16 Design of Trans-Splicing Adeno-Associated Viral Vectors

16
Design of Trans-Splicing Adeno-Associated Viral Vectors
for Duchenne Muscular Dystrophy Gene Therapy
Yi Lai, Dejia Li, Yongping Yue, and Dongsheng Duan
Summary
The development of trans-splicing vectors opens the door for delivering a large therapeutic gene with adeno-associated viral vectors (AAV). One potential application is to
deliver the 6 kb mini-dystrophin gene for Duchenne muscular dystrophy (DMD) gene
therapy. However, early attempts have been very disappointing because of low transduction efficiency. We have recently identified mRNA accumulation as a critical barrier
for the trans-splicing AAV vectors. This barrier can be overcome by rational selection of
the gene splitting site. Here we outline a detailed RNase protection assay-based strategy
to determine the optimal gene splitting site for the mini-dystrophin gene. We also provide
methods to evaluate transduction efficiency of the mini-dystrophin trans-splicing vectors
in mdx mouse, a model for DMD.
Key Words: AAV; adeno-associated virus; Duchenne muscular
dystrophin; mini-dystrophin; trans-splicing; gene therapy; muscle; mdx.
dystrophy;
1. Introduction
Duchenne muscular dystrophy (DMD) is the most common lethal childhood
muscle-wasting disease affecting all body muscles. It is caused by mutations
in the dystrophin gene. Current treatment can only alleviate certain symptoms
but cannot cure the disease. An ultimate solution to DMD requires replacing
the mutated dystrophin gene with a functional gene. To achieve this goal, one
needs to have a vehicle that can efficiently deliver a therapeutic gene to all
muscles in the body. Adeno-associated viral vector (AAV) seems an ideal tool
From: Methods in Molecular Biology, vol. 433: Volume 1: Production and In Vivo Applications
of Gene Transfer Vectors
Edited by: J. M. Le Doux © Humana Press, Totowa, NJ
259
260
Lai et al.
because it readily transduces muscle fibers either by direct muscle injection
or through systemic delivery. The challenge with AAV-mediated DMD gene
therapy lies in the small viral packaging capacity.
Wild type AAV carries a ∼4.7 kb single-stranded DNA genome. It contains
two flanking inverted terminal repeats (ITRs) at the ends and two internal open
reading frames encoding viral capsid (cap gene) and replication proteins (rep
gene), respectively. In a recombinant vector, cap and rep genes can be replaced
by a reporter and/or therapeutic expression cassette. This dictates a ≤5 kb vector
genome size for an AAV vector. The full-length dystrophin protein is 427 kD
and contains the N-terminal, central rod, cysteine-rich, and C-terminal domains.
It is encoded in an 11.6 kb coding sequence. Apparently, this exceeds the
packaging capacity of a single AAV virion. To solve this problem, investigators
have developed the mini- and micro-dystrophin genes (see Fig. 1A) (1,2). The
microgenes are less than 4 kb and do not carry the C-terminal domain. They
Fig. 1. Dystrophin isoform structure and the effect of the gene splitting site on
mRNA accumulation in mini-dystrophin. (A) Schematic outline of the full-length,
micro- and mini-dystrophin proteins. Four functional domains in the full-length protein
are the N-terminal domain (N), the rod domain (including 24 spectrin-like repeats and
four hinges, H1 to H4), the cysteine-rich domain (CR) and the C-terminal domain.
Regions that are deleted in micro- and mini-dystrophins are shown as white boxes.
Specific force data are derived from Harper et al. (2002) Nat Med (2) (B) Relative
mRNA levels according to RPA results from the mini-cassette depicted in Fig. 2B.
The data are derived from Lai et al. (2005) Nat Biotech (7). The cartoon on the top of
the panel B depicts the exon/intron/exon junctions where the minigene is split in each
pair of the trans-splicing vectors. The dotted lines refer to the corresponding locations
in the rod domain.
Trans-Splice the Dystrophin Gene
261
can fit into a single AAV vector but cannot restore specific force to the normal
level (2). The 6 kb minigene is an optimized version of a truncated, but fairly
functional human dystrophin gene (3). It contains all the functional domains of
the full-length protein. The original gene is capable of supporting daily activity
in a 60-year-old patient (3). The optimized gene performed even better than
the original gene, and it resulted in a muscle-specific force indistinguishable
from that of wildtype mice (2,4). Efficient delivering of the 6 kb minigene with
AAV vector may lead to a cure to DMD.
The trans-splicing dual vector approach effectively doubles the AAV
packaging capacity and raises the hope of delivering the 6 kb minigene with
AAV vector (5–7). In this context trans -splicing is defined as the reconstruction of an intact transcript by splicing in “trans” between two covalently
linked vector genomes each carrying a part of the transgene (see Fig. 2).
This approach stems from a unique feature in AAV transduction biology.
After entering cells, viral genomes form head-to-tail concatamers through ITRmediated recombination. By taking advantage of cellular splicing machinery,
one can engineer splicing signals at the viral genome junction to remove
the noncoding component at the junction and restore a functional expression
cassette (see Fig. 2). The trans-splicing system is composed of two vectors.
Fig. 2. Trans-splicing AAV-mediated expression of the mini-dystrophin gene. (A)
Schematic outline of the transgene reconstitution in mini-dystrophin trans-splicing
vectors. (B) The mini-cassette used in RPA to screen for the best gene splitting site.
