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Patel PA, LaConte LEW, Liang C, Cecere T, Rajan D, Srivastava S, Mukherjee K. Genetic evidence for splicing-dependent structural and functional plasticity in CASK protein. J Med Genet 2024; 61:759-768. [PMID: 38670634 PMCID: PMC11290809 DOI: 10.1136/jmg-2023-109747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Pontocerebellar hypoplasia (PCH) may present with supratentorial phenotypes and is often accompanied by microcephaly. Damaging mutations in the X-linked gene CASK produce self-limiting microcephaly with PCH in females but are often lethal in males. CASK deficiency leads to early degeneration of cerebellar granule cells but its role in other regions of the brain remains uncertain. METHOD We generated a conditional Cask knockout mice and deleted Cask ubiquitously after birth at different times. We examined the clinical features in several subjects with damaging mutations clustered in the central part of the CASK protein. We have performed phylogenetic analysis and RT-PCR to assess the splicing pattern within the same protein region and performed in silico structural analysis to examine the effect of splicing on the CASK's structure. RESULT We demonstrate that deletion of murine Cask after adulthood does not affect survival but leads to cerebellar degeneration and ataxia over time. Intriguingly, damaging hemizygous CASK mutations in boys who display microcephaly and cerebral dysfunction but without PCH are known. These mutations are present in two vertebrate-specific CASK exons. These exons are subject to alternative splicing both in forebrain and hindbrain. Inclusion of these exons differentially affects the molecular structure and hence possibly the function/s of the CASK C-terminus. CONCLUSION Loss of CASK function disproportionately affects the cerebellum. Clinical data, however, suggest that CASK may have additional vertebrate-specific function/s that play a role in the mammalian forebrain. Thus, CASK has an ancient function shared between invertebrates and vertebrates as well as novel vertebrate-specific function/s.
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Affiliation(s)
- Paras A Patel
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
| | - Leslie E W LaConte
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
- Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - Chen Liang
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
| | - Thomas Cecere
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Deepa Rajan
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sarika Srivastava
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
- Department of Genetics, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, USA
| | - Konark Mukherjee
- Fralin Biomedical Research Institute at VTC, Roanoke, Virginia, USA
- Department of Genetics, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, USA
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Lughmani H, Patel H, Chakravarti R. Structural Features and Physiological Associations of Human 14-3-3ζ Pseudogenes. Genes (Basel) 2024; 15:399. [PMID: 38674334 PMCID: PMC11049341 DOI: 10.3390/genes15040399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they have functional and regulatory roles. We study 14-3-3ζ, an adaptor protein that regulates cytokine signaling and inflammatory diseases, including rheumatoid arthritis, cancer, and neurological disorders. To understand how 14-3-3ζ (gene symbol YWHAZ) performs diverse functions, we examined the human genome and identified nine YWHAZ pseudogenes spread across many chromosomes. Unlike the 32 kb exon-to-exon sequence in YWHAZ, all pseudogenes are much shorter and lack introns. Out of six, four YWHAZ exons are highly conserved, but the untranslated region (UTR) shows significant diversity. The putative amino acid sequence of pseudogenes is 78-97% homologous, resulting in striking structural similarities with the parent protein. The OMIM and Decipher database searches revealed chromosomal loci containing pseudogenes are associated with human diseases that overlap with the parent gene. To the best of our knowledge, this is the first report on pseudogenes of the 14-3-3 family protein and their implications for human health. This bioinformatics-based study introduces a new insight into the complexity of 14-3-3ζ's functions in biology.
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Affiliation(s)
| | | | - Ritu Chakravarti
- Department of Physiology and Pharmacology, The University of Toledo, Toledo, OH 43614, USA; (H.L.); (H.P.)
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Mori T, Zhou M, Tabuchi K. Diverse Clinical Phenotypes of CASK-Related Disorders and Multiple Functional Domains of CASK Protein. Genes (Basel) 2023; 14:1656. [PMID: 37628707 PMCID: PMC10454856 DOI: 10.3390/genes14081656] [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: 08/07/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
CASK-related disorders are a form of rare X-linked neurological diseases and most of the patients are females. They are characterized by several symptoms, including microcephaly with pontine and cerebellar hypoplasia (MICPCH), epilepsy, congenital nystagmus, and neurodevelopmental disorders. Whole-genome sequencing has identified various mutations, including nonsense and missense mutations, from patients with CASK-related disorders, revealing correlations between specific mutations and clinical phenotypes. Notably, missense mutations associated with epilepsy and intellectual disability were found throughout the whole region of the CASK protein, while missense mutations related to microcephaly and MICPCH were restricted in certain domains. To investigate the pathophysiology of CASK-related disorders, research groups have employed diverse methods, including the generation of CASK knockout mice and the supplementation of CASK to rescue the phenotypes. These approaches have yielded valuable insights into the identification of functional domains of the CASK protein associated with a specific phenotype. Additionally, recent advancements in the AI-based prediction of protein structure, such as AlphaFold2, and the application of genome-editing techniques to generate CASK mutant mice carrying missense mutations from patients with CASK-related disorders, allow us to understand the pathophysiology of CASK-related disorders in more depth and to develop novel therapeutic methods for the fundamental treatment of CASK-related disorders.
