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| Status |
Public on Jan 31, 2023 |
| Title |
RNAi-mediated rheostat for dynamic control of AAV-delivered transgenes |
| Organisms |
Homo sapiens; Mus musculus; Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Adeno-associated virus (AAV)-based gene therapy could be facilitated by the development of molecular switches to control the magnitude and timing of expression of therapeutic transgenes. RNA interference (RNAi)-based approaches hold unique potential as a clinically proven modality to pharmacologically regulate AAV gene dosage in a sequence-specific manner. We present a generalizable RNAi-based rheostat wherein AAV transgene expression is silenced using the clinically validated modality of chemically modified short interfering RNA (siRNA) conjugates or vectorized co-expression of short hairpin RNA (shRNA). For transgene induction, we employ REVERSIR technology, a synthetic high-affinity oligonucleotide complementary to the siRNA or shRNA guide strand to reverse RNAi activity and rapidly recover transgene expression. For potential clinical development, we report potent and specific siRNA sequences that may allow selective regulation of transgenes while minimizing unintended off-target effects. Our results establish a conceptual framework for RNAi-based regulatory switches with potential for infrequent dosing in clinical settings to dynamically modulate expression of virally-delivered gene therapies.
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| Overall design |
The high specificity of transgene-targeting siRNAs is demonstrated in vitro using measures of differential expression derived from RNA-seq data.
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| Contributor(s) |
Subramanian M, McIninch J, Zlatev I, Schlegel MK, Kaittanis C, Nguyen T, Agarwal S, Racie T, Alvarado MA, Wassarman K, Collins TS, Chickering T, Brown CR, Schmidt K, Castoreno AB, Shulga-Morskaya S, Stamenova E, Buckowing K, Berman D, Barry JD, Bisbe A, Maier MA, Fitzgerald K, Jadhav V |
| Citation(s) |
37031257 |
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| Submission date |
Sep 23, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Joseph Barry |
| E-mail(s) |
jbarry@alnylam.com
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| Organization name |
Alnylam Pharmaceuticals
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| Street address |
675 West Kendall St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (3) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (66)
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| Relations |
| BioProject |
PRJNA883694 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214065_Hep3B_groupsiRNA.ctrl_10nM.vs.mock.DESeq2.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE214065_Hep3B_groupsiRNA1_10nM.vs.mock.DESeq2.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE214065_Hep3B_groupsiRNA2_10nM.vs.mock.DESeq2.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE214065_Hep3B_groupsiRNA3_10nM.vs.mock.DESeq2.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE214065_PMH_groupsiRNA.ctrl_50nM.vs.mock.DESeq2.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE214065_PMH_groupsiRNA1_50nM.vs.mock.DESeq2.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE214065_PMH_groupsiRNA2_50nM.vs.mock.DESeq2.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE214065_PMH_groupsiRNA3_50nM.vs.mock.DESeq2.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE214065_RAW.tar |
12.4 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE214065_SuppRat_groupsiRNA1_100mkg.vs.NaCl.DESeq2.txt.gz |
995.8 Kb |
(ftp)(http) |
TXT |
| GSE214065_SuppRat_groupsiRNA1_30mkg.vs.NaCl.DESeq2.txt.gz |
949.8 Kb |
(ftp)(http) |
TXT |
| GSE214065_SuppRat_groupsiRNA2_100mkg.vs.NaCl.DESeq2.txt.gz |
992.0 Kb |
(ftp)(http) |
TXT |
| GSE214065_SuppRat_groupsiRNA2_30mkg.vs.NaCl.DESeq2.txt.gz |
986.0 Kb |
(ftp)(http) |
TXT |
| GSE214065_SuppRat_groupsiRNA3_100mkg.vs.NaCl.DESeq2.txt.gz |
991.3 Kb |
(ftp)(http) |
TXT |
| GSE214065_SuppRat_groupsiRNA3_30mkg.vs.NaCl.DESeq2.txt.gz |
981.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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