Integrating Epigenetic Modulators into NanoScript for Enhanced Chondrogenesis of Stem Cells

Article abstract of DOI:10.1021/ja511298n

N-(4-Chloro-3-(trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB) is a small molecule that functions by altering the chromatin architecture to modulate gene expression. We report a new CTB derivative with increased solubility and demonstrate CTB's functionality by conjugating it on the recently established NanoScript platform to enhance gene expression and induce stem cell differentiation. NanoScript is a nanoparticle-based artificial transcription factor that emulates the structure and function of transcription factor proteins (TFs) to effectively regulate endogenous gene expression. Modifying NanoScript with CTB will more closely replicate the TF structure and enhance CTB functionality and gene expression. To this end, we first conjugated CTB onto NanoScript and initiated a time-dependent increase in histone acetyltransferase activity. Next, because CTB is known to trigger the pathway involved in regulating Sox9, a master regulator of chondrogenic differentiation, we modifed a Sox9-specific NanoScript with CTB to enhance chondrogenic gene activity and differentiation. Because NanoScript is a tunable and robust platform, it has potential for various gene-regulating applications, such as stem cell differentiation.

Full text of DOI:10.1021/ja511298n

Communication
pubs.acs.org/JACS
Integrating Epigenetic Modulators into NanoScript for Enhanced
Chondrogenesis of Stem Cells
Sahishnu Patel,† Thanapat Pongkulapa,† Perry T. Yin,‡ Ganesh N. Pandian,§ Christopher Rathnam,‡
Toshikazu Bando,∥ Thangavel Vaijayanthi,∥ Hiroshi Sugiyama,*,§,∥ and Ki-Bum Lee*,†,‡
†Department of Chemistry and Chemical Biology and ‡Department of Biomedical Engineering, Rutgers, The State University of New
Jersey, Piscataway, New Jersey 08854-8087, United States
∥
§Institute for Integrated Cell-Material Sciences (iCeMS) and Department of Chemistry, Graduate School of Science, Kyoto
University, Kyoto 606-8501, Japan
S
* Supporting Information
ABSTRACT: N-(4-Chloro-3-(trifluoromethyl)phenyl)-2-
ethoxybenzamide (CTB) is a small molecule that functions
by altering the chromatin architecture to modulate gene
expression. We report a new CTB derivative with
increased solubility and demonstrate CTB’s functionality
by conjugating it on the recently established NanoScript
platform to enhance gene expression and induce stem cell
differentiation. NanoScript is a nanoparticle-based artificial
transcription factor that emulates the structure and
function of transcription factor proteins (TFs) to
effectively regulate endogenous gene expression. Modify-
ing NanoScript with CTB will more closely replicate the
TF structure and enhance CTB functionality and gene
expression. To this end, we first conjugated CTB onto
NanoScript and initiated a time-dependent increase in
histone acetyltransferase activity. Next, because CTB is
known to trigger the pathway involved in regulating Sox9,
a master regulator of chondrogenic differentiation, we
modifed a Sox9-specific NanoScript with CTB to enhance
chondrogenic gene activity and differentiation. Because
NanoScript is a tunable and robust platform, it has
potential for various gene-regulating applications, such as
stem cell differentiation.
Figure 1. Schematic representation of CTB’s function and role in
initiating chondrogenesis. (a) If DNA (black line) is tightly coiled
around histone proteins (blue cylinders), transcriptional activity and
subsequent gene expression are inhibited. Activation of histone
acetyltransferase (HAT) via the CTB molecule loosens the DNA,
making target binding sites available for transcription. (b) CTB is
functionalized on the NanoScript platform, and the resulting construct is
delivered to adipose-derived mesenchymal stem cells (ADMSCs) to
enhance overexpression of targeted genes. The NanoScript construct is
also modified with additional small molecules that target and
overexpress the Sox9 gene. (c) Activation of the Sox9 gene in ADMSCs
guides enhanced differentiation into the chondrogenic lineage.
