Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models

Derek J C Tai; Parisa Razaz; Serkan Erdin; Dadi Gao; Jennifer Wang; Xander Nuttle; Celine E de Esch; Ryan L Collins; Benjamin B Currall; Kathryn O'Keefe; Nicholas D Burt; Rachita Yadav; Lily Wang; Kiana Mohajeri; Tatsiana Aneichyk; Ashok Ragavendran; Alexei Stortchevoi; Elisabetta Morini; Weiyuan Ma; Diane Lucente; Alex Hastie; Raymond J Kelleher; Roy H Perlis; Michael E Talkowski; James F Gusella

doi:10.1016/j.ajhg.2022.08.012

Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models

Am J Hum Genet. 2022 Oct 6;109(10):1789-1813. doi: 10.1016/j.ajhg.2022.08.012. Epub 2022 Sep 23.

Authors

Derek J C Tai¹, Parisa Razaz², Serkan Erdin³, Dadi Gao², Jennifer Wang⁴, Xander Nuttle¹, Celine E de Esch², Ryan L Collins², Benjamin B Currall², Kathryn O'Keefe², Nicholas D Burt², Rachita Yadav², Lily Wang⁵, Kiana Mohajeri², Tatsiana Aneichyk¹, Ashok Ragavendran², Alexei Stortchevoi², Elisabetta Morini⁶, Weiyuan Ma⁶, Diane Lucente⁶, Alex Hastie⁷, Raymond J Kelleher⁸, Roy H Perlis⁴, Michael E Talkowski⁹, James F Gusella¹⁰

Affiliations

¹ Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
² Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
³ Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁴ Center for Quantitative Health, Division of Clinical Research, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
⁵ Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁶ Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
⁷ Bionano Genomics, San Diego, CA 92121, USA.
⁸ Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
⁹ Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: [email protected].
¹⁰ Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address: [email protected].

Abstract

Chromosome 16p11.2 reciprocal genomic disorder, resulting from recurrent copy-number variants (CNVs), involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia, but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, and white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue-, cell-type-, and dosage-specific, although more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2,163 differentially expressed genes), and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated, loss-of-function constraint, and fragile X messenger ribonucleoprotein target gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, and single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Changes both in neuronal ratios and in gene expression in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption that might contribute to changes in neurodevelopmental and cognitive function in 16p11.2 carriers. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes and that this disruption has relative impacts that are context specific.

Keywords: 16p11.2; CRISPR; RNAseq; cerebral organoid; copy-number variation; genomic disorder; transcriptome.

Publication types

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

MeSH terms

Animals
Autism Spectrum Disorder* / genetics
Calbindin 2 / genetics
Cerebral Cortex
Chromosome Deletion
Chromosome Disorders* / genetics
Chromosomes, Human, Pair 16 / genetics
DNA Copy Number Variations
Genomics
Humans
Intellectual Disability* / genetics
Mice
Neurons
RNA

Substances

Calbindin 2
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding