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Ben-Azu B, Adebayo OG, Fokoua AR, Oritsemuelebi B, Chidebe EO, Nwogueze CB, Kumanwee L, Uyere GE, Emuakpeje MT. Antipsychotic effect of diosgenin in ketamine-induced murine model of schizophrenia: Involvement of oxidative stress and cholinergic transmission. IBRO Neurosci Rep 2024; 16:86-97. [PMID: 38282757 PMCID: PMC10818187 DOI: 10.1016/j.ibneur.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024] Open
Abstract
A decrease in the levels of antioxidant arsenals exacerbate generation of reactive oxygen/nitrogen species, leading to neurochemical dysfunction, with significant impact on the pathogenesis of psychotic disorders such as schizophrenia. This study examined the preventive and reversal effects of diosgenin, a phyto-steroidal saponin with antioxidant functions in mice treated with ketamine which closely replicates schizophrenia-like symptoms in human and laboratory animals. In the preventive phase, adult mice cohorts were clustered into 5 groups (n = 9). Groups 1 and 2 received saline (10 mL/kg, i.p.), groups 3 and 4 were pretreated with diosgenin (25 and 50 mg/kg), and group 5 received risperidone (0.5 mg/kg) orally for 14 days. Mice in groups 2-5 additionally received a daily dose of ketamine (20 mg/kg, i.p.) or saline (10 mL/kg/day, i.p.). In the reversal phase, mice received intraperitoneal injection of ketamine or saline for 14 consecutive days prior to diosgenin (25 and 50 mg/kg/p.o./day) and risperidone (0.5 mg/kg/p.o./day) treatment from days 8-14. Mice were assessed for behavioral changes. Oxidative, nitrergic markers, and cholinergic (acetylcholinesterase activity) transmission were examined in the striatum, prefrontal-cortex and hippocampus. Diosgenin prevented and reversed hyperlocomotion, cognitive and social deficits in mice treated with ketamine relative to ketamine groups. The increased acetylcholinesterase, malondialdehyde and nitrite levels produced by ketamine were reduced by diosgenin in the striatum, prefrontal-cortex and hippocampus, but did not reverse striatal nitrite level. Diosgenin increased glutathione, and catalase levels, except for hippocampal catalase activity when compared with ketamine controls. Conclusively, these biochemical changes might be related to the behavioral deficits in ketamine-treated mice, which were prevented and reversed by diosgenin.
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Affiliation(s)
- Benneth Ben-Azu
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
| | - Olusegun G. Adebayo
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
- Neurophysiology Unit, Department of Physiology, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Aliance Romain Fokoua
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
- Research unit of Neuroinflammatory and Cardiovascular Pharmacology, Department of Animal Biology, Faculty of Sciences, University of Dschang, Cameroon
| | - Benjamin Oritsemuelebi
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
| | - Emmanuel O. Chidebe
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
| | - Chukwuebuka B. Nwogueze
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
| | - Lenatababari Kumanwee
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
| | - God'swill E. Uyere
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
| | - Micheal T. Emuakpeje
- DELSU Joint Canada-Israel Neuroscience and Biopsychiatry Laboratory, Department of Pharmacology, Faculty of Basic Medical Sciences, College of Health Sciences, Delta State University, Abraka, Delta State, Nigeria
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Bamford RA, Zuko A, Eve M, Sprengers JJ, Post H, Taggenbrock RLRE, Fäβler D, Mehr A, Jones OJR, Kudzinskas A, Gandawijaya J, Müller UC, Kas MJH, Burbach JPH, Oguro-Ando A. CNTN4 modulates neural elongation through interplay with APP. Open Biol 2024; 14:240018. [PMID: 38745463 DOI: 10.1098/rsob.240018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 05/16/2024] Open
Abstract
The neuronal cell adhesion molecule contactin-4 (CNTN4) is genetically associated with autism spectrum disorder (ASD) and other psychiatric disorders. Cntn4-deficient mouse models have previously shown that CNTN4 plays important roles in axon guidance and synaptic plasticity in the hippocampus. However, the pathogenesis and functional role of CNTN4 in the cortex has not yet been investigated. Our study found a reduction in cortical thickness in the motor cortex of Cntn4 -/- mice, but cortical cell migration and differentiation were unaffected. Significant morphological changes were observed in neurons in the M1 region of the motor cortex, indicating that CNTN4 is also involved in the morphology and spine density of neurons in the motor cortex. Furthermore, mass spectrometry analysis identified an interaction partner for CNTN4, confirming an interaction between CNTN4 and amyloid-precursor protein (APP). Knockout human cells for CNTN4 and/or APP revealed a relationship between CNTN4 and APP. This study demonstrates that CNTN4 contributes to cortical development and that binding and interplay with APP controls neural elongation. This is an important finding for understanding the physiological function of APP, a key protein for Alzheimer's disease. The binding between CNTN4 and APP, which is involved in neurodevelopment, is essential for healthy nerve outgrowth.