histone acetyltransferases (HATs), function by weakening the
association of DNA with histones, making the DNA more
accessible for transcription and gene activation (Figure 1a).5 Of
the many HAT activator small molecules, N-(4-chloro-3-
(trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB), is known
to be effective in regulating HAT activity.6 CTB functions by
triggering the p300 signaling pathway, which influences
chromatin structure by facilitating the assembly of chromatin
remodeling proteins to DNA binding sites (Figure 1a).7 As a
result, CTB enhances p300 HAT-dependent transcriptional
activation and regulates expression of p300-related genes.8 One
gene regulated by the p300 signaling pathway is Sox9,9 which
plays a critical role for inducing stem cell chondrogenesis.10
We recently demonstrated a new gene-regulating platform
called NanoScript, which mimics the fundamental structure and
function of TFs.11 NanoScript effectively induced gene
tem-cell-based therapies and cellular reprogramming hold
S
immense potential for regenerative medicine. Significant
effort has been invested in developing methods for effectively
controlling the differentiation of stem cells into specific lineages.
One promising approach for enhancing gene expression and
inducing stem cell differentiation involves epigenetic modifica-
tion.1 Epigenetic modification refers to changes in gene activity
and expression by modifying chromatin structure rather than
altering the DNA sequence.2 The eukaryotic genome is packed
into chromatin, in which the DNA wraps around proteins called
histones, and gene expression is regulated in part by the dynamics
of chromatin structure.3 Moreover, epigenetic modification plays
a critical role in enabling transcription factor proteins (TFs)
master regulators of gene expressionto regulate chromatin
structure for inducing transcriptional activity.4
Specifically, epigenetic modification involves DNA histone
deacetylation and acetylation, which regulate the chromatin
structure. One class of epigenetic modification molecules,
Received: November 6, 2014
Published: March 19, 2015
© 2015 American Chemical Society
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expression of both a reporter plasmid and endogenous genes on
native DNA in a nonviral manner, establishing it as an attractive
platform for applications requiring gene regulation.11 NanoScript
was designed to mimic the two fundamental domains on TFs: the
activation domain (AD) and the DNA binding domain (DBD).
The DBD seeks and binds to target gene sequences on DNA,
while the AD recruits the transcriptional basal machinery to
initiate transcriptional activity.12 These two domains function
synergistically to induce targeted gene expression. Through a
simple modification of the DBD, NanoScript can be designed to
target and activate the Sox9 gene. Moreover, studies have shown
CTB to trigger the p300 pathway, and the p300 pathway to
recruit the transcriptional basal machinery to initiate transcrip-
tional activity.13 Thus, we hypothesize that by modifying
NanoScript with a CTB molecule, an AD molecule, and a
Sox9-targeting molecule, we can utilize the NanoScript platform
to achieve enhanced Sox9 expression in stem cells to accelerate
their chondrocyte differentiation.
We combined the NanoScript platform with an epigenetic
modulator (i.e., CTB) and a Sox9-targeting molecule to activate
Sox9 expression in adipose-derived mesenchymal stem cells
(ADMSCs) to induce enhanced chondrogenic differentiation
(Figure 1b). First, we developed a new functional CTB derivative
modified with a thiol-PEG linker molecule to increase solubility
and enable conjugation on NanoScript. Second, the NanoScript
platform was modified with CTB, whereupon it more closely
mimicked TF protein structure because TFs contain an
epigenetic modification domain. Finally, when the CTB-
modified NanoScript specific for Sox9 (termed NanoScript-
Sox9) was delivered to ADMSCs, enhanced gene expression of
Sox9 and subsequent chondrogenic differentiation were
observed.
The NanoScript platform was designed and constructed to
replicate the fundamental structure of multidomain TFs.
