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Polakkattil BK, Vellichirammal NN, Nair IV, Nair CM, Banerjee M. Methylome-wide and meQTL analysis helps to distinguish treatment response from non-response and pathogenesis markers in schizophrenia. Front Psychiatry 2024; 15:1297760. [PMID: 38516266 PMCID: PMC10954811 DOI: 10.3389/fpsyt.2024.1297760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
Schizophrenia is a complex condition with entwined genetic and epigenetic risk factors, posing a challenge to disentangle the intermixed pathological and therapeutic epigenetic signatures. To resolve this, we performed 850K methylome-wide and 700K genome-wide studies on the same set of schizophrenia patients by stratifying them into responders, non-responders, and drug-naïve patients. The key genes that signified the response were followed up using real-time gene expression studies to understand the effect of antipsychotics at the gene transcription level. The study primarily implicates hypermethylation in therapeutic response and hypomethylation in the drug-non-responsive state. Several differentially methylated sites and regions colocalized with the schizophrenia genome-wide association study (GWAS) risk genes and variants, supporting the convoluted gene-environment association. Gene ontology and protein-protein interaction (PPI) network analyses revealed distinct patterns that differentiated the treatment response from drug resistance. The study highlights the strong involvement of several processes related to nervous system development, cell adhesion, and signaling in the antipsychotic response. The ability of antipsychotic medications to alter the pathology by modulating gene expression or methylation patterns is evident from the general increase in the gene expression of response markers and histone modifiers and the decrease in class II human leukocyte antigen (HLA) genes following treatment with varying concentrations of medications like clozapine, olanzapine, risperidone, and haloperidol. The study indicates a directional overlap of methylation markers between pathogenesis and therapeutic response, thereby suggesting a careful distinction of methylation markers of pathogenesis from treatment response. In addition, there is a need to understand the trade-off between genetic and epigenetic observations. It is suggested that methylomic changes brought about by drugs need careful evaluation for their positive effects on pathogenesis, course of disease progression, symptom severity, side effects, and refractoriness.
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Affiliation(s)
- Binithamol K. Polakkattil
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- Research Center, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Neetha N. Vellichirammal
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Indu V. Nair
- Mental Health Centre, Thiruvananthapuram, Kerala, India
| | | | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Zhou W, Jiang Z, Yi Z, Ouyang J, Li X, Zhang Q, Wang P. Defect of TIMP4 Is Associated with High Myopia and Participates in Rat Ocular Development in a Dose-Dependent Manner. Int J Mol Sci 2023; 24:16928. [PMID: 38069250 PMCID: PMC10707432 DOI: 10.3390/ijms242316928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Thinning of the sclera happens in myopia eyes owing to extracellular matrix (ECM) remodeling, but the initiators of the ECM remodeling in myopia are mainly unknown. The matrix metalloproteinase (MMPs) and tissue inhibitors of matrix metalloproteinase (TIMPs) regulate the homeostasis of the ECM. However, genetic studies of the MMPs and TIMPs in the occurrence of myopia are poor and limited. This study systematically investigated the association between twenty-nine genes of the TIMPs and MMPs families and early-onset high myopia (eoHM) based on whole exome sequencing data. Two TIMP4 heterozygous loss-of-function (LoF) variants, c.528C>A in six patients and c.234_235insAA in one patient, were statistically enriched in 928 eoHM probands compared to that in 5469 non-high myopia control (p = 3.7 × 10-5) and that in the general population (p = 2.78 × 10-9). Consequently, the Timp4 gene editing rat was further evaluated to explore the possible role of Timp4 on ocular and myopia development. A series of ocular morphology abnormalities in a dose-dependent manner (Timp4-/- < Timp4+/- < Timp4+/+) were observed in a rat model, including the decline in the retinal thickness, the elongation in the axial length, more vulnerable to the form deprivation model, morphology changes in sclera collagen bundles, and the decrease in collagen contents of the sclera and retina. Electroretinogram revealed that the b-wave amplitudes of Timp4 defect rats were significantly reduced, consistent with the shorter length of the bipolar axons detected by HE and IF staining. Heterozygous LoF variants in the TIMP4 are associated with early onset high myopia, and the Timp4 defect disturbs ocular development by influencing the morphology and function of the ocular tissue.
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Affiliation(s)
| | | | | | | | | | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510000, China; (W.Z.); (Z.J.); (Z.Y.); (J.O.); (X.L.)
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510000, China; (W.Z.); (Z.J.); (Z.Y.); (J.O.); (X.L.)
