Modifications in Small Interfering RNA That
Separate Immunostimulation from RNA
Interference
This information is current as
of June 16, 2017.
Florian Eberle, Kerstin Gießler, Christopher Deck, Klaus
Heeg, Mirjam Peter, Clemens Richert and Alexander H.
Dalpke
J Immunol 2008; 180:3229-3237; ;
doi: 10.4049/jimmunol.180.5.3229
http://www.jimmunol.org/content/180/5/3229
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References
The Journal of Immunology
Modifications in Small Interfering RNA That Separate
Immunostimulation from RNA Interference1
Florian Eberle,* Kerstin Gießler,† Christopher Deck,† Klaus Heeg,* Mirjam Peter,*
Clemens Richert,† and Alexander H. Dalpke2*
R
ibonucleic acid interference (RNAi)3 is an evolutionary
conserved mechanism in plant and animal cells that leads
to the sequence-specific degradation of messenger RNA.
The exact molecular mechanisms of all steps are not known, but
RNAi involves formation of small interfering RNA (siRNA) duplexes that are 21–28 nucleotides in length with 3⬘-overhangs of
two nucleotides at either terminus (1). The siRNAs are incorporated in an RNA-induced silencing complex (RISC) that cleaves
target mRNA complementary to the antisense or leading strand of
the siRNA. A hallmark for siRNA biology in mammals has been
the observation that chemically synthesized short siRNA duplexes
can induce this process (2). siRNA has become a widespread molecular tool, and it is thought that siRNA has a potential for therapeutic inhibition of gene expression in a variety of diseases (3–5).
Type I IFN induction is a common response of mammalian cells
to long double-stranded RNA that serves as an antiviral defense. It
*Department of Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg; and †Institute for Organic Chemistry, University of Karlsruhe, Karlsruhe,
Germany
Received for publication October 23, 2007. Accepted for publication December
21, 2007.
The costs of publication of this article were defrayed in part by the payment of page
charges. This article must therefore be hereby marked advertisement in accordance
with 18 U.S.C. Section 1734 solely to indicate this fact.
1
This work was supported by a grant of the Landesstiftung Baden-Württemberg to
K.H., C.R., and A.D. (P-LS-RNS/25).
2
Address correspondence and reprint requests to Dr. Alexander H. Dalpke, Department of Medical Microbiology and Hygiene, Hygiene-Institute, University of Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany. E-mail address:
[email protected]
3
Abbreviations used in this paper: RNAi, RNA interference; DOTAP, N-[1-(2,3dioleoyloxy)propyl]-N,N,N-trimethylammonium methylsulfate; eGFP, enhanced
green fluorescent protein; MFI, mean fluorescence intensity; RISC, RNA-induced
silencing complex; siRNA, small interfering RNA; TBDMS, tert-butyldimethylsilyl.
Copyright © 2008 by The American Association of Immunologists, Inc. 0022-1767/08/$2.00
www.jimmunol.org
is induced by various RNA-recognizing molecules, including retinoic acid-inducible gene I and melanoma differentiation-associated
gene 5 (6, 7). During the last few years, additional receptors for the
recognition of RNA have been identified. Single-stranded RNA
has been shown to be recognized by TLR7 and TLR8 (8 –10),
whereas double-stranded RNA is a ligand for TLR3 (11). Results
from several groups now show that synthetic siRNA is also recognized in a TLR3/TLR7/TLR8-dependent manner (12–15). Sequence analysis revealed several possible immunostimulatory sequences characterized by a high content of guanosine and uridine
residues (12, 16).
Recognition of siRNA by plasmacytoid dendritic cells that express TLR7 results in the secretion of IFN-␣. Although the finding
was initially controversial (17), it is now clear that synthetic
siRNA duplexes induce the up-regulation of IFN-stimulated genes
(18 –20), potentially leading to severe side effects. The absence of
a molecular understanding of this activity makes it impossible to
predict the immunostimulatory risk associated with specific siRNA
sequences, creating an untenable situation for medical applications
and complicating drug development.
It has been shown that modified nucleosides can alter the immunostimulatory potential of RNA oligomers (21). The 2⬘-hydroxy group of RNA is apparently not absolutely required for
RNAi activity (22), leading to the speculation that the introduction
of noncanonical nucleosides could separate immunostimulation
from gene-silencing activity (23). Modifications at the 2⬘-position
of uridines diminish immunostimulation (24 –28). Modified
strands have been shown to reduce immunostimulation induced
both by otherwise stimulatory RNA strands and by CpG DNA
strands activating TLR7 or TLR9, respectively (25, 26). However,
firm principles are missing of how a siRNA may have to be modified to be safe for clinical applications.
