1
|
Wu S, Fan J, Tang F, Chen L, Zhang X, Xiao D, Li X. The role of RIM in neurotransmitter release: promotion of synaptic vesicle docking, priming, and fusion. Front Neurosci 2023; 17:1123561. [PMID: 37179554 PMCID: PMC10169678 DOI: 10.3389/fnins.2023.1123561] [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: 12/14/2022] [Accepted: 04/06/2023] [Indexed: 05/15/2023] Open
Abstract
There are many special sites at the end of a synapse called active zones (AZs). Synaptic vesicles (SVs) fuse with presynaptic membranes at these sites, and this fusion is an important step in neurotransmitter release. The cytomatrix in the active zone (CAZ) is made up of proteins such as the regulating synaptic membrane exocytosis protein (RIM), RIM-binding proteins (RIM-BPs), ELKS/CAST, Bassoon/Piccolo, Liprin-α, and Munc13-1. RIM is a scaffold protein that interacts with CAZ proteins and presynaptic functional components to affect the docking, priming, and fusion of SVs. RIM is believed to play an important role in regulating the release of neurotransmitters (NTs). In addition, abnormal expression of RIM has been detected in many diseases, such as retinal diseases, Asperger's syndrome (AS), and degenerative scoliosis. Therefore, we believe that studying the molecular structure of RIM and its role in neurotransmitter release will help to clarify the molecular mechanism of neurotransmitter release and identify targets for the diagnosis and treatment of the aforementioned diseases.
Collapse
Affiliation(s)
- Shanshan Wu
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jiali Fan
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Fajuan Tang
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Lin Chen
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaoyan Zhang
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Dongqiong Xiao
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xihong Li
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| |
Collapse
|
2
|
Simsek-Kiper PO, Jacob P, Upadhyai P, Taşkıran ZE, Guleria VS, Karaosmanoglu B, Imren G, Gocmen R, Bhavani GS, Kausthubham N, Shah H, Utine GE, Boduroglu K, Girisha KM. Biallelic loss-of-function variants in EXOC6B are associated with impaired primary ciliogenesis and cause spondylo-epi-metaphyseal dysplasia with joint laxity type 3. Hum Mutat 2022; 43:2116-2129. [PMID: 36150098 PMCID: PMC7615863 DOI: 10.1002/humu.24478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/30/2022] [Accepted: 09/21/2022] [Indexed: 01/25/2023]
Abstract
Spondylo-epi-metaphyseal dysplasias with joint laxity, type 3 (SEMDJL3) is a genetic skeletal disorder characterized by multiple joint dislocations, caused by biallelic pathogenic variants in the EXOC6B gene. Only four individuals from two families have been reported to have this condition to date. The molecular pathogenesis related to primary ciliogenesis has not been enumerated in subjects with SEMDJL3. In this study, we report two additional affected individuals from unrelated families with biallelic pathogenic variants, c.2122+15447_2197-59588del and c.401T>G in EXOC6B identified by exome sequencing. One of the affected individuals had an intellectual disability and central nervous system anomalies, including hydrocephalus, hypoplastic mesencephalon, and thin corpus callosum. Using the fibroblast cell lines, we demonstrate the primary evidence for the abrogation of exocytosis in an individual with SEMDLJ3 leading to impaired primary ciliogenesis. Osteogenesis differentiation and pathways related to the extracellular matrix were also found to be reduced. Additionally, we provide a review of the clinical and molecular profile of all the mutation-proven patients reported hitherto, thereby further characterizing SEMDJL3. SEMDJL3 with biallelic pathogenic variants in EXOC6B might represent yet another ciliopathy with central nervous system involvement and joint dislocations.
Collapse
Affiliation(s)
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Zihni Ekim Taşkıran
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Vishal S. Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Beren Karaosmanoglu
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gozde Imren
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gandham S. Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopaedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gulen Eda Utine
- Department of Pediatric Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Koray Boduroglu
- Department of Pediatric Genetics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Katta M. Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
3
|
Masola V, Greco N, Tozzo P, Caenazzo L, Onisto M. The role of SPATA2 in TNF signaling, cancer, and spermatogenesis. Cell Death Dis 2022; 13:977. [PMID: 36402749 PMCID: PMC9675801 DOI: 10.1038/s41419-022-05432-1] [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: 03/04/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/20/2022]
Abstract
The activation of TNF receptors can lead to cell death with a mechanism of cell necrosis regulated genetically and distinct from apoptosis which is defined as necroptosis. Necroptosis has been one of the most studied emerging cell death/signaling pathways in recent years, especially in light of the role of this process in human disease. However, not all regulatory components of TNF signaling have been identified in relation to both physiological and pathological conditions. In 2008, Spata2 (Spermatogenesis-associated protein 2) was identified as one of the seven fundamental genes for the cellular signaling network that regulates necroptosis and apoptosis. This gene had been cloned by our group and named Spata2 as its expression was found to be elevated in the testis compared to other tissues, localized at the Sertoli cell level and FSH-dependent. More recently, it has been demonstrated that deletion of Spata2 gene causes increased inhibin α expression and attenuated fertility in male mice. However, more importantly, five recently published reports have highlighted that SPATA2 is crucial for recruiting CYLD to the TNFR1 signaling complex thus promoting its activation leading to TNF-induced cell death. Loss of SPATA2 increases transcriptional activation of NF-kB and limits TNF-induced necroptosis. Here we will discuss these important findings regarding SPATA2 and, in particular, focus attention on the evidence that suggests a role for this protein in the TNF signaling pathway.
