significant (*Po0.05; #Po0.01) (analysis performed by the
Student’s t-test)
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Defects of ATM-deficient neural-specified hiPSCs
L Carlessi et al
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Figure 8 A-T post-mitotic neurons accumulate abnormal levels of Top1-cc. Total intracellular levels of Top1 protein were analyzed by western blot in proliferating hNPCs
and post-mitotic neurons (a left). The levels of endogenous Top1-ccs were quantified in Ctrl and A-T post-mitotic neurons (D30) subjected to 30 mM CPT for 40 min by MACA
from 50 cells per sample per experiment (a right). Data are the average of three independent experiments (mean±S.D.). For each time point, the difference between Ctrl and
A-T was statistically significant (#Po0.01) except where indicated. In b, Ctrl or A-T post-mitotic neuronal cells were untreated or treated with 30 mM CPT for 60 min or
incubated and harvested 3 h after washing. The DNA was purified from cells after lyses with a denaturing buffer (MB) as reported in Materials and methods section. The
indicated amount of DNA was vacuum blotted on a nitrocellulose membrane, which was then tested with anti-Top1 antibody and ECL (left) and with DAPI (middle). b-Actin
(left) represents the control for non-covalently bound contaminant proteins. The densitometry analysis of Top1-cc signals after normalization for blotted DNA (DAPI) from three
biological replicates (mean±S.D.) is reported in the graph. Y axis represents the relative signal intensity. Where indicated the difference between Ctrl and A-T was statistically
significant (#Po0.01; analysis performed by the Student’s t-test)
concordant with previous works showing pre- and postsynaptic degeneration in ATM knockout mice,42 the requirement of cytoplasmic ATM for phosphorylation of the synaptic
vesicle proteins VAMP2 and Synapsin-1, and that ATM
deficiency affects spontaneous vesicle release and establishment of long-term potentiation.8 We also showed that
A-T neurons are defective in the expression of SCG10
and KChip, altogether underpinning defects in neuronal
maturation.
Cell Death and Disease
In agreement with the role of ATM in establishing the G1/S
checkpoint arrest to prevent cells with damaged DNA from
entering the S-phase,1 primary Ctrl fibroblasts effectively
arrested at the G1/S boundary after IR, but once reprogrammed into hiPSCs lost this G1/S checkpoint arrest to
regain it at the stage of hNPCs. Instead, A-T cells showed a
disrupted G1/S checkpoint, whatever the developmental
stage. Notably, the absence of the G1/S checkpoint arrest in
Ctrl hiPSCs is a characteristic of ESCs, where the cells
Defects of ATM-deficient neural-specified hiPSCs
L Carlessi et al
11
subjected to DNA damage in G1 enter S-phase to be eliminated
by apoptosis, thus avoiding the propagation of mutations
detrimental for the whole organism.43,44 Accordingly, hiPSCs
showed a great accumulation of p53-pS15 and faint induction
of p21waf1, compatible with a p53-dependent apoptotic
response rather than with a G1/S checkpoint activation.
Moreover, we found that Ctrl hiPSCs upregulate homologous
recombination components such as Rad51, concordant with
the fact that ESCs predominantly use this high fidelity pathway
to avoid the accumulation of mutations, in contrast to somatic
cells, which rely on the error-prone non-homologous end
joining to repair DNA damage occurring in G1.45
BER is the major pathway for repair of oxidatively damaged
DNA and various SSB intermediates,22 and previous findings
demonstrate that ATM and Chk2 facilitate the recruitment of
downstream BER proteins to the initial damage recognition/
excision step to promote BER.46 Here, we found no significant
differences in SP-BER activity between Ctrl and A-T
proliferative hNPCs and post-mitotic neurons, while conversely, LP-BER activity was reduced in post-mitotic neurons. It
should be noted that both SP-BER and LP-BER enzymatic
efficiencies have been found to decrease, along with the
respective protein components, in a neuroblastoma cell line
upon differentiation,24 and while our data on LP-BER concord
with these results, those on SP-BER are clearly at variance.