The dotted boxes in panels A and B represent the same region. SD, splicing donor;
SA, splicing acceptor; ITR, AAV inverted terminal repeat; dD-ITR, the double D ITR
structure formed in recombination.
262
Lai et al.
An AV.Donor vector carries the promoter, the 5´ transgene, and the splicing
donor signal. An AV.Acceptor vector carries the splicing acceptor signal, the
3´ transgene, and the polyA sequence.
Successful transduction of the trans-splicing vectors depends on efficient
co-infection of AV.Donor and AV.Acceptor, efficient viral genome recombination, and mRNA production from the reconstituted genome. We have
previously demonstrated that co-infection is not a barrier. However, mRNA
accumulation represents a predominant rate-limiting step (8). On the basis of
this observation, we have developed an RNase-protection assay (RPA)-based
screening strategy to rationally design the trans-splicing vectors for the 6 kb
minigene. Using the conserved splicing value as a guide, we have analyzed
a series of potential gene splitting sites in the mini-dystrophin gene. Our
screening has yielded a pair of extremely efficient minigene trans-splicing
vectors. This pair of vectors is based on splitting the gene at endogenous intron
60. Their transduction efficiency has reached that of a single AAV vector
(see Fig. 3).
In this protocol, we outline the procedures used in screening the gene splitting
site, generating the mini-dystrophin trans-splicing vectors, and confirming
mini-dystrophin expression in the mdx mouse model of DMD.
Fig. 3. Transduction efficiency of the intron 60 trans-splicing vectors reaches that
of the single intact vector. (A) Representative photomicrographs of the mdx EDL
muscles infected by AV.Micro-dys (single intact vector). (B) Representative photomicrographs of the mdx EDL muscles co-infected by AV.Mini-dys.Donor and AV.Minidys.Acceptor (the intron 60 trans-splicing vectors). (C) Quantitative comparison of the
transduction efficiency of the single intact vector and the trans-splicing vectors. Data
are means ± standard error of mean. N = 8 for AV.Micro-dys infection; N =15 for
trans-splicing vector infection; p = 0.43.
Trans-Splice the Dystrophin Gene
263
2. Materials
2.1. Generating the Mini-dystrophin Trans-Splicing Vectors
2.1.1. Selection of the Potential Gene Splitting Sites
There is no special material needed besides the dystrophin gene sequence
itself.
2.1.2. RPA-Mediated Screening of the Potential Gene Splitting Site
1. 293 cells (ATCC). This is an adenovirus E1 gene transformed human kidney
cell line. They are used as a packaging cell line for recombinant AAV
production. These cells are propagated in high-glucose Dulbecco’s modified
Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and 1%
penicillin G/streptomycin (see below).
2. Cell culture medium: DMEM, high glucose with l-glutamine (Gibco-BRL,
Grand Island, NY, USA). Store at 4 ºC.
3. FBS (Hyclone). Store at –20 ºC.
4. Penicillin G-Streptomycin: Penicillin 100 U/ml DMEM culture medium and
Streptomycin 100 μg/ml DMEM culture medium (Gibco-BRL). Store at
–20 ºC.
5. 1× Trypsin–EDTA: 0.25% Trypsin, 1 mM EDTA/4Na (Gibco-BRL). Store at 4 ºC.
6. Lipofectamine and Plus reagent (Invitrogen, Carlsbad, CA, USA).
7. Mini-dystrophin gene plasmid pH2-R19. This plasmid is obtained from Dr.
Jeffrey Chamberlain (University of Washington, Seattle, WA, USA).
8. pcDNA3.1(+) (Invitrogen).
9. pGL3-control (Promega, Madison, WI, USA).
10. pGEM3Z (Promega).
11. pTRI--actin-human antisense control template (Ambion, Austin, TX, USA).
12. Guanidine isothiocyanate (Amresco, Solon, OH, USA).
13. Cesium chloride (Research Products International Corp, Mount. Prospect, IL,
USA).
14. SP6 RNA polymerase (Invitrogen).
15. RNasin (RNase inhibitor, Roche Applied Science, Indianapolis, IN, USA).
16. 5 mM rNTP (Amersham Pharmacia, Piscataway, NJ, USA).
17. P32 rUTP (Perkin Elmer, Boston, MA, USA).
18. Vanadyl Ribonucleoside complex (VRC) (Gibco-BRL), an RNase inhibitor used
during anti-sense RNA probe purification.
19. RQ1 DNase (Promega) to remove the DNA template after RNA probe is
generated from in vitro transcription.
20. tRNA (Sigma).
21. RNase A (Roche Applied Science).
22. RNase T1 (Roche Applied Science).
264
Lai et al.
2.1.3. Generating the cis-Plasmids for Recombinant AAV Packaging
1. Vent DNA Polymerase (New England Biolabs): This is a high-fidelity
thermophilic DNA polymerase. It has a low polymerase chain reaction (PCR)related mutation rate.
2. Electroporation-competent Escherichia coli SURE cells (Stratagene, LA Jolla,
CA, USA): AAV ITRs can be rearranged or deleted by endogenous DNA repair
systems when they are propagated in bacterial cells. SURE cells are defective
in DNA repair and recombination pathways (such as uvrC, umuC, SbcC, RecJ,
recB, and recJ). Store at –80 ºC.
3. E. coli Pulser (Bio-Rad).
4. Gene Pulser cuvets, 0.1 cm gap (Bio-Rad).
5. 14-ml polypropylene round-bottomed tubes (Becton Dickinson Labware, Franklin
Lakes, NJ, USA).
