Abstract
Background
The 15q13.3 microdeletion is associated with several neuropsychiatric disorders, including
autism and schizophrenia. Previous association and functional studies have investigated
the potential role of several genes within the deletion in neuronal dysfunction, but
the molecular effects of the deletion as a whole remain largely unknown.
Methods
Induced pluripotent stem cells, from 3 patients with the 15q13.3 microdeletion and
3 control subjects, were generated and converted into induced neurons. We analyzed
the effects of the 15q13.3 microdeletion on genome-wide gene expression, DNA methylation,
chromatin accessibility, and sensitivity to cisplatin-induced DNA damage. Furthermore,
we measured gene expression changes in induced neurons with CRISPR (clustered regularly
interspaced short palindromic repeats) knockouts of individual 15q13.3 microdeletion
genes.
Results
In both induced pluripotent stem cells and induced neurons, gene copy number change
within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression
and no compensatory changes in DNA methylation or chromatin accessibility, supporting
the model that haploinsufficiency of genes within the deleted region drives the disorder.
Furthermore, we observed global effects of the microdeletion on the transcriptome
and epigenome, with disruptions in several neuropsychiatric disorder–associated pathways
and gene families, including Wnt signaling, ribosome function, DNA binding, and clustered
protocadherins. Individual gene knockouts mirrored many of the observed changes in
an overlapping fashion between knockouts.
Conclusions
Our multiomics analysis of the 15q13.3 microdeletion revealed downstream effects in
pathways previously associated with neuropsychiatric disorders and indications of
interactions between genes within the deletion. This molecular systems analysis can
be applied to other chromosomal aberrations to further our etiological understanding
of neuropsychiatric disorders.
Keywords
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References
- Further delineation of the 15q13 microdeletion and duplication syndromes: A clinical spectrum varying from non-pathogenic to a severe outcome.J Med Genet. 2009; 46: 511-523
- A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures.Nat Genet. 2008; 40: 322-328
- Delineating the 15q13.3 microdeletion phenotype: A case series and comprehensive review of the literature.Genet Med. 2015; 17: 149-157
- Pharmaco-genetically guided treatment of recurrent rage outbursts in an adult male with 15q13.3 deletion syndrome.Am J Med Genet A. 2011; 155: 805-810
- Functional consequences of CHRNA7 copy-number alterations in induced pluripotent stem cells and neural progenitor cells.Am J Hum Genet. 2017; 101: 874-887
- Evidence in postmortem brain tissue for decreased numbers of hippocampal nicotinic receptors in schizophrenia.Biol Psychiatry. 1995; 38: 22-33
- Neuronal nicotinic acetylcholine receptor subunits in autism: An immunohistochemical investigation in the thalamus.Neurobiol Dis. 2005; 19: 366-377
- Hippocampal α7 nicotinic acetylcholine receptor levels in patients with schizophrenia, bipolar disorder, or major depressive disorder.Bipolar Disord. 2011; 13: 701-707
- OTUD7A regulates neurodevelopmental phenotypes in the 15q13.3 microdeletion syndrome.Am J Hum Genet. 2018; 102: 278-295
- Otud7a Knockout Mice Recapitulate Many Neurological Features of 15q13.3 Microdeletion Syndrome.Am J Hum Genet. 2018; 102: 296-308
- Scan statistic-based analysis of exome sequencing data identifies FAN1 at 15q13.3 as a susceptibility gene for schizophrenia and autism.Proc Natl Acad Sci U S A. 2014; 111: 343-348
- FAN1 mutations cause karyomegalic interstitial nephritis, linking chronic kidney failure to defective DNA damage repair.Nat Genet. 2013; 44: 910-915
- Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion.Science. 2015; 347: 1465-1470
