RNA interference: new tool,
ancient immune system
MNBTS 9000 lecture – Oslo – October 16th 2008
Torgeir Holen, CMBN and Institute for
Basal Medical Sciences (IMB), University of Oslo
1
29/05/2016
Lectures are online


folk.uio.no/torgeirh/transfer/
generell link til liste med verktøy:

folk.uio.no/torgeirh/fag.html
2
29/05/2016
Aims of this talk
Part I: To give a short introduction to the newly discovered
immune system RNA interference (RNAi) in various species
Part II: To look at some practical limitations to knocking
down mRNA gene expression by RNAi & siRNA, and some
recent solutions...
Part III: siRNA is already old hat – what’s going on now...?
short RNA : DNA/chromatin interactions...
3
29/05/2016
Part I: Gene silencing exist in
many multicellular organisms
roundworm
Petunias
Transgenic Petunias C. elegans
Transgenic potatoes
resist virus infection
fungus
Neurospora
4
fruitfly
Drosophila
29/05/2016
Gene silencing go back to the
earliest epochs of life on Earth

This ancient immune
system seems conserved
over 1.5 billion years
...thus we can learn about
different aspects of gene
and RNA silencing wherever
it is easiest... plants...
roundworms... flies...
human cell lines...
Wang, Kumar & Hedges, 1999
5
29/05/2016
A brief history of RNA silencing

1998: Andrew Fire and Craig Mello
show that double-stranded RNA
induce gene silencing in C. elegans
• 1999: Hamilton & Baulcombe find
small RNA where genes are silenced in
plants
• 2000: Greg Hannon and colleagues
isolate Dicer, the siRNA producing
RNase-III enzyme in Drosophila
• 2001: Thomas Tuschl and
colleagues show that synthetic
small
RNA
introduced

Nobel
Prize
2006 into human
cells can silence human genes
6
29/05/2016
7
29/05/2016
Plasmid produced siRNA
•Brummelkamp, 2002; Paddision, 2002; Miyahishi, 2002; Paul, 2002; Sui, 2002;
Lee, 2002; Jacque, 2002; Yu, 2002; Yang, 2002
8
29/05/2016
The PRK/interferon response




immune-system virus-response system in
mammalian cells
activated by long dsRNA
mechanism: shuts down all translation by by
phosphorylating eIF2-alpha (see Williams,
Oncogene, 1999)
the siRNA break-through of Thomas Tuschl
consisted of the PKR/interferon response not
being activated (Elbashir et al, Nature, 2001;
also shown by Natasha Caplen, PNAS, 2001)
9
29/05/2016
Part II: Limits to siRNA activity
- some other limitations to these great, but still new, tools
1.
siRNA exhibit position effects – some target positions superior to others
2.
siRNA activity fades out – in our case 3-4 days after transfection
3.
siRNA activity can be blocked by competition with less active siRNA
4.
Some siRNA have great tolerance for chemical modifications
5.
Some siRNA tolerate mutations
6.
Main problem of RNAi-field today: delivery, in vitro & in vivo
10
29/05/2016
Finding good target positions:
TF-luciferase-reporter assay
- Holen et al (Nucleic Acids Research, 2002).
- Tissue Factor (TF), is the principal coagulation trigger and
has been implicated in cardiac diseases. TF is also involved in
angiogenesis and metastasis of cancer.
Fusion Reporter Construct
...
TF (47-951)
LUC (37-2255)
pTRE
...





pTRE
hTF167i
5'-GCGCUUCAGGCACUACAAATT
TTCGCGAAGUCCGUGAUGUUU-5'
Fen1, Aqp4 and GlnS Constructs
pTRE
Fen1/Aqp4/GS
LUC (37-2255)
pTRE
...





...
11
29/05/2016
Why the position effects?
hTF562i
hTF478i
hTF372i
hTF167i
PSK314i
HeLa
mRNA
AGGUGGCCGGCGCUUCAGGCACUACAAAUACUGUGGC
hTF158i
AGGUGGCCGGCGCUUCAGGTT
hTF161i
UGGCCGGCGCUUCAGGCACTT
hTF164i
CCGGCGCUUCAGGCACUACTT
hTF167i
hTF562i
hTF478i
hTF372i
hTF167i
PSK314i
293
GCGCUUCAGGCACUACAAATT
hTF170i
CUUCAGGCACUACAAAUACTT
hTF173i
CAGGCACUACAAAUACUGUTT
hTF176i
hTF562i
hTF478i
hTF372i
hTF167i
PSK314i
GCACUACAAAUACUGUGGCTT
Cos-1
Cotransfections with siRNAs targeting sites around hTF167
hTF929i
hTF562i
hTF478i
hTF459i
hTF372i
hTF256i
hTF167i
hTF77i
PSK739i
PSK566i
PSK546i
PSK314i
HaCaT
TF-LUC/RLUC
Normalised
Re lativ e hTF-Fluc/Rluc
120
100
80
60
40
20
0
PSK314i
20
40
60
80
hTF158i
hTF161i
hTF164i
hTF167i
hTF170i
hTF173i
100 120 140
Normalised TF-LUC/RLUC
12
29/05/2016
hTF176i
Knock-downs must be verified...
PSK739i
PSK566i
PSK546i
PSK314i
hTF562i
hTF478i
hTF372i
hTF167i
mock
- position effect consistent also in Northern assays, protein
assays and coagulation assays…
Inhibition of TF mRNA, procoagulant activity
Protein
&andCoagulation
antigen by siRNA
TF
GAPDH
TF
hTF176i
hTF173i
hTF170i
hTF167i
hTF164i
hTF161i
hTF158i
mock
Northerns
Normalised TF expression
120
100
80
mRNA
procoag
antigen
60
40
20
0
mock
hTF167i
hTF372i
PSK314i
Legend: mRNA (filled bars), procoagulant activity
(dotted bars) and TF protein (hatched bars)
GAPDH
13
29/05/2016
Some computational solutions
to position effects:







Khvorova, Cell, 2003: 5’end of active antisense
unstable...
Ui-Tei et al, Nucleic Acids Research, 2004:
(i) A/U at the 5' end of the antisense strand
(ii) G/C at the 5' end of the sense strand
(iii) at least five A/U residues in the 5' terminal one-third of the
antisense strand
Holen, RNA, 2006 - siRNArules 1.0 - open source software for
siRNA predictions - free download
also, several commercial companies provide in-house service as
part of siRNA design and sale
14
29/05/2016
RNAi silencing sets in
slowly…
…why?
Normalised TF expression
Normalised TF/GAPDH mRNA
Time-dependence of hTF167i effect
100
procoag
80
mRNA
60
LUC
40
20
0
48 h
72 h
96 h
120 h
Measurements at 4 h, 8 h, 24 h, 48 h
…and fades out even more slowly,
but steadily…
15
29/05/2016
Tolerance for chemical modifications
P1+1
5’-g*c-gcuucaggcacuaca-a-a-u*a-3’
3’-g*c-c-g-cgaaguccgugaugu-u*u-5’
P0+2
5’-g-c-gcuucaggcacuaca-a-a*u*a-3’
3’-g*c*c-g-cgaaguccgugaugu-u-u-5’
P2+2
5’-g*c*gcuucaggcacuaca-a-a*u*a-3’
3’-g*c*c-g-cgaaguccgugaugu*u*u-5’
P2+4
5’-g*c*gcuucaggcacuaca*a*a*u*a-3’
3’-g*c*c*g*cgaaguccgugaugu*u*u-5’
M1+1
5’-GcgcuucaggcacuacaaauA-3’
3’-GccgcgaaguccgugauguuU-5’
M0+2
5’-gcgcuucaggcacuacaaaUA-3’
3’-GCcgcgaaguccgugauguuu-5’
M2+2
5’-GCgcuucaggcacuacaaaUA-3’
3’-GCcgcgaaguccgugauguUU-5’
M2+4
5’-GCgcuucaggcacuacaAAUA-3’
3’-GCCGcgaaguccgugauguUU-5’
Normalized TF/GAPDH mRNA
Normalised TF/GAPDH mRNA
120
100
80
60
40
20
0
mock
wt
A1+1
5’-GcgcuucaggcacuacaaauA-3’
3’-GccgcgaaguccgugauguuU-5’
A0+2
5’-gcgcuucaggcacuacaaaUA-3’
3’-GCcgcgaaguccgugauguuu-5’
P1+1 P0+2 M1+1 M0+2 A1+1 A0+2
P2+2 P2+4 M2+2 M2+4
16
29/05/2016
Pre-clinical studies by Alnylam Inc:
Inhibition of cholesterol synthesis
by siRNA



"...Administration of chemically modified siRNAs
resulted in silencing of the apoB messenger RNA in
liver and jejunum, decreased plasma levels of apoB
protein, and reduced total cholesterol. "
Soutschek et al, Nature, 2004
"RNAi-mediated gene silencing in non-human
primates", Zimmermann et al, Nature, 2006
John et al, Nature, 2007
17
29/05/2016
siRNA against macular
degeneration (blindness) in eye
siRNA
Vitravene (ISIS Pharmaceuticals), anti-sense drug
18
29/05/2016
developed against late-stage HIV opportunistic
infections
Several siRNAs against VEGF
and VEGFR in clinical trials





