Transcriptional linkage analysis with in vivo AAV-Perturb-seq.
Antonio J SantinhaEsther KlinglerMaria KuhnRick FarouniSandra LaglerGeorgios KalamakisUlrike LischettiDenis JabaudonRandall J PlattPublished in: Nature (2023)
The ever-growing compendium of genetic variants associated with human pathologies demands new methods to study genotype-phenotype relationships in complex tissues in a high-throughput manner 1,2 . Here we introduce adeno-associated virus (AAV)-mediated direct in vivo single-cell CRISPR screening, termed AAV-Perturb-seq, a tuneable and broadly applicable method for transcriptional linkage analysis as well as high-throughput and high-resolution phenotyping of genetic perturbations in vivo. We applied AAV-Perturb-seq using gene editing and transcriptional inhibition to systematically dissect the phenotypic landscape underlying 22q11.2 deletion syndrome 3,4 genes in the adult mouse brain prefrontal cortex. We identified three 22q11.2-linked genes involved in known and previously undescribed pathways orchestrating neuronal functions in vivo that explain approximately 40% of the transcriptional changes observed in a 22q11.2-deletion mouse model. Our findings suggest that the 22q11.2-deletion syndrome transcriptional phenotype found in mature neurons may in part be due to the broad dysregulation of a class of genes associated with disease susceptibility that are important for dysfunctional RNA processing and synaptic function. Our study establishes a flexible and scalable direct in vivo method to facilitate causal understanding of biological and disease mechanisms with potential applications to identify genetic interventions and therapeutic targets for treating disease.
Keyphrases
- genome wide
- single cell
- high throughput
- rna seq
- gene expression
- dna methylation
- gene therapy
- transcription factor
- prefrontal cortex
- high resolution
- copy number
- mouse model
- heat shock
- endothelial cells
- crispr cas
- spinal cord
- case report
- risk assessment
- physical activity
- genome editing
- subarachnoid hemorrhage
- antiretroviral therapy
- tandem mass spectrometry
- young adults