6. S.O.C. medium (Gibco-BRL). Store at room temperature.
7. Amp selection LB agar plates (100 μg/ml, Ampicillin). Store at 4 ºC.
8. Standard materials for large-scale plasmid preparation. To achieve the best transfection efficiency for AAV production, we recommend preparing the plasmids by
CsCl2 /ethidium bromide equilibrium centrifugation.
2.1.4. Recombinant AAV-6 Production
1. Adenoviral helper plasmid: (pHelper, Stratagene).
2. Helper plasmid for AAV-2 rep gene (pMT-Rep2): This plasmid provides the
Rep gene required for recombinant AAV replication and packaging (9). AAV2 rep proteins can fully support AAV-6 production. This plasmid is obtained
from Dr. A. Dusty Miller (Fred Hutchinson Cancer Research Center, Seattle,
WA, USA).
3. Helper plasmid for AAV-6 capsids (pCMVCap6): This plasmid provides the
Cap gene required for rAAV-6 packaging (9). This plasmid is obtained from
Dr. A. Dusty Miller (Fred Hutchinson Cancer Research Center).
4. 2.5 M CaCl2 . Sterilize by filtration and store at –20 ºC.
5. 2× HBS buffer: 0.3 M NaCl, 1.5 mM Na2 HPO4 , and 40 mM HEPES, pH
7.05 ± 0.05. Sterilize by filtration and store at –20 ºC. As pH affects transduction efficiency, it is highly suggested to double check pH before each
usage.
6. DNase I (Sigma, 11 mg protein/vial, total 33 K [kuniz] units).
7. 0.25% Trypsin (Gibco-BRL). Store at 4 ºC.
8. 10% Sodium deoxycholate. Store at room temperature.
9. Misonic Cell Disruptor S3000 (Misonix, NY).
10. Cell lifter (Corning Incorporated, Corning, NY, USA).
11. HEPES AAV dialysis buffer: 20 mM HEPES, 150 mM NaCl, pH 7.8. Filtersterilize and store at 4 ºC.
12. Dialysis tubing: 12,000 MW cutoffs (Gibco-BRL). Store at 4 ºC.
13. AAV digestion buffer: 0.4 M NaOH, 20 mM EDTA. Freshly made before use.
Trans-Splice the Dystrophin Gene
265
14. Slot blot hybridization solution [5× SSC, 5× Denhardts’s solution, 1% sodium
dodecyl sulfate (SDS), and 50 % formamide, add 100 μg/ml denatured salmon
sperm DNA just before use].
15. HiTrap heparin column (Amersham).
2.2. In Vivo Evaluation of the Mini-Dystrophin Trans-Splicing Vectors
2.2.1. Local Muscle Injection
Two-month-old dystrophin-null mdx mice (C57BL/10ScSn-Dmdmdx/J; The
Jackson Laboratory). Dystrophin expression is aborted in this inbreed strain
because of a nonsense mutation in exon 23 (10,11). (see Note 1).
1. Anesthetic reagents and instruments for local muscle injection: 4 μl/g body
weight anesthetic cocktail (ketamine 25 mg/ml, xylazine 2.5mg/ml, acepromazine
0.5mg/ml in physiological saline). Sterile forceps and scissors (World Precision
Instruments, Inc., Sarasota, FL, USA), needle holders (Accurate Surgical & Scientific Instruments Corp., Westbury, NY, USA) and Guthrie double hook retractor
(Fine Science Tools, Inc., Foster City, CA, USA). 5-0 sofsilk suture (Auto Suture
Company, Norwalk, CT, USA). 33G gas-tight Hamilton syringe and needle
(Hamilton Company Reno, NV, USA).
2. Polyethylene mouse Elizabethan collar (E-collar, Harvard Apparatus).
3. Banamine (also called Flunixin, 1.5 mg/kg) (Schering-Plough Animal Health
Corp., Union, NJ, USA)
2.2.2. Quantifying Mini-Dystrophin Expression by Western Blot
1. Muscle homogenization solution: 20 mM Na4 P2 O4 , 20 mM NaHPO4 , 1 mM
MgCl2 , 0.5 mM EDTA, and 303 mM sucrose.
2. Muscle microsome preparation wash buffer: 20 mM Tris–HCl (pH 7.0), 60 mM
KCl, 303 mM sucrose.
3. Muscle microsome storage solution: 20 mM Tris–HCl (pH 7.0) and 303 mM
sucrose.
4. Cheese-cloth (Fisher Scientific, Pittsburgh, PA, USA).
5. Tissue-Tek OCT compound (Sakura Finetek Inc., Torrance, CA, USA).
2.2.3. Quantifying Mini-Dystrophin Expression by Immunostaining
1. Mouse monoclonal antibodies for different regions of the dystrophin protein:
Dys-3 (clone Dy10/12B2, IgG2a), an antibody that specifically recognizes the
hinge 1 region of human dystrophin (Novocastra, Newcastle, UK). Dys-2 (clone
Dy8/6C5, IgG1), an antibody that reacts with the dystrophin C-terminal domain
(Novocastra). Mandys-8 (clone 8H11, IgG2b), an antibody that specifically
recognizes spectrin-like repeat 11 (exon 32) (Sigma) (see Note 2).
2. Polyclonal antibodies for different regions of the dystrophin protein: rabbit
anti-dystrophin N-terminal antibody, an affinity-purified antibody obtained from
266
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
Lai et al.