This could be because the expression of the SP-BER
component XRCC1 is totally ablated in differentiated neuroblastoma cells,24 while being only partially downregulated in
our neurons. Regardless of this discrepancy, the variations in
LP-BER activity between post-mitotic neurons and proliferative hNPCs were totally independent of ATM expression.
In accordance with our previous findings using hNSCs,19
here we found that the DDR was vigorously activated in postmitotic Ctrl neurons, according to the strong phosphorylation
of ATM substrates, whereas in A-T post-mitotic neurons this
response was almost ablated. We also highlighted relevant
DSB repair defects in A-T neurons, which indicated that ATM
deficiency delays the repair of DSBs, in accordance with
previous reports19,47 and with the observation that ATM is
required for the repair of heterochromatic DSBs.48 Furthermore, we demonstrated that A-T neurons show less apoptosis-related sub-diploid DNA content and a lower cleaved
PARP induction after IR-treatment than Ctrl neurons. Indeed,
ATM deficiency has been found to attenuate the apoptotic
response to IR in A-T lymphoblastoid cells and in hNSCs19,29
and ATM is required for the p53-mediated apoptosis of
developing post-mitotic neurons exposed to IR.49,50
Although ATM appears involved in sensing and modulating
the cellular response to ROS,7 in our study A-T post-mitotic
neurons were as sensitive to oxidative agents as Ctrl postmitotic neurons, in agreement with the alkaline comet assays
showing that these neurons equally repair SSBs, and in the
case of H2O2, with results obtained with A-T lymphoblastoid
cells.33 By contrast, A-T post-mitotic neurons were significantly
more resistant than Ctrl neurons to the genotoxic agents CPT
and Trabectedin, probably because, in the absence of ATM,
drug-induced DSBs in transcribed genes fail to activate a p53dependent apoptotic response. This finding is concordant with
results showing that ATM inhibition suppresses the genotoxic
response in rat cerebellar granule neurons.51
Finally, as it has been recently shown that post-mitotic
neural cells from ATM-deficient mice accumulate Top1-ccs
and fail to recover global transcription after Top1-cc trapping
by CPT,34 and given that Top1-ccs can promote transcription
elongation arrest and decay,52 a phenomenon underlying
neurodegeneration,53–55 we analyzed Top1-ccs by two
different assays and found greater levels of these intermediates in A-T than in Ctrl neurons. This finding, which to our
knowledge has never been reported in human A-T neurons,
warrants further studies to determine the impact of Top1-cc on
genome-wide global transcription.
In conclusion, we have shown that A-T post-mitotic neurons
display normal electrophysiological activity, defective expression of maturation markers, attenuated response to and repair
of DSBs, but normal capacity to repair SSBs and normal BER
activities. Strikingly, A-T neurons exhibit elevated levels of
Top1-ccs, which may potentially impair transcriptional fidelity,
a possibility that requires further investigation. Finally, we
have shown that hiPSCs, like ESCs, provide a unique in vitro
model to study the G1/S cell cycle checkpoint in a developmental context.
Materials and Methods
Primary cell culture. A-T patient-derived primary dermal fibroblasts
(GM03487 and GM02530) were purchased from the Coriell Institute for Medical
Research (Camden, NJ, USA). Both carry compound heterozygous mutations in
ATM gene: GM03487 (c.8266A4T and c.1141_1142ins4), GM02530
(c.5675_5762del in trans with c.2251-1G4A and c.6573_6653del). Dermal
fibroblasts of a healthy, ethnically matched donor and their iPSCs derivatives were
previously described by us.18 Fibroblasts were cultured at 37 1C in a 5% CO2 in
E-MEM supplemented with 15% heat-inactivated FCS, 100 units/ml penicillin,
100 mg/ml streptomycin, 100 mM non-essential amino acids and 2 mM glutamine.
Primary MEFs (PMEF-CFL, Millipore, Bedford, MA, USA) were cultured in
DMEM/F12 supplemented with 20% heat-inactivated FCS, 100 units/ml penicillin,
100 mg/ml streptomycin, 100 mM non-essential amino acids and 2 mM glutamine.
