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Zhang C, Gao J, Chen HY, Kong L, Cao G, Guo X, Liu W, Ren B, Wei DQ. STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. PLoS Comput Biol 2024; 20:e1011935. [PMID: 38416785 PMCID: PMC10927115 DOI: 10.1371/journal.pcbi.1011935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/11/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Spatial transcriptomic (ST) clustering employs spatial and transcription information to group spots spatially coherent and transcriptionally similar together into the same spatial domain. Graph convolution network (GCN) and graph attention network (GAT), fed with spatial coordinates derived adjacency and transcription profile derived feature matrix are often used to solve the problem. Our proposed method STGIC (spatial transcriptomic clustering with graph and image convolution) is designed for techniques with regular lattices on chips. It utilizes an adaptive graph convolution (AGC) to get high quality pseudo-labels and then resorts to dilated convolution framework (DCF) for virtual image converted from gene expression information and spatial coordinates of spots. The dilation rates and kernel sizes are set appropriately and updating of weight values in the kernels is made to be subject to the spatial distance from the position of corresponding elements to kernel centers so that feature extraction of each spot is better guided by spatial distance to neighbor spots. Self-supervision realized by Kullback-Leibler (KL) divergence, spatial continuity loss and cross entropy calculated among spots with high confidence pseudo-labels make up the training objective of DCF. STGIC attains state-of-the-art (SOTA) clustering performance on the benchmark dataset of 10x Visium human dorsolateral prefrontal cortex (DLPFC). Besides, it's capable of depicting fine structures of other tissues from other species as well as guiding the identification of marker genes. Also, STGIC is expandable to Stereo-seq data with high spatial resolution.
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Affiliation(s)
- Chen Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Junhui Gao
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Yu Chen
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Lingxin Kong
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guangshuo Cao
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang
| | - Xiangyu Guo
- Smart-Health Initiative, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Wei Liu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Bin Ren
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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2
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Contribution of parasol-magnocellular pathway ganglion cells to foveal retina in macaque monkey. Vision Res 2023; 202:108154. [PMID: 36436365 DOI: 10.1016/j.visres.2022.108154] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/18/2022] [Accepted: 10/28/2022] [Indexed: 11/25/2022]
Abstract
Parasol-magnocellular pathway ganglion cells form an important output stream of the primate retina and make a major contribution to visual motion detection. They are known to comprise ON and OFF type response polarities but the relative numbers of ON and OFF parasol cells, and the overall contribution of parasol cells to high-acuity foveal vision are not well understood. Here we use antibodies against carbonic anhydrase 8 (CA8) and intracellular injections of the liphilic dye DiI to show that CA8 selectively labels OFF parasol cells in macaque retina. By combined labeling with CA8 antibodies and a previously-described marker for parasol cells (GABAA receptor antibodies), we show that ON and OFF parasol cells each comprise ∼ 6% of all ganglion cells in central retina (each peak density ∼ 3000 cells/mm2 at 5 deg.), and each population comprises ∼ 10% of all ganglion cells in peripheral temporal retina. Thus, the spatial density of parasol cells in central retina is greater than reported by previous anatomical studies, and the central-peripheral gradient in parasol cell density is shallower than previously reported. The data nevertheless predict decline in spatial acuity with visual field eccentricity for both midget-parvocellular pathway and parasol-magnocellular pathway mediated visual functions. The spatial resolving power of the OFF parasol array (peak ∼ 7 cpd) falls short of macaque behavioral grating acuity by at least a factor of three throughout the retina.
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Wu QW, Kapfhammer JP. The Emerging Key Role of the mGluR1-PKCγ Signaling Pathway in the Pathogenesis of Spinocerebellar Ataxias: A Neurodevelopmental Viewpoint. Int J Mol Sci 2022; 23:ijms23169169. [PMID: 36012439 PMCID: PMC9409119 DOI: 10.3390/ijms23169169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/19/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are a heterogeneous group of autosomal dominantly inherited progressive disorders with degeneration and dysfunction of the cerebellum. Although different subtypes of SCAs are classified according to the disease-associated causative genes, the clinical syndrome of the ataxia is shared, pointing towards a possible convergent pathogenic pathway among SCAs. In this review, we summarize the role of SCA-associated gene function during cerebellar Purkinje cell development and discuss the relationship between SCA pathogenesis and neurodevelopment. We will summarize recent studies on molecules involved in SCA pathogenesis and will focus on the mGluR1-PKCγ signaling pathway evaluating the possibility that this might be a common pathway which contributes to these diseases.
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4
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Mezey SE, Kapfhammer JP, Shimobayashi E. Transcriptome Profile of a New Mouse Model of Spinocerebellar Ataxia Type 14 Implies Changes in Cerebellar Development. Genes (Basel) 2022; 13:genes13081417. [PMID: 36011327 PMCID: PMC9407720 DOI: 10.3390/genes13081417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 12/13/2022] Open
Abstract
The autosomal dominant inherited spinocerebellar ataxias (SCAs) are a group of neurodegenerative disorders characterized by cerebellar atrophy and loss of Purkinje neurons. Spinocerebellar ataxia type 14 (SCA14) is a rare variant of SCAs caused by missense mutations or deletions in the PRKCG gene encoding the protein kinase C γ (PKCγ). Although mutated PKCγs are responsible for SCA14, it is still unclear exactly how mutated PKCγs are involved in SCA14 pathogenesis. Therefore, it is important to study how PKCγ signaling is altered in the cerebellum, which genes or signaling pathways are affected, and how this leads to neurological disease. In this study, we used a mouse line carrying a knock-in pseudo-substrate domain mutation in PKCγ (PKCγ-A24E) as an SCA14 model and performed RNA sequencing (RNA-seq) analysis at an early developmental timepoint (postnatal day 15) to investigate changes in the gene profile compared to wildtype mice. We analyzed both heterozygous (Het) PKCγ-A24E mice and homozygous (Homo) PKCγ-A24E mice for transcriptomic changes. The Het PKCγ-A24E mice reflects the situation observed in human SCA14 patient, while Homo PKCγ-A24E mice display stronger phenotypes with respect to Purkinje cell development and behavior. Our findings highlight an abundance of modifications affecting genes involved in developmental processes, suggesting that at least a part of the final phenotype is shaped by altered cerebellar development and is not only caused by changes in mature animals.
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Lin GY, Ma CY, Kuo LC, Hsieh BY, Wang H, Liu CS, Hsieh M. Altered glucose metabolism and its association with carbonic anhydrase 8 in Machado-Joseph Disease. Metab Brain Dis 2022; 37:2103-2120. [PMID: 35488942 DOI: 10.1007/s11011-022-00994-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/26/2022] [Indexed: 11/27/2022]
Abstract
Machado-Joseph disease (MJD), also known as spinocerebellar ataxia type 3 (SCA3), is an autosomal dominant neurodegenerative disease. This disorder is caused by polyglutamine (polyQ)-containing mutant ataxin-3, which tends to misfold and aggregate in neuron cells. We previously demonstrated a protective function of carbonic anhydrase 8 (CA8) in MJD disease models and a decreased glycolytic activity associated with down-regulated CA8 in a human osteosarcoma (OS) cell model. Given that a reduction in body weight accompanied by gait and balance instability was observed in MJD patients and transgenic (Tg) mice, in this study, we aimed to examine whether metabolic defects are associated with MJD and whether CA8 expression is involved in metabolic dysfunction in MJD. Our data first showed that glucose uptake ability decreases in cells harboring mutant ataxin-3, but increases in cells overexpressing CA8. In addition, the expressions of glucose transporter 3 (GLUT3) and phosphofructokinase-1 (PFK1) were significantly decreased in the presence of mutant ataxin-3. Consistently, immunohistochemistry (IHC) showed that GLUT3 was less expressed in cerebella of aged MJD Tg mice, indicating that the dysfunction of GLUT3 may be associated with late-stage disease. On the other hand, transient down-regulation of CA8 revealed decreased expressions of GLUT3 and PFK1 in HEK293 cells harboring wild-type (WT) ataxin-3, but no further reduction of GLUT3 and PFK1 expressions were observed in HEK293 cells harboring mutant ataxin-3. Moreover, immunoprecipitation (IP) and immunofluorescence (IF) demonstrated that interactions exist between ataxin-3, CA8 and GLUT3 in MJD cellular and Tg models. These lines of evidence suggest that CA8 plays an important role in glucose metabolism and has different impacts on cells with or without mutant ataxin-3. Interestingly, the decreased relative abundance of Firmicutes/Bacteroidetes (F/B) ratio in the feces of aged MJD Tg mice coincided with weight loss and metabolic dysfunction in MJD. Taken together, our results are the first to demonstrate the effects of CA8 on glucose metabolism and its involvement in the metabolic defects in MJD disease. Further investigations will be required to clarify the underlying mechanisms for the metabolic defects associated with MJD.
