Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity

Mary H Wertz; Mollie R Mitchem; S Sebastian Pineda; Lea J Hachigian; Hyeseung Lee; Vanessa Lau; Alex Powers; Ruth Kulicke; Gurrein K Madan; Medina Colic; Martine Therrien; Amanda Vernon; Victoria F Beja-Glasser; Mudra Hegde; Fan Gao; Manolis Kellis; Traver Hart; John G Doench; Myriam Heiman

doi:10.1016/j.neuron.2020.01.004

Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity

Neuron. 2020 Apr 8;106(1):76-89.e8. doi: 10.1016/j.neuron.2020.01.004. Epub 2020 Jan 30.

Authors

Mary H Wertz¹, Mollie R Mitchem¹, S Sebastian Pineda², Lea J Hachigian³, Hyeseung Lee¹, Vanessa Lau¹, Alex Powers¹, Ruth Kulicke¹, Gurrein K Madan⁴, Medina Colic⁵, Martine Therrien¹, Amanda Vernon³, Victoria F Beja-Glasser⁶, Mudra Hegde⁷, Fan Gao⁸, Manolis Kellis⁹, Traver Hart⁵, John G Doench⁷, Myriam Heiman¹⁰

Affiliations

¹ Picower Institute for Learning and Memory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA.
³ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁴ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA.
⁵ University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁶ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁸ Picower Institute for Learning and Memory, Cambridge, MA 02139, USA; Bioinformatics Resource Center in the Beckman Institute at Caltech, Pasadena, CA 91125, USA.
⁹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA.
¹⁰ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: [email protected].

Abstract

Unbiased in vivo genome-wide genetic screening is a powerful approach to elucidate new molecular mechanisms, but such screening has not been possible to perform in the mammalian central nervous system (CNS). Here, we report the results of the first genome-wide genetic screens in the CNS using both short hairpin RNA (shRNA) and CRISPR libraries. Our screens identify many classes of CNS neuronal essential genes and demonstrate that CNS neurons are particularly sensitive not only to perturbations to synaptic processes but also autophagy, proteostasis, mRNA processing, and mitochondrial function. These results reveal a molecular logic for the common implication of these pathways across multiple neurodegenerative diseases. To further identify disease-relevant genetic modifiers, we applied our screening approach to two mouse models of Huntington's disease (HD). Top mutant huntingtin toxicity modifier genes included several Nme genes and several genes involved in methylation-dependent chromatin silencing and dopamine signaling, results that reveal new HD therapeutic target pathways.

Keywords: Huntington’s disease; Nme1; genome-wide screening; neuronal essential genes.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Behavior, Animal
CRISPR-Cas Systems
Cell Survival / genetics*
Gene Knockdown Techniques
Gene Library
Genes, Essential / genetics
Huntingtin Protein / genetics*
Huntington Disease / genetics*
Mice
Mice, Transgenic
NM23 Nucleoside Diphosphate Kinases / genetics
Neostriatum / metabolism*
Neurons / metabolism*
Nucleoside Diphosphate Kinase D / genetics
Protein Aggregates
RNA Interference
RNA, Guide, CRISPR-Cas Systems
RNA, Small Interfering
Receptors, Dopamine D2 / genetics
Sequence Analysis, RNA

Substances

DRD2 protein, mouse
HTT protein, human
Huntingtin Protein
NM23 Nucleoside Diphosphate Kinases
Protein Aggregates
RNA, Guide, CRISPR-Cas Systems
RNA, Small Interfering
Receptors, Dopamine D2
Nme1 protein, mouse
Nme3 protein, mouse
Nme4 protein, mouse
Nucleoside Diphosphate Kinase D

Abstract

Publication types

MeSH terms

Substances

Grants and funding