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Affiliation(s)
- Takuma Mori
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Mengyun Zhou
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
| | - Katsuhiko Tabuchi
- Department of Neuroinnovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto 390-8621, Japan;
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto 390-8621, Japan;
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Bayanova M, Bolatov AK, Bazenova A, Nazarova L, Nauryzbayeva A, Tanko NM, Rakhimova S, Satvaldina N, Samakyzy D, Kozhamkulov U, Kairov U, Akilzhanova A, Sarbassov D. Whole-Genome Sequencing Among Kazakhstani Children with Early-Onset Epilepsy Revealed New Gene Variants and Phenotypic Variability. Mol Neurobiol 2023; 60:4324-4335. [PMID: 37095367 PMCID: PMC10293429 DOI: 10.1007/s12035-023-03346-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
In Kazakhstan, there is insufficient data on genetic epilepsy, which has its own clinical and management implications. Thus, this study aimed to use whole genome sequencing to identify and evaluate genetic variants and genetic structure of early onset epilepsy in the Kazakhstani pediatric population. In this study, for the first time in Kazakhstan, whole genome sequencing was carried out among epilepsy diagnosed children. The study involved 20 pediatric patients with early onset epilepsy and no established cause of the disease during the July-December, 2021. The average age at enrolment was 34.5 months, with a mean age at seizure onset of 6 months. Six patients (30%) were male, and 7 were familial cases. We identified pathogenic and likely pathogenic variants in 14 (70%) cases, among them, 6 novel disease gene variants (KCNQ2, CASK, WWOX, MT-CO3, GRIN2D, and SLC12A5). Other genes associated with the disease were SCN1A (x2), SLC2A1, ARX, CACNA1B, PCDH19, KCNT1, and CHRNA2. Identification of the genetic causes in 70% of cases confirms the general structure of the etiology of early onset epilepsy and the necessity of using NGS in diagnostics. Moreover, the study describes new genotype-phenotypic correlations in genetic epilepsy. Despite certain limitations of the study, it can be concluded that the genetic etiology of pediatric epilepsy in Kazakhstan is very broad and requires further research.
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Affiliation(s)
- Mirgul Bayanova
- University Medical Center CF, Kerey-Zhanibek Handar St. 5/1, Z05P3Y4, Astana, Kazakhstan
| | - Aidos K. Bolatov
- University Medical Center CF, Kerey-Zhanibek Handar St. 5/1, Z05P3Y4, Astana, Kazakhstan
- Astana Medical University, Beybitshilik St. 49A, Z10K9D9, Astana, Kazakhstan
| | - Assiya Bazenova
- University Medical Center CF, Kerey-Zhanibek Handar St. 5/1, Z05P3Y4, Astana, Kazakhstan
| | - Lyazzat Nazarova
- University Medical Center CF, Kerey-Zhanibek Handar St. 5/1, Z05P3Y4, Astana, Kazakhstan
| | - Alissa Nauryzbayeva
- University Medical Center CF, Kerey-Zhanibek Handar St. 5/1, Z05P3Y4, Astana, Kazakhstan
| | - Naanlep Matthew Tanko
- University Medical Center CF, Kerey-Zhanibek Handar St. 5/1, Z05P3Y4, Astana, Kazakhstan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan 010000
| | - Saule Rakhimova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
| | - Nazerke Satvaldina
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
| | - Diana Samakyzy
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
| | - Ulan Kozhamkulov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
| | - Ulykbek Kairov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
| | - Ainur Akilzhanova
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
| | - Dos Sarbassov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
- School of Sciences and Humanities, Nazarbayev University, Kabanbay batyr Ave 53, Astana, Kazakhstan 010000
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Zhang Q, Huang Y, Wu A, Duan Q, He P, Huang H, Gao Y, Nie K, Liu Q, Wang L. Calcium/calmodulin-dependent serine protein kinase exacerbates mitochondrial calcium uniporter-related mitochondrial calcium overload by phosphorylating α-synuclein in Parkinson's disease. Int J Biochem Cell Biol 2023; 157:106385. [PMID: 36754160 DOI: 10.1016/j.biocel.2023.106385] [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: 10/29/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