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Affiliation(s)
- Guan-Yu Lin
- Department of Life Science, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 407, Taiwan, Republic of China
| | - Chung-Yung Ma
- Department of Life Science, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 407, Taiwan, Republic of China
| | - Li-Chung Kuo
- Department of Life Science, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 407, Taiwan, Republic of China
| | - Benjamin Y Hsieh
- Department of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, Republic of China
| | - Hanbing Wang
- Department of Life Science, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 407, Taiwan, Republic of China
| | - Chin-San Liu
- Vascular and Genomic Center, Changhua Christian Hospital, Changhua, Taiwan, Republic of China
| | - Mingli Hsieh
- Department of Life Science, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 407, Taiwan, Republic of China.
- Life Science Research Center, Tunghai University, Taichung, Taiwan, Republic of China.
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6
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Bertile F, Plumel M, Maes P, Hirschler A, Challet E. Daytime Restricted Feeding Affects Day-Night Variations in Mouse Cerebellar Proteome. Front Mol Neurosci 2021; 14:613161. [PMID: 33912010 PMCID: PMC8072461 DOI: 10.3389/fnmol.2021.613161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
The cerebellum harbors a circadian clock that can be shifted by scheduled mealtime and participates in behavioral anticipation of food access. Large-scale two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry was used to identify day–night variations in the cerebellar proteome of mice fed either during daytime or nighttime. Experimental conditions led to modified expression of 89 cerebellar proteins contained in 63 protein spots. Five and 33 spots were changed respectively by time-of-day or feeding conditions. Strikingly, several proteins of the heat-shock protein family (i.e., Hsp90aa1, 90ab1, 90b1, and Hspa2, 4, 5, 8, 9) were down-regulated in the cerebellum of daytime food-restricted mice. This was also the case for brain fatty acid protein (Fabp7) and enzymes involved in oxidative phosphorylation (Ndufs1) or folate metabolism (Aldh1l1). In contrast, aldolase C (Aldoc or zebrin II) and pyruvate carboxylase (Pc), two enzymes involved in carbohydrate metabolism, and vesicle-fusing ATPase (Nsf) were up-regulated during daytime restricted feeding, possibly reflecting increased neuronal activity. Significant feeding × time-of-day interactions were found for changes in the intensity of 20 spots. Guanine nucleotide-binding protein G(o) subunit alpha (Gnao1) was more expressed in the cerebellum before food access. Neuronal calcium-sensor proteins [i.e., parvalbumin (Pvalb) and visinin-like protein 1 (Vsnl1)] were inversely regulated in daytime food-restricted mice, compared to control mice fed at night. Furthermore, expression of three enzymes modulating the circadian clockwork, namely heterogeneous nuclear ribonucleoprotein K (Hnrnpk), serine/threonine-protein phosphatases 1 (Ppp1cc and Ppp1cb subunits) and 5 (Ppp5), was differentially altered by daytime restricted feeding. Besides cerebellar proteins affected only by feeding conditions or daily cues, specific changes in in protein abundance before food access may be related to behavioral anticipation of food access and/or feeding-induced shift of the cerebellar clockwork.
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Affiliation(s)
- Fabrice Bertile
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Université de Strasbourg, Centre National de la Recherche Scientifique, Strasbourg, France
| | - Marine Plumel
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Université de Strasbourg, Centre National de la Recherche Scientifique, Strasbourg, France
| | - Pauline Maes
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Université de Strasbourg, Centre National de la Recherche Scientifique, Strasbourg, France
| | - Aurélie Hirschler
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Université de Strasbourg, Centre National de la Recherche Scientifique, Strasbourg, France
| | - Etienne Challet
- Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Centre National de la Recherche Scientifique, Strasbourg, France
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A New Mouse Model Related to SCA14 Carrying a Pseudosubstrate Domain Mutation in PKCγ Shows Perturbed Purkinje Cell Maturation and Ataxic Motor Behavior. J Neurosci 2021; 41:2053-2068. [PMID: 33478986 PMCID: PMC7939089 DOI: 10.1523/jneurosci.1946-20.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 01/15/2023] Open
Abstract
Spinocerebellar ataxias (SCAs) are diseases characterized by cerebellar atrophy and loss of Purkinje neurons caused by mutations in diverse genes. In SCA14, the disease is caused by point mutations or small deletions in protein kinase C γ (PKCγ), a crucial signaling protein in Purkinje cells. It is still unclear whether increased or decreased PKCγ activity may be involved in the SCA14 pathogenesis. In this study, we present a new knock-in mouse model related to SCA14 with a point mutation in the pseudosubstrate domain, PKCγ-A24E, known to induce a constitutive PKCγ activation. In this protein conformation, the kinase domain of PKCγ is activated, but at the same time the protein is subject to dephosphorylation and protein degradation. As a result, we find a dramatic reduction of PKCγ protein expression in PKCγ-A24E mice of either sex. Despite this reduction, there is clear evidence for an increased PKC activity in Purkinje cells from PKCγ-A24E mice. Purkinje cells derived from PKCγ-A24E have short thickened dendrites typical for PKC activation. These mice also develop a marked ataxia and signs of Purkinje cell dysfunction making them an interesting new mouse model related to SCA. Recently, a similar mutation in a human patient was discovered and found to be associated with overt SCA14. RNA profiling of PKCγ-A24E mice showed a dysregulation of related signaling pathways, such as mGluR1 or mTOR. Our results show that the induction of PKCγ activation in Purkinje cells results in the SCA-like phenotype indicating PKC activation as one pathogenetic avenue leading to a SCA.SIGNIFICANCE STATEMENT Spinocerebellar ataxias (SCAs) are hereditary diseases affecting cerebellar Purkinje cells and are a one of neurodegenerative diseases. While mutation in several genes have been identified as causing SCAs, it is unclear how these mutations cause the disease phenotype. Mutations in PKCγ cause one subtype of SCAs, SCA14. In this study, we have generated a knock-in mouse with a mutation in the pseudosubstrate domain of PKCγ, which keeps PKCγ in the constitutive active open conformation. We show that this mutation leading to a constant activation of PKCγ results in a SCA-like phenotype in these mice. Our findings establish the constant activation of PKC signaling as one pathogenetic avenue leading to an SCA phenotype and a mechanism causing a neurodegenerative disease.
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8
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Wu QW, Kapfhammer JP. Modulation of Increased mGluR1 Signaling by RGS8 Protects Purkinje Cells From Dendritic Reduction and Could Be a Common Mechanism in Diverse Forms of Spinocerebellar Ataxia. Front Cell Dev Biol 2021; 8:569889. [PMID: 33553137 PMCID: PMC7858651 DOI: 10.3389/fcell.2020.569889] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are a group of hereditary neurodegenerative diseases which are caused by diverse genetic mutations in a variety of different genes. We have identified RGS8, a regulator of G-protein signaling, as one of the genes which are dysregulated in different mouse models of SCA (e.g., SCA1, SCA2, SCA7, and SCA14). In the moment, little is known about the role of RGS8 for pathogenesis of spinocerebellar ataxia. We have studied the expression of RGS8 in the cerebellum in more detail and show that it is specifically expressed in mouse cerebellar Purkinje cells. In a mouse model of SCA14 with increased PKCγ activity, RGS8 expression was also increased. RGS8 overexpression could partially counteract the negative effects of DHPG-induced mGluR1 signaling for the expansion of Purkinje cell dendrites. Our results suggest that the increased expression of RGS8 is an important mediator of mGluR1 pathway dysregulation in Purkinje cells. These findings provide new insights in the role of RGS8 and mGluR1 signaling in Purkinje cells and for the pathology of SCAs.
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Affiliation(s)
- Qin-Wei Wu
- Institute of Anatomy, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josef P Kapfhammer
- Institute of Anatomy, Department of Biomedicine, University of Basel, Basel, Switzerland
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9
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Winkler SC, Shimobayashi E, Kapfhammer JP. PKCγ-Mediated Phosphorylation of CRMP2 Regulates Dendritic Outgrowth in Cerebellar Purkinje Cells. Mol Neurobiol 2020; 57:5150-5166. [PMID: 32860158 PMCID: PMC7541385 DOI: 10.1007/s12035-020-02038-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/22/2020] [Indexed: 11/02/2022]
Abstract
The signalling protein PKCγ is a major regulator of Purkinje cell development and synaptic function. We have shown previously that increased PKCγ activity impairs dendritic development of cerebellar Purkinje cells. Mutations in the protein kinase Cγ gene (PRKCG) cause spinocerebellar ataxia type 14 (SCA14). In a transgenic mouse model of SCA14 expressing the human S361G mutation, Purkinje cell dendritic development is impaired in cerebellar slice cultures similar to pharmacological activation of PKC. The mechanisms of PKCγ-driven inhibition of dendritic growth are still unclear. Using immunoprecipitation-coupled mass spectrometry analysis, we have identified collapsin response mediator protein 2 (CRMP2) as a protein interacting with constitutive active PKCγ(S361G) and confirmed the interaction with the Duolink™ proximity ligation assay. We show that in cerebellar slice cultures from PKCγ(S361G)-mice, phosphorylation of CRMP2 at the known PKC target site Thr555 is increased in Purkinje cells confirming phosphorylation of CRMP2 by PKCγ. miRNA-mediated CRMP2 knockdown decreased Purkinje cell dendritic outgrowth in dissociated cerebellar cultures as did the transfection of CRMP2 mutants with a modified Thr555 site. In contrast, dendritic development was normal after wild-type CRMP2 overexpression. In a novel knock-in mouse expressing only the phospho-defective T555A-mutant CRMP2, Purkinje cell dendritic development was reduced in dissociated cultures. This reduction could be rescued by transfecting wild-type CRMP2 but only partially by the phospho-mimetic T555D-mutant. Our findings establish CRMP2 as an important target of PKCγ phosphorylation in Purkinje cells mediating its control of dendritic development. Dynamic regulation of CRMP2 phosphorylation via PKCγ is required for its correct function.