Collapse
Affiliation(s)
- Valentina Masola
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Nicola Greco
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Pamela Tozzo
- grid.5608.b0000 0004 1757 3470Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Luciana Caenazzo
- grid.5608.b0000 0004 1757 3470Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Maurizio Onisto
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padova, Padua, Italy
| |
Collapse
|
4
|
Li S, Wang W, Zhang D, Li W, Lund J, Kruse T, Mengel-From J, Christensen K, Tan Q. Differential regulation of the DNA methylome in adults born during the Great Chinese Famine in 1959-1961. Genomics 2021; 113:3907-3918. [PMID: 34600028 DOI: 10.1016/j.ygeno.2021.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/24/2021] [Accepted: 09/25/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Extensive epidemiological studies have established the association between exposure to early-life adversity and health status and diseases in adults. Epigenetic regulation is considered as a key mediator for this phenomenon but analysis on humans is sparse. The Great Chinese Famine lasting from 1958 to 1961 is a natural string of disasters offering a precious opportunity for elucidating the underlying epigenetic mechanism of the long-term effect of early adversity. METHODS Using a high-throughput array platform for DNA methylome profiling, we conducted a case-control epigenome-wide association study on early-life exposure to Chinese famine in 79 adults born during 1959-1961 and compared to 105 unexposed subjects born 1963-1964. RESULTS The single CpG site analysis of whole epigenome revealed a predominant pattern of decreased DNA methylation levels associated with fetal exposure to famine. Four CpG sites were detected with p < 1e-06 (linked to EHMT1, CNR1, UBXN7 and ESM1 genes), 16 CpGs detected with 1e-06 < p < 1e-05 and 157 CpGs with 1e-05 < p < 1e-04, with a predominant pattern of hypomethylation. Functional annotation to genes and their enriched biological pathways mainly involved neurodevelopment, neuropsychological disorders and metabolism. Multiple sites analysis detected two top-rank differentially methylated regions harboring RNF39 on chromosome 6 and PTPRN2 on chromosome 7, both showing epigenetic association with stress-related conditions. CONCLUSION Early-life exposure to famine could mediate DNA methylation regulations that persist into adulthood with broad impacts in the activities of genes and biological pathways. Results from this study provide new clues to the epigenetic embedding of early-life adversity and its impacts on adult health.
Collapse
Affiliation(s)
- Shuxia Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Weijing Wang
- Qingdao University School of Public Health, Qingdao, China
| | - Dongfeng Zhang
- Qingdao University School of Public Health, Qingdao, China
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark; Population Research Unit, Faculty of Social Sciences, University of Helsinki, Finland.
| | - Jesper Lund
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark; Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, Potsdam, Germany.
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Jonas Mengel-From
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Kaare Christensen
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
5
|
Liang C, Huang S, Zhao Y, Chen S, Li Y. TOX as a potential target for immunotherapy in lymphocytic malignancies. Biomark Res 2021; 9:20. [PMID: 33743809 PMCID: PMC7981945 DOI: 10.1186/s40364-021-00275-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
TOX (thymocyte selection-associated HMG BOX) is a member of a family of transcriptional factors that contain the highly conserved high mobility group box (HMG-box) region. Increasing studies have shown that TOX is involved in maintaining tumors and promoting T cell exhaustion. In this review, we summarized the biological functions of TOX and its contribution as related to lymphocytic malignancies. We also discussed the potential role of TOX as an immune biomarker and target in immunotherapy for hematological malignancies.