In our current work, we tested oligoribonucleotides both for
their immunostimulatory activity and their RNAi efficacy, using a
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Synthetic small interfering RNA (siRNA) can suppress the expression of endogenous mRNA through RNA interference. It has
been reported that siRNA can induce type I IFN production from plasmacytoid dendritic cells, leading to off-target effects. To
separate immunostimulation from the desired gene-specific inhibitory activity, we designed RNA strands with chemical modifications at strategic positions of the ribose or nucleobase residues. Substitution of uridine residues by 2ⴕ-deoxyuridine or thymidine
residues was found to decrease type I IFN production upon in vitro stimulation of human PBMC. Thymidine residues in both
strands of a siRNA duplex further decreased immunostimulation. Fortunately, the thymidine residues did not affect gene-silencing
activity. In contrast, 2ⴕ-O-methyl groups at adenosine and uridine residues reduced both IFN-␣ secretion and gene-silencing
activity. Oligoribonucleotides with 2ⴕ-O-methyladenosine residues actively inhibited IFN-␣ secretion induced by other immunostimulatory RNAs, an effect not observed for strands with 2ⴕ-deoxynucleosides. Furthermore, neither 5-methylcytidine nor 7-deazaguanosine residues in the stimulatory strands affected IFN-␣ secretion, suggesting that recognition does not involve sites in the
major groove of duplex regions. The activity data, together with structure prediction and exploratory UV-melting analyses,
suggest that immunostimulatory sequences adopt folded structures. The results show that immunostimulation can be suppressed
by suitable chemical modifications without losing siRNA potency by introducing seemingly minor structural changes. The Journal of Immunology, 2008, 180: 3229 –3237.
3230
combination of two assay systems. We studied the effect of sterically demanding 2⬘-O-methyl groups as well as deletion of the OH
function at the 2⬘-position and nucleobase modifications in a
screen involving residue-specific changes in the entirety of the
RNA strands. Only thymidine residues replacing uridines gave
RNAs with gene-silencing activity comparable to that of unmodified siRNA, but they markedly reduced induction of IFN-␣ in
human peripheral blood cells. We also identified a 2⬘-O-methyladenosine-containing RNA that led to complete loss of IFN-␣
induction and suppression of the effect of other stimulatory RNA
strands.
Materials and Methods
Reagents for RNA synthesis
SILENCING IMMUNOSTIMULATION BY siRNA
used for HPLC purification with a gradient from 0 to 30% CH3CN in 30
min, at a flow of 1 ml/min. A single, conventional HPLC step on a C18
reversed-phase column provided the oligoribonucleotides in high yields
and purity, as demonstrated by MALDI-TOF mass spectrometry (supporting information can be found online: http://chip.chemie.uni-karlsruhe.de/
sup_inf/). Control experiments with a sample of RNA 1 synthesized inhouse showed the same activity in terms of IFN-␣ induction as that of the
same compound prepared and purified by IBA, confirming that results with
samples from either source produce comparable results.
Annealing to duplexes
To generate double-stranded siRNA duplexes, sense (s) and complementary antisense (as) strands of each siRNA were mixed at equimolar concentrations in annealing buffer (20 mM of HEPES, 150 mM of NaCl (pH
7.4)), heated to 90°C for 5 min, followed by cooling-down slowly to room
temperature.
Cell isolation
Spectrometric characterization
All used RNA molecules were encapsulated with DOTAP (N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium methylsulfate) (Roth) in a ratio of 1:2.5 according to the manufacturer’s protocol. Cells were stimulated
for 16 h. Cell-free supernatant was removed and analyzed for human IFN-␣
secretion using a sandwich enzyme-linked immunosorbent assay (Bender
MedSystems). Analysis was done in duplicates, and all experiments were
performed at least three times unless indicated otherwise. To account for
donor heterogeneity, stimulation with 1 ␮g/ml unmodified RNA oligoribonucleotide 1 was normalized to 100%.
MALDI-TOF mass spectra were acquired on a Bruker Reflex IV spectrometer in negative, linear mode, using a mixture of 2,4,6-trihydroxy-acetophenone (0.3 M in EtOH) and diammonium citrate (0.1 M in H2O) at a
ratio of 2:1 (v/v) as matrix. UV-Vis spectra were recorded on a NanoDrop
ND-1000 spectrophotometer. Purification of the oligonucleotides was performed on a Hitachi HPLC L-6200 system using C18 reversed-phase columns (Machery-Nagel) or C18 Sep-Pak cartridge (Waters).
Media and Abs
RPMI 1640 and sodium pyruvate were obtained from Biochrom. FCS was
from Biowest, PBS was obtained from PAA, and DMEM was purchased
from Invitrogen.
RNA oligoribonucleotides
The sequences of all RNA strands that were produced are depicted in Figs.
1–3. Unmodified RNA strands, as well as 2⬘-O-methyluridine-containing
strands (1mU), were obtained from IBA. All other oligoribonucleotides
were custom-synthesized in-house on an Expedite 8909 DNA synthesizer
(ABI/PerSeptive Biosystems) on a 1 ␮mol scale, starting from preloaded
controlled pore glass. RNA oligoribonucleotides were deprotected and
cleaved from the solid support using concentrated aqueous ammonia (25%)
(1 ml) for 35 min at 55°C. The supernatant was collected and the residue
was washed with deionized water. Excess ammonia was removed from the
combined aqueous solutions with a gentle stream of compressed air directed onto the surface of the solutions.