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Affiliation(s)
- Sabine C Winkler
- Anatomical Institute, Department of Biomedicine, University of Basel, Pestalozzistrasse 20, CH - 4056, Basel, Switzerland
| | - Etsuko Shimobayashi
- Anatomical Institute, Department of Biomedicine, University of Basel, Pestalozzistrasse 20, CH - 4056, Basel, Switzerland
| | - Josef P Kapfhammer
- Anatomical Institute, Department of Biomedicine, University of Basel, Pestalozzistrasse 20, CH - 4056, Basel, Switzerland.
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10
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Sanyanga TA, Tastan Bishop Ö. Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function. Int J Mol Sci 2020; 21:E2764. [PMID: 32316137 PMCID: PMC7215520 DOI: 10.3390/ijms21082764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Human carbonic anhydrase 8 (CA-VIII) is an acatalytic isoform of the α -CA family. Though the protein cannot hydrate CO2, CA-VIII is essential for calcium (Ca2+) homeostasis within the body, and achieves this by allosterically inhibiting the binding of inositol 1,4,5-triphosphate (IP3) to the IP3 receptor type 1 (ITPR1) protein. However, the mechanism of interaction of CA-VIII to ITPR1 is not well understood. In addition, functional defects to CA-VIII due to non-synonymous single nucleotide polymorphisms (nsSNVs) result in Ca2+ dysregulation and the development of the phenotypes such as cerebellar ataxia, mental retardation and disequilibrium syndrome 3 (CAMRQ3). The pathogenesis of CAMRQ3 is also not well understood. The structure and function of CA-VIII was characterised, and pathogenesis of CAMRQ3 investigated. Structural and functional characterisation of CA-VIII was conducted through SiteMap and CPORT to identify potential binding site residues. The effects of four pathogenic nsSNVs, S100A, S100P, G162R and R237Q, and two benign S100L and E109D variants on CA-VIII structure and function was then investigated using molecular dynamics (MD) simulations, dynamic cross correlation (DCC) and dynamic residue network (DRN) analysis. SiteMap and CPORT analyses identified 38 unique CA-VIII residues that could potentially bind to ITPR1. MD analysis revealed less conformational sampling within the variant proteins and highlighted potential increases to variant protein rigidity. Dynamic cross correlation (DCC) showed that wild-type (WT) protein residue motion is predominately anti-correlated, with variant proteins showing no correlation to greater residue correlation. DRN revealed variant-associated increases to the accessibility of the N-terminal binding site residues, which could have implications for associations with ITPR1, and further highlighted differences to the mechanism of benign and pathogenic variants. SNV presence is associated with a reduction to the usage of Trp37 in all variants, which has implications for CA-VIII stability. The differences to variant mechanisms can be further investigated to understand pathogenesis of CAMRQ3, enhancing precision medicine-related studies into CA-VIII.