Collapse
Affiliation(s)
- Chaofeng Liang
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China.,Department of Anatomy and Molecular Embryology, Institute of Anatomy, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Shuxin Huang
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yujie Zhao
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shaohua Chen
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China.
| | - Yangqiu Li
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
6
|
Jiang L, Liu X, He X, Jin Y, Cao Y, Zhan X, Griffin CH, Gragnoli C, Wu R. A behavioral model for mapping the genetic architecture of gut-microbiota networks. Gut Microbes 2021; 13:1820847. [PMID: 33131416 PMCID: PMC8381822 DOI: 10.1080/19490976.2020.1820847] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota may play an important role in affecting human health. To explore the genetic mechanisms underlying microbiota-host relationships, many genome-wide association studies have begun to identify host genes that shape the microbial composition of the gut. It is becoming increasingly clear that the gut microbiota impacts host processes not only through the action of individual microbes but also their interaction networks. However, a systematic characterization of microbial interactions that occur in densely packed aggregates of the gut bacteria has proven to be extremely difficult. We develop a computational rule of thumb for addressing this issue by integrating ecological behavioral theory and genetic mapping theory. We introduce behavioral ecology theory to derive mathematical descriptors of how each microbe interacts with every other microbe through a web of cooperation and competition. We estimate the emergent properties of gut-microbiota networks reconstructed from these descriptors and map host-driven mutualism, antagonism, aggression, and altruism QTLs. We further integrate path analysis and mapping theory to detect and visualize how host genetic variants affect human diseases by perturbing the internal workings of the gut microbiota. As the proof of concept, we apply our model to analyze a published dataset of the gut microbiota, showing its usefulness and potential to gain new insight into how microbes are organized in human guts. The new model provides an analytical tool for revealing the "endophenotype" role of microbial networks in linking genotype to end-point phenotypes.
Collapse
Affiliation(s)
- Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinjuan Liu
- Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xiaoqing He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yige Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiang Zhan
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Christopher H. Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA, USA
| | - Claudia Gragnoli
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
- Division of Endocrinology, Diabetes, and Metabolic Disease, Translational Medicine, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Molecular Biology Laboratory, Bios Biotech Multi Diagnostic Health Center, Rome, Italy
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| |
Collapse
|
7
|
Faudi E, Brischoux-Boucher E, Huber C, Dabudyk T, Lenoir M, Baujat G, Michot C, Van Maldergem L, Cormier-Daire V, Piard J. A new case of KIAA0753-related variant of Jeune asphyxiating thoracic dystrophy. Eur J Med Genet 2019; 63:103823. [PMID: 31816441 DOI: 10.1016/j.ejmg.2019.103823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 10/14/2019] [Accepted: 12/05/2019] [Indexed: 11/24/2022]
Abstract
A narrow thorax with shortening of long bones is usually pointing to dysfunction of the primary cilia corresponding clinically to ciliopathies with major skeletal involvement. Mutations in at least 23 genes are likely to correspond to this clinical presentation: IFT43/52/80/81/122/140/172, WDR19/34/35/60, DYNC2H1, DYNC2LI1, CEP120, NEK1, TTC21B, TCTEX1D2, INTU, TCTN3, EVC 1/2 and KIAA0586. In addition to these, KIAA0753 variants were recently described in seven patients with Jeune asphyxiating thoracic dystrophy (ATD) (two first cousins, one unrelated patient and one fetus), Joubert syndrome (two siblings) and orofaciodigital syndrome type 6 (one patient). We present the clinical characteristics of a eighth such patient. This 4 year-old boy with narrow thorax, short limbs, severe respiratory and feeding difficulties from birth on had a history of hypotonia and developmental delay. On skeletal survey, short tubular bones (height - 5,5 SD) and a trident appearance of the pelvis were seen. Brain MRI showed cervical canal stenosis. Renal function was normal and moderate hepatomegaly was noted. A homozygous c.943C > T mutation in KIAA0753 was identified on whole exome sequencing, resulting in Gln315Ter premature termination of the corresponding protein. This case provides confirmation of an additional molecular basis for skeletal dysplasia and illustrates how ciliopathies due to mutations in a single gene may present as apparently distinct syndromes.
Collapse
Affiliation(s)
- Emilien Faudi
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Céline Huber
- Service de génétique clinique, CRMR maladies osseuses constitutionnelles, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Thibaud Dabudyk
- Service de Réanimation Infantile, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| | - Marion Lenoir
- Service de Radiologie, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| | - Geneviève Baujat
- Service de génétique clinique, CRMR maladies osseuses constitutionnelles, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Caroline Michot
- Service de génétique clinique, CRMR maladies osseuses constitutionnelles, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France; Unité de recherche en neurosciences intégratives et cognitives EA481, Université de Franche-Comté, Besançon, France; Centre d'investigation clinique 1431, INSERM, Besançon, France
| | - Valérie Cormier-Daire
- Service de génétique clinique, CRMR maladies osseuses constitutionnelles, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker Enfants Malades, Paris, France
| | - Juliette Piard
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France; Unité de recherche en neurosciences intégratives et cognitives EA481, Université de Franche-Comté, Besançon, France.