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Affiliation(s)
- Rosemary A Bamford
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Amila Zuko
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University , Nijmegen, The Netherlands
| | - Madeline Eve
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Jan J Sprengers
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht, Institute for Pharmaceutical Sciences, Utrecht University , Utrecht, The Netherlands
- Netherlands Proteomics Centre , Utrecht, The Netherlands
| | - Renske L R E Taggenbrock
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
| | - Dominique Fäβler
- Institute for Pharmacy and Molecular Biotechnology (IPMB), Functional Genomics, University of Heidelberg , Heidelberg 69120, Germany
| | - Annika Mehr
- Institute for Pharmacy and Molecular Biotechnology (IPMB), Functional Genomics, University of Heidelberg , Heidelberg 69120, Germany
| | - Owen J R Jones
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Aurimas Kudzinskas
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Josan Gandawijaya
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
| | - Ulrike C Müller
- Institute for Pharmacy and Molecular Biotechnology (IPMB), Functional Genomics, University of Heidelberg , Heidelberg 69120, Germany
| | - Martien J H Kas
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen , Groningen, The Netherlands
| | - J Peter H Burbach
- Department of Translational Neuroscience, UMC Utrecht Brain Center, UMC Utrecht , Utrecht 3508 AB, The Netherlands
| | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, Tokyo University of Science , Noda, Chiba, Japan
- Research Institute for Science and Technology, Tokyo University of Science , Tokyo, Japan
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3
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Pu H, Gao C, Zou Y, Zhao L, Li G, Liu C, Zhao L, Zheng M, Sheng G, Sun X, Hao X, Wang C, He X, Xiao J. Single cell transcriptome profiling of infrapatellar fat pad highlights the role of interstitial inflammatory fibroblasts in osteoarthritis. Int Immunopharmacol 2024; 131:111888. [PMID: 38522139 DOI: 10.1016/j.intimp.2024.111888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES Osteoarthritis (OA) is a whole-joint disease in which the role of the infrapatellar fat pad (IFP) in its pathogenesis is unclear. Our study explored the cellular heterogeneity of IFP to understand OA and identify therapeutic targets. METHODS Single-cell and single-nuclei RNA sequencing were used to analyze 10 IFP samples, comprising 5 from OA patients and 5 from healthy controls. Analyses included differential gene expression, enrichment, pseudotime trajectory, and cellular communication, along with comparative studies with visceral and subcutaneous fats. Key subcluster and pathways were validated using multiplex immunohistochemistry. RESULTS The scRNA-seq performed on the IFPs of the OA and control group profiled the gene expressions of over 49,674 cells belonging to 11 major cell types. We discovered that adipose stem and progenitor cells (ASPCs), contributing to the formation of both adipocytes and synovial-lining fibroblasts (SLF). Interstitial inflammatory fibroblasts (iiFBs) were a subcluster of ASPCs that exhibit notable pro-inflammatory and proliferative characteristics. We identified four adipocyte subtypes, with one subtype showing a reduced lipid synthesis ability. Furthermore, iiFBs modulated the activities of macrophages and T cells in the IFP. Compared to subcutaneous and visceral adipose tissues, iiFBs represented a distinctive subpopulation of ASPCs in IFP that regulated cartilage proliferation through the MK pathway. CONCLUSION This study presents a comprehensive single-cell transcriptomic atlas of IFP, uncovering its complex cellular landscape and potential impact on OA progression. Our findings highlight the role of iiFBs in OA, especially through MK pathway, opening new avenues for understanding OA pathogenesis and developing novel targeted therapies.