PMEF-CFLs were mitotically inactivated (Mito-MEFs) with 1 mg/ml Mytomycin C
(Kiowa Hakko Kirin, Milan, Italy) in DMEM high glucose (Euroclone, Pero, Italy) for
3 h and were then collected and plated into 0.1% gelatin-coated six-well plates at a
concentration of 1.8 105 cells/cm2.
hiPSC generation and culture. Human primary fibroblasts were infected
with the STEMCCA Cre-Excisable Constitutive Polycistronic Lentivirus (Millipore)
following the manufacturer’s instructions. After 20–25 days, hiPSC clones were
picked and transferred onto a Mito-MEF feeder in human embryonic stem cell
(hESC) medium composed of DMEM/F12 supplemented with 20% KnockOut
serum replacement (Life Technologies, Monza, Italy), 100 units/ml penicillin,
100 mg/ml streptomycin, 100 mM non-essential amino acids, 2 mM glutamine,
1 mM sodium pyruvate, 100 mM 2-mercaptoethanol and 20 ng/ml basic fibroblast
growth factor (bFGF; Peprotech, Rocky Hill, NJ, USA). For passaging, hiPSCs
were incubated with DMEM/F12 containing 1 mg/ml collagenase IV (Sigma, Milan,
Italy) at 37 1C for 10 min. Cells were then scraped, collected and transferred at a
split ratio of 1 : 3 to a new plate on Mito-MEFs in hESC medium. For feeder-free
culture, hiPSCs were seeded on Matrigel (hESC-qualified matrix, BD Biosciences,
San Jose, CA, USA)-coated plates in Nutristem culture medium (Stemgent,
Cambridge, MA, USA) supplemented with 100 units/ml penicillin and 100 mg/ml
streptomycin. For differentiation into derivatives of all three primary germ layers,
hiPSCs were collected as for passaging and transferred to a gelatin-coated plate
in DMEM/F12 supplemented with 20% heat-inactivated FCS, 100 units/ml
penicillin, 100 mg/ml streptomycin, 100 mM non-essential amino acids and
2 mmol/l glutamine.
Generation of hNPCs and terminal differentiation. hiPSC colonies
were harvested as for passaging, resuspended in hESC medium without bFGF
and plated into a 6 cm low binding dish (HydroCell, Nunc, Cornaredo, Italy) for
floating cultivation. After 5 days in suspension culture, EBs were collected and
plated into a Matrigel (growth factor reduced, BD Biosciences)-coated dish for
Cell Death and Disease
Defects of ATM-deficient neural-specified hiPSCs
L Carlessi et al
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additional 7 days in hESC media supplemented with 1X N2 (Gibco, Monza, Italy).
After 7 days, rosettes were manually picked, mechanically dissociated into single
cells and resuspended in Neural Precursor Medium (NPMedium) composed of
DMEM/F12 supplemented with 2 mM glutamax, 100 units/ml penicillin, 100 mg/ml
streptomycin, 1 : 500 B27 (Gibco), 1X N2, 20 ng/ml epidermal growth factor (EGF)
and 20 ng/ml bFGF (Società Italiana Chimici, Roma, Italy) and plated into Matrigelcoated flasks. NPMedium was changed every 2 days. For passaging, 90%
confluent cells were detached using Accutase (PAA; Piscataway, NJ, USA) and
split at a ratio of 1 : 4. hNPCs displayed a homogenous population starting at
passage 3. To obtain terminally differentiated neurons, proliferating hNPCs were
plated in NPMedium at a concentration of 5 103 cells/cm2; 24 h later medium
was changed to NPMedium without bFGF and EGF and replaced every 2–3 days
thereafter.
0.2 mM EGTA, 10 mM HEPES, 20 mM P-creatine, 2 mM ATP-Na2, 0.2 mM GTPNa2 and 0.1 mM Leupeptine, pH 7.2 with KOH. Cell capacitance and series
resistance errors were carefully compensated (B85%) throughout the experiment.