Phosphoramidites with TBDMS (29) or triisopropylsilyloxymethyl
(TOM) groups (30) protecting for the 2⬘-hydroxy groups gave similar
yields in the chain assembly process. The former are considerably less
expensive than the latter, and TBMDS-protected building blocks were
therefore used exclusively. A seemingly minor modification to the protocol
recommended by the supplier of the phosphoramidites significantly improved yields. The dimethoxytrityl group of the 5⬘-terminal nucleotide was
removed before release from the solid support, and neat triethylamine hydrofluoride was used for the deprotection step, rather than tetrabutylammonium fluoride in tetrahydrofuran (THF), whose tetrabutylammonium
ions were found difficult to remove during cartridge purification. The more
acidic hydrogen fluoride reagent also minimizes strand cleavage during
work-up of the deprotection solution, which is caused by fluoride ions. So,
after lyophilization, triethylamine trihydrofluoride (NEt3 3 HF) (250 ␮l)
was added. After 16 h, methoxytrimethylsilane (550 ␮l) was added to
precipitate the oligoribonucleotide. The use of trimethylsilyl methyl ether
as quenching agent at the end of the deprotection of the 2⬘-TBDMS groups
not only removed residual hydrogen fluoride (a very toxic reagent), but also
ensured that the RNA formed an easy-to-harvest pellet upon centrifugation.
Therefore, after 20 min, the RNA was spun down by centrifugation on a
microcentrifuge for 1 min. The supernatant was aspired, and the pellet was
dissolved in doubly distilled water (150 ␮l), filtered (0.2 ␮m pore size), and
Human PBMCs were isolated from whole blood of young healthy donors.
Isolation was performed by standard Ficoll-Hypaque density centrifugation. Blood was diluted 1/2 (v/v) with PBS, underlaid by Ficoll (Biochrom), and centrifuged at 485 ⫻ g for 20 min. PBMCs were washed twice
with PBS and resuspended in complete medium (RPMI 1640, 2% heatinactivated autologous serum). PBMCs were plated at 4 ⫻ 105 cells/well in
a 96-well flat-bottom plate for stimulation assays.
Cell stimulation and IFN detection
Determination of gene-silencing activity
Human embryonic kidney cells (1.5 ⫻ 105 per well of a 24-well culture
plate, HEK293) were plated in DMEM containing 10% FCS and no antibiotics. The following day, cells were cotransfected either with 400 ng
pEGFP-N1 (BD Clontech), encoding enhanced GFP (eGFP), or with 500
ng pSV-␤-galactosidase control vector (Promega), encoding for ␤-galactosidase together with the respective siRNA in the indicated concentration.
Transfection was performed with Lipofectamine 2000 (Invitrogen). After 24 h, cells were washed with PBS, and reporter gene expression was
analyzed. Expression of eGFP was determined by flow cytometry
(FACSCanto, BD Biosciences) in the FITC channel (530/30 nm). Mean
fluorescence intensity (MFI) of 20,000 live cells gated according to forward/side-scatter characteristics was detected. ␤-Galactosidase activity
was determined by incubation of the cells for 4 h at 37°C in lysis buffer
(100 mM of 2-ME, 9 mM of MgCl2, 0.125% NP40, and 0.15 mM of
chlorophenol red-␤-galactopyranoside). The reaction was stopped by addition of stopping solution (300 mM of glycine, 15 mM of EDTA), and OD
was measured at 570 nm with a 650-nm reference wavelength.
Statistical analysis
Data were analyzed by GraphPad Prism 4.03 program (GraphPad Software). Significant differences were assessed by ANOVA to compare three
or more groups followed by Dunnetts test to compare selected groups. In
all figures, ⴱ represents p values ⬍0.05.
Results
We assumed that the receptor(s) causing the immunostimulatory
side effects of siRNA are structurally more discriminating than is
the enzymatic machinery of RNAi. The former have to ensure
highly selective differentiation of self from nonself structures,
whereas the latter may have been evolved to attack doublestranded RNA from a variety of sources. The choice of modifications to be tested was governed by the following considerations: 1)
structural diversity at positions that are likely to be recognized by
a high-fidelity receptor of the innate immune system, 2) negligible
effects on the base pairing required for siRNA activity (dsRNA), 3)
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5-[Bis(3,5-trifluoromethyl)phenyl]-1H-tetrazole (activator), tetrahydrofuran (THF), pyridine, iodine and water (oxidizer; 0.02 M), acetonitrile, trichloroacetic acid in acetonitrile (deblock), tert-butylphenoxyacetyl acetic
anhydride in THF (Cap A), pyridine and N-methylimidazole (Cap B), the
solid support (cpg), tert-butyldimethylsilyl (TBDMS)-protected RNA
phosphoramidites, and modified RNA phosphoramidites were purchased
from Proligo or ChemGenes. Triethylammonium acetate buffer (0.1 M (pH
7)) was used for HPLC purification against a gradient of CH3CN. Hydrofluoric acid in triethylamine (“triethylamine trihydrofluoride”) and methoxytrimethylsilane were from Acros Organics or from Fluka.