Dr. Jeffrey Chamberlain’s laboratory (University of Washington, Seattle, WA,
USA). Goat anti-dystrophin C-terminal antibody (Santa Cruz). Rabbit antidystrophin spectrin-like repeat 4–6 antibody (Santa Cruz).
2-methylbutane (Sigma).
Tissue-Tek OCT (Sakura Finetek Inc., USA).
Rabbit anti-mouse IgG (Sigma, final concentration 0.46 mg/ml).
Papain (Sigma, final concentration 45 μg/ml).
L-cystein (Sigma, final concentration 22 mM).
Iodoacetic acid (Sigma, final concentration 10 mM).
20% rabbit serum (Jackson ImmunoResearch Laboratories, Inc.).
Alex 488 conjugated rabbit anti-mouse antibodies (Molecular Probe).
Alex 594 conjugated rabbit anti-mouse antibodies (Molecular Probe).
KPBS: 356 μM KH2 PO4 , 1.64 mM K2 HPO4 , 160 mM NaCl.
Gelatin (Sigma).
M.O.M kit (Vector Laboratories, Inc.).
3. Methods
3.1. Generating the Mini-dystrophin Trans-Splicing Vectors
3.1.1. Selection of the Potential Gene Splitting Sites
There are several considerations when deciding on the potential sites to split
the mini-dystrophin gene. These include the size of the individual vector, the
gene structure, and the relative efficiency of transcription and splicing. Specifically, both AV.Donor and AV.Acceptor have to fit into a single AAV virion
themselves, respectively; the minigene should be split at a natural exon/exon
junction rather than within an exon; and the site should yield the highest level
of mRNA in the context of a reconstituted/recombined viral genome.
1. Preliminary selection of the gene splitting site according to the size constraint of
a single AAV virion. There are a total of 79 exons in the full-length dystrophin
gene. However, the minigene only contains the coding sequence from 44 exons.
The 5´ half of the minigene is ∼2.2 kb (exon 1 to the beginning of exon 17)
spanning the region from the N-terminus to repeat 3. The 3´ half of the minigene
is ∼3.8 kb (the end of exon 49 to the beginning of exon 79) covering the region
from hinge 3 to the C-terminus. Considering the size of the ITR (two ITRs,
total ∼0.3 kb), the CMV promoter (∼0.6 kb), the pA signal (∼0.4 kb), and the
splicing signals (∼ 0.3 kb), any exon boundary between exons 51 and 65 would
be appropriate to divide the minigene.
2. Preliminary screening of the gene splitting site according to the conserved splicing
value in the wildtype dystrophin gene. Sironi et al. (12) has systematically calculated the conserved splicing value (CV) and U1 small nuclear RNA binding
energy for all the exon/intron/exon junctions in the dystrophin gene (see Note 3).
The mean CVs for the 5´ and 3´ splicing sites are (0.83 ± 0.07) and (0.87 ± 0.09),
Trans-Splice the Dystrophin Gene
267
respectively. The mean binding energy is –7.76 ± 2.21 kcal/mole (12). We selected
three sites that have the highest CV and lowest binding energy as potential sites
for gene splitting. These are 56/56/57 (exon/intron/exon), 60/60/61, and 63/63/64
junctions. Their respective CVs and binding energy are (in the order of 5´ splicing
site CV, 3´ splicing site CV, and binding energy) 0.84. 0.97, and –10.4 kcal/mole
(for the 56/56/57 junction), 0.94, 0.98, and –11.7 kcal/mole (for the 60/60/61
junction), and 0.95, 0.90, and –10.6 kcal/mole (for the 63/63/64 junction). As a
control, we also selected the 53/53/54 junction, which has an average binding
energy (–7.7 kcal/mole) and moderate CVs (0.90 and 0.60 for the 5´ and 3´
splicing sites, respectively).
3.1.2. RPA-Mediated Screening of the Potential Gene Splitting Site
Formation of the double-D ITR structure is a unique feature in the recombined AAV genome (13). Importantly, the double-D ITR structure in intron
down-regulates mRNA accumulation (8). An ideal gene splitting site should
yield the highest level of mRNA in the presence of the double-D ITR structure.
To identify the best site, we constructed a series of mini-cassettes to mold
the reconstituted vector genome. An RPA assay was then used to quantify the
relative level of mRNA accumulation (see Fig. 2).
1. Cloning the endogenous dystrophin intron splicing signal from a human
cell line. Use 293 cell genomic DNA as the PCR template. Design the
primers to amplify the exon/intron junctions. The primer sequences for each
junction can be found in the online supplementary material in Lai et al.
(http://www.nature.com/nbt/journal/v23/n11/suppinfo/nbt1153_S1.html) (7). To
facilitate subsequent cloning, include restriction site overhangs in the primers as
needed (see Note 4).
2. Reconstituting the mini-cassette in the backbone of pcDNA3.1(+). First, introduce
the respective exon/intron junctions in pcDNA3.1(+). For the 53/53/54 junction,
insert the splicing donor between the Kpn I/BamH I sites and insert the splicing
acceptor between the Xho I/Xba I sites. For the 56/56/57 junction, insert the
splicing donor between the Hind III/Kpn I sites and insert the splicing acceptor
between the EcoR V/Xba I site. For the 60/60/63 junction, insert the splicing
donor between the Kpn I/BamH I sites and insert the splicing acceptor between
the Xho I/Xba I sites. For the 63/63/64 junction, insert the splicing donor between
the Hind III/Kpn I sites and insert the splicing acceptor between the Xho I/Xba
I sites. After inserting splicing signals, clone the double-D ITR structure in the
intron region between the EcoR I/EcoR V sites (see Fig. 2B).