The remaining linear capacity and leakage currents were eliminated online using a
P/4 subtraction paradigm. Pipette resistance was between 2.6 and 3.0 MO. For
the recordings of total voltage-gated ion currents, signals were filtered at 10 kHz
and sampled at 100 kHz. For the recordings of postsynaptic currents, signals were
filtered at 3 kHz and sampled at 10 kHz. When we switched the amplifier to current
clamp mode, we applied the bridge balance compensation and held the resting
potential at ÿ 70 mV by injecting the appropriate holding current. Neuronal firing
was recorded injecting depolarizing current pulses of increasing amplitude. The
neurons with unstable resting potential and/or unstable firing were discarded. In
current clamp mode signals were filtered at 10 kHz and sampled at 20 kHz.
Western blotting. Western blot analysis was performed as previously
described.56 Briefly, cells were lysed in Laemmli buffer (0.125 M Tris-HCl pH 6.8,
5% SDS) and lysates were sonicated, size-fractionated by SDS-PAGE and
electroblotted onto PVDF membranes (Millipore), which were then incubated with
primary antibodies and binding detected by ECL (Pierce, Rockford, IL, USA) on
autoradiographic films. Bands were acquired with a digital scanner. The primary
mouse monoclonal antibodies used were against the following molecules: OCT3/
4(clone C-10), p53, Cdc2 (p34), p21waf1 (Santa Cruz Biotechnology, Inc., Dallas,
TX, USA), b-tubulin III (clone 2G10), SYP, Vinculin, b-actin (Sigma), Tra-1-81
(eBioscience, San Diego, CA, USA), anti-Sox2, CDC25A (Abcam, Cambridge,
UK), cyclin B1 (clone GNS-1, BD Pharmigen, Franklin Lakes, NJ, USA), gH2AX
(H2AX-pSer139, clone JBW301, Millipore), PSD95, SCG10, Pan-KChIP, SYP
(NeuroMab, Davis, CA, USA), Nestin, MAP2 (clone AP20, Chemicon International,
Billerica, MA, USA), KAP1 (TIF1b, clone 4E1, Cell Signaling Technology,
Danvers, MA, USA), Chk2 (clone DCS270-273, MBL Intl Corp., Des Plaines, IL,
USA) and Top1 (BD Biosciences); rabbit antibodies specific for ATM (clone Y170,
Epitomics, Burlingame, CA, USA), ATM pS1981 (Rockland Inc., Gilbertsville, PA,
USA), cleaved PARP, XRCC1, KAP1-pS824, Chk2-pThr68, p53-pSer15 (Cell
Signaling Technology), GFAP (Millipore), VGAT (Synaptic System, Goettingen,
Germany), Polb, Fen1 (Abcam), APE1 (Santa Cruz Biotechnology, Inc.),
SMC1, SMC1-pSer966 (Bethyl Laboratories, Inc., Montgomery, TX, USA) and
KAP1-pS473 (Biolabs, San Diego, CA, USA).
Cell cycle phase analysis. Cells at different developmental stages were
irradiated with 5 Gy IR, incubated for 24 h and then fixed with 70% ethanol,
washed, treated PBS-RNAse A, at 37 1C for 30 min and finally stained with
propidium iodide. Cells were analyzed with a FACSCalibur flow cytofluorimeter
instrument fitted with a Cell Quest software package (Becton Dickinson,
Sunnyvale, CA, USA).
Immunofluorescence. Cells grown on coverslips were fixed in 4% buffered
paraformaldehyde and permeabilized with 0.1% Triton X-100 in PBS for 10 min.19
After blocking with PBS plus 10% normal goat serum for 40 min, cells were
incubated overnight with primary antibodies at 4 1C. The following primary
antibodies were used: monoclonal anti-Oct 3/4 (Clone C-10, Santa Cruz
Biotechnology, Inc.), anti-SSEA4 (eBioscience), anti-Tra-1-81 (eBioscience),
anti-a-SMA (clone 1A4, Sigma), anti-Sox17 (clone 245013, R&D System,
Minneapolis, MN, USA), anti-b-tubulin III (clone TUJ1, Covance, Princeton, NJ,
USA), anti-Nestin, anti-MAP2 (clone AP20, Chemicon International), anti-Vimentin
(DAKO, Cernusco sul Naviglio, Italy), and polyclonal anti-GFAP (Millipore), antiGABA, and anti-Ki67 (Thermo Scientific, Milan, Italy). After three washes with
PBS, cells were incubated with Alexa fluor-labeled goat anti-mouse or anti-rabbit
antibodies (Life Technologies) for 45 min. Cells were washed, counterstained with
DAPI, mounted on glass-slides with Prolong Gold Antifade (Life Technologies) and
analyzed using an Eclipse E1000 Nikon fluorescence microscope equipped with a
DMX1200F CCD camera (Torino, Italy). For the assessment of nuclear foci, cells
on coverslips were washed with 0.9% NaCl, air dried, fixed in 3% buffered
paraformaldehyde and permeabilized for 5 min at 4 1C in 0.5% Triton. Cells were
then blocked in PBS containing 5% BSA and 0.2% Tween20, labeled with
antibodies specific for H2AX-pS139 antibody (clone JBW301, Upstate Biotechnology,
New York, NY, USA) and 53BP1 (NB100-304; Novus Biologicals, Cambridge, UK)
and foci from three independent experiments and duplicate slides were
enumerated.
Electrophysiology analysis. Electrophysiological recordings were done as
reported18,57 at room temperature (22–25 1C) using a Multiclamp 700 A patch
clamp amplifier and pClamp 10.2 software (Molecular Devices, Sunnyvale, CA,
USA). Recordings usually started 5 min after the rupture of the membrane patch,
to allow intracellular dialysis with the pipette solution. External bath solution
consisted of 129 mM NaCl, 1.25 mM NaH2PO4, 35 mM glucose, 1.8 mM MgSO2,
1.6 mM CaCl2, 3 mM KCl and 10 mM HEPES, pH 7.4 with NaOH. The internal
pipette solution consisted of 120 mM K gluconate, 15 mM KCl, 2 mM MgCl2,
Cell Death and Disease
In vitro BER assay. Whole-cell extracts for BER assays were prepared from
15 106 cells that were harvested, resuspended in 400 ml buffer I (10 mM Tris pH
7.8, 200 mM KCl) and then lysed by adding an equal volume of Buffer II (10 mM
Tris pH 7.8, 200 mM KCl, 2 mM EDTA, 40% glycerol, 0.2% Nonidet-P40, 2 mM
DTT and protease inhibitors). After stirring for 1 h at 4 1C and centrifugation, the
supernatant was aliquoted and stored at ÿ 80 1C. Closed circular DNA molecules
containing a single lesion were constructed as described58 by priming singlestranded pGem-3Zf( þ ) DNA with the oligonucleotides containing the modified
base of interest (uracil and tetrahydrofuran (THF). These oligonucleotides were [g32P]ATP 50 end-labeled. The in vitro DNA synthesis was performed by using DNA
T4 DNA polymerase holoenzyme, single-stranded DNA-binding protein, dNTPs
and T4 DNA ligase. The plasmid DNA containing a single uracil residue was
digested with UDG to produce a single abasic site. Repair of the plasmid DNA
containing the lesions (pGEM-AP/THF) was conducted as described.58 Briefly,
reaction mixtures (50 ml) contained 40 mM HEPES/KOH (pH 7.9), 75 mM KCl,
5 mM MgCl2, 0.5 mM dithiothreitol, 50 mM of each dNTP, 2 mM ATP, 40 mM
phosphocreatine, 2.5 mg of creatine phosphokinase (type I), 3.4% glycerol, 18 mg
of bovine serum albumin and 50 mg of cell extracts. After incubation at 30 1C, the
plasmid DNA was recovered and loaded onto agarose gels. The relative yield of
the different plasmid forms was measured. All experiments were repeated at least
three times, and representative experiments are shown.