| |
Collapse
|
8
|
Bikkul MU, Faragher RGA, Worthington G, Meinke P, Kerr ARW, Sammy A, Riyahi K, Horton D, Schirmer EC, Hubank M, Kill IR, Anderson RM, Slijepcevic P, Makarov E, Bridger JM. Telomere elongation through hTERT immortalization leads to chromosome repositioning in control cells and genomic instability in Hutchinson-Gilford progeria syndrome fibroblasts, expressing a novel SUN1 isoform. Genes Chromosomes Cancer 2019; 58:341-356. [PMID: 30474255 PMCID: PMC6590296 DOI: 10.1002/gcc.22711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023] Open
Abstract
Immortalizing primary cells with human telomerase reverse transcriptase (hTERT) has been common practice to enable primary cells to be of extended use in the laboratory because they avoid replicative senescence. Studying exogenously expressed hTERT in cells also affords scientists models of early carcinogenesis and telomere behavior. Control and the premature ageing disease—Hutchinson‐Gilford progeria syndrome (HGPS) primary dermal fibroblasts, with and without the classical G608G mutation have been immortalized with exogenous hTERT. However, hTERT immortalization surprisingly elicits genome reorganization not only in disease cells but also in the normal control cells, such that whole chromosome territories normally located at the nuclear periphery in proliferating fibroblasts become mislocalized in the nuclear interior. This includes chromosome 18 in the control fibroblasts and both chromosomes 18 and X in HGPS cells, which physically express an isoform of the LINC complex protein SUN1 that has previously only been theoretical. Additionally, this HGPS cell line has also become genomically unstable and has a tetraploid karyotype, which could be due to the novel SUN1 isoform. Long‐term treatment with the hTERT inhibitor BIBR1532 enabled the reduction of telomere length in the immortalized cells and resulted that these mislocalized internal chromosomes to be located at the nuclear periphery, as assessed in actively proliferating cells. Taken together, these findings reveal that elongated telomeres lead to dramatic chromosome mislocalization, which can be restored with a drug treatment that results in telomere reshortening and that a novel SUN1 isoform combined with elongated telomeres leads to genomic instability. Thus, care should be taken when interpreting data from genomic studies in hTERT‐immortalized cell lines.
Collapse
Affiliation(s)
- Mehmet U. Bikkul
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | | | - Gemma Worthington
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Peter Meinke
- Friedrich‐Baur‐InstitutKlinikum der Universität MünchenMünchenGermany
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Alastair R. W. Kerr
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Aakila Sammy
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Kumars Riyahi
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Daniel Horton
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell BiologyInstitute of Cell Biology, and Centre for Translational and Chemical Biology, University of EdinburghEdinburghEngland
| | - Michael Hubank
- Centre for Molecular PathologyThe Royal Marsden HospitalLondonEngland
| | - Ian R. Kill
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Rhona M. Anderson
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Predrag Slijepcevic
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Evgeny Makarov
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| | - Joanna M. Bridger
- Genome Engineering and Maintenance NetworkInstitute for Environment, Health and Societies, Brunel University LondonUxbridgeEngland
| |
Collapse
|
9
|
Chirita Emandi A, Dobrescu AI, Doros G, Hyon C, Miclea D, Popoiu C, Puiu M, Arghirescu S. A Novel 3q29 Deletion in Association With Developmental Delay and Heart Malformation-Case Report With Literature Review. Front Pediatr 2019; 7:270. [PMID: 31338352 PMCID: PMC6628938 DOI: 10.3389/fped.2019.00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/14/2019] [Indexed: 01/16/2023] Open
Abstract
3q29 deletion syndrome is a rare disorder, causing a complex phenotype. Clinical features are variable and relatively non-specific. Our report aims to present an atypical, de novo deletion in chromosome band 3q29 in a preschool boy, first child of healthy non-consanguineous parents, presenting a particular phenotype (microcephaly, "full moon" face, flattened facial profile, large ears, auricular polyp, and dental dystrophies), motor and cognitive delay, characteristics of autism spectrum disorder and aggressive behavior. He also presented intrauterine growth restriction (birth weight 2,400 g) and a ventricular septal defect. SNP Array revealed a 962 kb copy number loss, on the chromosome 3q29 band (195519857-196482211), consistent with 3q29 microdeletion syndrome. FISH analysis using a RP11-252K11 probe confirmed the deletion in the proband, which was not present in the parents. Although the patient's deletion is relatively small, it partly overlaps the canonical 3q29 deletion (defined between TFRC and DLG1 gene) and extends upstream, associating a different facial phenotype compared to the classic 3q29 deletion, nonetheless showing a similar psychiatric disorder. This deletion is different from the canonical region, as it does not include the PAK2 and DLG1 genes, considered as candidates for causing intellectual disability. Thus, narrowing the genotype-phenotype correlation for the 3q29 band, FBX045 is suggested as a candidate gene for the neuropsychiatric phenotype.