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The Biology and Function of Tissue Inhibitor of Metalloproteinase 2 in the Lungs. Pulm Med 2022; 2022:3632764. [PMID: 36624735 PMCID: PMC9825218 DOI: 10.1155/2022/3632764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/02/2023] Open
Abstract
Tissue inhibitors of matrix metalloproteinases (TIMP) are a family of four endogenous proteins that primarily function to inhibit the activities of proteases such as the matrix metalloproteinases (MMP). Altered MMP/TIMP ratios are frequently observed in several human diseases. During aging and disease progression, the extracellular matrix (ECM) undergoes structural changes in which elastin and collagens serve an essential role. MMPs and TIMPs significantly influence the ECM. Classically, elevated levels of TIMPs are suggested to result in ECM accumulation leading to fibrosis, whereas loss of TIMP responses leads to enhanced matrix proteolysis. Here, we outline the known roles of the most abundant TIMP, TIMP2, in pulmonary diseases but also discuss future perspectives in TIMP2 research that could impact the lungs. TIMP2 directly inhibits MMPs, in particular MMP2, but TIMP2 is also required for the activation of MMP2 through its interaction with MMP14. The protease and antiprotease imbalance of MMPs and TIMPs are extensively studied in diseases but recent discoveries suggest that TIMPs, specifically, TIMP2 could play other roles in aging and inflammation processes.
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Toma C, Shaw AD, Heath A, Pierce KD, Mitchell PB, Schofield PR, Fullerton JM. A linkage and exome study of multiplex families with bipolar disorder implicates rare coding variants of ANK3 and additional rare alleles at 10q11-q21. J Psychiatry Neurosci 2021; 46:E247-E257. [PMID: 33729739 PMCID: PMC8061732 DOI: 10.1503/jpn.200083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bipolar disorder is a highly heritable psychiatric condition for which specific genetic factors remain largely unknown. In the present study, we used combined whole-exome sequencing and linkage analysis to identify risk loci and dissect the contribution of common and rare variants in families with a high density of illness. METHODS Overall, 117 participants from 15 Australian extended families with bipolar disorder (72 with affective disorder, including 50 with bipolar disorder type I or II, 13 with schizoaffective disorder-manic type and 9 with recurrent unipolar disorder) underwent whole-exome sequencing. We performed genome-wide linkage analysis using MERLIN and conditional linkage analysis using LAMP. We assessed the contribution of potentially functional rare variants using a genebased segregation test. RESULTS We identified a significant linkage peak on chromosome 10q11-q21 (maximal single nucleotide polymorphism = rs10761725; exponential logarithm of the odds [LODexp] = 3.03; empirical p = 0.046). The linkage interval spanned 36 protein-coding genes, including a gene associated with bipolar disorder, ankyrin 3 (ANK3). Conditional linkage analysis showed that common ANK3 risk variants previously identified in genome-wide association studies - or variants in linkage disequilibrium with those variants - did not explain the linkage signal (rs10994397 LOD = 0.63; rs9804190 LOD = 0.04). A family-based segregation test with 34 rare variants from 14 genes under the linkage interval suggested rare variant contributions of 3 brain-expressed genes: NRBF2 (p = 0.005), PCDH15 (p = 0.002) and ANK3 (p = 0.014). LIMITATIONS We did not examine non-coding variants, but they may explain the remaining linkage signal. CONCLUSION Combining family-based linkage analysis with next-generation sequencing data is effective for identifying putative disease genes and specific risk variants in complex disorders. We identified rare missense variants in ANK3, PCDH15 and NRBF2 that could confer disease risk, providing valuable targets for functional characterization.
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Affiliation(s)
- Claudio Toma
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
| | - Alex D Shaw
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
| | - Anna Heath
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
| | - Kerrie D Pierce
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
| | - Philip B Mitchell
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
| | - Peter R Schofield
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
| | - Janice M Fullerton
- From Neuroscience Research Australia, Sydney, Australia (Toma, Shaw, Heath, Pierce, Schofield); the School of Medical Sciences, University of New South Wales, Sydney, Australia (Toma, Shaw, Schofield, Fullerton); the Centro de Biología Molecular 'Severo Ochoa', Universidad Autónoma de Madrid/CSIC, Madrid, Spain (Toma); the School of Psychiatry, University of New South Wales, Sydney, Australia (Mitchell); and the Black Dog Institute, Prince of Wales Hospital, Sydney, Australia (Mitchell)
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Multiple rare inherited variants in a four generation schizophrenia family offer leads for complex mode of disease inheritance. Schizophr Res 2020; 216:288-294. [PMID: 31813803 PMCID: PMC8958857 DOI: 10.1016/j.schres.2019.11.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/23/2019] [Accepted: 11/24/2019] [Indexed: 02/01/2023]
Abstract
Schizophrenia is a clinically and genetically heterogeneous neuropsychiatric disorder, with a polygenic basis but identification of the specific determinants is a continuing challenge. In this study, we analyzed a multigenerational family, with all healthy individuals in the first two generations, and four progeny affected with schizophrenia in the subsequent two generations, using whole exome sequencing. We identified five rare protein sequence altering heterozygous variants, in five different genes namely SMARCA5, PDE1B, TNIK, SMARCA2 and FLRT shared among all affected members and predicted to be damaging. Variants in SMARCA5 and PDE1B were inherited from the unaffected father whereas variants in TNIK, SMARCA2 and FLRT1 were inherited from the unaffected mother in all the three affected individuals in the third generation; and notably all these five variants were transmitted by an affected mother to her affected son. Microsatellite based analysis lent a modest linkage support (LOD score of 1.2; θ=0.0 at each variant). Of note, analysis of exome data of an ancestry matched unrelated schizophrenia cohort (n = 350), revealed a total of 16 rare variants (MAF < 0.01) in these five genes. Interestingly, these five genes involved in neurodevelopmental and/or neurotransmitter signaling processes are implicated in the etiology of schizophrenia previously. This study provides good evidence for a likely cumulative contribution of multiple rare variants from disease relevant genes with a threshold effect in disease development and seems to explain the unusual disease transmission pattern generally witnessed in such conditions, but warrants extensive replication efforts in families with similar complex disease inheritance profiles.