Comet assay and MACA. To prepare the Comet slides, the day before
analysis microscope glass slides were washed with methanol, air dried and
immersed in molten Normal Melting-Agarose (1%) to obtain the first agarose layer,
before being stored overnight at 4 1C. To evaluate DNA strand breaks, post-mitotic
neurons were incubated with 20 mM H2O2 (Sigma) for 20 min or irradiated with
5 Gy. After treatment with Accutase, the cell suspension was added to 180 ml of
molten Low Melting-Agarose (0.7% LM-agarose) at 37 1C, and immediately
layered onto Comet slides, covered with a coverslip and stored at 4 1C in the dark.
After 25 min, the coverslip was removed and a second LM-Agarose layer was
layered onto the slides. The slides were then transferred to a pre-chilled lysis
solution (2.5 M NaCl, 100 mM EDTA, 10 mM Tris-base, 300 mM NaOH, pH 10,
and 1% freshly added Triton X-100) for 2 h at 4 1C in the dark. In the alkaline
condition, the slides were placed in a horizontal electrophoresis chamber and the
denaturation step was performed in pre-chilled electrophoresis solution (300 mM
NaOH, 1 mM EDTA, pH413) at 4 1C in the dark. After 20 min, the slides were
electrophoresed (1 V/cm, 300 mA) for 20 min, and washed with neutralization
buffer (0.4 M Tris-HCl, pH 7.4). In the neutral condition, after the lysis the slides
were washed twice with 1 Tris-borate EDTA buffer solution pH 8.3 (TBE) for
10 min. Electrophoresis was carried out at the rate of 1.0 V/cm for 20 min. The
slides were then washed in deionized water for 5 min. MACA on post-mitotic
neurons was performed as described.34 After electrophoresis, Comet slides were
fixed with pre-chilled methanol, air dried overnight, stained with ethidium bromide
(0.1 mg/ml) for 10 min, and images acquired with an Eclipse E1000 Nikon
fluorescence microscope equipped with a DMX1200F CCD camera. Comet
images were processed with Comet Score software (v1.5; TriTek Corporation,
Sumerduck, VA, USA).
Defects of ATM-deficient neural-specified hiPSCs
L Carlessi et al
13
Rapid approach to DNA adduct recovery. Post-mitotic neurons (D30)
were incubated with or without 30 mM CPT for 1 h. Following treatment, part of the
cells was immediately lysed, while the remaining washed with PBS and incubated
in fresh medium for 3 h before lysis. For DNA–protein covalent complexes
isolation, cells were lysed in the culture plates by addition of 2 ml of MB lysis
reagent (6 M GTC, 10 mM Tris-HCl, pH 6.5, 20 mM EDTA, 4% Triton X100, 1%
Sarkosyl and 1% dithiothreitol) and processed as described.35 Purified DNA was
vacuum blotted on nitrocellulose membranes and Top1 detected using a mouse
monoclonal anti-Top1 antibody (BD Biosciences) and ECL. Sample loadings were
normalized for DNA content using DAPI.
Neuronal viability assay. Neuronal viability was evaluated using the Cell
Titer-Glo luminescent assay (Promega, Madison, WI, USA). Briefly, hNPCs were
seeded into Matrigel-coated 96-well plates (10 000 cells per well) and let to
differentiate for 30 days, after which they were treated in triplicate with CPT, H2O2,
Paraquat (all from Sigma) or trabectedin (Yondelis; ET-743) for 72 h. H2O2 was
removed after 20 min. Afterward, a volume of CellTiter-Glo Reagent was added to
each well and luminescence measured using a Tecan Genios instrument
(Männedorf, Switzerland).
Conflict of Interest
The authors declare no conflict of interest.
Acknowledgements. This work was financially supported by Comitato
Telethon Fondazione Onlus (grant # GGP10066 to DD) and by the Italian Association
for Cancer Research (AIRC) (grant # IG-10248 to DD). Dr. Carlessi Luigi is recipient of
a post-doctoral fellowships award from Fondazione Umberto Veronesi. We wish to
thank Dr. Sherif El-Kamisy, Department of Molecular Biology and Biotechnology,
Sheffield University, UK, for kindly providing the detailed MACA protocol, and
Dr. Christian Unger, Centre for Stem Cell Biology, Sheffield University, UK, for
providing training (to DL) and expertise in the field of iPSCs, as well as reagents.
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