The Journal of Immunology
3231
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synthetic accessibility at moderate costs (to facilitate drug development), and 4) precedents in the literature.
The 2⬘-position was considered critical, as it is the very position
where RNA and DNA differ structurally. Two types of modifications at this position were included: those that lack the 2⬘-oxygen
(deoxy derivatives) and those that feature a methyl group at this
position (2⬘-O-methyl derivatives; Fig. 1A). The latter should induce a steric conflict in complexes where the 2⬘-hydroxy group is
located in a specific pocket of a receptor (Fig. 1B). Thymidine as
replacement for uridine residues was also included, together with
5-methylcytidine and 7-deazaguanosine residues. In either of these
nucleobase-modified residues, a position is altered that affects recognition in the major groove of duplexes. The major groove is the
site most frequently involved in sequence-specific recognition of
DNA by proteins (31). Duplex-forming potential is known to affect
RNAi and the structural characteristics of certain immunostimulatory CpG oligonucleotides (32). Thymidine and 5-methylcytidine are sterically more demanding, and 7-deazaguanosine lacks
N7 as a hydrogen bond acceptor (Fig. 1B).
Based on the parent sequence 1 (Fig. 2), which is both immunostimulatory and shows strong interference activity, derivatives
were prepared. All ribonucleotides of one given nucleobase were
replaced by their 2⬘-deoxy counterparts (1dA–1dU, Fig. 3A).
These were complemented by three base-modified oligoribonucleotides (Fig. 3B), of which 1dT contains residues with structural
changes in both the ribose and base. Additionally, 2⬘-O-methyl
derivatives were prepared (1mA–1mU, Fig. 3C). The most promising structural replacement (U/dT, vide infra) was also tested in
other sequence contexts (Fig. 3D). All compounds, except 1mU,
were prepared via the optimized protocol given in Materials and
Methods and were HPLC-purified to homogeneity, as shown by
MALDI-TOF mass spectrometry (supporting information can be
found online: http://chip.chemie.uni-karlsruhe.de/sup_inf/).
Analysis of 2⬘-deoxy-modified RNA oligomers regarding
immunostimulation
First, the 2⬘-deoxy derivatives (1dA–1dU) of single-stranded (ss)
oligoribonucleotide 1 representing the antisense strand of a siRNA
directed against eGFP (33) were tested. The RNA strands were
formulated with DOTAP (9) and tested for IFN-␣ secretion from
human PBMCs, which is mediated by activation of plasmacytoid
dendritic cells. Plasmacytoid dendritic cells had a frequency of
⬃1.6% (⫾0.3%) in PBMCs as determined by flow cytometry
analysis for expression of BDCA-2 and BDCA-4. Due to donor
heterogeneity, IFN-␣ output was normalized to an internal reference. We observed a dose-dependent increase in IFN-␣ secretion of unmodified RNA strand 1 over the tested concentration range from 0.01 to 1 ␮g/ml (Fig. 4A). Individual IFN-␣
secretion varied between 900 and 1400 pg/ml. Substitution of
all uridines in RNA 1 (5 of 22 nucleotides) by their 2⬘-deoxy
counterparts gave 1dU, which showed a significantly decreased
immunostimulatory activity. Residual IFN-␣ secretion was observed when 1dU was added at a concentration of 1 ␮g/ml. 1dC
also diminished IFN-␣ secretion; however, reduction was far
less than observed with 1dU. In contrast, the 2⬘-deoxynucleosides 1dA and 1dG showed no significant inhibition of
immunostimulation.
FIGURE 1. Structures of modified residues in RNA strands used in this
work. A, Top row: 2⬘-deoxynucleotides of A, C, U, and G (dA, dC, dU,
dG); middle row: 2⬘-O-methylribonucleotides of A, C, and U (AOMe,
COMe, UOMe); bottom row: nucleotides featuring 5⬘-methylcytosine (5MC),
(deoxy)thymidine (dT), and deazaguanine (DNG). B, Structural drawings
of AOMe and dT highlighting the effect of chemical modifications on the
steric demand and conformational flexibility of each nucleoside.
Immunostimulation with 2⬘-O-methyl derivatives
Next, oligonucleotides containing 2⬘-methoxy groups (Fig. 4B)
were analyzed. For the derivatives of 1 with 2⬘-O-methyl groups at
any A or U residue, IFN-␣ secretion in human PBMCs was completely abrogated. Both modified RNA oligoribonucleotides (1mA
or 1mU) showed a complete loss of immunostimulation, even at
the highest tested concentration, exceeding the effects of 2⬘-deoxyuridine (1dU) as replacement. In contrast, incorporation of 2⬘O-methyl-cytidine (1mC) did not lead to an alteration in IFN-␣
induction.
