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Santinha AJ, Klingler E, Kuhn M, Farouni R, Lagler S, Kalamakis G, Lischetti U, Jabaudon D, Platt RJ. Transcriptional linkage analysis with in vivo AAV-Perturb-seq. Nature 2023; 622:367-375. [PMID: 37730998 PMCID: PMC10567566 DOI: 10.1038/s41586-023-06570-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
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 manner1,2. 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 syndrome3,4 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.
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Affiliation(s)
- Antonio J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Esther Klingler
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Maria Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Pharma Research and Early Development (pRED), Roche, Basel, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sandra Lagler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ulrike Lischetti
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Botnar Research Center for Child Health, Basel, Switzerland.
- Department of Chemistry, University of Basel, Basel, Switzerland.
- NCCR Molecular Systems Engineering, Basel, Switzerland.
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Tomasello U, Klingler E, Niquille M, Mule N, Santinha AJ, de Vevey L, Prados J, Platt RJ, Borrell V, Jabaudon D, Dayer A. miR-137 and miR-122, two outer subventricular zone non-coding RNAs, regulate basal progenitor expansion and neuronal differentiation. Cell Rep 2022; 38:110381. [PMID: 35172154 PMCID: PMC8864305 DOI: 10.1016/j.celrep.2022.110381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/22/2021] [Accepted: 01/24/2022] [Indexed: 12/29/2022] Open
Abstract
Cortical expansion in primate brains relies on enlargement of germinal zones during a prolonged developmental period. Although most mammals have two cortical germinal zones, the ventricular zone (VZ) and subventricular zone (SVZ), gyrencephalic species display an additional germinal zone, the outer subventricular zone (oSVZ), which increases the number and diversity of neurons generated during corticogenesis. How the oSVZ emerged during evolution is poorly understood, but recent studies suggest a role for non-coding RNAs, which allow tight genetic program regulation during development. Here, using in vivo functional genetics, single-cell RNA sequencing, live imaging, and electrophysiology to assess progenitor and neuronal properties in mice, we identify two oSVZ-expressed microRNAs (miRNAs), miR-137 and miR-122, which regulate key cellular features of cortical expansion. miR-137 promotes basal progenitor self-replication and superficial layer neuron fate, whereas miR-122 decreases the pace of neuronal differentiation. These findings support a cell-type-specific role of miRNA-mediated gene expression in cortical expansion. oSVZ-expressed microRNAs 137 and 122 promote superficial layer identity of neurons miR-137 promotes basal progenitor proliferation and layer 2/3 neuron generation miR-122 slows down neuronal differentiation pace
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Affiliation(s)
- Ugo Tomasello
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, 03550 Alacant, Spain
| | - Esther Klingler
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland
| | - Mathieu Niquille
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Department of Psychiatry, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Nandkishor Mule
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland
| | - Antonio J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Laura de Vevey
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland
| | - Julien Prados
- Department of Psychiatry, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Victor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, 03550 Alacant, Spain
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Clinic of Neurology, Geneva University Hospital, 1205 Geneva, Switzerland.
| | - Alexandre Dayer
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Department of Psychiatry, Geneva University Hospital, 1205 Geneva, Switzerland
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