3. Generating the RPA probe. To quantify both spliced and unspliced RNA products,
generate an anti-sense RNA probe for each potential site to hybridize with the
respective 5´ exon and the intron donor sequence (see Fig. 2B). Then insert
the PCR products into the EcoR I/BamH I sites in pGEM3Z accordingly. After
linearization at the EcoR I site, synthesize the RPA probes by in vitro transcription
with SP6 RNA polymerase and [-32 P]-rUTP as the substrate (7,8).
268
Lai et al.
4. RPA screening. Co-transfect the plasmids carrying the mini-cassette (4 μg) and
a transfection control plasmid (0.5 μg; we used a luciferase plasmid pDD12. In
this plasmid, the entire expression cassette from pGL3-control (Promega) was
cloned into an AAV packaging plasmid) into 70–80% confluent 293 cells using
Lipofectamine and Plus reagent (Invitrogen). About 48 h later, extract protein
from one-fifth cells for luciferase assay to normalize transfection efficiency. Lyse
remaining cells in 4 M guanidine isothiocyanate and extract total RNA in 5.7 M
CsCl2 by ultra-centrifugation at the speed of 116,200 × g for at least 12 h at 20 ºC.
In each RPA reaction, use10 μg total RNA to hybridize with excessive amount
of 32 P-labeled probe and digest unprotected RNA by RNaseT1 (0.923 μg/ml) and
RNaseA (at 18.46 μg/ml). Elecctrophorese the reaction products in 8% denaturing
polyacrylamide gel and quantify the bands with the Molecular Imager FX and
Quantity One (version 4.2.2 image software; Bio-Rad, Heracules, CA). Normalize
the RPA reaction with endogenous human -actin using an independent probe
generated from pTRI--actin-human antisense. Normalize RNA signal intensity
by transfection efficiency, RPA reaction and the number of 32 P-labeled uridine in
each protected band. The 60/60/61 junction produces the highest level of mRNA
and the 63/63/64 junction is the second best (∼50% of that from the 60/60/61
junction) (see Fig. 1B).
3.1.3. Generating the cis -Plasmids for Recombinant AAV Packaging
Generate two pairs of the trans-splicing plasmids representing gene splitting
sites at the 60/60/61 and the 63/63/64 junctions, respectively. Each pair includes
a cis-donor plasmid and a cis-acceptor plasmid. To facilitate comparison,
both pairs are under transcriptional regulation of the CMV promoter and
the SV40 polyA. Use standard molecular cloning methods to generate these
constructs. The detailed step-by-step cloning procedure can be found in the
online supplementary material in Lai et al. (http://www.nature.com/nbt/journal/
v23/n11/suppinfo/nbt1153_S1.html) (7).
3.1.4. Recombinant AAV-6 Production see Notes 5 and 6
.
1. Two days before viral production, split 293 cells at 1:6 to 150 mm culture plates.
Seed a total of 15 plates for one production. Change to fresh culture media about
1–2 h before transfection.
2. Preparing DNA-calcium-phosphate precipitate. Co-transfect four plasmids to
make AAV-6 vector. These include the cis-plasmid, pMT-Rep2, pCMVCap6, and
pHelper. For each vector preparation (15 × 150 mm plates), use 187.5 μg of the
cis-plasmid, 187.5 μg pMT-Rep2, 562.5 μg pCMVCap6, and 562.5 μg pHelper
(at a ratio of 1:1:3:3). Mix all plasmids thoroughly in 15.2 ml H2 O. Add 1.68
ml of 2.5 M CaCl2 to a final concentration of 250 mM. Generate DNA-calciumphosphate precipitate by slowly dropping the DNA/CaCl2 mixture to 16.8 ml of
Trans-Splice the Dystrophin Gene
3.
4.
5.
6.
7.
8.
9.
269
2× HBS. In general, it takes 15–30 min room temperature incubation to form a
high quality precipitate (see Note 7).
Gently apply the DNA-calcium-phosphate precipitate to 293 cells drop-by-drop
while swirling the culture plate.
At 72 h after transfection, collect cell lysate with a cell lifter. After a 20 min spin
in a bench-top centrifuge (1,800 × g at 4 ºC), resuspend cell pellet in 9 ml of 10
mM Tris–HCl (pH 8.0). Freeze/thaw cell lysate 8–10 times using dry ice/ethanol
and a 40 ºC water bath. Sonicate cell lysate at the power output of 5.5 for 10
min (on ice). Digest cell lysate with DNase I at 37 ºC for 45 min (we normally
use half vial of Sigma DNase I for each 15 plates viral preparation). Sonicate
cell lysate again at the power output of 5.5 for 7 min (on ice). Digest lysate with
one-tenth volume of 0.05% trypsin and 10% sodium deoxycholate for 30 min at
37 ºC. Clear cell lysate by spinning at 3,200 × g for 30 min at 4 ºC. Carefully
transfer supernatant to a new tube.
Adjust the volume to 29 ml with 10 mM Tris–HCl (pH 8.0) and add 18.2 g CsCl2
(this is equal to 0.613 g/ml). The final volume should be about 32.5ml. Incubate
for 30 min at 37 ºC to dissolve CsCl2 . Spin at 3200 × g for 30 min at 4 ºC.
Carefully load the supernatant into six 5-ml Beckman ultracentrifugation tubes in
an SW55Ti rotor. Spin at 200,000 × g for 40 h at 4 ºC.
