Abstract
Whereas some rare genetic variants convey high risk for schizophrenia (SZ), common alleles conveying even moderate risk remain elusive. Long interspersed element-1s (L1) are mobile retrotransposons comprising ~17% of the human genome. L1 retrotransposition can cause somatic mosaicism during neurodevelopment by insertional mutagenesis. We hypothesized that, compared to controls, patients diagnosed with schizophrenia (PDS) may have increased numbers of deleterious L1 insertions, perhaps occurring de novo, in brain-expressed genes of dorsolateral prefrontal cortex (DLPFC) neurons. Neuronal and non-neuronal nuclei were separated by fluorescence-activated cell sorting from postmortem DLPFC of 36 PDS and 26 age-matched controls. Genomic sequences flanking the 3′-side of L1s were amplified from neuronal DNA, and neuronal L1 libraries were sequenced. Aligned sequences were analyzed for L1 insertions using custom bioinformatics programs. Ontology and pathway analyses were done on lists of genes putatively disrupted by L1s in PDS and controls. Cellular or population allele frequencies of L1s were assessed by droplet digital PCR or Taqman genotyping. We observed a statistically significant increase in the proportion of intragenic novel L1s in DLPFC of PDS. We found over-representation of L1 insertions within the gene ontologies ‘cell projection’ and ‘postsynaptic membrane’ in the gene lists derived from PDS samples, but not from controls. Cellular allele frequencies of examined L1 insertions indicated heterozygosity in genomes of DLPFC cells. An L1 within ERI1 exoribonuclease family member 3 (ERI3) was found to associate with SZ. These results extend prior work documenting increased L1 genetic burden in the brains of PDS and also identify unique genes that may provide new insight into the pathophysiology of schizophrenia.
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Acknowledgements
We thank Paul Hallberg for performing the fluorescence-activated cell sorter separations at the University of Pennsylvania Flow Cytometry Core Facility. We also thank the Children’s Hospital of Philadelphia Nucleic Acid/Protein core for performing the Sanger sequencing. We acknowledge the NIMH Center for Collaborative Genomic Studies on Mental Disorders established through the NIMH Human Genetics Initiative in conjunction with Washington University in Saint Louis, the University of Southern California’s Information Sciences Institute, and Rutgers University’s RUCDR Infinite Biologics for providing DNA samples collected from the following studies and investigators: subjects were obtained from the National Institute of Mental Health Schizophrenia Genetics Initiative (NIMH-GI); data and biomaterials were collected by the ‘Molecular Genetics of Schizophrenia II’ (MGS-2) collaboration. The investigators and coinvestigators are as follows: ENH/Northwestern University, Evanston, IL, MH059571, Pablo V Gejman, MD (Collaboration Coordinator, PI), and Alan R Sanders, MD; Emory University School of Medicine, Atlanta, GA, MH59587, Farooq Amin, MD (PI); Louisiana State University Health Sciences Center; New Orleans, LA, MH067257, Nancy Buccola, APRN, BC, MSN (PI); University of California-Irvine, Irvine, CA, MH60870, William Byerley, MD (PI); Washington University, St. Louis, MO, U01, MH060879, C Robert Cloninger, MD (PI); University of Iowa, Iowa City, IA, MH59566, Raymond Crowe, MD (PI) and Donald Black, MD; University of Colorado, Denver, CO, MH059565, Robert Freedman, MD (PI); University of Pennsylvania, Philadelphia, PA, MH061675, Douglas Levinson MD (PI); University of Queensland, Queensland, Australia, MH059588, Bryan Mowry, MD (PI); and Mt. Sinai School of Medicine, New York, NY, MH59586, Jeremy Silverman, PhD (PI). The samples were collected by Vishwajit Nimgaonkar’s group at the University of Pittsburgh, as part of a multi-institutional collaborative research project with Jordan Smoller, MD, DSc, and Pamela Sklar, MD, PhD, Massachusetts General Hospital (grant MH63420). Data and biomaterials generated in Study 6 were collected by the Molecular Genetics of Schizophrenia, part 1 (MGS1), and funded by collaborative NIMH grants to Evanston Northwestern Healthcare/Northwestern University, Evanston, IL, MH059571, Pablo V Gejman, MD (Collaboration Coordinator; PI), and Alan R Sanders, MD; Emory University School of Medicine, Atlanta, GA, MH59587, Farooq Amin, MD (PI); University of California, San Francisco, CA, MH60870, William Byerley, MD (PI); University of Iowa, Iowa City, IA, MH59566, Raymond Crowe, MD (PI), Donald Black, MD; Washington University, St. Louis, MO, U01, MH060879, C Robert Cloninger, MD (PI); University of Colorado, Denver, CO, MH059565, Robert Freedman, MD (PI), Ann Olincy, MD; University of Pennsylvania, Philadelphia, PA, MH061675, Douglas Levinson, MD (PI), Nancy Buccola, APRN, BC, MSN, New Orleans, LA; University of Queensland, Queensland, Australia, MH059588, Bryan Mowry, MD (PI); and Mt. Sinai School of Medicine, New York, NY, MH059586, Jeremy Silverman, PhD (PI). Data and biomaterials used in Study 23 were collected by the University of Pittsburgh and funded by an NIMH grant (Genetic Susceptibility in Schizophrenia, MH 56242) to Vishwajit Nimgaonkar, MD, PhD. Additional Principal Investigators on this grant include Smita Deshpande, MD, and Dr Ram Moanohar Lohia Hospital, New Delhi, India; and Michael Owen, MD, PhD, University of Wales College of Medicine, Cardiff, UK. Most importantly, we thank the families who have participated in and contributed to these studies.
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Doyle, G., Crist, R., Karatas, E. et al. Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia. Neuropsychopharmacol. 42, 2602–2611 (2017). https://doi.org/10.1038/npp.2017.115
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