α-Synuclein phosphorylation and mitochondrial calcium homeostasis are important mechanisms underlying mitochondrial dysfunction in Parkinson's disease, but the network regulating these mechanisms remains unclear. We identified the role of key phosphokinases and the pathological effects of α-synuclein phosphorylation on mitochondrial calcium influx and mitochondrial function in Parkinson's disease. The function of the key phosphokinase, calcium/calmodulin-dependent serine protein kinase, was investigated through loss- and gain-of-function experiments using a cell model of Parkinson's disease. The regulation of mitochondrial calcium uniporter-mediated mitochondrial calcium influx by calcium/calmodulin-dependent serine protein kinase was explored using a cellular model of Parkinson's disease. Coimmunoprecipitation experiments and α-synuclein mutation were used to explore the mechanism through which calcium/calmodulin-dependent serine protein kinase regulates mitochondrial calcium uniporter-mediated mitochondrial calcium influx and exacerbates mitochondrial damage in Parkinson's disease. Here, we show the pathogenic role of calcium/calmodulin-dependent serine protein kinase in Parkinson's disease progression. Calcium/calmodulin-dependent serine protein kinase phosphorylated α-synuclein to activate mitochondrial calcium uniporter and thus increase mitochondrial calcium influx, and these effects were blocked by α-synuclein S129A mutant expression. Furthermore, the calcium/calmodulin-dependent serine protein kinase inhibitor CASK-IN-1 exerted neuroprotective effects in Parkinson's disease. Collectively, our results suggest that calcium/calmodulin-dependent serine protein kinase phosphorylates α-synuclein to activate the mitochondrial calcium uniporter and thereby causes mitochondrial calcium overload and mitochondrial damage in Parkinson's disease. We elucidated a new role of calcium/calmodulin-dependent serine protein kinase in Parkinson's disease and revealed the potential therapeutic value of targeting calcium/calmodulin-dependent serine protein kinase in Parkinson's disease treatment.
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Affiliation(s)
- Qingxi Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510100, China; Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Yin Huang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Anbiao Wu
- Department of Cardiology, Laboratory of Heart Center; Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Qingrui Duan
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Peikun He
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Haifeng Huang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Yuyuan Gao
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Kun Nie
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Qicai Liu
- Department of Cardiology, Laboratory of Heart Center; Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China.
| | - Lijuan Wang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
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Wahbeh MH, Peng X, Bacharaki S, Hatzimanolis A, Dimitrakopoulos S, Wohler E, Yang X, Yovo C, Maher BJ, Sobreira N, Stefanis NC, Avramopoulos D. A Missense Variant in CASKIN1's Proline-Rich Region Segregates with Psychosis in a Three-Generation Family. Genes (Basel) 2023; 14:177. [PMID: 36672919 PMCID: PMC9859343 DOI: 10.3390/genes14010177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
The polygenic nature of schizophrenia (SCZ) implicates many variants in disease development. Rare variants of high penetrance have been shown to contribute to the disease prevalence. Whole-exome sequencing of a large three-generation family with SCZ and bipolar disorder identified a single segregating novel, rare, non-synonymous variant in the gene CASKIN1. The variant D1204N is absent from all databases, and CASKIN1 has a gnomAD missense score Z = 1.79 and pLI = 1, indicating its strong intolerance to variation. We find that introducing variants in the proline-rich region where the D1204N resides results in significant cellular changes in iPSC-derived neurons, consistent with CASKIN1’s known functions. We observe significant transcriptomic changes in 368 genes (padj < 0.05) involved in neuronal differentiation and nervous system development. We also observed nominally significant changes in the frequency of action potentials during differentiation, where the speed at which the edited and unedited cells reach the same level of activity differs. Our results suggest that CASKIN1 is an excellent gene candidate for psychosis development with high penetrance in this family.
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Affiliation(s)
- Marah H. Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Predoctoral Training Program in Human Genetics and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21201, USA
| | - Xi Peng
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sofia Bacharaki
- Department of Psychiatry, General Hospital of Syros, 84100 Cyclades, Greece
| | - Alexandros Hatzimanolis
- Department of Psychiatry, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 15772 Athens, Greece
| | - Stefanos Dimitrakopoulos
- Department of Psychiatry, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 15772 Athens, Greece
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Xue Yang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Brady J. Maher
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Nikos C. Stefanis
- Department of Psychiatry, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 15772 Athens, Greece
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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