Collect fractions from the bottom of the tube with a 20-G needle. Identify the
viral containing fractions by slot blot (see below).
Combine fractions with the highest viral titer and centrifuge again at 200,000 ×
g for 40 h at 4 ºC. Collect fractions as described in step 6 and identify highest
viral fraction by slot blot (see below).
Dialyze viral stock in HEPES buffer (4 ºC for 2 × 24 h).
Slot blot viral titer determination. Use duplicated sets of viral stock aliquots
(1, 5, and 10 μl) and plasmid copy number controls (107 , 108 , 109 , 1010 , 1011
molecules/μl) in slot blot. Denature samples in 50 μl AAV digestion buffer at
100 ºC for 10 min. Then immediately chill samples on ice and bring up volume
to 400 μl with digestion buffer. Load samples onto Hybond-N plus membrane
with a Bio-Dot SF manifold microfiltration apparatus. After blotting, crosslink
DNA to the membrane with UV irradiation. Prehybridize the membrane. Then
hybridize the membrane with a 32 P-labeled transgene-specific probe in the slot
blot hybridization solution. Determine the viral particle titer by comparing the
intensity of the viral stock band to that of the plasmid standards.
3.2. In Vivo Evaluation of the Mini-Dystrophin Trans-Splicing Vectors
3.2.1. Local Muscle Injection
For all animal experiments, get approval from the institute Animal Care
and Use Committee and follow NIH guidelines. Two muscles have been used
to evaluate AAV transduction efficiency including the tibialis anterior (TA)
muscle and the extensor digitorum longus (EDL) muscle. In trans-splicing
270
Lai et al.
vector transduction studies, mix equal amount of AV.Donor and AV.Acceptor
particles before muscle injection. Then anesthetize experimental animal.
1. Gene delivery to the TA muscle. Expose the proximal end of the TA muscle
with a 2∼3 mm incision. Insert a 33-G Hamilton needle into the middle belly of
the TA muscle. Slowly inject 30 μl trans-splicing AAV vectors into the muscle
while slowly backing out the injection needle. Suture the wound and monitor the
animal until it recovers.
2. Gene delivery to the EDL muscle. Make a 0.5 × 5 mm incision along the
longitudinal axis in the lateral surface of the distal hind limb. Separate the EDL
tendon from the TA tendon and then gently pull the TA muscle aside with a
Guthrie double hook retractor to expose the EDL muscle. Perform two injections
from the proximal and the distal ends respectively with a 33G Hamilton syringe.
In each injection, directly inject 5 μl virus into the muscle body (a total of 10 μl
AAV for each EDL muscle). Suture the wound and monitor the animal until it
recovers (see Note 8).
3.2.2. Quantifying Mini-Dystrophin Expression by Western Blot
1. Muscle microsome preparation. Pulverize muscle in liquid nitrogen by hand
grinding. Resuspend the muscle powder in 6 ml muscle homogenization solution.
Transfer muscle lysate to a clean Oakridge tube. Spin at 250,000 × g for 15
min at 4 ºC in a Sorval RC-5B supercentrifuge. Filter supernatant through six
layers of cheese cloth. Load the filtered supernatant (∼5 ml) to a 5.2-ml SW55
centrifuge tube. Spin at 110,000 × g for 30 min at 4 ºC. Discard supernatant.
Gently resuspend the pellet in 5 ml wash buffer. Spin again at 110,000 × g for 30
min at 4 ºC. Resuspend the pellet (muscle microsome) in 200 μl storage solution
and store at –80 ºC.
2. Western blot. Electrophorese 50 μg of muscle microsome preparation in a
6% SDS-polyacrylamide gel. Detect mini-dystrophin with either Dys-2 (1:100
dilution) or Dys-3 (1:20 dilution) antibodies.
3.2.3. Quantifying Mini-Dystrophin Expression by Immunostaining
1. Snap freeze freshly isolated muscle sample in liquid nitrogen-cooled
2-methylbutane in Tissue-Tek OCT.
2. Immunostaining with monoclonal antibody. To use mouse monoclonal antibody
in murine tissue, one must first block the binding of the secondary antibody to
endogenous mouse immunoglobulins (Igs) (14). We used papain digested rabbit
anti-mouse IgG (including Fab and Fc fragments) for blocking (see Note 9).
Briefly, digest rabbit anti-mouse IgG with Papain in the presence of 1 mM EDTA
and 22 mM l-cystein at 37 ºC for 16 h. Stop digestion reaction with iodoaceticacid. For immunostaining, first block 8 μm air-dried cryosections in anti-mouse
IgG blocking solution at room temperature for 60 min. After washing in PBS,
block the cryosections again with 20% rabbit serum at room temperature for 30
Trans-Splice the Dystrophin Gene
271
min. After washing in PBS, apply the primary antibody (diluted in 1% rabbit
serum, such as Dys-3, Dys-2, or Mandy-8) at a dilution of 1:100 and incubate at
4 ºC overnight. After washing in PBS, detect signals with Alex 488 or Alex 594
conjugated rabbit anti-mouse antibodies, respectively.
3. Immunostaining with polyclonal antibody. Briefly rinse 8 μm air-dried cryosections with KPBS. Block with 1% goat serum KPBS at room temperature for 15
min. Wash with 0.2% gelatin KPBS. Apply primary antibody at 4 ºC overnight
(1:600 for Chamberlain’s affinity purified N-terminal antibody; 1:200 for Santa
Cruz’s C-terminal antibody, and 1:400 for Santa Cruz’s repeat 4–6 antibody).