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John J, Kukshal P, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare variant based evidence for oligogenic contribution of neurodevelopmental pathway genes to schizophrenia. Schizophr Res 2019; 210:296-298. [PMID: 30612842 PMCID: PMC7018639 DOI: 10.1016/j.schres.2018.12.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/23/2018] [Accepted: 12/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St., Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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John J, Kukshal P, Sharma A, Bhatia T, Nimgaonkar VL, Deshpande SN, Thelma BK. Rare variants in Protein tyrosine phosphatase, receptor type A (PTPRA) in schizophrenia: Evidence from a family based study. Schizophr Res 2019; 206:75-81. [PMID: 30594456 PMCID: PMC7321970 DOI: 10.1016/j.schres.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/25/2018] [Accepted: 12/08/2018] [Indexed: 12/23/2022]
Abstract
The contribution of both common and rare risk variants to the genetic architecture of schizophrenia (SZ) has been documented in genome-wide association studies, whole exome and whole genome sequencing approaches. As SZ is highly heritable and segregates in families, highly penetrant rare variants are more likely to be identified through analyses of multiply affected families. Further, much of the gene mapping studies in SZ have utilized individuals of Caucasian ancestry. Analysis of other ethnic groups may be informative. In this study, we aimed at identification of rare, penetrant risk variants utilizing whole exome sequencing (WES) in a three-generation Indian family with multiple members affected. Filtered data from WES, combined with in silico analyses revealed a novel heterozygous missense variant (NM_080841:c.1730C>G:p.T577R; exon18) in Protein tyrosine phosphatase, receptor type A (PTPRA 20p13). The variant was located in an evolutionarily conserved position and predicted to be damaging. Screening for variants in this gene in the WES data of an independent SZ cohort (n = 350) of matched ethnicity, identified five additional rare missense variants with MAF < 0.003, which were also predicted to be damaging. In conclusion, the rare missense variants in PTPRA identified in this study could confer risk for SZ. This has also derived support from concordant data from prior linkage and association, as well as animal studies which indicated a role for PTPRA in glutamate function.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Aditya Sharma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - V L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, DeSoto St, Pittsburgh, PA 15213, USA
| | - S N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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Rhoades R, Jackson F, Teng S. Discovery of rare variants implicated in schizophrenia using next-generation sequencing. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2019; 3:1-20. [PMID: 33981965 PMCID: PMC8112455 DOI: 10.20517/jtgg.2018.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Schizophrenia is a highly heritable psychiatric disorder that affects 1% of the population. Genome-wide association studies have identified common variants in candidate genes associated with schizophrenia, but the genetics mechanisms of this disorder have not yet been elucidated. The discovery of rare genetic variants that contribute to schizophrenia symptoms promises to help explain the missing heritability of the disease. Next generation sequencing techniques are revolutionizing the field of psychiatric genetics. Various statistical approaches have been developed for rare variant association testing in case-control and family studies. Targeted resequencing, whole exome sequencing and whole genome sequencing combined with these computational tools are used for the discovery of rare genetic variations in schizophrenia. The findings provide useful information for characterizing the rare mutations and elucidating the genetic mechanisms by which the variants cause schizophrenia.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Fatimah Jackson
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC 20059, USA
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Igeta H, Watanabe Y, Morikawa R, Ikeda M, Otsuka I, Hoya S, Koizumi M, Egawa J, Hishimoto A, Iwata N, Someya T. Rare compound heterozygous missense SPATA7 variations and risk of schizophrenia; whole-exome sequencing in a consanguineous family with affected siblings, follow-up sequencing and a case-control study. Neuropsychiatr Dis Treat 2019; 15:2353-2363. [PMID: 31695380 PMCID: PMC6707433 DOI: 10.2147/ndt.s218773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Whole-exome sequencing (WES) of multiplex families is a promising strategy for identifying causative variations for common diseases. To identify rare recessive risk variations for schizophrenia, we performed a WES study in a consanguineous family with affected siblings. We then performed follow-up sequencing of SPATA7 in schizophrenia-affected families. In addition, we performed a case-control study to investigate association between SPATA7 variations and schizophrenia. PATIENTS AND METHODS WES was performed on two affected siblings and their unaffected parents, who were second cousins, of a multiplex schizophrenia family. Subsequently, we sequenced the coding region of SPATA7, a potential risk gene identified by the WES analysis, in 142 affected offspring from 137 families for whom parental DNA samples were available. We further tested rare recessive SPATA7 variations, identified by WES and sequencing, for associations with schizophrenia in 2,756 patients and 2,646 controls. RESULTS Our WES analysis identified rare compound heterozygous missense SPATA7 variations, p.Asp134Gly and p.Ile332Thr, in both affected siblings. Sequencing SPATA7 coding regions from 137 families identified no rare recessive variations in affected offspring. In the case-control study, we did not detect the rare compound heterozygous SPATA7 missense variations in patients or controls. CONCLUSION Our data does not support the role of the rare compound heterozygous SPATA7 missense variations p.Asp134Gly and p.Ile332Thr in conferring a substantial risk of schizophrenia.
