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Wu X, Zhang Z, Qiu Z, Wu X, Chen J, Liu L, Liu X, Zhao S, Yang Y, Zhao Y. TNIK in disease: from molecular insights to therapeutic prospects. Apoptosis 2024:10.1007/s10495-024-01987-w. [PMID: 38853204 DOI: 10.1007/s10495-024-01987-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
TRAF2 and NCK interacting kinase (TNIK), a critical interacting protein kinase, is currently receiving wide attention. TNIK is found in various human body organs and tissues and participates in cell motility, proliferation, and differentiation. On the one hand, its aberrant expression is related to the onset and progression of numerous malignant tumors. On the other hand, TNIK is important in neuronal growth, proliferation, differentiation, and synaptic formation. Thus, the novel therapeutic strategies for targeting TNIK offer a promising direction for cancer, neurological or psychotic disorders. Here, we briefly summarized the biological information of TNIK, reviewed the role and regulatory mechanism in cancer and neuropsychiatric diseases, and introduced the research progress of inhibitors targeting TNIK. Taken together, this review hopes to contribute to the in-depth understanding of the function and regulatory mechanism of TNIK, which is of great significance for revealing the role of TNIK in the occurrence and treatment of diseases.
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Affiliation(s)
- Xue Wu
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
| | - Zhe Zhang
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Zhenye Qiu
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Xiaopeng Wu
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Junmin Chen
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Lu Liu
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Xiaoyi Liu
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Shiyan Zhao
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China
| | - Yang Yang
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China.
- Department of Cardiology, Faculty of Life Sciences and Medicine, Northwest University First Hospital, Northwest University, Xi'an, 710069, China.
| | - Ye Zhao
- Xi'an Key Laboratory of Innovative Drug Research for Heart Failure, Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710069, China.
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Thapaliya B, Ray B, Farahdel B, Suresh P, Sapkota R, Holla B, Mahadevan J, Chen J, Vaidya N, Perrone-Bizzozero NI, Benegal V, Schumann G, Calhoun VD, Liu J. Cross-continental environmental and genome-wide association study on children and adolescent anxiety and depression. Front Psychiatry 2024; 15:1384298. [PMID: 38827440 PMCID: PMC11141390 DOI: 10.3389/fpsyt.2024.1384298] [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: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 06/04/2024] Open
Abstract
Anxiety and depression in children and adolescents warrant special attention as a public health concern given their devastating and long-term effects on development and mental health. Multiple factors, ranging from genetic vulnerabilities to environmental stressors, influence the risk for the disorders. This study aimed to understand how environmental factors and genomics affect children and adolescents anxiety and depression across three cohorts: Adolescent Brain and Cognitive Development Study (US, age of 9-10; N=11,875), Consortium on Vulnerability to Externalizing Disorders and Addictions (INDIA, age of 6-17; N=4,326) and IMAGEN (EUROPE, age of 14; N=1888). We performed data harmonization and identified the environmental impact on anxiety/depression using a linear mixed-effect model, recursive feature elimination regression, and the LASSO regression model. Subsequently, genome-wide association analyses with consideration of significant environmental factors were performed for all three cohorts by mega-analysis and meta-analysis, followed by functional annotations. The results showed that multiple environmental factors contributed to the risk of anxiety and depression during development, where early life stress and school support index had the most significant and consistent impact across all three cohorts. In both meta, and mega-analysis, SNP rs79878474 in chr11p15 emerged as a particularly promising candidate associated with anxiety and depression, despite not reaching genomic significance. Gene set analysis on the common genes mapped from top promising SNPs of both meta and mega analyses found significant enrichment in regions of chr11p15 and chr3q26, in the function of potassium channels and insulin secretion, in particular Kv3, Kir-6.2, SUR potassium channels encoded by the KCNC1, KCNJ11, and ABCCC8 genes respectively, in chr11p15. Tissue enrichment analysis showed significant enrichment in the small intestine, and a trend of enrichment in the cerebellum. Our findings provide evidences of consistent environmental impact from early life stress and school support index on anxiety and depression during development and also highlight the genetic association between mutations in potassium channels, which support the stress-depression connection via hypothalamic-pituitary-adrenal axis, along with the potential modulating role of potassium channels.
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Affiliation(s)
- Bishal Thapaliya
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Bhaskar Ray
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Britny Farahdel
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Pranav Suresh
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Ram Sapkota
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Bharath Holla
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Jayant Mahadevan
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Nilakshi Vaidya
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
- Centre for Population Neuroscience and Stratified Medicine, Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Vivek Benegal
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine, Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine, Institute for Science and Technology of Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in NeuroImaging and Data Science, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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Wang M, Gu Y, Li Q, Feng B, Lv X, Zhang H, Kong Q, Dong Z, Tian X, Zhang Y. The Traf2 and NcK interacting kinase inhibitor NCB-0846 suppresses seizure activity involving the decrease of GRIA1. Genes Dis 2024; 11:100997. [PMID: 38292191 PMCID: PMC10826163 DOI: 10.1016/j.gendis.2023.03.036] [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: 01/03/2023] [Revised: 03/09/2023] [Accepted: 03/29/2023] [Indexed: 02/01/2024] Open
Abstract
Epilepsy, one of the most common neurological disorders, is characterized by spontaneous recurrent seizures. Temporal lobe epilepsy (TLE) is one of the most common medically intractable seizure disorders. Traf2-and NcK-interacting kinase (TNIK) has recently attracted attention as a critical modulation target of many neurological and psychiatric disorders, but its role in epilepsy remains unclear. In this study, we hypothesized the involvement of TNIK in epilepsy and investigated TNIK expression in patients with intractable TLE and in a pilocarpine-induced rat model of epilepsy by western blotting, immunofluorescence, and immunohistochemistry. A pentylenetetrazole (PTZ)-induced epilepsy rat model was used to determine the effect of the TNIK inhibitor NCB-0846 on behavioral manifestations of epilepsy. Coimmunoprecipitation (Co-IP)/mass spectrometry (MS) was used to identify the potential mechanism. Through Co-IP, we detected and confirmed the main potential TNIK interactors. Subcellular fractionation was used to establish the effect of NCB-0846 on the expression of the main interactors in postsynaptic density (PSD) fractions. We found that TNIK was primarily located in neurons and decreased significantly in epilepsy model rats and TLE patients compared with controls. NCB-0846 delayed kindling progression and decreased seizure severity. Co-IP/MS identified 63 candidate TNIK interactors in rat hippocampi, notably CaMKII. Co-IP showed that TNIK might correlate with endogenous GRIA1, SYN2, PSD-95, CaMKIV, GABRG1, and GABRG2. In addition, the significant decrease in GRIA1 in hippocampal total lysate and PSDs after NCB-0846 treatment might help modify the progression of PTZ kindling. Our results suggest that TNIK contributes to epileptic pathology and is a potential antiepileptic drug target.
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Affiliation(s)
- Min Wang
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, China
| | - Yixue Gu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Qiubo Li
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, China
| | - Bangzhe Feng
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, China
| | - Xinke Lv
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Hao Zhang
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, China
| | - Qingxia Kong
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, China
| | - Zhifang Dong
- Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Xin Tian
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Yanke Zhang
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
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Jiang J, Wilkinson B, Flores I, Hartel N, Mihaylov SR, Clementel VA, Flynn HR, Alkuraya FS, Ultanir S, Graham NA, Coba MP. Mutations in the postsynaptic density signaling hub TNIK disrupt PSD signaling in human models of neurodevelopmental disorders. Front Mol Neurosci 2024; 17:1359154. [PMID: 38638602 PMCID: PMC11024424 DOI: 10.3389/fnmol.2024.1359154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024] Open
Abstract
A large number of synaptic proteins have been recurrently associated with complex brain disorders. One of these proteins, the Traf and Nck interacting kinase (TNIK), is a postsynaptic density (PSD) signaling hub, with many variants reported in neurodevelopmental disorder (NDD) and psychiatric disease. While rodent models of TNIK dysfunction have abnormal spontaneous synaptic activity and cognitive impairment, the role of mutations found in patients with TNIK protein deficiency and TNIK protein kinase activity during early stages of neuronal and synapse development has not been characterized. Here, using hiPSC-derived excitatory neurons, we show that TNIK mutations dysregulate neuronal activity in human immature synapses. Moreover, the lack of TNIK protein kinase activity impairs MAPK signaling and protein phosphorylation in structural components of the PSD. We show that the TNIK interactome is enriched in NDD risk factors and TNIK lack of function disrupts signaling networks and protein interactors associated with NDD that only partially overlap to mature mouse synapses, suggesting a differential role of TNIK in immature synapsis in NDD.
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Affiliation(s)
- Jianzhi Jiang
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Brent Wilkinson
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ilse Flores
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Nicolas Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, United States
| | - Simeon R. Mihaylov
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Veronica A. Clementel
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Helen R. Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Fowsan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sila Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Nicholas A. Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, United States
| | - Marcelo P. Coba
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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Minale EMP, De Falco A, Agolini E, Novelli A, Russo R, Andolfo I, Iolascon A, Piscopo C. First Case of a Dominant De Novo SEC23A Mutation with Neurological and Psychiatric Features: New Insights into Cranio-Lenticulo-Sutural Dysplasia with Literature Review. Genes (Basel) 2024; 15:130. [PMID: 38275611 PMCID: PMC10815465 DOI: 10.3390/genes15010130] [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: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Cranio-lenticulo-sutural dysplasia (CLSD, OMIM #607812) is a rare genetic condition characterized by late-closing fontanels, skeletal defects, dysmorphisms, and congenital cataracts that are caused by bi-allelic or monoallelic variants in the SEC23A gene. Autosomal recessive inheritance (AR-CLSD) has been extensively documented in several cases with homozygous or compound heterozygous variants in SEC23A, whereas autosomal dominant inheritance (AD-CLSD) involving heterozygous inherited variants has been reported just in three patients. The SEC23A gene encodes for one of the main components of a protein coat complex known as coat-protein-complex II (COPII), responsible for the generation of the envelope of the vesicles exported from the endoplasmic reticulum (ER) toward the Golgi complex (GC). AR-CLSD and AD-CLSD exhibit common features, although each form also presents distinctive and peculiar characteristics. Herein, we describe a rare case of a 10-year-old boy with a history of an anterior fontanel that closed only at the age of 9. The patient presents with short proportionate stature, low weight, and neurological impairment, including intellectual disability, global developmental delay, abnormal coordination, dystonia, and motor tics, along with dysmorphisms such as a wide anterior fontanel, hypertelorism, frontal bossing, broad nose, high-arched palate, and micrognathia. Trio clinical exome was performed, and a de novo heterozygous missense variant in SEC23A (p.Arg716Cys) was identified. This is the first reported case of CLSD caused by a de novo heterozygous missense variant in SEC23A presenting specific neurological manifestations never described before. For the first time, we have conducted a comprehensive phenotype-genotype correlation using data from our patient and the eight most well-documented cases in the literature. Our work has allowed us to identify the main specific and characteristic signs of both forms of CLSD (AR-CLSD, AD CLSD), offering valuable insights that can guide physicians in the diagnostic process. Notably, detailed descriptions of neurological features such as intellectual disability, global developmental delay, and motor impairment have not been documented before. Furthermore, our literature overview is crucial in the current landscape of CLSD due to the absence of guidelines for the clinical diagnosis and proper follow-up of these patients, especially during childhood.
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Affiliation(s)
- Elia Marco Paolo Minale
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy; (E.M.P.M.); (A.D.F.); (A.I.)
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (R.R.); (I.A.)
| | - Alessandro De Falco
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy; (E.M.P.M.); (A.D.F.); (A.I.)
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (R.R.); (I.A.)
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (E.A.); (A.N.)
| | - Antonio Novelli
- Laboratory of Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (E.A.); (A.N.)
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (R.R.); (I.A.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (R.R.); (I.A.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Achille Iolascon
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy; (E.M.P.M.); (A.D.F.); (A.I.)
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (R.R.); (I.A.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetic Unit, Antonio Cardarelli Hospital, 80131 Naples, Italy
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Sha Z, Schijven D, Fisher SE, Francks C. Genetic architecture of the white matter connectome of the human brain. SCIENCE ADVANCES 2023; 9:eadd2870. [PMID: 36800424 PMCID: PMC9937579 DOI: 10.1126/sciadv.add2870] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
White matter tracts form the structural basis of large-scale brain networks. We applied brain-wide tractography to diffusion images from 30,810 adults (U.K. Biobank) and found significant heritability for 90 node-level and 851 edge-level network connectivity measures. Multivariate genome-wide association analyses identified 325 genetic loci, of which 80% had not been previously associated with brain metrics. Enrichment analyses implicated neurodevelopmental processes including neurogenesis, neural differentiation, neural migration, neural projection guidance, and axon development, as well as prenatal brain expression especially in stem cells, astrocytes, microglia, and neurons. The multivariate association profiles implicated 31 loci in connectivity between core regions of the left-hemisphere language network. Polygenic scores for psychiatric, neurological, and behavioral traits also showed significant multivariate associations with structural connectivity, each implicating distinct sets of brain regions with trait-relevant functional profiles. This large-scale mapping study revealed common genetic contributions to variation in the structural connectome of the human brain.
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Affiliation(s)
- Zhiqiang Sha
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Dick Schijven
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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7
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Thapaliya B, Ray B, Farahdel B, Suresh P, Sapkota R, Holla B, Mahadevan J, Chen J, Vaidya N, Perrone-Bizzozero N, Benegal V, Schumann G, Calhoun VD, Liu J. Cross-continental environmental and genome-wide association study on children and adolescent anxiety and depression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285530. [PMID: 36798402 PMCID: PMC9934785 DOI: 10.1101/2023.02.06.23285530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Anxiety and depression in children and adolescents warrant special attention as a public health issue given their devastating and long-term effects on development and mental health. Multiple factors, ranging from genetic vulnerabilities to environmental stressors, influence the risk for the disorders. This study aimed to understand how environmental factors and genomics affect children and adolescents anxiety and depression across three cohorts: Adolescent Brain and Cognitive Development Study (US, age of 9-10), Consortium on Vulnerability to Externalizing Disorders and Addictions (INDIA, age of 6-17) and IMAGEN (EUROPE, age of 14). We performed data harmonization and identified the environmental impact on anxiety/depression using a linear mixed-effect model, recursive feature elimination regression, and the LASSO regression model. Subsequently, genome-wide association analyses with consideration of significant environmental factors were performed for all three cohorts by mega-analysis and meta-analysis, followed by functional annotations. The results showed that multiple environmental factors contributed to the risk of anxiety and depression during development, where early life stress and school risk had the most significant and consistent impact across all three cohorts. Both meta and mega-analysis identified a novel SNP rs79878474 in chr11p15 to be the most promising SNP associated with anxiety and depression. Gene set analysis on the common genes mapped from top promising SNPs of both meta and mega analyses found significant enrichment in regions of chr11p15 and chr3q26, in the function of potassium channels and insulin secretion, in particular Kv3, Kir-6.2, SUR potassium channels encoded by the KCNC1, KCNJ11, and ABCCC8 genes respectively, in chr11p15. Tissue enrichment analysis showed significant enrichment in the small intestine and a trend of enrichment in the cerebellum. Our findings provide evidence of consistent environmental impact from early life stress and school risks on anxiety and depression during development and also highlight the genetic association between mutations in potassium channels along with the potential role of the cerebellum region, which are worthy of further investigation.
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Affiliation(s)
- Bishal Thapaliya
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Bhaskar Ray
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Britny Farahdel
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Pranav Suresh
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Ram Sapkota
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
| | | | | | - Bharath Holla
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Jayant Mahadevan
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Nilakshi Vaidya
- Centre for Population Neuroscience and Stratified Medicine, Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Germany
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Vivek Benegal
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine, Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine, Institute for Science and Technology of Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, USA
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in Neuro Imaging and Data Science
- Department of Computer Science, Georgia State University, Atlanta, USA
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Xu Q, Li Y, Li M, Qin S, Ning A, Yuan R, Fu Y, Wang D, Zhang R, Zeng D, Yu W, Li H, Yu S. The influence of polymorphisms in TNIK gene on risperidone response in a Chinese Han population. Pharmacogenomics 2022; 23:575-583. [PMID: 35698907 DOI: 10.2217/pgs-2022-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate whether the TNIK gene affects risperidone treatment outcomes in the Chinese population. Methods: A total of 148 unrelated inpatients who received risperidone for six weeks were enrolled. The selected single nucleotide polymorphisms (SNPs; rs2088885, rs7627954 and rs13065441) were genotyped using the MassARRAY® SNP IPLEX platform. Results: The analysis showed that one novel SNP of TNIK, rs7627954, had a significant association with the response to risperidone (χ2 = 4.472; p = 0.034). This work also identified rs2088885 as significantly associated with risperidone response (χ2 = 5.257; p = 0.022). The result revealed that the rs2088885-rs7627954 C-T haplotype was more prevalent in good responders than in poor responders (p = 0.0278). Conclusion: This study revealed that the rs2088885 and rs7627954 SNPs of TNIK are associated with risperidone treatment response.
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Affiliation(s)
- Qingqing Xu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaojing Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,958 Hospital of PLA Army, Chongqing, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for The Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for The Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Ailing Ning
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruixue Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingmei Fu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongxiang Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ran Zhang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Duan Zeng
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjuan Yu
- Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huafang Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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9
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Functions of CNKSR2 and Its Association with Neurodevelopmental Disorders. Cells 2022; 11:cells11020303. [PMID: 35053419 PMCID: PMC8774548 DOI: 10.3390/cells11020303] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
The Connector Enhancer of Kinase Suppressor of Ras-2 (CNKSR2), also known as CNK2 or MAGUIN, is a scaffolding molecule that contains functional protein binding domains: Sterile Alpha Motif (SAM) domain, Conserved Region in CNK (CRIC) domain, PSD-95/Dlg-A/ZO-1 (PDZ) domain, Pleckstrin Homology (PH) domain, and C-terminal PDZ binding motif. CNKSR2 interacts with different molecules, including RAF1, ARHGAP39, and CYTH2, and regulates the Mitogen-Activated Protein Kinase (MAPK) cascade and small GTPase signaling. CNKSR2 has been reported to control the development of dendrite and dendritic spines in primary neurons. CNKSR2 is encoded by the CNKSR2 gene located in the X chromosome. CNKSR2 is now considered as a causative gene of the Houge type of X-linked syndromic mental retardation (MRXHG), an X-linked Intellectual Disability (XLID) that exhibits delayed development, intellectual disability, early-onset seizures, language delay, attention deficit, and hyperactivity. In this review, we summarized molecular features, neuronal function, and neurodevelopmental disorder-related variations of CNKSR2.
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10
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Yuan R, Li Y, Fu Y, Ning A, Wang D, Zhang R, Yu S, Xu Q. TNIK influence the effects of antipsychotics on Wnt/β-catenin signaling pathway. Psychopharmacology (Berl) 2021; 238:3283-3292. [PMID: 34350475 DOI: 10.1007/s00213-021-05943-3] [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: 01/21/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
RationaleTraf2- and Nck-interacting kinase (TNIK), a member of germinal center kinase (GCK) family, has been implicated as a risk factor in schizophrenia and bipolar disorder as well as the action of antipsychotics. TNIK is an essential activator of Wnt/β-catenin signaling pathway which has been identified involved in the mechanism underlying the effects of antipsychotics. Thus, the effects of TNIK on antipsychotics may be achieved by influencing Wnt/β-catenin signaling pathway proteins.Objectives and methodsIn the current study, the effects of up- or downregulated TNIK on β-catenin, T-cell factor 4 (TCF-4), glycogen synthase kinase-3β (GSK3β), and phosphorylated GSK3β (p-GSK3β) were examined in the human glioma U251 cells. Then, we observed the effects of antipsychotics (clozapine and risperidone) on the above proteins and evaluated the role of differentially expressed TNIK on antipsychotic-treated cell groups.ResultsThe result showed that clozapine treatment decreased β-catenin and TCF-4 levels in U251 cells, and risperidone had the similar effects on β-catenin and p-GSK3β. The downregulated TNIK using siRNA impeded the regulation of antipsychotics on Wnt pathway proteins via increasing the expression levels of TCF-4, β-catenin, or p-GSK3β, whereas the upregulated TNIK made no significant change.ConclusionsThe influence of TNIK on the effects of antipsychotics may be partly through Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Ruixue Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaojing Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingmei Fu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ailing Ning
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongxiang Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ran Zhang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Qingqing Xu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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11
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Childebayeva A, Harman T, Weinstein J, Day T, Brutsaert TD, Bigham AW. Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp Trek. Front Physiol 2021; 12:660906. [PMID: 34262470 PMCID: PMC8273439 DOI: 10.3389/fphys.2021.660906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
The individual physiological response to high-altitude hypoxia involves both genetic and non-genetic factors, including epigenetic modifications. Epigenetic changes in hypoxia factor pathway (HIF) genes are associated with high-altitude acclimatization. However, genome-wide epigenetic changes that are associated with short-term hypoxia exposure remain largely unknown. We collected a series of DNA samples from 15 participants of European ancestry trekking to Everest Base Camp to identify DNA methylation changes associated with incremental altitude ascent. We determined genome-wide DNA methylation levels using the Illumina MethylationEPIC chip comparing two altitudes: baseline 1,400 m (day 0) and elevation 4,240 m (day 7). The results of our epigenome-wide association study revealed 2,873 significant differentially methylated positions (DMPs) and 361 significant differentially methylated regions (DMRs), including significant positions and regions in hypoxia inducible factor (HIF) and the renin–angiotensin system (RAS) pathways. Our pathway enrichment analysis identified 95 significant pathways including regulation of glycolytic process (GO:0006110), regulation of hematopoietic stem cell differentiation (GO:1902036), and regulation of angiogenesis (GO:0045765). Lastly, we identified an association between the ACE gene insertion/deletion (I/D) polymorphism and oxygen saturation, as well as average ACE methylation. These findings shed light on the genes and pathways experiencing the most epigenetic change associated with short-term exposure to hypoxia.
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Affiliation(s)
- Ainash Childebayeva
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States.,Department of Environmental Sciences, School of Public Health, Ann Arbor, MI, United States.,Department of Archaeogenetics, Max Planck Institute for the Study of Human History, Jena, Germany
| | - Taylor Harman
- Department of Anthropology, Syracuse University, Syracuse, NY, United States
| | - Julien Weinstein
- Department of Anthropology, University of Michigan, Ann Arbor, MI, United States
| | - Trevor Day
- Department of Biology, Mount Royal University, Calgary, AB, Canada
| | - Tom D Brutsaert
- Department of Exercise Science, Syracuse University, Syracuse, NY, United States
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA, United States
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12
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Disease-associated synaptic scaffold protein CNK2 modulates PSD size and influences localisation of the regulatory kinase TNIK. Sci Rep 2020; 10:5709. [PMID: 32235845 PMCID: PMC7109135 DOI: 10.1038/s41598-020-62207-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/05/2020] [Indexed: 01/13/2023] Open
Abstract
Scaffold proteins are responsible for structural organisation within cells; they form complexes with other proteins to facilitate signalling pathways and catalytic reactions. The scaffold protein connector enhancer of kinase suppressor of Ras 2 (CNK2) is predominantly expressed in neural tissues and was recently implicated in X-linked intellectual disability (ID). We have investigated the role of CNK2 in neurons in order to contribute to our understanding of how CNK2 alterations might cause developmental defects, and we have elucidated a functional role for CNK2 in the molecular processes that govern morphology of the postsynaptic density (PSD). We have also identified novel CNK2 interaction partners and explored their functional interdependency with CNK2. We focussed on the novel interaction partner TRAF2- and NCK-interacting kinase TNIK, which is also associated with ID. Both CNK2 and TNIK are expressed in neuronal dendrites and concentrated in dendritic spines, and staining with synaptic markers indicates a clear postsynaptic localisation. Importantly, our data highlight that CNK2 plays a role in directing TNIK subcellular localisation, and in neurons, CNK2 participates in ensuring that this multifunctional kinase is present in the correct place at desirable levels. In summary, our data indicate that CNK2 expression is critical for modulating PSD morphology; moreover, our study highlights that CNK2 functions as a scaffold with the potential to direct the localisation of regulatory proteins within the cell. Importantly, we describe a novel link between CNK2 and the regulatory kinase TNIK, and provide evidence supporting the idea that alterations in CNK2 localisation and expression have the potential to influence the behaviour of TNIK and other important regulatory molecules in neurons.
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13
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Coste de Bagneaux P, von Elsner L, Bierhals T, Campiglio M, Johannsen J, Obermair GJ, Hempel M, Flucher BE, Kutsche K. A homozygous missense variant in CACNB4 encoding the auxiliary calcium channel beta4 subunit causes a severe neurodevelopmental disorder and impairs channel and non-channel functions. PLoS Genet 2020; 16:e1008625. [PMID: 32176688 PMCID: PMC7176149 DOI: 10.1371/journal.pgen.1008625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 04/22/2020] [Accepted: 01/23/2020] [Indexed: 12/27/2022] Open
Abstract
P/Q-type channels are the principal presynaptic calcium channels in brain functioning in neurotransmitter release. They are composed of the pore-forming CaV2.1 α1 subunit and the auxiliary α2δ-2 and β4 subunits. β4 is encoded by CACNB4, and its multiple splice variants serve isoform-specific functions as channel subunits and transcriptional regulators in the nucleus. In two siblings with intellectual disability, psychomotor retardation, blindness, epilepsy, movement disorder and cerebellar atrophy we identified rare homozygous variants in the genes LTBP1, EMILIN1, CACNB4, MINAR1, DHX38 and MYO15 by whole-exome sequencing. In silico tools, animal model, clinical, and genetic data suggest the p.(Leu126Pro) CACNB4 variant to be likely pathogenic. To investigate the functional consequences of the CACNB4 variant, we introduced the corresponding mutation L125P into rat β4b cDNA. Heterologously expressed wild-type β4b associated with GFP-CaV1.2 and accumulated in presynaptic boutons of cultured hippocampal neurons. In contrast, the β4b-L125P mutant failed to incorporate into calcium channel complexes and to cluster presynaptically. When co-expressed with CaV2.1 in tsA201 cells, β4b and β4b-L125P augmented the calcium current amplitudes, however, β4b-L125P failed to stably complex with α1 subunits. These results indicate that p.Leu125Pro disrupts the stable association of β4b with native calcium channel complexes, whereas membrane incorporation, modulation of current density and activation properties of heterologously expressed channels remained intact. Wildtype β4b was specifically targeted to the nuclei of quiescent excitatory cells. Importantly, the p.Leu125Pro mutation abolished nuclear targeting of β4b in cultured myotubes and hippocampal neurons. While binding of β4b to the known interaction partner PPP2R5D (B56δ) was not affected by the mutation, complex formation between β4b-L125P and the neuronal TRAF2 and NCK interacting kinase (TNIK) seemed to be disturbed. In summary, our data suggest that the homozygous CACNB4 p.(Leu126Pro) variant underlies the severe neurological phenotype in the two siblings, most likely by impairing both channel and non-channel functions of β4b.
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Affiliation(s)
| | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marta Campiglio
- Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
| | - Jessika Johannsen
- Childrens Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gerald J. Obermair
- Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
- Division Physiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bernhard E. Flucher
- Department of Physiology and Medical Physics, Medical University Innsbruck, Innsbruck, Austria
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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14
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Li Q, Nirala NK, Chen HJ, Nie Y, Wang W, Zhang B, Czech MP, Wang Q, Xu L, Mao J, Tony Ip Y. The Misshapen subfamily of Ste20 kinases regulate proliferation in the aging mammalian intestinal epithelium. J Cell Physiol 2019; 234:21925-21936. [PMID: 31042012 PMCID: PMC6711781 DOI: 10.1002/jcp.28756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/17/2022]
Abstract
The intestinal epithelium has a high rate of cell turn over and is an excellent system to study stem cell-mediated tissue homeostasis. The Misshapen subfamily of the Ste20 kinases in mammals consists of misshapen like kinase 1 (MINK1), mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), and TRAF2 and NCK interacting kinase (TNIK). Recent reports suggest that this subfamily has a novel function equal to the Hippo/MST subfamily as upstream kinases for Warts/Large tumor suppressor kinase (LATS) to suppress tissue growth. To study the in vivo functions of Mink1, Map4k4, and Tnik, we generated a compound knockout of these three genes in the mouse intestinal epithelium. The intestinal epithelia of the mutant animals were phenotypically normal up to approximately 12 months. The older animals then exhibited mildly increased proliferation throughout the lower GI tract. We also observed that the normally spatially organized Paneth cells in the crypt base became dispersed. The expression of one of the YAP pathway target genes Sox9 was increased while other target genes including CTGF did not show a significant change. Therefore, the Misshapen and Hippo subfamilies may have highly redundant functions to regulate growth in the intestinal epithelium, as illustrated in recent tissue culture models.
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Affiliation(s)
- Qi Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Niraj K. Nirala
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Hsi-Ju Chen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yingchao Nie
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Wei Wang
- Guangzhou RiboBio Co., Ltd., Guangzhou 510663, China
| | - Biliang Zhang
- Guangzhou RiboBio Co., Ltd., Guangzhou 510663, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Michael P. Czech
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Qi Wang
- Neuroscience Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Lan Xu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Junhao Mao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Y. Tony Ip
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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15
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Gumina V, Colombrita C, Fallini C, Bossolasco P, Maraschi AM, Landers JE, Silani V, Ratti A. TDP-43 and NOVA-1 RNA-binding proteins as competitive splicing regulators of the schizophrenia-associated TNIK gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194413. [PMID: 31382054 DOI: 10.1016/j.bbagrm.2019.194413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 01/09/2023]
Abstract
The RNA-binding protein TDP-43, associated to amyotrophic lateral sclerosis and frontotemporal dementia, regulates the alternative splicing of several genes, including the skipping of TNIK exon 15. TNIK, a genetic risk factor for schizophrenia and causative for intellectual disability, encodes for a Ser/Thr kinase regulating negatively F-actin dynamics. Here we show that in the human adult nervous system TNIK exon 15 is mostly included compared to the other tissues and that, during neuronal differentiation of human induced pluripotent stem cells and of human neuroblastoma cells, TNIK exon 15 inclusion increases independently of TDP-43 protein content. By studying the possible molecular interplay of TDP-43 with brain-specific splicing factors, we found that the neuronal NOVA-1 protein competitively inhibits both TDP-43 and hnRNPA2/B1 skipping activity on TNIK by means of a RNA-dependent interaction and that this competitive mechanism is common to other TDP-43 RNA targets. We also show that the TNIK protein isoforms including/excluding exon 15 differently regulate cell spreading in non-neuronal cells and neuritogenesis in primary cortical neurons. Our data suggest a complex regulation between the ubiquitous TDP-43 and the neuron-specific NOVA-1 splicing factors in the brain that may help better understand the pathobiology of both neurodegenerative diseases and schizophrenia.
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Affiliation(s)
- Valentina Gumina
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Via F. Sforza 35, 20122 Milan, Italy
| | - Claudia Colombrita
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, ASC 6-1053, Worcester, MA 01605, USA.
| | - Patrizia Bossolasco
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy
| | - Anna Maria Maraschi
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy.
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, ASC 6-1053, Worcester, MA 01605, USA.
| | - Vincenzo Silani
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Via F. Sforza 35, 20122 Milan, Italy; "Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Via A. di Rudinì 8, 20142 Milan, Italy.
| | - Antonia Ratti
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090, Segrate, Milan, Italy.
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16
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An T, Zhang J, Ma Y, Lian J, Wu YX, Lv BH, Ma MH, Meng JH, Zhou YT, Zhang ZY, Liu Q, Gao SH, Jiang GJ. Relationships of Non-coding RNA with diabetes and depression. Sci Rep 2019; 9:10707. [PMID: 31341180 PMCID: PMC6656886 DOI: 10.1038/s41598-019-47077-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/07/2019] [Indexed: 01/12/2023] Open
Abstract
In order to study the molecular differences between type 2 diabetes mellitus (T2DM) and T2DM with depression (DD), we aimed to screen the differential expression of lncRNA, mRNA, and circRNA in the blood of patients with T2DM and DD. Based on the self-rating depression scale (SDS), patient health questionnaire 9 (PHQ9), blood glucose and HbA1c, we divided the patients into T2DM and DD group. Peripheral blood was collected from the two groups of patients to perform lncRNA, mRNA, and circRNA expression profiling and screening DD-related specific molecules. Subsequently, bioinformatics analysis was performed to investigate the functions of differentially expressed genes (DEgenes). Finally, RT-PCR and lncRNA-mRNA regulatory network was performed to verify the expressions of lncRNAs and mRNAs related to the occurrence and development of DD. 28 lncRNAs, 107 circRNAs, and 89 mRNAs were identified in DD differential expression profiles. GO and pathway analysis found that 20 biological process (BP) related entities and 20 pathways associated with DD. The analysis shows that the genes that are differentially expressed in the DD group involved in the development of the neuropsychiatric system, immunity, and inflammation. Then, we screening for the important DElncRNA and mRNA associated with DD were verified by RT-PCR experiments and the results of RT-PCR were consistent with the sequencing results. LncRNA, circRNA, and mRNA differential expression profiles exist in DD patients compared with T2DM. The lncRNA-mRNA regulatory network analysis confirmed the crosslinking and complex regulation patterns of lncRNA and mRNA expression and verified the authenticity of the regulatory network.
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Affiliation(s)
- Tian An
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jing Zhang
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, 063000, China
| | - Yue Ma
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Juan Lian
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yan-Xiang Wu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Bo-Han Lv
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Meng-Hua Ma
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, 063000, China
| | - Jun-Hua Meng
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, 063000, China
| | - Yun-Tao Zhou
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, 063000, China
| | - Zhi-Yong Zhang
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, 063000, China
| | - Qing Liu
- Beijing Medicine and Food Co., Ltd., Beijing, 100029, China
| | - Si-Hua Gao
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Guang-Jian Jiang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China.
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17
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Hendi A, Kurashina M, Mizumoto K. Intrinsic and extrinsic mechanisms of synapse formation and specificity in C. elegans. Cell Mol Life Sci 2019; 76:2719-2738. [PMID: 31037336 PMCID: PMC11105629 DOI: 10.1007/s00018-019-03109-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
Precise neuronal wiring is critical for the function of the nervous system and is ultimately determined at the level of individual synapses. Neurons integrate various intrinsic and extrinsic cues to form synapses onto their correct targets in a stereotyped manner. In the past decades, the nervous system of nematode (Caenorhabditis elegans) has provided the genetic platform to reveal the genetic and molecular mechanisms of synapse formation and specificity. In this review, we will summarize the recent discoveries in synapse formation and specificity in C. elegans.
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Affiliation(s)
- Ardalan Hendi
- Department of Zoology, The University of British Columbia, 2406-2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Mizuki Kurashina
- Department of Zoology, The University of British Columbia, 2406-2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Kota Mizumoto
- Department of Zoology, The University of British Columbia, 2406-2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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18
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Wilkinson B, Evgrafov O, Zheng D, Hartel N, Knowles JA, Graham NA, Ichida J, Coba MP. Endogenous Cell Type-Specific Disrupted in Schizophrenia 1 Interactomes Reveal Protein Networks Associated With Neurodevelopmental Disorders. Biol Psychiatry 2019; 85:305-316. [PMID: 29961565 PMCID: PMC6251761 DOI: 10.1016/j.biopsych.2018.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 04/03/2018] [Accepted: 05/03/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Disrupted in schizophrenia 1 (DISC1) has been implicated in a number of psychiatric diseases along with neurodevelopmental phenotypes such as the proliferation and differentiation of neural progenitor cells. While there has been significant effort directed toward understanding the function of DISC1 through the determination of its protein-protein interactions within an in vitro setting, endogenous interactions involving DISC1 within a cell type-specific setting relevant to neural development remain unclear. METHODS Using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) genome engineering technology, we inserted an endogenous 3X-FLAG tag at the C-terminus of the canonical DISC1 gene in human induced pluripotent stem cells (iPSCs). We further differentiated these cells and used affinity purification to determine protein-protein interactions involving DISC1 in iPSC-derived neural progenitor cells and astrocytes. RESULTS We were able to determine 151 novel cell type-specific proteins present in DISC1 endogenous interactomes. The DISC1 interactomes can be clustered into several subcomplexes that suggest novel DISC1 cell-specific functions. In addition, the DISC1 interactome in iPSC-derived neural progenitor cells associates in a connected network containing proteins found to harbor de novo mutations in patients affected by schizophrenia and contains a subset of novel interactions that are known to harbor syndromic mutations in neurodevelopmental disorders. CONCLUSIONS Endogenous DISC1 interactomes within iPSC-derived human neural progenitor cells and astrocytes are able to provide context to DISC1 function in a cell type-specific setting relevant to neural development and enables the integration of psychiatric disease risk factors within a set of defined molecular functions.
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Affiliation(s)
- Brent Wilkinson
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Oleg Evgrafov
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | - DongQing Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90033, USA
| | - Nicolas Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90033, USA
| | - James A. Knowles
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Nicholas A. Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90033, USA
| | - Justin Ichida
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC
| | - Marcelo P. Coba
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Corresponding Author: Marcelo P. Coba, Keck School of Medicine, University of Southern California, Zilkha Neurogenetic Institute, 1501 San Pablo St, Los Angeles, CA 90033, USA. Phone: 323-442-4345.
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19
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Salih MAM, Swar MO. The odyssey of diagnosing genetic disorders in evolving health services. Sudan J Paediatr 2019; 19:2-5. [PMID: 31384081 PMCID: PMC6589806 DOI: 10.24911/sjp.106-1557046594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/05/2019] [Indexed: 11/11/2022]
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Chen X, Shibata AC, Hendi A, Kurashina M, Fortes E, Weilinger NL, MacVicar BA, Murakoshi H, Mizumoto K. Rap2 and TNIK control Plexin-dependent tiled synaptic innervation in C. elegans. eLife 2018; 7:38801. [PMID: 30063210 PMCID: PMC6067881 DOI: 10.7554/elife.38801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022] Open
Abstract
During development, neurons form synapses with their fate-determined targets. While we begin to elucidate the mechanisms by which extracellular ligand-receptor interactions enhance synapse specificity by inhibiting synaptogenesis, our knowledge about their intracellular mechanisms remains limited. Here we show that Rap2 GTPase (rap-2) and its effector, TNIK (mig-15), act genetically downstream of Plexin (plx-1) to restrict presynaptic assembly and to form tiled synaptic innervation in C. elegans. Both constitutively GTP- and GDP-forms of rap-2 mutants exhibit synaptic tiling defects as plx-1 mutants, suggesting that cycling of the RAP-2 nucleotide state is critical for synapse inhibition. Consistently, PLX-1 suppresses local RAP-2 activity. Excessive ectopic synapse formation in mig-15 mutants causes a severe synaptic tiling defect. Conversely, overexpression of mig-15 strongly inhibited synapse formation, suggesting that mig-15 is a negative regulator of synapse formation. These results reveal that subcellular regulation of small GTPase activity by Plexin shapes proper synapse patterning in vivo. Genes do more than just direct the color of our hair or eyes. They produce proteins that are involved in almost every process in the body. In humans, the majority of active genes can be found in the brain, where they help it to develop and work properly – effectively controlling how we move and behave. The brain’s functional units, the nerve cells or neurons, communicate with each other by releasing messenger molecules in the gap between them, the synapse. These molecules are then picked up from specific receptor proteins of the receiving neuron. In the nervous system, neurons only form synapses with the cells they need to connect with, even though they are surrounded by many more cells. This implies that they use specific mechanisms to stop neurons from forming synapses with incorrect target cells. This is important, because if too many synapses were present or if synapses formed with incorrect target cells, it would compromise the information flow in the nervous system. This would ultimately lead to various neurological conditions, including Autism Spectrum Disorder. In 2013, researchers found that in the roundworm Caenorhabditis elegans, a receptor protein called Plexin, is located at the surface of the neurons and can inhibit the formation of nearby synapses. Now, Chen et al. – including one author involved in the previous research – wanted to find out what genes Plexin manipulates when it stops synapses from growing. Knowing what each of those genes does can help us understand how neurons can inhibit synapses. The results revealed that Plexin appears to regulate two genes, Rap2 and TNIK. Plexin reduced the activity of Rap2 in the neuron that released the messenger, which hindered the formation of synapses. The gene TNIK and its protein on the other hand, have the ability to modify other proteins and could so inhibit the growth of synapses. When TNIK was experimentally removed, the number of synapses increased, but when its activity was increased, the number of synapses was strongly reduced. These findings could help scientists understand how mutations in Rap2 or TNIK can lead to various neurological conditions. A next step will be to test if these genes also affect the formation of synapses in other species such as mice, which have a more complex nervous system that is structurally and functionally more similar to that of humans.
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Affiliation(s)
- Xi Chen
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Akihiro Ce Shibata
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Ardalan Hendi
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Mizuki Kurashina
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Ethan Fortes
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | | | - Brian A MacVicar
- Department of Psychiatry, The University of British Columbia, Vancouver, Canada
| | - Hideji Murakoshi
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Japan
| | - Kota Mizumoto
- Department of Zoology, The University of British Columbia, Vancouver, Canada
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21
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Baltussen LL, Rosianu F, Ultanir SK. Kinases in synaptic development and neurological diseases. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:343-352. [PMID: 29241837 DOI: 10.1016/j.pnpbp.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
Abstract
Neuronal morphogenesis and synapse development is essential for building a functioning nervous system, and defects in these processes are associated with neurological disorders. Our understanding of molecular components and signalling events that contribute to neuronal development and pathogenesis is limited. Genes associated with neurodevelopmental and neurodegenerative diseases provide entry points for elucidating molecular events that contribute to these conditions. Several protein kinases, enzymes that regulate protein function by phosphorylating their substrates, are genetically linked to neurological disorders. Identifying substrates of these kinases is key to discovering their function and providing insight for possible therapies. In this review, we describe how various methods for kinase-substrate identification helped elucidate kinase signalling pathways important for neuronal development and function. We describe recent advances on roles of kinases TAOK2, TNIK and CDKL5 in neuronal development and the converging pathways of LRRK2, PINK1 and GAK in Parkinson's Disease.
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Affiliation(s)
- Lucas L Baltussen
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Flavia Rosianu
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom.
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22
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Khan MA, Khan S, Windpassinger C, Badar M, Nawaz Z, Mohammad RM. The Molecular Genetics of Autosomal Recessive Nonsyndromic Intellectual Disability: a Mutational Continuum and Future Recommendations. Ann Hum Genet 2017; 80:342-368. [PMID: 27870114 DOI: 10.1111/ahg.12176] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022]
Abstract
Intellectual disability (ID) is a clinical manifestation of the central nervous system without any major dysmorphologies of the brain. Biologically it affects learning capabilities, memory, and cognitive functioning. The basic defining features of ID are characterized by IQ<70, age of onset before 18 years, and impairment of at least two of the adaptive skills. Clinically it is classified in a syndromic (with additional abnormalities) and a nonsyndromic form (with only cognitive impairment). The study of nonsyndromic intellectual disability (NSID) can best explain the pathophysiology of cognition, intelligence and memory. Genetic analysis in autosomal recessive nonsyndrmic ID (ARNSID) has mapped 51 disease loci, 34 of which have revealed their defective genes. These genes play diverse physiological roles in various molecular processes, including methylation, proteolysis, glycosylation, signal transduction, transcription regulation, lipid metabolism, ion homeostasis, tRNA modification, ubiquitination and neuromorphogenesis. High-density SNP array and whole exome sequencing has increased the pace of gene discoveries and many new mutations are being published every month. The lack of uniform criteria has assigned multiple identifiers (or accession numbers) to the same MRT locus (e.g. MRT7 and MRT22). Here in this review we describe the molecular genetics of ARNSID, prioritize the candidate genes in uncharacterized loci, and propose a new nomenclature to reorganize the mutation data that will avoid the confusion of assigning duplicate accession numbers to the same ID locus and to make the data manageable in the future as well.
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Affiliation(s)
- Muzammil Ahmad Khan
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.,Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan, 29050 KPK, Pakistan
| | - Saadullah Khan
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.,Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | | | - Muhammad Badar
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan, 29050 KPK, Pakistan
| | - Zafar Nawaz
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Ramzi M Mohammad
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
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23
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Makrythanasis P, Guipponi M, Santoni FA, Zaki M, Issa MY, Ansar M, Hamamy H, Antonarakis SE. Exome sequencing discloses KALRN homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree. Hum Genomics 2016; 10:26. [PMID: 27421267 PMCID: PMC4947303 DOI: 10.1186/s40246-016-0082-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The recent availability of whole-exome sequencing has opened new possibilities for the evaluation of individuals with genetically undiagnosed intellectual disability. RESULTS We report two affected siblings, offspring of first-cousin parents, with intellectual disability, hypotonia, short stature, growth hormone deficiency, and delayed bone age. All members of the nuclear family were genotyped, and exome sequencing was performed in one of the affected individuals. We used an in-house algorithm (CATCH v1.1) that combines homozygosity mapping with exome sequencing results and provides a list of candidate variants. One identified novel homozygous missense variant in KALRN (NM_003947.4:c.3644C>A: p.(Thr1215Lys)) was predicted to be pathogenic by all pathogenicity prediction software used (SIFT, PolyPhen, Mutation Taster). KALRN encodes the protein kalirin, which is a GTP-exchange factor protein with a reported role in cytoskeletal remodeling and dendritic spine formation in neurons. It is known that mice with ablation of Kalrn exhibit age-dependent functional deficits and behavioral phenotypes. CONCLUSION Exome sequencing provided initial evidence linking KALRN to monogenic intellectual disability in man, and we propose that KALRN is the causative gene for the autosomal recessive phenotype in this family.
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Affiliation(s)
- Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Michel Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Maha Zaki
- Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Issa
- Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland. .,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland. .,iGE3, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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