Specifically, to replicate the structure of TFs, we designed
NanoScript with six components: (1) the CTB molecule that
mimics the epigenetic modification domain to initiate HAT
activity for enhanced gene expression,6 (2) a hairpin polyamide
molecule that mimics the DBD to target and bind to the Sox9
gene,12,14 (3) a transactivation peptide that mimics the AD to
initiate transcriptional activity,15 (4) a membrane-penetrating
peptide,16 (5) polyethleyne glycol (PEG)-based molecules to
increase stability and solubility,17 and (6) a gold nanoparticle
(AuNP) to tether these molecules onto a single construct.18
Assembling these individual small molecules on an AuNP
enables the resulting NanoScript platform to emulate TF protein
structure and function.
The CTB molecule interacts with the p300 protein, which in
turn interacts with lysine amino acids on histone proteins. This
results in reduced electrostatic attraction between the histone
and the DNA, causing the DNA to decrease its affinity, thus
exposing more binding sites for transcription. This CTB binds to
the target through hydrogen-bonding and hydrophobic inter-
actions, with the -Cl and -CF3 positions having the strongest
influence on binding affinity (Figure 2a).8 Moreover, the ortho
position on the aromatic hydrocarbon does not play a critical role
in overall binding.19 Thus, we modified the ortho position with a
PEG-thiol chain to increase solubility in physiological environ-
ments and enable conjugation onto the AuNPs (Figure 2a). In
doing so, we synthesized a CTB analogue.
Figure 2. CTB’s function is enhanced when conjugated on NanoScript.
(a) The CTB molecule is modified with a thiol-PEG chain and
functionalized on NanoScript. The remaining components on Nano-
Script include the AD, which recruits endogenous factors to initiate
transcription, and the DBD (refer to Figure S1 for structure details),
which targets and binds to the target Sox9 sequence on DNA. (b) The
HAT activity of this NanoScript-Sox9 construct was shown to increase
across three time points (days 1−3). Controls with only the AD
(without CTB), only CTB (without AD), or unconjugated CTB in
media showed comparatively less HAT activity. All conditions and
controls were transfected with 1 nM of the constructs. The increase of
HAT activity for all samples was determined by normalizing to the
untreated control. Standard error is from three independent trials.
A-T base pairs on the DNA, respectively, with nanomolar
affinity.20 The Sox9 gene has a consensus promoter sequence of
5′-ACAATGG-3′,21 so we designed a hairpin polyamide to target
this sequence (Figure S1a). Reported protocols using solid-phase
synthesis enabled us to build the hairpin with a sequence of
PyPyPy-β-PyImPy-γ-PyPyPy-β-PyImIm-β-Dp-NH2, comple-
mentary to the target Sox9 gene.22 In vitro binding association
studies were performed using surface plasmon resonance to
verify the binding affinity of the Sox9 polyamide. Results showed
a high sequence-specific binding affinity of the Sox9 polyamide to
the target sequence as compared to controls, including scrambled
polyamides and scrambled DNA sequences (Figure S1b).
The third molecule is the transactivation peptide, which
emulates the AD and recruits the transcriptional basal machinery
required to initiate transcription.23 This peptide is a potent
inducer of transcriptional activity.15 The fourth molecule is the
cell-penetrating peptide that enables plasma and nuclear
membrane penetration. Specifically, we used a modified TAT
peptide to shuttle AuNPs into the nucleus.16
The hairpin polyamide, transactivation peptide, and TAT
peptide were conjugated to a PEG-thiol molecule (21-chain
PEG) via EDC/NHS coupling, which enables functionalization
onto AuNPs. AuNPs were chosen because they are highly
biocompatible and nontoxic in cells and, most importantly,
because their multifunctional surface enables conjugation of
multiple molecules on a single NP.18 After 10 nm AuNPs were
functionalized with these PEG-terminated molecules, along with
the CTB, the resulting NanoScript platform (NanoScript-Sox9)
targeted the Sox9 gene (Figure 2a). Characterization of
NanoScript-Sox9 revealed a successive shift in the UV
absorbance, indicative of functionalization (Figure S2), and the
hydrodynamic diameter was found to be 57.9 nm (Figure S3).