3232
SILENCING IMMUNOSTIMULATION BY siRNA
Immunostimulation with base-modified derivates
Furthermore, nucleobase-modified residues, which should affect
recognition processes involving the major groove of duplexes (Fig.
4C), were tested. We observed that the derivative of 1 containing
2⬘-thymidine residues (1dT) showed significant reduction of
IFN-␣ secretion over all concentrations tested, comparable to that
observed with 1dU (Fig. 4A). 5-methylcytidine (1C5Me)-modified
RNA strands did not show altered IFN-␣ secretion as compared
with the unmodified parental strand (1), and 7-deazaguanosine
(1NG) modified strands were slightly less active at only two
concentrations.
Thymidine-containing siRNAs show superior gene-silencing
activity
Next, we assessed whether modifications that decrease the immunostimulatory activity of the oligoribonucleotides affect gene-silencing activity of the corresponding siRNA duplexes. The antisense, or leading strands, with their respective modifications (1,
1dT, 1dU, 1mA, or 1mU) were annealed to their unmodified complementary strand (2). By cotransfection of a plasmid encoding
eGFP with the duplexes, it was shown that the unmodified siRNA
(2/1) efficiently silenced eGFP expression to ⬍5% at all concentrations tested (Fig. 5). Control duplex (8/7) with a different sequence did not even decrease eGFP expression slightly, suggesting
that this was a sequence-specific effect. The minor increase observed might be due to an increased transfection efficacy. Among
the modified siRNAs, only the one containing the thymidine residues (2/1dT) displayed the same efficiency of silencing to 5% of
gene expression as the unmodified counterpart 2/1. Moreover,
siRNA 2/1dT was active at all three concentrations tested. In contrast, 2⬘-deoxyuridine (2/1dU) and 2⬘-O-methyluridine (2/1mU) as
replacements in the siRNAs suppressed eGFP expression much
less, with inhibition to 43 and 38% at 1.5 nM of strand concentration. Increasing the siRNA concentration resulted in slightly improved gene silencing, but even with 10-fold higher concentrations, the suppression activity was not as high as that with
unmodified (2/1) or thymidine-containing (2/1dT) siRNA. The 2⬘-
FIGURE 3. Modified RNA sequences used. Oligoribonucleotides containing modified residues are shown. A, Sequence 1 with deoxy nucleotides
dA, dC, dU, or dG; B, derivatives of sequence 1 with base-modified residues 5MC, dT, and DNG; C, versions of sequence 1 featuring 2⬘-O-methyl
nucleotides AOMe, COMe, and UOme; and D, sequences 2, 3, and 5 with dT
replacing uridine residues.
O-methyladenosine-containing 2/1mA was even less effective,
showing only a marginal inhibition to 88% of control expression.
Thymidine residues separate immunostimulation from gene
silencing
These results indicated that thymidine is a favorable residue for
siRNAs, which decreases immunostimulation without affecting
gene-silencing activity. To determine whether these observations
were specific for the individual siRNA 2/1dT or hold true for
siRNA duplexes in general, further siRNAs, targeting GFP at another position (4/3, 4/3dT) or targeting ␤-galactosidase (6/5,
6/5dT), were designed. Sequences with high GU-content were
chosen to allow for immunostimulation. Thymidine residues were
again introduced in the leading strands (3dT, 5dT) (Fig. 3). Singlestranded, modified RNA oligoribonucleotides were applied to human PBMCs and IFN-␣ secretion was measured (Fig. 6, A–C). We
observed that all three unmodified RNA strands tested (1, 3, 5)
induced IFN-␣ with rather similar dose-activity profiles, and maximum activity was found in two independent donors. In each case,
incorporation of thymidines (1dT, 3dT, 5dT) resulted in a strong
reduction of IFN-␣ secretion, confirming our hypothesis. As observed for RNA strand 1dT, application of ⬎1 ␮g/ml 5dT resulted
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FIGURE 2. RNA sequence motives used. RNA duplexes featuring
oligoribonucleotides 1– 8 are shown in the form used for RNAi assays.
Complementary strands are written in antiparallel fashion; s denotes
sense strands; as, antisense strands. Modified duplexes contained the
nucleotides shown in Fig. 1 as replacements for their natural counterparts (compare Fig. 3).
The Journal of Immunology
3233
FIGURE 4. Effects of 2⬘-deoxy, 2⬘-O-methyl, or nucleobase modifications on IFN-␣ secreting capacity of RNA oligoribonucleotides. Human
PBMCs were stimulated with single-stranded RNA oligoribonucleotide
sequence 1 either unmodified or with the indicated 2⬘-deoxy (1dA,
1dG, 1dC, 1dU) (A) or 2⬘-O-methyl (1mC, 1mA, 1mU) (B) modifications or with the nucleobase modifications thymidine, 7-deazaguanosine, or 5-methylcytidine (1dT, 1C5Me, 1NG) (C) incorporated.