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MESH Headings
- Binding Sites
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cerebellar Ataxia/genetics
- Cerebellar Ataxia/pathology
- Databases, Genetic
- Humans
- Inositol 1,4,5-Trisphosphate Receptors/chemistry
- Inositol 1,4,5-Trisphosphate Receptors/metabolism
- Intellectual Disability/genetics
- Intellectual Disability/pathology
- Molecular Dynamics Simulation
- Mutation, Missense
- Polymorphism, Single Nucleotide
- Protein Binding
- Protein Interaction Maps
- Protein Stability
- Protein Structure, Tertiary
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Affiliation(s)
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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11
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Miterko LN, Sillitoe RV. Climbing Fiber Development Is Impaired in Postnatal Car8 wdl Mice. THE CEREBELLUM 2019; 17:56-61. [PMID: 28940157 DOI: 10.1007/s12311-017-0886-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The cerebellum is critical for an array of motor functions. During postnatal development, the Purkinje cells (PCs) guide afferent topography to establish the final circuit. Perturbing PC morphogenesis or activity during development can result in climbing fiber (CF) multi-innervation or mis-patterning. Structural defects during circuit formation typically have long-term effects on behavior as they contribute to the phenotype of movement disorders such as cerebellar ataxia. The Car8 wdl mouse is one model in which early circuit destruction influences movement. However, although the loss of Car8 leads to the mis-wiring of afferent maps and abnormal PC firing, adult PC morphology is largely intact and there is no neurodegeneration. Here, we sought to uncover how defects in afferent connectivity arise in Car8 wdl mutants to resolve how functional deficits persist in motor diseases with subtle neuropathology. To address this problem, we analyzed CF development during the first 3 weeks of life. By immunolabeling CF terminals with VGLUT2, we found evidence of premature CF synapse elimination and delayed translocation from PC somata at postnatal day (P) 10 in Car8 wdl mice. Surprisingly, by P15, the wiring normalized, suggesting that CAR8 regulates the early but not the late stages of CF development. The data support the hypothesis of a defined sequence of events for cerebellar circuits to establish function.
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Affiliation(s)
- Lauren N Miterko
- Department of Pathology and Immunology, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Roy V Sillitoe
- Department of Pathology and Immunology, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA. .,Program in Developmental Biology, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA. .,Department of Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.
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12
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Zanni G, Nardella M, Barresi S, Bellacchio E, Niceta M, Ciolfi A, Pro S, D'Arrigo S, Tartaglia M, Bertini E. De novo p.T362R mutation in MORC2 causes early onset cerebellar ataxia, axonal polyneuropathy and nocturnal hypoventilation. Brain 2019; 140:e34. [PMID: 28402445 DOI: 10.1093/brain/awx083] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ginevra Zanni
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Nardella
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Pro
- Department of Neurosciences, Unit of Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano D'Arrigo
- Developmental Neurology Division, IRCCS Fondazione Istituto Neurologico C. Besta, Milan, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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13
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Fogelholm J, Inkabi S, Höglund A, Abbey-Lee R, Johnsson M, Jensen P, Henriksen R, Wright D. Genetical Genomics of Tonic Immobility in the Chicken. Genes (Basel) 2019; 10:genes10050341. [PMID: 31067744 PMCID: PMC6562468 DOI: 10.3390/genes10050341] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/17/2019] [Accepted: 04/30/2019] [Indexed: 11/17/2022] Open
Abstract
Identifying the molecular mechanisms of animal behaviour is an enduring goal for researchers. Gaining insight into these mechanisms enables us to gain a greater understanding of behaviour and their genetic control. In this paper, we perform Quantitative Trait Loci (QTL) mapping of tonic immobility behaviour in an advanced intercross line between wild and domestic chickens. Genes located within the QTL interval were further investigated using global expression QTL (eQTL) mapping from hypothalamus tissue, as well as causality analysis. This identified five candidate genes, with the genes PRDX4 and ACOT9 emerging as the best supported candidates. In addition, we also investigated the connection between tonic immobility, meat pH and struggling behaviour, as the two candidate genes PRDX4 and ACOT9 have previously been implicated in controlling muscle pH at slaughter. We did not find any phenotypic correlations between tonic immobility, struggling behaviour and muscle pH in a smaller additional cohort, despite these behaviours being repeatable within-test.
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Affiliation(s)
- Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
| | - Samuel Inkabi
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
| | - Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
| | - Robin Abbey-Lee
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
| | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland EH25 9RG, UK.
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden.
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden.