- Genome-wide gene expression in a patient with 15q13.3 homozygous microdeletion syndrome.Eur J Hum Genet. 2013; 21: 1093-1099
- Epigenetic regulations in neuropsychiatric disorders.Front Genet. 2019; 10: 1-30
- Rapid single-step induction of functional neurons from human pluripotent stem cells.. 2013; 78: 785-798
- Fast and accurate long-read alignment with Burrows-Wheeler transform.Bioinformatics. 2010; 26: 589-595
- BEDTools: A flexible suite of utilities for comparing genomic features.Bioinformatics. 2010; 26: 841-842
- CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.Genome Res. 2011; 21: 974-984
- TopHat: Discovering splice junctions with RNA-Seq.Bioinformatics. 2009; 25: 1105-1111
- Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.Genome Biol. 2014; 15: 550
- WebGestalt 2017: A more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.Nucleic Acids Res. 2017; 45: 130-137
- Fast gapped-read alignment with Bowtie 2.Nat Methods. 2012; 9: 357-359
- Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications.Bioinformatics. 2011; 27: 1571-1572
- methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles.Genome Biol. 2012; 13: R87
- Metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.Genome Res. 2016; 26: 256-262
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.Nat Methods. 2013; 10: 1213-1218
- Model-based analysis of ChIP-Seq (MACS).Genome Biol. 2008; 9: R137
- DiffBind: Differential binding analysis of ChIP-Seq peak data.(Available at:) (Accessed June 1, 2020)
- Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.Mol Cell. 2010; 38: 576-589
- Modeling gene regulation from paired expression and chromatin accessibility data.Proc Natl Acad Sci U S A. 2017; 114: E4914-E4923
- UniProt: The universal protein knowledgebase.Nucleic Acids Res. 2017; 45: D158-D169
- Copy number variants in schizophrenia: Confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications.Am J Psychiatry. 2011; 168: 302-316
- Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia.Nature. 2011; 471: 499-503
- Dominant KCNA2 mutation causes episodic ataxia and pharmacoresponsive epilepsy.Neurology. 2016; 87: 1975-1984
- Europe PMC funders group linkage and association analysis of CACNG3 in childhood absence epilepsy.. 2008; 15: 463-472
- SCN8A-related epilepsy with encephalopathy.(Available at:) (Accessed June 1, 2020)
- Mutations in SPATA5 are associated with microcephaly, intellectual disability, seizures, and hearing loss.Am J Hum Genet. 2015; 97: 457-464
- Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment.Hum Mol Genet. 2015; 24: 3172-3180
- Loss of the scavenger mRNA decapping enzyme DCPS causes syndromic intellectual disability with neuromuscular defects.Hum Mol Genet. 2015; 24: 3163-3171
- Novel LINS1 missense mutation in a family with non-syndromic intellectual disability.Am J Med Genet A. 2017; 173: 1041-1046
- Genetic variation at the 22q11 PRODH2/DGCR6 locus presents an unusual pattern and increases susceptibility to schizophrenia.Proc Natl Acad Sci U S A. 2002; 99: 3717-3722
- Recurrent rearrangements in synaptic and neurodevelopmental genes and shared biologic pathways in schizophrenia, autism, and mental retardation.Arch Gen Psychiatry. 2009; 66: 947-956
- Signal Transduction in Ribosome Biogenesis: A Recipe to Avoid Disaster.Int J Mol Sci. 2019; 20: 2718
- Regulation of Wnt signaling by protocadherins.Semin Cell Dev Biol. 2017; 69: 158-171
- Epigenetic dysregulation of protocadherins in human disease.Semin Cell Dev Biol. 2017; 69: 172-182
- Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model.bioRxiv. 2020; https://doi.org/10.1101/2020.02.09.940965
- Haplotype of single nucleotide polymorphisms in exon 6 of the MZF-1 gene and Alzheimer’s disease.J Alzheimers Dis. 2013; 34: 439-447
- Mutations in two large pedigrees highlight the role of ZNF711 in X-linked intellectual disability.Gene. 2017; 605: 92-98
- Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.Nat Genet. 2018; 50: 668-681
- Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis.Arch Neurol. 2011; 68: 587-593
- Silencing of the Drosophila ortholog of SOX5 leads to abnormal neuronal development and behavioral impairment.Hum Mol Genet. 2017; 26: 1472-1482
- Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features.Hum Mutat. 2012; 33: 728-740
- Social stress in adolescents induces depression and brain-region-specific modulation of the transcription factor MAX.Transl Psychiatry. 2016; 6: e914
- Identification of protein biomarkers for schizophrenia and bipolar disorder in the postmortem prefrontal cortex using SELDI-TOF-MS ProteinChip profiling combined with MALDI-TOF-PSD-MS analysis.Neurobiol Dis. 2006; 23: 61-76
- Distribution and functional properties of human KCNH8 (Elk1) potassium channels.Am J Physiol Cell Physiol. 2003; 285: C1356-C1366
- Contactin 4 as an autism susceptibility locus.Autism Res. 2011; 4: 189-199
- Psychophysiological endophenotypes to characterize mechanisms of known schizophrenia genetic loci.Psychol Med. 2017; 47: 1116-1125
- Zinc deficiency and low enterocyte zinc transporter expression in human patients with autism related mutations in SHANK3.Sci Rep. 2017; 7: 45190
- Vps10 family proteins and the retromer complex in aging-related neurodegeneration and diabetes.J Neurosci. 2012; 32: 14080-14086
- Regulation of neuronal function by choline and 4OH-GTS-21 through alpha 7 nicotinic receptors.J Neurophysiol. 2003; 89: 1797-1806
- The nicotinic acetylcholine receptor: The founding father of the pentameric ligand-gated ion channel superfamily.Jf Biol Chem. 2012; 287: 40207-40215
- Mitochondrial dysfunction in schizophrenia: Evidence for compromised brain metabolism and oxidative stress.Mol Psychiatry. 2004; 9: 684-697
- Mitochondrial involvement in psychiatric disorders.Ann Med. 2008; 40: 281-295
- Perturbation in mitochondrial network dynamics and in complex I dependent cellular respiration in schizophrenia.Biol Psychiatry. 2011; 69: 980-988
- Frequency and association of mitochondrial genetic variants with neurological disorders.Mitochondrion. 2019; 46: 345-360
- Transcriptomic networks implicate neuronal energetic abnormalities in three mouse models harboring autism and schizophrenia-associated mutations.Mol Psychiatry. 2019; ([published online ahead of print Nov 8])
- ScNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.Nat Commun. 2018; 9: 781
- Open chromatin dynamics reveals stage-specific transcriptional networks in hiPSC-based neurodevelopmental model.Stem Cell Res. 2018; 29: 88-98
- Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion.BMC Syst Biol. 2016; 10: 105
- Consistently altered expression of gene sets in postmortem brains of individuals with major psychiatric disorders.Transl Psychiatry. 2016; 6e890
- Meta-analysis of differentially expressed genes in autism based on gene expression data.. 2015; 14: 2146-2155
- Reduced protein synthesis in schizophrenia patient-derived olfactory cells.Transl Psychiatry. 2015; 5: e663
- Increased abundance of translation machinery in stem cell-derived neural progenitor cells from four schizophrenia patients.Transl Psychiatry. 2015; 5e662
- DNA damage and repair in schizophrenia and autism: Implications for cancer comorbidity and beyond.Int J Mol Sci. 2016; 17: 856
- DNA damage in major psychiatric diseases.Neurotox Res. 2016; 30: 251-267
- A human neurodevelopmental model for Williams syndrome.Nature. 2016; 536: 338-343
- Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons.Mol Autism. 2019; 10: 51
- Wnt signaling in the nervous system and in Alzheimer’s disease.J Mol Cell Biol. 2014; 6: 64-74
- Wnt signaling in neuropsychiatric disorders: Ties with adult hippocampal neurogenesis and behavior.Neurosci Biobehav Rev. 2014; 47: 369-383
- Altered WNT signaling in human induced pluripotent stem cell neural progenitor cells derived from four schizophrenia patients.Biol Psychiatry. 2015; 78: e29-e34
