Lentiviral vector preparation. We previously developed a chimeric
HIV-1–based lentiviral vector system (χHIV vector) in which the HIV-1 genome is
packaged into simian immunodeficiency virus capsid with vesicular stomatitis virus
glycoprotein envelope, to efficiently transduce rhesus hematopoietic cells.10 (link),11 (link) The χHIV vectors
encoding GFP or YFP were prepared by cotransfection of four plasmids into 293T cells,
which contain gag/pol, rev/tat, envelope, and vector plasmids.10 (link),25 (link) The HIV-1 vector plasmids were
kindly provided by Dr Arthur Nienhuis (St Jude Children's Research Hospital,
Memphis, TN).26 (link),27 (link) Two days after transfection, conditioned media from the transfected
293T cells were 100-fold concentrated by ultracentrifugation. The vector stocks were
stored in a −80 °C freezer. Deoxyribonucleases were not used for our viral
preparation.
Rhesus HSC transplantation with lentiviral transduction. We previously developed
a large animal model for HSC transplantation with lentiviral transduction in rhesus
macaques.10 (link),12 (link) Granulocyte colony-stimulating factor (Amgen, Thousand Oaks, CA) and
stem cell factor (Amgen) or plerixafor (Genzyme, Cambridge, MA)-mobilized rhesus
CD34+ cells were cultured in X-VIVO10 media (Lonza, Allendale, NJ) containing
stem cell factor, FMS-related tyrosine kinase 3 ligand, and thrombopoietin (all
100 ng/ml; R&D Systems, Minneapolis, MN).15 (link) After 1 day prestimulation, the CD34+ cells were
transduced with χHIV vectors at a multiplicity of infection of 50, and next day, these
cells were infused into rhesus macaques following a split dose (2 × 5
Gy) of 10 Gy total body irradiation. A small amount of the transduced CD34+cells were cultured in vitro in fresh media with same cytokines.
Real-time PCR. Genomic DNA was extracted from the transduced rhesus
CD34+ cells 6 days after transduction and from both granulocytes and
lymphocytes 6 months after transplantation, which were separated by Ficoll-Paque PLUS
density gradient centrifugation (GE Healthcare, Uppsala, Sweden). The extracted DNA
(10 ng) was used as templates, and specific sequences were amplified by real-time
PCR (Mx3000P QPCR Systems; Agilent Technologies, Santa Clara, CA) using GFP or YFP
probe/primers,10 (link),11 (link) SIN-LTR probe/primers (Table 1 and Figure 4a ), and AmpR probe/primers28 (link) for 40 cycles of 30 seconds at 95 °C, 30 seconds at
60 °C, and 15 seconds at 72 °C. TaqMan Ribosomal RNA control reagents (Applied
Biosystems, Foster City, CA) were used to determine the amount of genomic DNA. Average VCN
per cell was calculated by total VCN per total cell number, which was compared to a
monoclonal cell line with single copy of integrated provirus (VCN = 1).10 (link) The relative plasmid signals using AmpR probe/primers
were calculated by compared to average plasmid signal in lymphocytes.
In addition, transgene expression rates (%GFP or %YFP) were evaluated by flow cytometry
(FACSCalibur; BD Biosciences, Franklin Lakes, NJ) 3–4 days after transduction among
CD34+ cells and 6 months after transplantation among both granulocytes and
lymphocytes from 16 transplanted rhesus macaques. In rhesus macaques undergoing
competitive repopulation assays, twofold scores of VCN and %GFP or %YFP were used in both
granulocytes and lymphocytes since each represented only half of the transduced
product.
Statistical analyses. Statistical analyses were performed using the JMP 9
software (SAS Institute, Cary, NC). We evaluated correlation using two factors of (i)
significance of relationship expressed by t-test for coefficient of correlation,
and (ii) strength of relationship measured by R 2 in regression
analysis. A P value of <0.01 or 0.05 was deemed significant. SEM are shown as
error bars in figures. We excluded outliers (in vivo VCN >6 and in
vitro VCN >600 inFigure 1c and in
vivo VCN >6 inFigure 5a ), which were defined
by more than the upper limit of “(third quartile) + 1.5 × (interquartile
range)” or less than the lower limit of “(first quartile) − 1.5 ×
(interquartile range).”