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14
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Miterko LN, White JJ, Lin T, Brown AM, O'Donovan KJ, Sillitoe RV. Persistent motor dysfunction despite homeostatic rescue of cerebellar morphogenesis in the Car8 waddles mutant mouse. Neural Dev 2019; 14:6. [PMID: 30867000 PMCID: PMC6417138 DOI: 10.1186/s13064-019-0130-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/20/2019] [Indexed: 12/19/2022] Open
Abstract
Background Purkinje cells play a central role in establishing the cerebellar circuit. Accordingly, disrupting Purkinje cell development impairs cerebellar morphogenesis and motor function. In the Car8wdl mouse model of hereditary ataxia, severe motor deficits arise despite the cerebellum overcoming initial defects in size and morphology. Methods To resolve how this compensation occurs, we asked how the loss of carbonic anhydrase 8 (CAR8), a regulator of IP3R1 Ca2+ signaling in Purkinje cells, alters cerebellar development in Car8wdl mice. Using a combination of histological, physiological, and behavioral analyses, we determined the extent to which the loss of CAR8 affects cerebellar anatomy, neuronal firing, and motor coordination during development. Results Our results reveal that granule cell proliferation is reduced in early postnatal mutants, although by the third postnatal week there is enhanced and prolonged proliferation, plus an upregulation of Sox2 expression in the inner EGL. Modified circuit patterning of Purkinje cells and Bergmann glia accompany these granule cell adjustments. We also find that although anatomy eventually normalizes, the abnormal activity of neurons and muscles persists. Conclusions Our data show that losing CAR8 only transiently restricts cerebellar growth, but permanently damages its function. These data support two current hypotheses about cerebellar development and disease: (1) Sox2 expression may be upregulated at sites of injury and contribute to the rescue of cerebellar structure and (2) transient delays to developmental processes may precede permanent motor dysfunction. Furthermore, we characterize waddles mutant mouse morphology and behavior during development and propose a Sox2-positive, cell-mediated role for rescue in a mouse model of human motor diseases. Electronic supplementary material The online version of this article (10.1186/s13064-019-0130-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lauren N Miterko
- Department of Pathology and Immunology, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Joshua J White
- Department of Pathology and Immunology, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Department of Neuroscience, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Tao Lin
- Department of Pathology and Immunology, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Amanda M Brown
- Department of Pathology and Immunology, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Department of Neuroscience, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Kevin J O'Donovan
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York, 10996, USA.,Burke Neurological Institute, Weill Cornell Medicine, White Plains, 10605, USA
| | - Roy V Sillitoe
- Department of Pathology and Immunology, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA. .,Department of Neuroscience, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA. .,Program in Developmental Biology, Baylor College of Medicine, Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA. .,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.
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15
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Trzesniewski J, Altmann S, Jäger L, Kapfhammer JP. Reduced Purkinje cell size is compatible with near normal morphology and function of the cerebellar cortex in a mouse model of spinocerebellar ataxia. Exp Neurol 2018; 311:205-212. [PMID: 30312605 DOI: 10.1016/j.expneurol.2018.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/27/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022]
Abstract
Spinocerebellar ataxia type 14 (SCA14) is a dominantly inherited neurodegenerative disease caused by diverse mutations in the Protein Kinase C gamma (PKCγ) gene which is one of the crucial signaling molecules of Purkinje cells. We have previously created a mouse model of SCA14 by transgenic expression of a mutated PKCγ gene causing SCA14 with a mutation in the catalytic domain. Purkinje cells from the mutated mice have a strong reduction of their dendritic tree in organotypic slice cultures typical for increased PKC activity. There was no overt degeneration of Purkinje cells in vivo and the cerebellum appeared morphologically normal with the exception of lobule 7 where abnormal Purkinje cells were present. Besides from mild motor deficits the mice have no major phenotype. We have now done a more extensive study of cerebellar morphology in these mice and show by rapid Golgi staining that there is a marked reduction of Purkinje cell dendritic tree size throughout the cerebellum. Despite this reduction in dendritic tree size, climbing fiber innervation of Purkinje cells as visualized by immunostaining for the vesicular glutamate transporter 2 (vGlut2) appeared normal in most parts of the cerebellum. The same was true for the expression of the activity and plasticity markers pS6, c-Fos and Arc. These finding suggest that the cerebellar cortex in the transgenic mice is functioning fairly normal and that the reduction of dendritic tree size and the increased PKC activity can be compensated in most Purkinje cells. Around cerebellar lobule 7 there was high transgene expression from the L7 promotor and Purkinje cells showed abnormal morphologies. Climbing fiber innervation as well as the expression of the activity and plasticity markers was strongly disturbed in this area. Our results show that there is substantial potential for functional compensation in the cerebellar cortex. In lobule 7, an area with high transgene expression, compensation failed resulting in Purkinje cell degeneration and dysfunction.
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Affiliation(s)
- Jakub Trzesniewski
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, CH - 4056 Basel, Switzerland
| | - Sandrine Altmann
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, CH - 4056 Basel, Switzerland
| | - Levy Jäger
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, CH - 4056 Basel, Switzerland
| | - Josef P Kapfhammer
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, CH - 4056 Basel, Switzerland.