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Affiliation(s)
- Hongxu Pu
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chenghao Gao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Zou
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liming Zhao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guanghao Li
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changyu Liu
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Libo Zhao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meng Zheng
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Gaohong Sheng
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuying Sun
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jun Xiao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Zakharova IS, Shevchenko AI, Arssan MA, Sleptcov AA, Nazarenko MS, Zarubin AA, Zheltysheva NV, Shevchenko VA, Tmoyan NA, Saaya SB, Ezhov MV, Kukharchuk VV, Parfyonova YV, Zakian SM. iPSC-Derived Endothelial Cells Reveal LDLR Dysfunction and Dysregulated Gene Expression Profiles in Familial Hypercholesterolemia. Int J Mol Sci 2024; 25:689. [PMID: 38255763 PMCID: PMC10815294 DOI: 10.3390/ijms25020689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Defects in the low-density lipoprotein receptor (LDLR) are associated with familial hypercholesterolemia (FH), manifested by atherosclerosis and cardiovascular disease. LDLR deficiency in hepatocytes leads to elevated blood cholesterol levels, which damage vascular cells, especially endothelial cells, through oxidative stress and inflammation. However, the distinctions between endothelial cells from individuals with normal and defective LDLR are not yet fully understood. In this study, we obtained and examined endothelial derivatives of induced pluripotent stem cells (iPSCs) generated previously from conditionally healthy donors and compound heterozygous FH patients carrying pathogenic LDLR alleles. In normal iPSC-derived endothelial cells (iPSC-ECs), we detected the LDLR protein predominantly in its mature form, whereas iPSC-ECs from FH patients have reduced levels of mature LDLR and show abolished low-density lipoprotein uptake. RNA-seq of mutant LDLR iPSC-ECs revealed a unique transcriptome profile with downregulated genes related to monocarboxylic acid transport, exocytosis, and cell adhesion, whereas upregulated signaling pathways were involved in cell secretion and leukocyte activation. Overall, these findings suggest that LDLR defects increase the susceptibility of endothelial cells to inflammation and oxidative stress. In combination with elevated extrinsic cholesterol levels, this may result in accelerated endothelial dysfunction, contributing to early progression of atherosclerosis and other cardiovascular pathologies associated with FH.
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Affiliation(s)
- Irina S. Zakharova
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.S.Z.); (A.I.S.); (M.A.A.); (N.V.Z.); (V.A.S.)
| | - Alexander I. Shevchenko
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.S.Z.); (A.I.S.); (M.A.A.); (N.V.Z.); (V.A.S.)
| | - Mhd Amin Arssan
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.S.Z.); (A.I.S.); (M.A.A.); (N.V.Z.); (V.A.S.)
| | - Aleksei A. Sleptcov
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Science, 634050 Tomsk, Russia; (A.A.S.); (M.S.N.); (A.A.Z.)
| | - Maria S. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Science, 634050 Tomsk, Russia; (A.A.S.); (M.S.N.); (A.A.Z.)
| | - Aleksei A. Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Science, 634050 Tomsk, Russia; (A.A.S.); (M.S.N.); (A.A.Z.)
| | - Nina V. Zheltysheva
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.S.Z.); (A.I.S.); (M.A.A.); (N.V.Z.); (V.A.S.)
| | - Vlada A. Shevchenko
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.S.Z.); (A.I.S.); (M.A.A.); (N.V.Z.); (V.A.S.)
| | - Narek A. Tmoyan
- Federal State Budgetary Institution, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, Ministry of Health of Russian Federation, 121552 Moscow, Russia; (N.A.T.); (M.V.E.); (V.V.K.); (Y.V.P.)
| | - Shoraan B. Saaya
- E.N. Meshalkin National Medical Research Centre, Ministry of Health Care of the Russian Federation, 630055 Novosibirsk, Russia;
| | - Marat V. Ezhov
- Federal State Budgetary Institution, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, Ministry of Health of Russian Federation, 121552 Moscow, Russia; (N.A.T.); (M.V.E.); (V.V.K.); (Y.V.P.)
| | - Valery V. Kukharchuk
- Federal State Budgetary Institution, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, Ministry of Health of Russian Federation, 121552 Moscow, Russia; (N.A.T.); (M.V.E.); (V.V.K.); (Y.V.P.)
| | - Yelena V. Parfyonova
- Federal State Budgetary Institution, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, Ministry of Health of Russian Federation, 121552 Moscow, Russia; (N.A.T.); (M.V.E.); (V.V.K.); (Y.V.P.)
| | - Suren M. Zakian
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.S.Z.); (A.I.S.); (M.A.A.); (N.V.Z.); (V.A.S.)
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Parikh K, Quintero Reis A, Wendt FR. Association between suicidal ideation and tandem repeats in contactins. Front Psychiatry 2024; 14:1236540. [PMID: 38239902 PMCID: PMC10794671 DOI: 10.3389/fpsyt.2023.1236540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
Background Death by suicide is one of the leading causes of death among adolescents. Genome-wide association studies (GWAS) have identified loci that associate with suicidal ideation and related behaviours. One such group of loci are the six contactin genes (CNTN1-6) that are critical to neurodevelopment through regulating neurite structure. Because single nucleotide polymorphisms (SNPs) detected by GWAS often map to non-coding intergenic regions, we investigated whether repetitive variants in CNTNs associated with suicidality in a young cohort aged 8 to 21. Understanding the genetic liability of suicidal thought and behavior in this age group will promote early intervention and treatment. Methods Genotypic and phenotypic data were obtained from the Philadelphia Neurodevelopment Cohort (PNC). Across six CNTNs, 232 short tandem repeats (STRs) were analyzed in up to 4,595 individuals of European ancestry who expressed current, previous, or no suicidal ideation. STRs were imputed into SNP arrays using a phased SNP-STR haplotype reference panel from the 1000 Genomes Project. We tested several additive and interactive models of locus-level burden (i.e., sum of STR alleles) with respect to suicidal ideation. Additive models included sex, birth year, developmental stage ("DevStage"), and the first 10 principal components of ancestry as covariates; interactive models assessed the effect of STR-by-DevStage considering all other covariates. Results CNTN1-[T]N interacted with DevStage to increase risk for current suicidal ideation (CNTN1-[T]N-by-DevStage; p = 0.00035). Compared to the youngest age group, the middle (OR = 1.80, p = 0.0514) and oldest (OR = 3.82, p = 0.0002) participant groups had significantly higher odds of suicidal ideation as their STR length expanded; this result was independent of polygenic scores for suicidal ideation. Discussion These findings highlight diversity in the genetic effects (i.e., SNP and STR) acting on suicidal thoughts and behavior and advance our understanding of suicidal ideation across childhood and adolescence.
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Affiliation(s)
- Kairavi Parikh
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
| | - Andrea Quintero Reis
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R. Wendt
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
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6
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Glessner JT, Khan ME, Chang X, Liu Y, Otieno FG, Lemma M, Slaby I, Hain H, Mentch F, Li J, Kao C, Sleiman PMA, March ME, Connolly J, Hakonarson H. Rare recurrent copy number variations in metabotropic glutamate receptor interacting genes in children with neurodevelopmental disorders. J Neurodev Disord 2023; 15:14. [PMID: 37120522 PMCID: PMC10148449 DOI: 10.1186/s11689-023-09483-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/06/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs), such as attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD), are examples of complex and partially overlapping phenotypes that often lack definitive corroborating genetic information. ADHD and ASD have complex genetic associations implicated by rare recurrent copy number variations (CNVs). Both of these NDDs have been shown to share similar biological etiologies as well as genetic pleiotropy. METHODS Platforms aimed at investigating genetic-based associations, such as high-density microarray technologies, have been groundbreaking techniques in the field of complex diseases, aimed at elucidating the underlying disease biology. Previous studies have uncovered CNVs associated with genes within shared candidate genomic networks, including glutamate receptor genes, across multiple different NDDs. To examine shared biological pathways across two of the most common NDDs, we investigated CNVs across 15,689 individuals with ADHD (n = 7920), ASD (n = 4318), or both (n = 3,416), as well as 19,993 controls. Cases and controls were matched by genotype array (i.e., Illumina array versions). Three case-control association studies each calculated and compared the observed vs. expected frequency of CNVs across individual genes, loci, pathways, and gene networks. Quality control measures of confidence in CNV-calling, prior to association analyses, included visual inspection of genotype and hybridization intensity. RESULTS Here, we report results from CNV analysis in search for individual genes, loci, pathways, and gene networks. To extend our previous observations implicating a key role of the metabotropic glutamate receptor (mGluR) network in both ADHD and autism, we exhaustively queried patients with ASD and/or ADHD for CNVs associated with the 273 genomic regions of interest within the mGluR gene network (genes with one or two degrees protein-protein interaction with mGluR 1-8 genes). Among CNVs in mGluR network genes, we uncovered CNTN4 deletions enriched in NDD cases (P = 3.22E - 26, OR = 2.49). Additionally, we uncovered PRLHR deletions in 40 ADHD cases and 12 controls (P = 5.26E - 13, OR = 8.45) as well as clinically diagnostic relevant 22q11.2 duplications and 16p11.2 duplications in 23 ADHD + ASD cases and 9 controls (P = 4.08E - 13, OR = 15.05) and 22q11.2 duplications in 34 ADHD + ASD cases and 51 controls (P = 9.21E - 9, OR = 3.93); those control samples were not with previous 22qDS diagnosis in their EHR records. CONCLUSION Together, these results suggest that disruption in neuronal cell-adhesion pathways confers significant risk to NDDs and showcase that rare recurrent CNVs in CNTN4, 22q11.2, and 16p11.2 are overrepresented in NDDs that constitute patients predominantly suffering from ADHD and ASD. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02286817 First Posted: 10 November 14, ClinicalTrials.gov Identifier: NCT02777931 first posted: 19 May 2016, ClinicalTrials.gov Identifier: NCT03006367 first posted: 30 December 2016, ClinicalTrials.gov Identifier: NCT02895906 first posted: 12 September 2016.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Munir E Khan
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - F George Otieno
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Maria Lemma
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Isabella Slaby
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Jin Li
- Department of Cell Biology, the Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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7
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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Wang N, Lv L, Huang X, Shi M, Dai Y, Wei Y, Xu B, Fu C, Huang H, Shi H, Liu Y, Hu X, Qin D. Gene editing in monogenic autism spectrum disorder: animal models and gene therapies. Front Mol Neurosci 2022; 15:1043018. [PMID: 36590912 PMCID: PMC9794862 DOI: 10.3389/fnmol.2022.1043018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) is a lifelong neurodevelopmental disease, and its diagnosis is dependent on behavioral manifestation, such as impaired reciprocal social interactions, stereotyped repetitive behaviors, as well as restricted interests. However, ASD etiology has eluded researchers to date. In the past decades, based on strong genetic evidence including mutations in a single gene, gene editing technology has become an essential tool for exploring the pathogenetic mechanisms of ASD via constructing genetically modified animal models which validates the casual relationship between genetic risk factors and the development of ASD, thus contributing to developing ideal candidates for gene therapies. The present review discusses the progress in gene editing techniques and genetic research, animal models established by gene editing, as well as gene therapies in ASD. Future research should focus on improving the validity of animal models, and reliable DNA diagnostics and accurate prediction of the functional effects of the mutation will likely be equally crucial for the safe application of gene therapies.
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Affiliation(s)
- Na Wang
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Longbao Lv
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaoyi Huang
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Mingqin Shi
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Youwu Dai
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yuanyuan Wei
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Bonan Xu
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Chenyang Fu
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Haoyu Huang
- Department of Pediatric Rehabilitation Medicine, Kunming Children’s Hospital, Kunming, Yunnan, China
| | - Hongling Shi
- Department of Rehabilitation Medicine, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yun Liu
- Department of Pediatric Rehabilitation Medicine, Kunming Children’s Hospital, Kunming, Yunnan, China,*Correspondence: Dongdong Qin Yun Liu Xintian Hu
| | - Xintian Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,*Correspondence: Dongdong Qin Yun Liu Xintian Hu
| | - Dongdong Qin
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China,*Correspondence: Dongdong Qin Yun Liu Xintian Hu
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9
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Fernandez A, Gomez MT, Vidal R. Lack of ApoE inhibits ADan amyloidosis in a mouse model of familial Danish dementia. J Biol Chem 2022; 299:102751. [PMID: 36436561 PMCID: PMC9792896 DOI: 10.1016/j.jbc.2022.102751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022] Open
Abstract