SUPPLEMENTARY MATERIAL Figure S1. Vector copy number per cell in GFP-positive and GFP-negative fractions
in peripheral blood cells of transplanted rhesus macaques.
HIV-1–based lentiviral vector system (χHIV vector) in which the HIV-1 genome is
packaged into simian immunodeficiency virus capsid with vesicular stomatitis virus
glycoprotein envelope, to efficiently transduce rhesus hematopoietic cells.10 (link),11 (link) The χHIV vectors
encoding GFP or YFP were prepared by cotransfection of four plasmids into 293T cells,
which contain gag/pol, rev/tat, envelope, and vector plasmids.10 (link),25 (link) The HIV-1 vector plasmids were
kindly provided by Dr Arthur Nienhuis (St Jude Children's Research Hospital,
Memphis, TN).26 (link),27 (link) Two days after transfection, conditioned media from the transfected
293T cells were 100-fold concentrated by ultracentrifugation. The vector stocks were
stored in a −80 °C freezer. Deoxyribonucleases were not used for our viral
preparation.
Rhesus HSC transplantation with lentiviral transduction. We previously developed
a large animal model for HSC transplantation with lentiviral transduction in rhesus
macaques.10 (link),12 (link) Granulocyte colony-stimulating factor (Amgen, Thousand Oaks, CA) and
stem cell factor (Amgen) or plerixafor (Genzyme, Cambridge, MA)-mobilized rhesus
CD34+ cells were cultured in X-VIVO10 media (Lonza, Allendale, NJ) containing
stem cell factor, FMS-related tyrosine kinase 3 ligand, and thrombopoietin (all
100 ng/ml; R&D Systems, Minneapolis, MN).15 (link) After 1 day prestimulation, the CD34+ cells were
transduced with χHIV vectors at a multiplicity of infection of 50, and next day, these
cells were infused into rhesus macaques following a split dose (2 × 5
Gy) of 10 Gy total body irradiation. A small amount of the transduced CD34+cells were cultured in vitro in fresh media with same cytokines.
Real-time PCR. Genomic DNA was extracted from the transduced rhesus
CD34+ cells 6 days after transduction and from both granulocytes and
lymphocytes 6 months after transplantation, which were separated by Ficoll-Paque PLUS
density gradient centrifugation (GE Healthcare, Uppsala, Sweden). The extracted DNA
(10 ng) was used as templates, and specific sequences were amplified by real-time
PCR (Mx3000P QPCR Systems; Agilent Technologies, Santa Clara, CA) using GFP or YFP
probe/primers,10 (link),11 (link) SIN-LTR probe/primers (
60 °C, and 15 seconds at 72 °C. TaqMan Ribosomal RNA control reagents (Applied
Biosystems, Foster City, CA) were used to determine the amount of genomic DNA. Average VCN
per cell was calculated by total VCN per total cell number, which was compared to a
monoclonal cell line with single copy of integrated provirus (VCN = 1).10 (link) The relative plasmid signals using AmpR probe/primers
were calculated by compared to average plasmid signal in lymphocytes.
In addition, transgene expression rates (%GFP or %YFP) were evaluated by flow cytometry
(FACSCalibur; BD Biosciences, Franklin Lakes, NJ) 3–4 days after transduction among
CD34+ cells and 6 months after transplantation among both granulocytes and
lymphocytes from 16 transplanted rhesus macaques. In rhesus macaques undergoing
competitive repopulation assays, twofold scores of VCN and %GFP or %YFP were used in both
granulocytes and lymphocytes since each represented only half of the transduced
product.
Statistical analyses. Statistical analyses were performed using the JMP 9
software (SAS Institute, Cary, NC). We evaluated correlation using two factors of (i)
significance of relationship expressed by t-test for coefficient of correlation,
and (ii) strength of relationship measured by R 2 in regression
analysis. A P value of <0.01 or 0.05 was deemed significant. SEM are shown as
error bars in figures. We excluded outliers (in vivo VCN >6 and in
vitro VCN >600 in
vivo VCN >6 in
by more than the upper limit of “(third quartile) + 1.5 × (interquartile
range)” or less than the lower limit of “(first quartile) − 1.5 ×
(interquartile range).”
in peripheral blood cells of transplanted rhesus macaques.