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Affiliation(s)
- Hirofumi Igeta
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Morikawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Satoshi Hoya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masataka Koizumi
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Xue CB, Xu ZH, Zhu J, Wu Y, Zhuang XH, Chen QL, Wu CR, Hu JT, Zhou HS, Xie WH, Yi X, Yu SS, Peng ZY, Yang HM, Hong XH, Chen JH. Exome Sequencing Identifies TENM4 as a Novel Candidate Gene for Schizophrenia in the SCZD2 Locus at 11q14-21. Front Genet 2018; 9:725. [PMID: 30745909 PMCID: PMC6360184 DOI: 10.3389/fgene.2018.00725] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/22/2018] [Indexed: 02/05/2023] Open
Abstract
Schizophrenia is a complex psychiatric disorder with high genetic heterogeneity, however, the contribution of rare mutations to the disease etiology remains to be further elucidated. We herein performed exome sequencing in a Han Chinese schizophrenia family and identified a missense mutation (c.6724C>T, p.R2242C) in the teneurin transmembrane protein 4 (TENM4) gene in the SCZD2 locus, a region previously linked to schizophrenia at 11q14-21. The mutation was confirmed to co-segregate with the schizophrenia phenotype in the family. Subsequent investigation of TENM4 exons 31, 32, and 33 adjacent to the p.R2242C mutation revealed two additional missense mutations in 120 sporadic schizophrenic patients. Residues mutated in these mutations, which are predicted to be deleterious to protein function, were highly conserved among vertebrates. These rare mutations were not detected in 1000 Genomes, NHLBI Exome Sequencing Project databases, or our in-house 1136 non-schizophrenic control exomes. Analysis of RNA-Seq data showed that TENM4 is expressed in the brain with high abundance and specificity. In line with the important role of TENM4 in central nervous system development, our findings suggested that increased rare variants in TENM4 could be associated with schizophrenia, and thus TENM4 could be a novel candidate gene for schizophrenia in the SCZD2 locus.
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Affiliation(s)
- Chao-Biao Xue
- Mental Health Center, Shantou University Medical College, Shantou, China
- Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Zhou-Heng Xu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Jun Zhu
- Mental Health Center, Shantou University Medical College, Shantou, China
- Shenzhen Kang Ning Hospital, Shenzhen, China
| | - Yu Wu
- Mental Health Center, Shantou University Medical College, Shantou, China
| | - Xi-Hang Zhuang
- Mental Health Center, Shantou University Medical College, Shantou, China
| | - Qu-Liang Chen
- Mental Health Center, Shantou University Medical College, Shantou, China
| | - Cai-Ru Wu
- Mental Health Center, Shantou University Medical College, Shantou, China
| | - Jin-Tao Hu
- Mental Health Center, Shantou University Medical College, Shantou, China
| | - Hou-Shi Zhou
- Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Wei-Hang Xie
- Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Xin Yi
- Beijing Genomics Institute – Shenzhen, Shenzhen, China
| | - Shan-Shan Yu
- Beijing Genomics Institute – Shenzhen, Shenzhen, China
| | - Zhi-Yu Peng
- Beijing Genomics Institute – Shenzhen, Shenzhen, China
| | | | - Xiao-Hong Hong
- Mental Health Center, Shantou University Medical College, Shantou, China
- *Correspondence: Xiao-Hong Hong, Jian-Huan Chen,
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
- *Correspondence: Xiao-Hong Hong, Jian-Huan Chen,
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