The Apolipoprotein E-ε4 allele (APOE-ε4) is the strongest genetic risk factor for late onset Alzheimer disease (AD). ApoE plays a critical role in amyloid-β (Aβ) accumulation in AD, and genetic deletion of the murine ApoE gene in mouse models results in a decrease or inhibition of Aβ deposition. The association between the presence of ApoE and amyloid in amyloidoses suggests a more general role for ApoE in the fibrillogenesis process. However, whether decreasing levels of ApoE would attenuate amyloid pathology in different amyloidoses has not been directly addressed. Familial Danish dementia (FDD) is an autosomal dominant neurodegenerative disease characterized by the presence of widespread parenchymal and vascular Danish amyloid (ADan) deposition and neurofibrillary tangles. A transgenic mouse model for FDD (Tg-FDD) is characterized by parenchymal and vascular ADan deposition. To determine the effect of decreasing ApoE levels on ADan accumulation in vivo, we generated a mouse model by crossing Tg-FDD mice with ApoE KO mice (Tg-FDD+/-/ApoE-/-). Lack of ApoE results in inhibition of ADan deposition up to 18 months of age. Additionally, our results from a genetic screen of Tg-FDD+/-/ApoE-/- mice emphasize the significant role for ApoE in neurodegeneration in FDD via glial-mediated mechanisms. Taken together, our findings suggest that the interaction between ApoE and ADan plays a key role in FDD pathogenesis, in addition to the known role for ApoE in amyloid plaque formation in AD.
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Affiliation(s)
- Anllely Fernandez
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Maria-Teresa Gomez
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, USA,For correspondence: Ruben Vidal
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10
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Choudhary A, Peles D, Nayak R, Mizrahi L, Stern S. Current progress in understanding schizophrenia using genomics and pluripotent stem cells: A meta-analytical overview. Schizophr Res 2022:S0920-9964(22)00406-6. [PMID: 36443183 DOI: 10.1016/j.schres.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/16/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022]
Abstract
Schizophrenia (SCZ) is a complex, heritable and polygenic neuropsychiatric disease, which disables the patients as well as decreases their life expectancy and quality of life. Common and rare variants studies on SCZ subjects have provided >100 genomic loci that hold importance in the context of SCZ pathophysiology. Transcriptomic studies from clinical samples have informed about the differentially expressed genes (DEGs) and non-coding RNAs in SCZ patients. Despite these advancements, no causative genes for SCZ were found and hence SCZ is difficult to recapitulate in animal models. In the last decade, induced Pluripotent Stem Cells (iPSCs)-based models have helped in understanding the neural phenotypes of SCZ by studying patient iPSC-derived 2D neuronal cultures and 3D brain organoids. Here, we have aimed to provide a simplistic overview of the current progress and advancements after synthesizing the enormous literature on SCZ genetics and SCZ iPSC-based models. Although further understanding of SCZ genetics and pathophysiological mechanisms using these technological advancements is required, the recent approaches have allowed to delineate important cellular mechanisms and biological pathways affected in SCZ.
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Affiliation(s)
- Ashwani Choudhary
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - David Peles
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Ritu Nayak
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Liron Mizrahi
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel.
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11
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Kushima I, Imaeda M, Tanaka S, Kato H, Oya-Ito T, Nakatochi M, Aleksic B, Ozaki N. Contribution of copy number variations to the risk of severe eating disorders. Psychiatry Clin Neurosci 2022; 76:423-428. [PMID: 35611833 PMCID: PMC9546291 DOI: 10.1111/pcn.13430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
Abstract
AIM Eating disorders (EDs) are complex, multifactorial psychiatric conditions. Previous studies identified pathogenic copy number variations associated with NDDs (NDD-CNVs) in ED patients. However, no statistical evidence for an association between NDD-CNVs and EDs has been demonstrated. Therefore, we examined whether NDD-CNVs confer risk for EDs. METHODS Using array comparative genomic hybridization (aCGH), we conducted a high-resolution CNV analysis of 71 severe female ED patients and 1045 female controls. According to the American College of Medical Genetics guidelines, we identified NDD-CNVs or pathogenic/likely pathogenic CNVs in NDD-linked loci. Gene set analysis was performed to examine the involvement of synaptic dysfunction in EDs. Clinical data were retrospectively examined for ED patients with NDD-CNVs. RESULTS Of the samples analyzed with aCGH, 70 severe ED patients (98.6%) and 1036 controls (99.1%) passed our quality control filtering. We obtained 189 and 2539 rare CNVs from patients and controls, respectively. NDD-CNVs were identified in 10.0% (7/70) of patients and 2.3% (24/1036) of controls. Statistical analysis revealed a significant association between NDD-CNVs and EDs (odds ratio = 4.69, P = 0.0023). NDD-CNVs in ED patients included 45,X and deletions at KATNAL2, DIP2A, PTPRT, RBFOX1, CNTN4, MACROD2, and FAM92B. Four of these genes were related to synaptic function. In gene set analysis, we observed a nominally significant enrichment of rare exonic CNVs in synaptic signaling in ED patients (odds ratio = 2.55, P = 0.0254). CONCLUSION Our study provides the first preliminary evidence that NDD-CNVs may confer risk for severe EDs. The pathophysiology may involve synaptic dysfunction.