IFN-␣ secretion was measured, and normalized values are displayed
(n ⫽ 3, mean ⫾ SD). ⴱ, p ⬍ 0.05 as compared with control RNA
oligoribonucleotide sequence 1.
in residual IFN-␣ secretion, whereas 3dT was completely inactive.
Next, siRNA duplexes containing the modified antisense (leading)
strand annealed to an unmodified sense (passenger) strand were
analyzed for gene-silencing activity (Fig. 6D). Gene expression of
both reporter genes (eGFP or galactosidase) in HEK293 cells was
suppressed efficiently to levels comparable to those with unmodified siRNAs (2/1 vs 2/1dT, 4/3 vs 4/3dT, 6/5 vs 6/5dT). These
results confirm that the thymidine modification in siRNA is separating immunostimulation from gene silencing in more than one
sequence context.
Effect of thymidine residues in both strands of siRNA duplexes
Having shown that thymidine-modified RNA oligoribonucleotides
are able to decrease IFN-␣ secretion induced by the singlestranded form, we examined to what extent thymidine residues
affect immunostimulatory activity induced by double-stranded
siRNA. SiRNA against eGFP had been chosen such that both
strands, sense (2) and antisense (1), were active in terms of IFN-␣
induction (see Fig. 8A). We generated siRNA duplexes composed
of unmodified and thymidine-modified strands in different orientations to analyze the immunostimulatory capacity of the siRNA
duplex as whole (Fig. 7A). Annealed, unmodified siRNA (2/1)
induced IFN-␣ in a dose-dependent manner. When the leading
strand was substituted with a thymidine modified strand (2/1dT),
IFN-␣ secretion was reduced to ⬃50% as compared with the unmodified siRNA (2/1). We speculated that the residual immunostimulation was due to the presence of the unmodified passenger
strand (2). To further decrease immunostimulation, thymidine residues were also introduced in the passenger strand of the siRNA
(2dT). This resulted in double-stranded siRNA (2dT/1dT) carrying thymidine residues in either strand. Using this doubly modified
siRNA duplex, IFN-␣ secretion in human PBMCs could be diminished further and was only observed at concentrations ⬎0.3 ␮g/ml.
In order to achieve sufficient reduction of immunostimulation
made it necessary to modify both strands of a siRNA targeting
eGFP with thymidines (Fig. 7A). Therefore, it was necessary to
verify that incorporation of these modifications in both strands did
not affect gene silencing (Fig. 7B). In fact, we observed that even
a siRNA consisting of two modified single strands (2dT/1dT) was
still as efficient in gene silencing as the unmodified counterpart
(2/1). The concentration necessary for gene silencing (0.02– 0.1
␮g/ml) was far below the concentration for which residual stimulation was observed.
Antagonistic effects on IFN-␣ secretion
It had been reported that 2⬘-O-methyluridine-, 2⬘-O-guanosine-,
and 2⬘-O-adenosine-modified RNA oligoribonucleotides act as
TLR7 antagonists (26). From the results presented above (Fig. 7A),
it seemed unlikely that thymidine-containing RNA strands act as
dominant antagonists. To address this issue, we repeated experiments from above including siRNA duplexes composed of an unmodified sense strand and 2⬘-O-methyladenosine residues (2/
1mA) or 2⬘-O-methyluridine residues (2/1mU). It was observed
that both single strands of the siRNA against eGFP (1, 2) induced
IFN-␣, with RNA strand 2 being slightly more active (Fig. 8A).
The annealed, unmodified siRNA 2/1 was as effective as the RNA
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FIGURE 5. Gene silencing using 2⬘-deoxy- and 2⬘-O-methyl-modified
siRNA duplexes. HEK293 cells were transfected with an eGFP expression
plasmid (gray bars). Additionally, annealed siRNA targeting eGFP composed of an unmodified strand in sense orientation and unmodified (2/1) or
thymidine (2/1dT)-, 2⬘-deoxyuridine (2/1dU)-, 2⬘-O-methyluridine (2/
1mU)-, or 2⬘-O-methyladenosine (2/1mA)-modified antisense strand was
added (black bars) in increasing concentrations of 1.5, 7.5, and 15 nM. A
control siRNA (8/7) was used to test specificity of gene silencing. GFP
expression was determined by flow cytometry (n ⫽ 3, mean ⫾ SD).