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16
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Shimobayashi E, Kapfhammer JP. Calcium Signaling, PKC Gamma, IP3R1 and CAR8 Link Spinocerebellar Ataxias and Purkinje Cell Dendritic Development. Curr Neuropharmacol 2018; 16:151-159. [PMID: 28554312 PMCID: PMC5883377 DOI: 10.2174/1570159x15666170529104000] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 01/05/2023] Open
Abstract
Background Spinocerebellar ataxias (SCAs) are a group of cerebellar diseases characterized by progressive ataxia and cerebellar atrophy. Several forms of SCAs are caused by missense mutations or deletions in genes related to calcium signaling in Purkinje cells. Among them, spinocerebellar ataxia type 14 (SCA14) is caused by missense mutations in PRKCG gene which encodes protein kinase C gamma (PKCγ). It is remarkable that in several cases in which SCA is caused by point mutations in an individual gene, the affected genes are involved in the PKCγ signaling pathway and calcium signaling which is not only crucial for proper Purkinje cell function but is also involved in the control of Purkinje cell dendritic development. In this review, we will focus on the PKCγ signaling related genes and calcium signaling related genes then discuss their role for both Purkinje cell dendritic development and cerebellar ataxia. Methods Research related to SCAs and Purkinje cell dendritic development is reviewed. Results PKCγ dysregulation causes abnormal Purkinje cell dendritic development and SCA14. Carbonic anhydrase related protein 8 (Car8) encoding CAR8 and Itpr1 encoding IP3R1were identified as upregulated genes in one of SCA14 mouse model. IP3R1, CAR8 and PKCγ proteins are strongly and specifically expressed in Purkinje cells. The common function among them is that they are involved in the regulation of calcium homeostasis in Purkinje cells and their dysfunction causes ataxia in mouse and human. Furthermore, disruption of intracellular calcium homeostasis caused by mutations in some calcium channels in Purkinje cells links to abnormal Purkinje cell dendritic development and the pathogenesis of several SCAs. Conclusion Once PKCγ signaling related genes and calcium signaling related genes are disturbed, the normal dendritic development of Purkinje cells is impaired as well as the integration of signals from other neurons, resulting in abnormal development, cerebellar dysfunction and eventually Purkinje cell loss.
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Affiliation(s)
- Etsuko Shimobayashi
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, CH-4056 Basel, Switzerland
| | - Josef P Kapfhammer
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, CH-4056 Basel, Switzerland
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17
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Shimobayashi E, Kapfhammer JP. Increased biological activity of protein Kinase C gamma is not required in Spinocerebellar ataxia 14. Mol Brain 2017; 10:34. [PMID: 28738819 PMCID: PMC5525338 DOI: 10.1186/s13041-017-0313-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/04/2017] [Indexed: 12/17/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is an autosomal dominant neurodegenerative disorder characterized by slowly progressive cerebellar dysfunction. Currently, 42 SCA types are known, some of which are caused by CAG repeat expansions, but others are caused by point mutations or deletions. Spinocerebellar ataxia type 14 (SCA14) is caused by missense mutations or deletions in the PRKCG gene, coding for protein kinase C gamma (PKCγ). It is still not well understood how these mutations eventually cause Purkinje cell dysfunction and death. Because PKCγ is a well characterized signaling protein highly expressed in Purkinje cells SCA14 offers the chance to better understand the pathogenesis of Purkinje cell dysfunction and death. Altered biological activity of PKCγ would be the simplest explanation for the disease phenotype. There are indeed indications that the enzymatic activity of mutated PKCγ proteins could be changed. Many mutations found in SCA14 families are located in the regulatory C1B and C1A domain, while a few mutations are also found in the C2 and in the catalytic C3 and C4 domains. For many of these mutations an increased enzymatic activity could be demonstrated in cell-based assays, but it remains unclear whether there is indeed an altered biological activity of the mutated PKCγ proteins within living Purkinje cells. In this study we used the dendritic morphology of developing Purkinje cells to detect increased biological activity of PKCγ after expression of different mutated PKCγ proteins. Our results indicate that two out of three known mutations in the catalytic domain of PKCγ did indeed show increased biological activity. On the other hand, none of the five tested mutations located in the regulatory C1 or the C2 domain showed an increased biological activity. Our findings indicate that SCA14 mutations located in different domains of the PRKCG gene cause SCA14 by different mechanisms and that an increased constitutive activity of PKCγ may be one, but cannot be the only mechanism to cause disease in SCA14.
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Affiliation(s)
- Etsuko Shimobayashi
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, 4056, Basel, Switzerland.
| | - Josef P Kapfhammer
- Anatomical Institute, Department of Biomedicine Basel, University of Basel, Pestalozzistrasse 20, 4056, Basel, Switzerland
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