RNA-seq analysis of mouse hearts over-expressing PTBP1 using an AAV9 vector
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA633802 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11811426_1.fastq.gz | Fastqsanger.gz | |||
| SRR11811426_2.fastq.gz | Fastqsanger.gz | |||
| SRR11811427_1.fastq.gz | Fastqsanger.gz | |||
| SRR11811427_2.fastq.gz | Fastqsanger.gz | |||
| SRR11811428_1.fastq.gz | Fastqsanger.gz |
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Project description:We describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions with 1 million HEK293 cells, and with public eCLIP and iCLIP PTBP1 data. There are 3 PTBP1 iiCLIP libraries, 1 input iiCLIP library and 1 PTBP1 iCLIP2 library produced in this study.
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Project description:Inherited retinal disorders (IRD) have become a primary focus of gene therapy research since the success of AAV-based therapeutics (voretigene neparvovec-rzyl) for Leber congenital amaurosis type 2 (LCA2). Dozens of monogenic IRDs could be potentially treated with a similar approach using adeno-associated virus (AAV) to transfer a functional gene into the retina. Here, we present the results of design, production and in vitro testing of the AAV serotype 9 (AAV9) vector carrying the codon-optimized (co) copy of aryl hydrocarbon receptor interacting protein like-1 (AIPL1) as a possible treatment for LCA4. The pAAV-AIPL1co was able to successfully transduce retinal pigment epithelium cells (ARPE-19) and initiate expression of human AIPL1. Intriguingly, cells transduced with AAV9-AIPL1co showed much less antiviral response than AAV9-AIPL1wt (wild type AIPL1 ) transduced. RNA-sequencing (RNA-seq) analysis of trans-differentiated ARPE-19 cells transduced with AAV9-AIPL1co demonstrated the significant differences in expression of genes involved in innate immune response. In contrast, AAV9-AIPL1wt induced prominent activation of multiple interferon-stimulated genes. The key part of possible regulatory molecular mechanism is activation of dsRNA-responsive antiviral oligoadenylate synthetases, and significant increase in level of histone coding genes’ transcripts overrepresented in RNA-seq data (i.e. H1, H2A, H2B, H3 and H4). The RNA-seq data suggests that AAV9-AIPL1co exhibiting less immunogenicity than AAV9-AIPL1wt can be used for potency testing using relevant animal models to develop future therapeutics for LCA4.
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