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SILENCING IMMUNOSTIMULATION BY siRNA
FIGURE 6. Thymidine-modified siRNAs separate gene-silencing activity from immunostimulation. A–C, Human PBMCs were stimulated with single-stranded, antisense RNA oligoribonucleotides 1
(A), 3 (B), or 5 (C) and compared with the thymidine-modified counterparts (1dT, 3dT, 5dT). IFN-␣
secretion from PBMCs of two individual donors
(D1, D2) is shown. D, HEK293 cells were transfected with the indicated reporter plasmids encoding
eGFP or ␤-galactosidase (gray bars). Annealed
siRNA duplexes composed of an unmodified sense
and thymidine-modified antisense strand and directed against eGFP (EGFP1, EGFP2) (2/1, 2/1dT,
4/3, 4/3dT) or ␤-galactosidase (BG) (6/5, 6/5dT)
were tested for gene-silencing activity (n ⫽ 2)
(black bars).
FIGURE 7. Effect of thymidine in the leading vs the passenger strand
on gene-silencing activity and IFN-␣ secretion. A, Human PBMCs were
stimulated with annealed siRNA (EGFP) that was composed of unmodified
strands (2/1), and with thymidine modification in the antisense (leading)
strand (2/1dT) or in both strands (2dT/1dT). IFN-␣ secretion was measured
(n ⫽ 3, mean ⫾ SD). ⴱ, p ⬍ 0.05 as compared with control siRNA 2/1. B,
The annealed siRNA duplexes were tested for gene-silencing activity
(black bars) on HEK293 cells transfected to express eGFP (gray bars) (n ⫽
3, mean ⫾ SD) at two concentrations of 1.5 or 7.5 nM.
strand 2 in trans. This dominant inhibitory effect was not observed
with the strand containing 2⬘-O-methyluridines (2/1mU).
To ascertain whether 2⬘-O-methyladenosines differ in their effect from thymidines in terms of their antagonistic activity, human
FIGURE 8. 2⬘-O-Methyladenosine-modified, but not thymidine-modified, RNA strands possess antagonistic activity. A, Human PBMCs were
stimulated with single-stranded RNA oligoribonucleotides 1, 2, or the
siRNA duplex thereof (EGFP), which was composed of unmodified strands
(2/1), thymidine (2/1dT), 2⬘-deoxyuridine (2/1dU), 2⬘-O-methyluridine (2/
1mU), or 2⬘-O-methyladenosine (2/1mA) modification in the antisense
(leading) strand. IFN-␣ secretion was measured (n ⫽ 3, mean ⫾ SD).
ⴱ, p ⬍ 0.05 as compared with control sirna duplex 2/1. B, Human PBMCs
were stimulated with antisense RNA oligoribonucleotide 1. The indicated
modified RNA oligoribonucleotides also in antisense orientation were
added in equal concentrations. IFN-␣ secretion was measured (n ⫽ 3,
mean ⫾ SD). ⴱ, p ⬍ 0.05 as compared with control with addition of
unmodified RNA 1.
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strand 1 when applied alone. In contrast to the siRNA with thymidines (2/1dT), a siRNA composed of 2⬘-O-methyladenosines in
the antisense strand (2/1mA) was completely unable to induce
IFN-␣ secretion. This indicates that the adenosine-modified antisense strand 1mA suppressed the otherwise stimulatory sense
The Journal of Immunology
PBMCs were stimulated by simultaneous addition of modified and
unmodified strands, with both being in the antisense orientation
(Fig. 8B). The result confirmed that 2⬘-O-methyladenosine is a
residue that completely suppresses the immunostimulatory activity
of the unmodified strand (1ⴙ1mA), acting as a dominant antagonist. In contrast, thymidine-containing RNA strands affected stimulation by the unmodified strand (1ⴙ1dT) only slightly, behaving
as an immunological more “silent” agent. Again, for 2⬘-O-methyl
uridine-modified RNA (1ⴙ1mU), only a weak antagonistic activity was observed.
UV-melting curves reveal structure formation
Our data suggest that uridine residues are critical for immunostimulatory activity, as do data from the literature (9, 12, 34). Uridine residues also play pivotal roles in the formation of defined
three-dimensional structures. For example, they can form two hydrogen bond base pairs with both adenine and guanine (35). We
therefore asked whether the immunostimulatory sequence 1 shows
signs of forming base pairs. A solution of sequence 1 in PBS buffer
FIGURE 10. Secondary structure of target strand 1. Predicted structures for unimolecular folding (A) and dimerization (B) of
oligoribonucleotide 1, as calculated with
Mfold software (42). Sequences were entered, with or without the corresponding
pairing partner, together with the following
conditions: 142 nM of strand concentration
(1 ␮g/ml) and 150 mM of NaCl.
was subjected to UV-monitored thermal denaturation, which
yielded the melting curve shown in Fig. 9A. This curve exhibits
two sigmoidal transitions, one just below room temperature, and
one at ⬃50°C. This is in agreement with the predicted structures
for intramolecular folding and dimerization (Fig. 10), both of
which feature two duplex regions, either of which contains uridine
residues. Although the region of lower stability may no longer be
predominant at body temperature, it is energetically close enough
to be relevant for molecular recognition events. Thymidine-containing 1dT does not show a significant low temperature transition
(Fig. 9A), while the high temperature transition is essentially unchanged. This may be the consequence of the steric effect of the
methyl groups of the thymine residues.
