Schizophrenia (SCZD) is a debilitating and typically incurable neuropsychiatric disease that affects 1% of the human population. Disease symptoms, which include hallucinations, paranoia, and impaired cognition, are thought to arise from impairments in neuronal connectivity and plasticity, but etiology of these defects remains unclear. Multiple lines of evidence suggest a strong genetic component to SCZD. Thus, identifying genetic variants associated with SCZD may provide critical tools for understanding and treating the disease. Indeed, recent genome wide association studies have identified >100 loci that are associated with SCZD, but these genetic variants account for only a small percentage of disease incidence. One potential explanation for this unsatisfying result is that SCZD risk alleles are not inherited through the germline, but instead arise through somatic mutations within neurons of affected individuals. Perhaps it is the propensity for somatic mosaicism that is inherited in patients with SCZD. It is now clear that somatic mosaicism of DNA sequence is much more common than previously thought (i.e., all cells within an individual do not contain the same genome), and that this phenomenon is particularly prevalent in the brain. These genomic differences may contribute to the diversity of neuronal function. However, dysregulation of processes that generate or control somatic mosaicism may lead to disease-related genomic instability. Our hypothesis, therefore, is that somatic mosaicism in neurons or their progenitors are a major contributor to SCZD pathogenesis.
Aim 1 will use single-cell genomic sequencing techniques to identify somatic copy number variants (CNVs) in neuronal and non-neuronal cell types from patients with SCZD or neurotypic controls. These analyses will focus on the frontal cortex and hippocampus, two brain regions associated with SCZD pathogenesis. Results will determine whether somatic CNVs are overrepresented in SCZD brains, and whether SCZD risk alleles are disproportionately affected by these CNVs.
Aim 2 will characterize somatic retrotransposon insertions within these same cell types, asking whether the frequency or location of retrotransposition events is altered in neurons from patients with SCZD compared with controls. A total of 8000 neurons will be analyzed in Aims 1 and 2, making this the most comprehensive analysis of neuronal somatic mosaicism to date.
In Aim 3, genomic variants most overrepresented in patients with SCZD (identified in Aims 1 and 2) will be engineered into hESCs for functional validation tests. It has been shown that cultured neurons derived from patients with SCZD exhibit reduced levels of connectivity and have underdeveloped neurites compared with controls. Similar analyses will be performed using isogenic and mosaic cultures of neurons derived from engineered hESCs. Results from these studies will determine whether the level, pattern, or type of somatic mosaicism is altered in SCZD neurons, and potentially identify genes and gene networks most affected by these changes. Identifying causal disease factors will provide new therapeutic targets and move us closer to finding a cure for this devastating disease.

Public Health Relevance

This project will use single-cell genomic sequencing techniques to identify genetic changes, such as deletions and retrotransposon insertions that are overrepresented in neurons of patients with schizophrenia. These experiments test the hypothesis that somatic mosaicism contributes to the schizophrenic disease state and seek to identify new therapeutic targets. Developing new treatments for schizophrenia is extremely critical to relieve the immeasurable suffering of affected families and individuals, and to reduce the public health burden.

Agency
National Institute of Health (NIH)
Institute
National Institute of Mental Health (NIMH)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01MH106882-04
Application #
9419200
Study Section
Special Emphasis Panel (ZMH1)
Program Officer
Senthil, Geetha
Project Start
2015-04-20
Project End
2020-01-31
Budget Start
2018-02-01
Budget End
2019-01-31
Support Year
4
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Salk Institute for Biological Studies
Department
Type
DUNS #
078731668
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Linker, Sara B; Marchetto, Maria C; Narvaiza, Iñigo et al. (2017) Examining non-LTR retrotransposons in the context of the evolving primate brain. BMC Biol 15:68
Paquola, Apuã C M; Erwin, Jennifer A; Gage, Fred H (2017) Insights into the role of somatic mosaicism in the brain. Curr Opin Syst Biol 1:90-94
Sarkar, Anindita; Marchetto, Maria C; Gage, Fred H (2017) Synaptic activity: An emerging player in schizophrenia. Brain Res 1656:68-75
McConnell, Michael J; Moran, John V; Abyzov, Alexej et al. (2017) Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 356:
Erwin, Jennifer A; Paquola, Apuã C M; Singer, Tatjana et al. (2016) L1-associated genomic regions are deleted in somatic cells of the healthy human brain. Nat Neurosci 19:1583-1591
Bedrosian, Tracy A; Linker, Sara; Gage, Fred H (2016) Environment-driven somatic mosaicism in brain disorders. Genome Med 8:58
Harbom, Lise J; Chronister, William D; McConnell, Michael J (2016) Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? Bioessays 38:157-61