Wash with 0.2% gelatin KPBS. Detect signal with Alex 488 or Alex 594
conjugated goat anti-rabbit antibody (for the N-terminal and repeat 4–6 primary
antibodies) or rabbit anti-goat antibody (for the C-terminal primary antibody) (see
Notes 10 and 11).
4. Notes
1. Despite the nonsense mutation, occasionally dystrophin positive revertant fibers
can be detected in mdx muscle (15). These are called revertant fibers. In revertant
fibers, the mutated exon 23 is skipped due to alternative splicing. Revertant
fibers can be distinguished from AAV-mediated mini-dystrophin expression by
the following criteria. First, revertant fibers can often be detected with antibodies
against the missing regions in the mini-dystrophin gene such as Mandy-8 (Sigma,
recognizes repeat 11) and Repeats 4–6 polyclonal antibody (Santa Cruz). Second,
revertant fibers cannot be recognized by human dystrophin-specific antibody
Dys-3.
2. In addition to the commercially available monoclonal antibodies mentioned here,
more than 60 monoclonal antibodies have been published. These antibodies
react with the different regions of the dystrophin protein. A collection of
these antibodies can be found in the website http://www.dmd.nl/antibody.html.
A large number of epitope-specific antibodies can be obtained from Prof.
Glenn E. Morris (Centre for Inherited Neuromuscular Disease, Leopold Muller
ARC Building, RJAH Orthopaedic Hospital, OSWESTRY, Shropshire, SY10
7AG, UK).
3. The conserved splicing value for a particular exon/intron/exon junction can be
calculated according to the following formula (16). For the 5´ splicing site, CV
= (X – 47)/548. X = the sum of all the reference values for the positions X and
x (see Table 1). For the 3´ splicing site, CV = (Y – 57)/640 + (Z – 11)/624. Y
= the sum of the eight highest values for all the y positions (see Table 1). Z =
the sum of all the reference values for the positions z and Z (see Table 1).
4. As mutations in intron may alter splicing profile and mutations in exon may
change amino acid sequence, we strongly recommend using high fidelity Taq
polymerase for all PCR-mediated cloning. It is also essential to confirm the
cloned PCR product by sequencing.
A
C
G
T
10
4
78
8
X
0
0
100
0
x
0
0
0
100
x
57
2
39
2
x
71
8
12
9
x
5
6
84
5
x
16
15
22
47
x
9
31
15
45
y
9
33
13
45
y
7
31
11
51
y
7
35
7
51
y
10
35
7
47
y
10
35
11
44
y
7
43
7
42
y
b
Adapted from Shapiro and Senapathy 1987 Nucleic Acid Res 15(17):7155.
Capital letters represent nucleotides in exon. Small letters represent nucleotides in intron.
c
Values at this nucleotide position is not used in calculation. n/a, not applicable.
a
58
13
15
15
Xb
Table 1
Reference Value for CV Calculation in a Primate Genea
9
41
8
42
y
6
39
6
48
y
6
40
8
46
y
n/a
n/a
n/a
n/a
oc
3
74
1
22
z
100
0
0
0
z
0
0
100
0
z
28
13
49
10
Z
Trans-Splice the Dystrophin Gene
273
5. AAV-6 has been shown as the best serotype for muscle transduction following
direct local injection (17,18). However, for systemic delivery one may also
consider other newly developed AAV serotypes such as AAV-8 and AAV-9.
6. In this protocol, we described a CsCl2 ultracentrifugation-based protocol for
AAV-6 purification. However, AAV-6 can also be purified with a HiTrap heparin
column using HPLC or FPLC (19).
7. A high-quality precipitate is essential to high viral yield. We recommend
routinely monitoring calcium phosphate precipitate on a coverslip using a phase
contrast microscope. Alternatively, the quality of the transfection reagents (such
as CaCl2 and 2× HBS) can be pre-tested with reporter plasmids such as GFP,
LacZ, or alkaline phosphatase plasmids.
8. To prevent gnawing on the suture and improve wound healing, we recommend
placing a polyethylene mouse Elizabethan collar around the mouse neck. This
device blocks the head from access to the rest of the body, but still enables
eating, drinking, and comfortable movement. To alleviate pain and discomfort at
the operation site, we suggest subcutaneous injection of a non-steroid analgesic
drug Banamine.
9. For immunostaining with monoclonal antibody, one can also use M.O.M kit.
10. To confirm trans-splicing AAV vector-mediated mini-dystrophin expression,
it is essential to perform immunostaining with at least three antibodies. Minidystrophin should be lighted up with antibodies against the N-terminal and
the C-terminal domains, respectively, but it will not be detected with antibody
against the regions that are deleted in mini-dystrophin (such as repeat 4–6).
11. The advantage of the polyclonal antibody is its low background staining in mouse
muscle. However, polyclonal antibody cannot distinguish between endogenously
mouse dystrophin in revertant myofibers and human mini-dystrophin expressed
from AAV vectors. Only Dys-3 monoclonal antibody can definitively diagnose
human originated mini-dystrophin.
Acknowledgments
We thank Dr. Jeffrey Chamberlain for providing the pH2-R19 minidystrophin plasmid. We also thank Dr. A. Dusty Miller for the AAV-6
packaging plasmids (pMT-Rep2 and pCMVCap6). This work is supported by
grants from the National Institutes of Health (AR-49419, DD) and the Muscular
Dystrophy Association (DD). We thank Mr. Arka Ghosh for optimizing AAV-6
preparation protocol. We thank Ms. Chun Long for animal care and Mr. Brian
Bostick for helpful discussion.