Collapse
Affiliation(s)
- Adela Chirita Emandi
- Discipline of Genetics, Victor Babeș University of Medicine and Pharmacy, Timișoara, Romania.,"Louis Turcanu" Clinical Emergency Hospital for Children, Timișoara, Romania
| | - Andreea Iulia Dobrescu
- Discipline of Genetics, Victor Babeș University of Medicine and Pharmacy, Timișoara, Romania.,"Louis Turcanu" Clinical Emergency Hospital for Children, Timișoara, Romania
| | - Gabriela Doros
- "Louis Turcanu" Clinical Emergency Hospital for Children, Timișoara, Romania.,IIIrd Pediatric Clinic, Pediatric Cardiology, Victor Babeș University of Medicine and Pharmacy, Timișoara, Romania
| | - Capucine Hyon
- Département de Génétique Médicale, AP-HP, GHUEP, Hôpital Armand Trousseau, Paris, France.,INSERM, UMRS 933, Hôpital Armand Trousseau, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Diana Miclea
- Genetics Department Cluj-Napoca, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Calin Popoiu
- "Louis Turcanu" Clinical Emergency Hospital for Children, Timișoara, Romania.,Discipline of Pediatric Surgery, Victor Babeș University of Medicine and Pharmacy, Timișoara, Romania
| | - Maria Puiu
- Discipline of Genetics, Victor Babeș University of Medicine and Pharmacy, Timișoara, Romania.,"Louis Turcanu" Clinical Emergency Hospital for Children, Timișoara, Romania
| | - Smaranda Arghirescu
- "Louis Turcanu" Clinical Emergency Hospital for Children, Timișoara, Romania.,IIIrd Pediatric Clinic, Victor Babeș University of Medicine and Pharmacy, Timișoara, Romania
| |
Collapse
|
10
|
Lintas C, Sacco R, Tabolacci C, Brogna C, Canali M, Picinelli C, Tomaiuolo P, Castronovo P, Baccarin M, Persico AM. An Interstitial 17q11.2 de novo Deletion Involving the CDK5R1 Gene in a High-Functioning Autistic Patient. Mol Syndromol 2018; 9:247-252. [PMID: 30733659 DOI: 10.1159/000491802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 11/19/2022] Open
Abstract
We describe a 32-year-old male patient diagnosed with high-functioning autism spectrum disorder carrying a de novo 196-kb interstitial deletion at chromosome 17q11.2. The deletion was detected by array CGH (180K Agilent) and confirmed by quantitative PCR on genomic DNA. The deleted region spans the entire PSMD11 and CDK5R1 genes and partially the MYO1D gene. The CDK5R1 gene encodes for a regulatory subunit of the cyclin-dependent kinase 5 responsible for its brain-specific activation. This gene has been previously associated with intellectual disability in humans. A reduction in CDK5R1 transcript was detected, consistent with the genomic deletion. Based on the functional role of CDK5R1, this gene appears as the best candidate to explain the clinical phenotype of our patient, whose neuropsychological profile has more resemblance with some of the higher brain function anomalies recently described in the CreER-p35 conditional knockout mouse model than previously described patients with intellectual disability.
Collapse
Affiliation(s)
- Carla Lintas
- Service for Neurodevelopmental Disorders, Department of Medicine, University Campus Bio-Medico, Rome, Italy.,Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - Roberto Sacco
- Service for Neurodevelopmental Disorders, Department of Medicine, University Campus Bio-Medico, Rome, Italy.,Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - Claudio Tabolacci
- Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - Claudia Brogna
- Service for Neurodevelopmental Disorders, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - Marco Canali
- Laboratory of Molecular Psychiatry and Neurogenetics, Department of Medicine, University Campus Bio-Medico, Rome, Italy
| | - Chiara Picinelli
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | | | - Paola Castronovo
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Marco Baccarin
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Antonio M Persico
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy.,Interdepartmental Program "Autism 0-90," "G. Martino" University Hospital, University of Messina, Messina, Italy
| |
Collapse
|
11
|
Du X, Zhou Y, Song L, Wang X, Zhang S. Zinc finger protein 365 is a new maternal LPS‐binding protein that defends zebrafish embryos against gram‐negative bacterial infections. FASEB J 2018; 32:979-994. [DOI: 10.1096/fj.201700694r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Xiaoyuan Du
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yang Zhou
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Lili Song
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Xia Wang
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Shicui Zhang
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| |
Collapse
|
12
|
Mata IF, Johnson CO, Leverenz JB, Weintraub D, Trojanowski JQ, Van Deerlin VM, Ritz B, Rausch R, Factor SA, Wood-Siverio C, Quinn JF, Chung KA, Peterson-Hiller AL, Espay AJ, Revilla FJ, Devoto J, Yearout D, Hu SC, Cholerton BA, Montine TJ, Edwards KL, Zabetian CP. Large-scale exploratory genetic analysis of cognitive impairment in Parkinson's disease. Neurobiol Aging 2017; 56:211.e1-211.e7. [PMID: 28526295 DOI: 10.1016/j.neurobiolaging.2017.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/19/2017] [Accepted: 04/12/2017] [Indexed: 11/25/2022]
Abstract