- alpha- and gamma-Protocadherins negatively regulate PYK2.J Biol Chem. 2008; 284: 2880-2890
- Protocadherin clusters and cell adhesion kinase regulate dendrite complexity through Rho GTPase.J Mol Cell Biol. 2012; 4: 362-376
- Bioinformatic evaluation of transcriptional regulation of WNT pathway genes with reference to diabetic nephropathy.J Diabetes Res 2016. 2016; : 7684038
- The Wnt-inducible transcription factor Twist1 inhibits chondrogenesis.J Biol Chem. 2006; 281: 1381-1388
- Mechanism for nicotine-induced up-regulation of Wnt signaling in human alveolar interstitial fibroblasts.Exp Lung Res. 2011; 37: 144-154
- Nicotine prevents synaptic impairment induced by amyloid-β oligomers through α7-nicotinic acetylcholine receptor activation.Neuromol Med. 2013; 15: 549-569
- Wnt/β-catenin signaling plays an essential role in α7 nicotinic receptor-mediated neuroprotection of dopaminergic neurons in a mouse Parkinson’s disease model.Biochem Pharmacol. 2017; 140: 115-123
- Deubiquitinase OTUD6B isoforms are important regulators of growth and proliferation.Mol Cancer Res. 2017; 15: 117-127
- Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized.eLife. 2020; 9e54023
- FAN1 acts with FANCI-FANCD2 to promote DNA interstrand cross-link repair.Science. 2010; 329: 693-696
- KIAA1018/FAN1 nuclease protects cells against genomic instability induced by interstrand cross-linking agents.Proc Natl Acad Sci U S A. 2010; 107: 21553-21557
- A genetic screen identifies FAN1, a Fanconi anemia-associated nuclease necessary for DNA interstrand crosslink repair.Mol Cell. 2010; 39: 36-47
- PTEN and myotubularin phosphatases: From 3-phosphoinositide dephosphorylation to disease.Trends Cell Biol. 2002; 12: 579-585
- A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.Mol Cell. 2009; 35: 228-239
- The Kruppel-like transcription factor KLF13 is a novel regulator of heart development.EMBO J. 2006; 25: 5201-5213
- The KLF family of transcriptional regulators in cardiomyocyte proliferation and differentiation.Cell Cycle. 2007; 6: 117-121
- Detection of de novo del(18)(q22.2) and a familial of 15q13.2-q13.3 microduplication in a fetus with congenital heart defects.Taiwan J Obstet Gynecol. 2019; 58: 704-708
- Chromosome 15q13 microduplication in a fetus with cardiac rhabdomyoma: A case report.Mol Cytogenet. 2019; 12: 24
- RFLAT-1: A new zinc finger transcription factor that activates RANTES gene expression in T lymphocytes.Immunity. 1999; 10: 93-103
- An interaction-based model for neuropsychiatric features of copy-number variants.PLoS Genet. 2019; 15e1007879
- Oligogenic effects of 16p11.2 copy-number variation on craniofacial development.Cell Rep. 2019; 28: 3320-3328.e4
Article info
Publication history
Published online: July 01, 2020
Accepted:
June 16,
2020
Received in revised form:
June 16,
2020
Received:
October 14,
2019
Identification
Copyright
© 2020 Society of Biological Psychiatry.
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- Cross-Platform Validation of 15q13.3 Microdeletion Network Effects in Human NeuronsBiological PsychiatryVol. 89Issue 5
- PreviewHeterozygous copy number variants are highly penetrant and pleiotropic deletions or duplications that confer risk to a variety of neuropsychiatric disease (1). Among these, 15q13.3 microdeletions (∼1.5–2.0 Mbp) result in developmental/intellectual disability, schizophrenia, autism spectrum disorder, and epilepsy, among other conditions, affecting a core set of 7 protein-coding genes (CHRNA7, FAN1, TRPM1, KLF13, OTUD7A, MTMR10, and ARHGAP11B), and 1 microRNA (MIR211) (2). While previous studies nominated candidate genes to explain the psychiatric symptoms associated with the microdeletion, the network effects of the gene cluster have yet to be explored under a human neuronal model.
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