After constructing the NanoScript-Sox9, we first wanted to
ensure successful nuclear localization, which is essential because
We next synthesized the hairpin polyamide specific for the
Sox9 gene. The hairpin polyamide, which acts as the DBD,
consists of imidazole and pyrrole motifs that bind to the G-C and
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Figure 3. Synergistic effect of CTB and AD on NanoScript enhances expression of chondrogenic markers. After 7 days post-transfection with
NanoScript-Sox9, ADMSCs were evaluated for their expression of distinct chondrogenic markers, (a) Aggrecan (green) and (b) Collagen II (red) (scale
bar = 50 μm). The intensity levels of both chondrogenic markers, (c) Aggrecan and (d) Collagen II, in the fluorescence images were quantified and
revealed a similar trend. (e) After 7 days post-treatment with NanoScript-Sox9, qPCR analysis revealed expression of distinct chondrogenic genes, as
compared to the untreated control. Gene expression levels were normalized to GAPDH. Error bars are from three independent experiments.
transcriptional activity occurs only in the nucleus. Hence, the
NanoScript-Sox9 was labeled with a fluorescent dye and
transfected into ADMSCs. After 24 h, fluorescence imaging
revealed that NanoScript-Sox9 was able to enter and localize
within the nucleus of 51.6% of the total cells (Figure S4a,b).
Next, we evaluated the function of the CTB molecule on the
NanoScript-Sox9. It is well known that CTB initiates HAT
activity.6 The effect of PEG modification on CTB was tested, and
both the unmodified CTB and PEG-modified CTB showed
similar HAT activity (Figure S5), indicating that the modified
CTB retained its functionality. Moreover, the function of CTB
conjugated to the NP was tested and revealed that increasing
CTB amounts on the NP resulted in increasing HAT activity
(Figure S6). We then tested various concentrations of Nano-
Script-Sox9 and observed a concentration-dependent HAT
activity increase (Figure S7). Next, NanoScript-Sox9-induced
HAT activity was evaluated at various time points. Remarkably,
the NanoScript-Sox9 with both the AD and CTB induced
maximal HAT activity at all the time points compared to the
controls, which included a free CTB molecule and NanoScript-
Sox9 that lacked either the CTB or AD (Figure 2b). While this
result shows induction of HAT activity when CTB or AD alone is
on NanoScript, the combined effect of CTB and AD on a single
NanoScript shows maximum increase in HAT activity.
overexpressing the Sox9 gene in ADMSCs to enhance
chondrogenic differentiation. ADMSCs were chosen as a
model cell line because they are excellent multipotent stem
cells with a capacity to differentiate into muscle, cartilage, bone,
and neuronal cells.24 Moreover, Sox9 was chosen as a target gene
because it is known to control chondrogenic differentiation and
its expression is regulated by both the p300 pathway and
conventional ADs.9 Thus, we expected to observe an enhance-
ment of Sox9 expression and other chondrogenic-related genes
when NanoScipt-Sox9 was delivered to ADMSCs.
NanoScript-Sox9 and chondrogenic differentiation media
were incubated with ADMSCs on days 0 and 2. After 7 days,
the ADMSCs were evaluated for expression of distinct
chondrogenic factors, Aggrecan and Collagen II, which are
prominent chondrogenic markers that are expressed based on
the progression of chondrogenic differentiation. After the
ADMSCs were fixed and stained, fluorescence imaging revealed
that the sample treated with NanoScript-Sox9 (having both CTB
and AD) showed enhanced expression of Aggrecan and Collagen
II as compared to controls (Figure 3a,b). Furthermore, the
fluorescence intensity of Aggrecan and Collagen II expression
from these images showed a remarkable trend that confirmed
maximal expression when both CTB and AD are present on
NanoScript-Sox9 (Figure 3c,d), with high cell viability (Figure
S8). Although all conditions and controls were treated identically
with differentiation media, maximum expression was observed
After determining that both CTB and AD are required on a
single NP to induce maximal HAT activity, we focused on
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when CTB and AD were both present on NanoScript-Sox9, thus
suggesting enhanced chondrogenic differentiation.
modification and ratios, and nuclear localization images. This
material is available free of charge via the Internet at http://pubs.
acs.org.
To further quantify the genetic expression patterns of
chondrogenic genes in NanoScript-Sox9-treated ADMSCs, we
performed qPCR. Analysis showed that NanoScript-Sox9
enhanced expression of all three distinct genes, Sox9, Aggrecan,
and Collagen II, as compared to controls and NanoScript lacking
either the AD or CTB (Figure 3e). Another control experiment,
incubating NanoScript-Sox9 with free CTB, suggested that CTB
has maximal function when attached to the AuNP (Figure S9).
Furthermore, expression levels of housekeeping genes remained
unchanged as compared to the control (Figure S10). Even
though NanoScript-Sox9 was designed to target the Sox9 gene,
which showed the highest expression among the three genes,
Sox9 is sufficient to trigger the chondrogenic pathway, including
the Aggrecan and Collagen II genes.
Taken together, the results from our three experiments (HAT
assay, immunofluorescence, and qPCR) indicate that the
presence of both CTB and AD on NanoScript initiates maximal
HAT activity and expression of chondrogenic genes. One
possible hypothesis for this is that the CTB and AD initiate HAT
activity through different pathways: previous reports showed that
CTB initiates HAT activity through the p300 pathway,6 while the
AD (specifically the transactivation peptide) initiates HAT
activity by recruiting factors such as SAGA and NuA4.23,25
Hence, it is possible that because two gene activation pathways
were induced, we observed an enhanced synergistic gene
expression when both CTB and AD were present on NanoScript.
However, the exact interplay between these signaling pathways is
unknown, and we will attempt to elucidate the mechanisms in
future studies.
In summary, the recently developed NanoScript platform was
modified with an epigenetic modification molecule, CTB, which
regulates histone proteins and enhances gene expression through
the HAT-dependent p300 pathway. Addition of CTB not only
moved NanoScript a step closer toward mimicking natural
transcription factors but also enhanced the gene expression
capabilities of NanoScript. The role and function of CTB on
NanoScript were evaluated and revealed that CTB is effective in
inducing HAT activity. Moreover, we observed that NanoScript
with both AD and CTB showed the greatest HAT activity,
possibly because the AD and CTB triggered two distinct
pathways for regulating HAT activity. When NanoScript-Sox9
was incubated with ADMSCs, we confirmed through fluo-
rescence imaging and qPCR that NanoScript-Sox9 activates
expression of chondrogenic markers.
Our NanoScript-based transcriptional activator can have a
significant impact in the fields of stem cell biology and cellular
reprogramming. Through this proof-of-concept demonstration,
we have established that NanoScript is an effective and tunable
platform that can manipulate targeted genes that are critical for
stem cell differentiation in a nonviral manner. Moreover, by
modifying NanoScript with epigenetic modification molecules
such as HAT activators (e.g., CTB), we optimized it to be more
effective in regulating gene expression. As a result, we are
confident that NanoScript can be utilized for other applications
requiring nonviral and effective gene regulation in stem cell
biology and cellular reprogramming.
AUTHOR INFORMATION
■
Corresponding Authors
*hs@kuchem.kyoto-u.ac.jp
*kblee@rutgers.edu
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We thank Anthony Dudzinski, Ruth Goldman, and Mike Moeller
(American CryoStem Corp.) for stem cells and media. K.-B.L.
acknowledges the NIH Director’s Innovator Award
(1DP20D006462-01), NIH R21 (1R21NS085569-01), New
Jersey Commission on Spinal Cord (CSR13ERG005), NSF
CHE-1429062, CBET-1236508, Busch Biomedical Grant
Program, and the Collaborative Research Travel Grant
(CRTG) from the Burroughs Wellcome Fund for funding.
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ASSOCIATED CONTENT
* Supporting Information
Sox9 polyamide structure and characteristics, absorbance,
NanoScript-Sox9 diameter, cell viability, effect of CTB
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DOI: 10.1021/ja511298n
J. Am. Chem. Soc. 2015, 137, 4598−4601