Cognitive impairment is a common and disabling problem in Parkinson's disease (PD). Identification of genetic variants that influence the presence or severity of cognitive deficits in PD might provide a clearer understanding of the pathophysiology underlying this important nonmotor feature. We genotyped 1105 PD patients from the PD Cognitive Genetics Consortium for 249,336 variants using the NeuroX array. Participants underwent assessments of learning and memory (Hopkins Verbal Learning Test-Revised [HVLT-R]), working memory/executive function (Letter-Number Sequencing and Trail Making Test [TMT] A and B), language processing (semantic and phonemic verbal fluency), visuospatial abilities (Benton Judgment of Line Orientation [JoLO]), and global cognitive function (Montreal Cognitive Assessment). For common variants, we used linear regression to test for association between genotype and cognitive performance with adjustment for important covariates. Rare variants were analyzed using the optimal unified sequence kernel association test. The significance threshold was defined as a false discovery rate-corrected p-value (PFDR) of 0.05. Eighteen common variants in 13 genomic regions exceeded the significance threshold for one of the cognitive tests. These included GBA rs2230288 (E326K; PFDR = 2.7 × 10-4) for JoLO, PARP4 rs9318600 (PFDR = 0.006), and rs9581094 (PFDR = 0.006) for HVLT-R total recall, and MTCL1 rs34877994 (PFDR = 0.01) for TMT B-A. Analysis of rare variants did not yield any significant gene regions. We have conducted the first large-scale PD cognitive genetics analysis and nominated several new putative susceptibility genes for cognitive impairment in PD. These results will require replication in independent PD cohorts.
Collapse
Affiliation(s)
- Ignacio F Mata
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA; Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Catherine O Johnson
- Department of Epidemiology, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel Weintraub
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA; Philadelphia Veterans Affairs Medical Center, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute on Aging, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beate Ritz
- Department of Epidemiology, School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Environmental Health Sciences, School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebecca Rausch
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stewart A Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Cathy Wood-Siverio
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Joseph F Quinn
- Portland Veterans Affairs Medical Center, Portland, OR, USA; Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Kathryn A Chung
- Portland Veterans Affairs Medical Center, Portland, OR, USA; Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Amie L Peterson-Hiller
- Portland Veterans Affairs Medical Center, Portland, OR, USA; Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Alberto J Espay
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Fredy J Revilla
- Division of Neurology at Greenville Health System and the University of South Carolina Medical School-Greenville, Greenville, SC, USA
| | - Johnna Devoto
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Dora Yearout
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA; Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Shu-Ching Hu
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA; Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Brenna A Cholerton
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA; Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thomas J Montine
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Karen L Edwards
- Department of Epidemiology, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Cyrus P Zabetian
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA; Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA.
| |
Collapse
|
13
|
Mak CCY, Chow PC, Liu APY, Chan KYK, Chu YWY, Mok GTK, Leung GKC, Yeung KS, Chau AKT, Lowther C, Scherer SW, Marshall CR, Bassett AS, Chung BHY. De novo large rare copy-number variations contribute to conotruncal heart disease in Chinese patients. NPJ Genom Med 2016; 1:16033. [PMID: 29263819 PMCID: PMC5685312 DOI: 10.1038/npjgenmed.2016.33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/02/2016] [Accepted: 08/05/2016] [Indexed: 01/05/2023] Open
Abstract
Conotruncal heart anomalies (CTDs) are particularly prevalent congenital heart diseases (CHD) in Hong Kong. We surveyed large (>500 kb), rare (<1% frequency in controls) copy-number variations (CNVs) in Chinese patients with CTDs to identify potentially disease-causing variations. Adults who tested negative for 22q11.2 deletions were recruited from the adult CHD clinic in Hong Kong. Using a stringent calling criteria, high-confidence CNV calls were obtained, and a large control set comprising 3,987 Caucasian and 1,945 Singapore Chinese subjects was used to identify rare CNVs. Ten large rare CNVs were identified, and 3 in 108 individuals were confirmed to harbour de novo CNVs. All three patients were syndromic with a more complex phenotype, and each of these CNVs overlapped regions likely to be important in CHD. One was a 611 kb deletion at 17p13.3, telomeric to the Miller-Dieker syndrome (MDS) critical region, overlapping the NXN gene. Another was a 5 Mb deletion at 13q33.3, within a previously described critical region for CHD. A third CNV, previously unreported, was a large duplication at 2q22.3 overlapping the ZEB2 gene. The commonly reported 1q21.1 recurrent duplication was not observed in this Chinese cohort. We provide detailed phenotypic and genotypic descriptions of large rare genic CNVs that may represent CHD loci in the East Asian population. Larger samples of Chinese origin will be required to determine whether the genome-wide distribution differs from that found in predominantly European CHD cohorts.