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Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Miho Imaeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital, Nagoya, Japan
| | - Satoshi Tanaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,National Hospital Organization Higashiowari National Hospital, Nagoya, Japan.,The Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoko Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Nutrition, Shubun University, Nagoya, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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12
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Luo W, Cruz-Ochoa NA, Seng C, Egger M, Lukacsovich D, Lukacsovich T, Földy C. Pcdh11x controls target specification of mossy fiber sprouting. Front Neurosci 2022; 16:888362. [PMID: 36117624 PMCID: PMC9475199 DOI: 10.3389/fnins.2022.888362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Circuit formation is a defining characteristic of the developing brain. However, multiple lines of evidence suggest that circuit formation can also take place in adults, the mechanisms of which remain poorly understood. Here, we investigated the epilepsy-associated mossy fiber (MF) sprouting in the adult hippocampus and asked which cell surface molecules define its target specificity. Using single-cell RNAseq data, we found lack and expression of Pcdh11x in non-sprouting and sprouting neurons respectively. Subsequently, we used CRISPR/Cas9 genome editing to disrupt the Pcdh11x gene and characterized its consequences on sprouting. Although MF sprouting still developed, its target specificity was altered. New synapses were frequently formed on granule cell somata in addition to dendrites. Our findings shed light onto a key molecular determinant of target specificity in MF sprouting and contribute to understanding the molecular mechanism of adult brain rewiring.
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13
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Zhou J, Chen Q, Braun PR, Perzel Mandell KA, Jaffe AE, Tan HY, Hyde TM, Kleinman JE, Potash JB, Shinozaki G, Weinberger DR, Han S. Deep learning predicts DNA methylation regulatory variants in the human brain and elucidates the genetics of psychiatric disorders. Proc Natl Acad Sci U S A 2022; 119:e2206069119. [PMID: 35969790 PMCID: PMC9407663 DOI: 10.1073/pnas.2206069119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
There is growing evidence for the role of DNA methylation (DNAm) quantitative trait loci (mQTLs) in the genetics of complex traits, including psychiatric disorders. However, due to extensive linkage disequilibrium (LD) of the genome, it is challenging to identify causal genetic variations that drive DNAm levels by population-based genetic association studies. This limits the utility of mQTLs for fine-mapping risk loci underlying psychiatric disorders identified by genome-wide association studies (GWAS). Here we present INTERACT, a deep learning model that integrates convolutional neural networks with transformer, to predict effects of genetic variations on DNAm levels at CpG sites in the human brain. We show that INTERACT-derived DNAm regulatory variants are not confounded by LD, are concentrated in regulatory genomic regions in the human brain, and are convergent with mQTL evidence from genetic association analysis. We further demonstrate that predicted DNAm regulatory variants are enriched for heritability of brain-related traits and improve polygenic risk prediction for schizophrenia across diverse ancestry samples. Finally, we applied predicted DNAm regulatory variants for fine-mapping schizophrenia GWAS risk loci to identify potential novel risk genes. Our study shows the power of a deep learning approach to identify functional regulatory variants that may elucidate the genetic basis of complex traits.
