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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 01, 2024 |
| Title |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [DNaseI-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. We designed a library of 15,000 short sequences (~200bp) derived from a set of developmentally active DHS elements during human ex vivo erythropoiesis and cloned them into a GFP reporter lentiviral vector. In an erythroid progenitor cell line, these elements display a gradient of transcriptional enhancer activity, with some demonstrating equivalent activity to the canonical β-globin μLCR despite a 9-fold smaller size. We show that these elements are both highly cell type restricted and developmental stage specific both in vitro and in vivo. Finally, we replace the μLCR element with one of the novel short enhancers in a β-thalassemia lentiviral therapeutic vector and efficiently correct the thalassemic phenotype in patient-derived HSPCs. More broadly, our approach provides further insights into enhancer biology with wider implications into the development of highly cell type specific and efficacious viral vectors for human gene therapy.
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| Overall design |
DNase I seq of WT and TALEN genome edited, homozygous for the deletion of either PVT1 or PPARA enhancer elements.
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| Contributor(s) |
Psatha N, Sova P, Georgolopoulos G, Paschoudi K, Iwata M, Bloom J, Ulyanova T, Wang H, Kirtsou A, Vasiloudis N, Wilken MS, Stamatoyannopoulos JA, Yannaki E, Papayanopoulou T, Stamatoyannopoulos G, Vierstra J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 27, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Jeff Vierstra |
| E-mail(s) |
jvierstra@altius.org
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| Organization name |
Altius Institute for Biomedical Sciences
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| Street address |
2211 Elliot Ave
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (3) |
| GSM7995348 |
HUDEP-2 WT DNase-I 60U/mL |
| GSM7995349 |
HUDEP-2 TL20804:TL20805 transfected, clone 124, rep 3, DNase-I 90U/mL |
| GSM7995350 |
HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 5, Dnase-I 120 U/mL |
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| This SubSeries is part of SuperSeries: |
| GSE252163 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors |
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| Relations |
| BioProject |
PRJNA1057940 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE252160_RAW.tar |
470.1 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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