Collapse
Affiliation(s)
- Christopher C Y Mak
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak Cheong Chow
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anthony P Y Liu
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kelvin Y K Chan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong, China
| | - Yoyo W Y Chu
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gary T K Mok
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gordon K C Leung
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kit San Yeung
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Adolphus K T Chau
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chelsea Lowther
- The Clinical Genetics Research Program at The Centre for Addiction and Mental Health, The Dalglish Family 22q Clinic at The University Health Network, and The Department of Psychiatry at The University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anne S Bassett
- The Clinical Genetics Research Program at The Centre for Addiction and Mental Health, The Dalglish Family 22q Clinic at The University Health Network, and The Department of Psychiatry at The University of Toronto, Toronto, ON, Canada
| | - Brian H Y Chung
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
14
|
Cortical gene expression correlates of temporal lobe epileptogenicity. ACTA ACUST UNITED AC 2016; 23:181-90. [PMID: 27354343 DOI: 10.1016/j.pathophys.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/19/2016] [Accepted: 05/27/2016] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Despite being one of the most common neurological diseases, it is unknown whether there may be a genetic basis to temporal lobe epilepsy (TLE). Whole genome analyses were performed to test the hypothesis that temporal cortical gene expression differs between TLE patients with high vs. low baseline seizure frequency. METHODS Baseline seizure frequency was used as a clinical measure of epileptogenicity. Twenty-four patients in high or low seizure frequency groups (median seizures/month) underwent anterior temporal lobectomy with amygdalohippocampectomy for intractable TLE. RNA was isolated from the lateral temporal cortex and submitted for expression analysis. Genes significantly associated with baseline seizure frequency on likelihood ratio test were identified based on >0.90 area under the ROC curve, P value of <0.05. RESULTS Expression levels of forty genes were significantly associated with baseline seizure frequency. Of the seven most significant, four have been linked to other neurologic diseases. Expression levels associated with high seizure frequency included low expression of Homeobox A10, Forkhead box A2, Lymphoblastic leukemia derived sequence 1, HGF activator, Kelch repeat and BTB (POZ) domain containing 11, Thanatos-associated protein domain containing 8 and Heparin sulfate (glucosamine) 3-O-sulfotransferase 3A1. CONCLUSIONS This study describes novel associations between forty known genes and a clinical marker of epileptogenicity, baseline seizure frequency. Four of the seven discussed have been previously related to other neurologic diseases. Future investigation of these genes could establish new biomarkers for predicting epileptogenicity, and could have significant implications for diagnosis and management of temporal lobe epilepsy, as well as epilepsy pathogenesis.
Collapse
|
15
|
Drabova J, Seemanova E, Hancarova M, Pourova R, Horacek M, Jancuskova T, Pekova S, Novotna D, Sedlacek Z. Long term follow-up in a patient with a de novo microdeletion of 14q11.2 involving CHD8. Am J Med Genet A 2015; 167A:837-41. [PMID: 25735987 DOI: 10.1002/ajmg.a.36957] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 12/21/2014] [Indexed: 11/07/2022]
Abstract
We identified a de novo deletion of 14q11.2 in a Czech patient with developmental delay, mild autistic features, macrosomy, macrocephaly, orthognathic deformities, and dysmorphic facial features. The clinical follow-up of the patient lasting 14 years documented changes in the facial dysmorphism from infancy to adolescence. The deletion affects approximately 200 kb of DNA with five protein-coding genes and two snoRNA genes. Two of the protein-coding genes, SUPT16H and CHD8, have been proposed as candidate genes for a new microdeletion syndrome. Our patient further supports the existence of this syndrome and extends its phenotypic spectrum, especially points to the possibility that orthognathic deformities may be associated with microdeletions of 14q11.2. CHD8 mutations have been found in patients with neurodevelopmental disorders and macrocephaly. The HNRNPC gene, repeatedly deleted in patients with developmental delay, is another candidate as its 5́ end is adjacent to the deletion, and the expression of this gene may be affected by position effect.