References
1. Wang, B., Li, J., and Xiao, X. (2000) Adeno-associated virus vector carrying
human minidystrophin genes effectively ameliorates muscular dystrophy in mdx
mouse model. Proc Natl Acad Sci USA 97, 13714–9.
274
Lai et al.
2. Harper, S. Q., Hauser, M. A., DelloRusso, C., Duan, D., Crawford, R. W.,
Phelps, S. F., Harper, H. A., Robinson, A. S., Engelhardt, J. F., Brooks, S. V., and
Chamberlain, J. S. (2002) Modular flexibility of dystrophin: implications for gene
therapy of Duchenne muscular dystrophy. Nat Med 8, 253–61.
3. England, S. B., Nicholson, L. V., Johnson, M. A., Forrest, S. M., Love, D. R.,
Zubrzycka-Gaarn, E. E., Bulman, D. E., Harris, J. B., and Davies, K. E. (1990)
Very mild muscular dystrophy associated with the deletion of 46% of dystrophin.
Nature 343, 180–2.
4. Phelps, S. F., Hauser, M. A., Cole, N. M., Rafael, J. A., Hinkle, R. T.,
Faulkner, J. A., and Chamberlain, J. S. (1995) Expression of full-length and
truncated dystrophin mini-genes in transgenic mdx mice. Hum Mol Genet 4,
1251–8.
5. Duan, D., Yue, Y., and Engelhardt, J. F. (2001) Expanding AAV packaging
capacity with trans-splicing or overlapping vectors: a quantitative comparison. Mol
Ther 4, 383–91.
6. Duan, D., Yue, Y., Yan, Z., and Engelhardt, J. F. (2003) Trans-splicing vectors
expand the packaging limits of adeno-associated virus for gene therapy applications. Methods Mol Med 76, 287–307.
7. Lai, Y., Yue, Y., Liu, M., Ghosh, A., Engelhardt, J. F., Chamberlain, J. S.,
and Duan, D. (2005) Efficient in vivo gene expression by trans-splicing adenoassociated viral vectors. Nat Biotechnol 23, 1435–9.
8. Xu, Z., Yue, Y., Lai, Y., Ye, C., Qiu, J., Pintel, D. J., and Duan, D. (2004)
Trans-splicing adeno-associated viral vector-mediated gene therapy is limited by
the accumulation of spliced mRNA but not by dual vector coinfection efficiency.
Hum Gene Ther 15, 896–905.
9. Halbert, C. L., Allen, J. M., and Miller, A. D. (2001) Adeno-associated virus type 6
(AAV6) vectors mediate efficient transduction of airway epithelial cells in mouse
lungs compared to that of AAV2 vectors. J Virol 75, 6615–24.
10. Bulfield, G., Siller, W. G., Wight, P. A., and Moore, K. J. (1984) X chromosomelinked muscular dystrophy (mdx) in the mouse. Proc Natl Acad Sci USA 81,
1189–92.
11. Sicinski, P., Geng, Y., Ryder-Cook, A. S., Barnard, E. A., Darlison, M. G., and
Barnard, P. J. (1989) The molecular basis of muscular dystrophy in the mdx mouse:
a point mutation. Science 244, 1578–80.
12. Sironi, M., Pozzoli, U., Cagliani, R., Comi, G. P., Bardoni, A., and Bresolin, N.
(2001) Analysis of splicing parameters in the dystrophin gene: relevance for physiological and pathogenetic splicing mechanisms. Hum Genet 109, 73–84.
13. Duan, D., Yan, Z., Yue, Y., and Engelhardt, J. F. (1999) Structural analysis of
adeno-associated virus transduction intermediates. Virology 261, 8–14.
14. Lu, Q. L., and Partridge, T. A. (1998) A new blocking method for application of
murine monoclonal antibody to mouse tissue sections. J Histochem Cytochem 46,
977–84.
15. Lu, Q. L., Morris, G. E., Wilton, S. D., Ly, T., Artem’yeva, O. V., Strong, P., and
Partridge, T. A. (2000) Massive idiosyncratic exon skipping corrects the nonsense
Trans-Splice the Dystrophin Gene
16.
17.
18.
19.
275
mutation in dystrophic mouse muscle and produces functional revertant fibers by
clonal expansion. J Cell Biol 148, 985–96.
Shapiro, M. B., and Senapathy, P. (1987) RNA splice junctions of different classes
of eukaryotes: sequence statistics and functional implications in gene expression.
Nucleic Acids Res 15, 7155–74.
Wang, Z., Zhu, T., Qiao, C., Zhou, L., Wang, B., Zhang, J., Chen, C., Li, J., and
Xiao, X. (2005) Adeno-associated virus serotype 8 efficiently delivers genes to
muscle and heart. Nat Biotechnol 23, 321–8.
Ghosh, A., Yue, Y., and Duan, D. (2006) Viral serotype and the transgene sequence
influence overlapping adeno-associated viral (AAV) vector-mediated gene transfer
in skeletal muscle. J Gene Med 8, 298–305.
Blankinship, M. J., Gregorevic, P., Allen, J. M., Harper, S. Q., Harper, H.,
Halbert, C. L., Miller, D. A., and Chamberlain, J. S. (2004) Efficient transduction
of skeletal muscle using vectors based on adeno-associated virus serotype 6. Mol
Ther 10, 671–8.