We then performed UV-melting analyses for EGFP3s, a sequence that is not immunostimulatory and lacks uridine residues.
A much broader transition with significantly reduced overall hyperchromicity was obtained (Fig. 9B). Structure prediction algorithms do not detect a significant folding or dimerization propensity for EGFP3s, with no more than two nucleotides engaging in
forming base pairs (supporting information can be found online:
http://chip.chemie.uni-karlsruhe.de/sup_inf/). The appearance of
the absorbance vs temperature plot of this nonstimulatory sequence is fairly similar to that of poly(C), a homopolymer that
does not have the propensity to fold into well-defined structures at
neutral pH (Fig. 9B). Exploratory assay on the immunostimulatory
effect of eight other RNA sequences, combined with structure predictions, showed that all sequences with immunostimulatory activity have the propensity to form uridine-containing duplex/stem
regions with predicted melting points above body temperature
(37°C) (supporting information can be found online: http://
chip.chemie.uni-karlsruhe.de/sup_inf/). Although they are not the
focus of our current study, these results may stimulate additional
experiments on the structure-forming propensity of RNAi agents.
Discussion
The discovery that certain synthetic siRNA duplexes activate the
RNAi machinery without stimulating a rigorous IFN response in
mammalian cells (2) was considered a breakthrough for the development of RNAi-based therapeutics (36). Closer scrutiny revealed
that although injection of naked siRNA does not necessarily result
in systemic IFN induction in vivo (17), a combination with lipidor polycation-based delivery systems does produce side effects.
Certain siRNAs induce a prominent IFN response (18 –20, 28),
which seems to be due to activation of plasmacytoid dendritic cells
via TLRs (12, 16, 20, 37). Therefore, therapeutic siRNAs should
be (chemically) modified for clinical use to minimize immune activation (23); otherwise, siRNAs could share the fate of antisense
therapeutics, for which immunostimulation via TLR9 was recognized only during clinical trials as a complicating factor (5).
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FIGURE 9. UV-melting curves. Transitions of (A) 1 and 1dT and (B)
nonstimulatory EGFP3s (5⬘-GAGCAAAGACCCCAACGAGAAG-3⬘)
and poly(C) (control) in PBS buffer as detected at 260-nm wavelength. The
strand concentration was 3.5 ␮M for the oligoribonucleotides, and the
poly(C) concentration was adjusted to the corresponding nucleotide concentration (77 ␮M).
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3236
finding may be significant, as a functional TLR7 may be necessary
for defense against some viruses (8).
The lack of specificity of the RNAi machinery deserves comment. It has been reported previously that the 2⬘-OH in the ribose
backbone is not absolutely necessary for RNAi (22). Certain modifications in the leading antisense strand of a siRNA seem to be
tolerated, with 2⬘-fluoro derivatives performing better than their
2⬘-O-methyl counterparts (38). However, it was shown that modifications had to be restricted to certain regions of a siRNA, yet the
exact requirements differ for various modifications (39, 40). In
general, it is thought that modifications in the middle of the duplex
are not well tolerated, as this part is important for RISC activity
(41). For example, 2⬘-O-methyluridines in the leading (antisense)
strand of a siRNA are not tolerated, while the same modification in
the passenger strand is less problematic (27). Our results confirm
that 2⬘-O-methyladenosine and 2⬘-O-methyluridine modifications
in the leading strand of a siRNA, while not entirely detrimental,
lead to lowered gene-silencing activity. In contrast, the thymidinecontaining siRNAs are fully inhibitory, even when both strands are
modified. This conclusion held true for two additional siRNA sequences, suggesting a general principle. We observed that the thymidine-containing siRNAs are consistently more inhibitory than
are their 2⬘-deoxyuridine counterparts, possibly because their
methyl group slightly increased duplex stability.
Although these findings are valuable for the design of future
RNAi agents, they do not necessarily resolve the issue as to what
are the molecular details of the molecular recognition event(s)
leading to IFN-␣ secretion. It is too early to speculate on the structural basis of the sequence-specific molecular recognition event(s)
leading to the immunostimulatory activity of sequences such as 1,
and the lack thereof for compounds like 1dT. The following can be
stated without any doubts, however: 1) compound 1 does show
signs of structure formation in its UV-melting curve, 2) the low
temperature transition in this curve is significantly reduced for
1dT, and 3) uridine residues are involved in forming base pairs in
all sequences evaluated with structure prediction algorithms thus
far. Because defined three-dimensional structures are advantageous for selective molecular recognition (32), this finding may
not be accidental.
In summary, we have identified thymidine as a modification that
can be introduced into siRNA without affecting gene-silencing activity while inhibiting IFN-␣ secretion from cells of human blood.
An oligoribonucleotide with 2⬘-O-methyladenosines that lacks
TLR7 antagonistic activity was found to be an active inhibitor of
immunostimulation.
Disclosures
The authors have no financial conflicts of interest.
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