Sirna-027
- Sirna Inc.
Cand5
- Acuity Inc
bevasiranib
- OPKO Ophthalmics
...much secrecy in drug development
However, Toll-like receptors show new pathway:
"Sequence- and target-independent angiogenesis
suppression by siRNA via TLR3", Kleinman,
Nature, 2008
19
29/05/2016
An siRNA mutation study
**** * ** * *
5'-GCGCUUCAGGCACUACAAAUA
GCCGCGAAGUCCGUGAUGUUU-5'
Normalized
TF/GAPDH mRNA
mRNA
TF/GAPDH
Normalised
120
100
80
60
40
20
s1
6
s1
3
s1
1
s1
0
s7
s4
s3
s2
s1
t
w
ds
7/
1
ds 0
10
/1
ds 1
10
/1
ds 3
10
/1
6
m
oc
k
0
Amarzguioui M, Holen T, Babaie E, Prydz H. Tolerance for
mutations and chemical modifications in a siRNA. Nucleic
Acids Res. 2003 Jan 15;31(2):589-95.
20
29/05/2016
Other genes possibly
targeted by laminB2
CLSTN2
5'-AAGAGGAGGAAGAAGCCGAGG-3'
|||||||||| |||||||||
3'-UUCUCCUCCUCCUUCGGCUCA-5'
HS6ST3
5'-AAGAGGAGGAGGAAGACGAGC-3'
||||||||||||||| ||||
3'-UUCUCCUCCUCCUUCGGCUCA-5'
NM_015897
5'-AAGAGGAGGAGGAAGACGAGG-3'
||||||||||||||| ||||
3'-UUCUCCUCCUCCUUCGGCUCA-5'
The dangers of siRNA in
functional genomics:
“…the two other lamins, B1 and B2,
are now identified as essential
proteins” (Harborth et al, JCS, 2001)
NM_015355
5'-ACUCGGCCUCCUCCUCCUCCU-3'
||||||| ||||||||||| |
3'-UGAGCCGAAGGAGGAGGAGAA-5'
ATBF1
5'-AAGAGGAGGAGGAAGACGAGG-3'
||||||||||||||| ||||
3'-UUCUCCUCCUCCUUCGGCUCA-5'
SPTB
5'-AAGAGGAGGAGGAAACAGAGU-3'
|||||||||||||| | ||||
3'-UUCUCCUCCUCCUUCGGCUCA-5'
21
29/05/2016
The delivery problem
- comparing different transfection agents
Lipofectamine2000, Lipofectamine, Oligofectamine and RNAifect…
140
120
100
80
60
40
20
as
-1
6
hT 7
F1
67
as
-P
i
SK
41
1
as
-1
6
hT 7
F1
67
as
-P
i
SK
41
1
as
-1
6
hT 7
F1
67
as
-P
i
SK
41
1
as
-1
6
hT 7
F1
67
as
-P
i
SK
41
1
0
22
29/05/2016
Indirect delivery in vivo
- Tissue Factor in cancer metastasis
Day 10

Day 15
set-up: metastatic B16 cells transfected
with siRNA against TF, then injected into
tail-vein of mice
tumors will then colonize lungs of mouse
mTF223i
D
mTF223i
hTF167i

mock
hTF167i
mTF
GAP
Day 20
mTF321i
mTF223i
hTF167i
23
Mohammed Amarzguioui, Qian
Peng, Torgeir Holen, Vlada
Vasovic, Eshrat Babaie, Jahn
29/05/2016
M. Nesland
& Hans Prydz
RNAi delivery by virus




Lentiviruses delivery especially interesting for
delivery to neuronal cells.
An et al, Human Gene Theraphy, 2003
Stewart et al, RNA, 2003
Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li
M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L,
Scobie K, Chang K, Westbrook T, Cleary M,
Sachidanandam R, McCombie WR, Elledge SJ,
Hannon GJ. A resource for large-scale RNAinterference-based screens in mammals.
Nature. 2004 Mar 25;428(6981):427-31.
24
29/05/2016
Hippocampal cultures
15
hours
post-plating
cultures
2 days
become
post-plating
very dense and opaque25
29/05/2016
Lentiviral labeling with GFP show
individual cells to be stable up to 35 days
day 23
26
29/05/2016
Regulatable knock-downs
What of it? Can’t the Cre/LoxP system or other
conditional knock-outs do the same?

From Matsukura et al (Nucleic Acids Research, 2003)

27
also see Moe,
Sorbo & Holen, J
Neuroscience
Methods, 2008
29/05/2016
The usefulness of siRNA
- a short summary of the pitfalls - repetition
1.
siRNA exhibit position effects – some target positions superior to others
2.
siRNA activity fades out – in our case 3-4 days after transfection
3.
siRNA activity can be blocked by competition with less active siRNA
4.
Some siRNA have great tolerance for chemical modifications
5.
Some siRNA tolerate mutations
6.
1.
The common theme: if siRNAs tolerate mismatches in relation to the
mRNA target, then similar, random targets in other mRNA are at risk
2.
Early studies: 3’ overhang mismatch tolerance & central mutations
3.
Screening disruptive G:C mutations: some positions more vulnerable than
others...
4.
What are the general consequences for the thousands of siRNA now in
common use? Can off-target hits be avoided? Some conclusions from a
bioinformatic study… some musings on micro-arrays
Some recent data from three new studies on mutations
28
29/05/2016
29
29/05/2016