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Affiliation(s)
- Jiyun Zhou
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Qiang Chen
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
| | - Patricia R. Braun
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kira A. Perzel Mandell
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Mental Health, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Hao Yang Tan
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94305
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shizhong Han
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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14
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Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol 2022; 6:630-643. [PMID: 35332281 PMCID: PMC9090980 DOI: 10.1038/s41559-022-01703-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 01/31/2023]
Abstract
Primates have adapted to numerous environments and lifestyles, but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of hematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers between populations. Compared to baboons at low altitude, we found that high-altitude geladas exhibit significantly expanded chest circumferences, potentially allowing for greater lung surface area for increased oxygen diffusion. We identified gelada-specific amino acid substitutions in the alpha-chain subunit of adult hemoglobin but found that gelada hemoglobin does not exhibit markedly altered oxygenation properties compared to lowland primates. We also found that geladas at high altitude do not exhibit elevated blood hemoglobin concentrations, in contrast to the normal acclimatization response to hypoxia in lowland primates. The absence of altitude-related polycythemia suggests that geladas are able to sustain adequate tissue-oxygen delivery despite environmental hypoxia. Finally, we identified numerous genes and genomic regions exhibiting accelerated rates of evolution, as well as gene families exhibiting expansions in the gelada lineage, potentially reflecting altitude-related selection. Our findings lend insight into putative mechanisms of high-altitude adaptation while suggesting promising avenues for functional hypoxia research.
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15
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Zhao R, Zhu T, Liu Q, Tian Q, Wang M, Chen J, Tong D, Yu B, Guo H, Xia K, Qiu Z, Hu Z. The autism risk gene CNTN4 modulates dendritic spine formation. Hum Mol Genet 2021; 31:207-218. [PMID: 34415325 DOI: 10.1093/hmg/ddab233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/03/2023] Open
Abstract
Contactin 4 (CNTN4) is a crucial synaptic adhesion protein that belongs to the contactin superfamily. Evidence from both human genetics and mouse models suggests that synapse formation and structural deficits strongly correlate with neurodevelopmental disorders, including autism. In addition, several lines of evidence suggest that CNTN4 is associated with the risk of autism. However, the biological functions of CNTN4 in neural development and disease pathogenesis are poorly understood. In this study, we investigated whether and how CNTN4 is autonomously involved in the development of dendrites and dendritic spines in cortical neurons. Disruption of Cntn4 decreased the number of excitatory synapses, which led to a reduction in neural activity. Truncated proteins lacking the signal peptide, FnIII domains, or GPI domain lacked the ability to regulate dendritic spine formation, indicating that CNTN4 regulates dendritic spine density through a mechanism dependent on FnIII domains. Importantly, we revealed that autism-related variants lacked the ability to regulate spine density and neural activity. In conclusion, our study suggests that CNTN4 is essential for promoting dendrite growth and dendritic spine formation and that disruptive variants of CNTN4 interfere with abnormal synapse formation and may increase the risk of autism.
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Affiliation(s)
- Rongjuan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Zhu
- Department of Critical Care Medicine, The Third people's hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China.,Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Qiong Liu
- Department of Neurology & Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qi Tian
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jingjing Chen
- Reproductive Medicine Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dali Tong
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bin Yu
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, China.,Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, Shanghai, China
| | - Zilong Qiu
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.,Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, Shanghai, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, China
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Connecting the Neurobiology of Developmental Brain Injury: Neuronal Arborisation as a Regulator of Dysfunction and Potential Therapeutic Target. Int J Mol Sci 2021; 22:ijms22158220. [PMID: 34360985 PMCID: PMC8348801 DOI: 10.3390/ijms22158220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Neurodevelopmental disorders can derive from a complex combination of genetic variation and environmental pressures on key developmental processes. Despite this complex aetiology, and the equally complex array of syndromes and conditions diagnosed under the heading of neurodevelopmental disorder, there are parallels in the neuropathology of these conditions that suggest overlapping mechanisms of cellular injury and dysfunction. Neuronal arborisation is a process of dendrite and axon extension that is essential for the connectivity between neurons that underlies normal brain function. Disrupted arborisation and synapse formation are commonly reported in neurodevelopmental disorders. Here, we summarise the evidence for disrupted neuronal arborisation in these conditions, focusing primarily on the cortex and hippocampus. In addition, we explore the developmentally specific mechanisms by which neuronal arborisation is regulated. Finally, we discuss key regulators of neuronal arborisation that could link to neurodevelopmental disease and the potential for pharmacological modification of arborisation and the formation of synaptic connections that may provide therapeutic benefit in the future.
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