Collapse
Affiliation(s)
- Jana Drabova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Shoubridge C, Walikonis RS, Gécz J, Harvey RJ. Subtle functional defects in the Arf-specific guanine nucleotide exchange factor IQSEC2 cause non-syndromic X-linked intellectual disability. Small GTPases 2014; 1:98-103. [PMID: 21686261 DOI: 10.4161/sgtp.1.2.13285] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 07/28/2010] [Accepted: 08/01/2010] [Indexed: 11/19/2022] Open
Abstract
Mutations in IQSEC2, a guanine nucleotide exchange factor for the ADP-ribosylation factor (Arf) family of small GTPases have recently been shown to cause non-syndromic X-linked intellectual disability (ID), characterised by substantial limitations in intellectual functioning and adaptive behaviour. This discovery was revealed by a combination of large-scale resequencing of the X chromosome, and key functional assays that revealed a reduction, but not elimination, of IQSEC2 GEF activity for mutations affecting conserved amino acids in the IQ-like and Sec7 domains. Compromised GTP binding activity of IQSEC2 leading to reduced activation of selected Arf substrates (Arf1, Arf6) is expected to impact on cytoskeletal organization, dendritic spine morphology and synaptic organisation. This study highlights the need for further investigation of the IQSEC gene family and Arf GTPases in neuronal morphology and synaptic function, and suggests that the genes encoding the ArfGEFs IQSEC1 and IQSEC3 should be considered as candidates for screening in autosomal ID.
Collapse
Affiliation(s)
- Cheryl Shoubridge
- Genetics and Molecular Pathology; SA Pathology; The University of Adelaide; Adelaide, Australia
| | | | | | | |
Collapse
|
17
|
Oka H, Kitagawa M, Takata T. F-spondin inhibits differentiation of clastic precursors via lipoprotein receptor-related protein 8 (LRP8). J Periodontol 2014; 86:465-72. [PMID: 25299387 DOI: 10.1902/jop.2014.140419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND F-spondin, known to be a secreted neuronal glycoprotein, is highly expressed on the tooth root surface. The authors previously reported that F-spondin is one of the specific markers of cementoblasts in periodontal tissue. In chronic periodontitis, significant cemental resorption rarely occurs on the root side, although alveolar bone resorption by osteoclasts is one of the major pathologic changes. Thus, it was hypothesized that secretory F-spondin from cementoblasts might be involved in differentiation of clastic cells on the root surface. The authors studied effects of secretory F-spondin from F-spondin-expressing cells and its pathway on receptor activator of nuclear factor-κB ligand (RANKL)-mediated differentiation of clastic cells. METHODS Osteoclast precursors were used in this study. With a chamber assay, the authors examined effects of secretory molecules from F-spondin-expressing cells of transgenic mice on RANKL-induced clastic cell differentiation. RESULTS Secretory molecules from F-spondin-overexpressing cells significantly inhibited the RANKL-mediated tartrate-resistant acid phosphatase (TRAP)-positive cells from primary progenitor cells with the chamber system. F-spondin suppressed RANKL-mediated nuclear factor of activated T-cells, cytoplasmic 1 (NFATc1); TRAP; cathepsin K; and dendritic cell-specific transmembrane protein (DC-STAMP) expression in the cells. The suppressive effect of F-spondin on RANKL-induced differentiation of clastic cells was partially blocked by knockdown of low-density lipoprotein receptor-related protein 8 (LRP8). CONCLUSIONS These findings indicate that secretory factors from F-spondin-expressing cells, including F-spondin, downregulate differentiation of clastic precursors. Moreover, F-spondin inhibits RANKL-mediated differentiation of clastic cells partially via LRP8. It is suggested that secretory F-spondin may act protectively from cemental resorption partially via LRP8 in periodontal tissue.
Collapse
Affiliation(s)
- Hiroko Oka
- Department of International Collaboration Development for Dentistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | | | | |
Collapse
|
18
|
Shavit Y, Lio' P. Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data. MOLECULAR BIOSYSTEMS 2014; 10:1576-85. [PMID: 24710657 DOI: 10.1039/c4mb00142g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Over the past few decades we have witnessed great efforts to understand the cellular function at the cytoplasm level. Nowadays there is a growing interest in understanding the relationship between function and structure at the nuclear, chromosomal and sub-chromosomal levels. Data on chromosomal interactions that are now becoming available in unprecedented resolution and scale open the way to address this challenge. Consequently, there is a growing need for new methods and tools that will transform these data into knowledge and insights. Here, we have developed all the steps required for the analysis of chromosomal interaction data (Hi-C data). The result is a methodology which combines a wavelet change point with the Bayes factor for useful correction, segmentation and comparison of Hi-C data. We further developed chromoR, an R package that implements the methods presented here. The chromoR package provides researchers with a means to analyse chromosomal interaction data using statistical bioinformatics, offering a new and comprehensive solution to this task.
Collapse
Affiliation(s)
- Yoli Shavit
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK.
| | | |
Collapse
|
19
|
Zhang C, Kho YS, Wang Z, Chiang YT, Ng GKH, Shaw PC, Wang Y, Qi RZ. Transmembrane and coiled-coil domain family 1 is a novel protein of the endoplasmic reticulum. PLoS One 2014; 9:e85206. [PMID: 24454821 PMCID: PMC3891740 DOI: 10.1371/journal.pone.0085206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/23/2013] [Indexed: 01/01/2023] Open
Abstract
The endoplasmic reticulum (ER) is a continuous membrane network in eukaryotic cells comprising the nuclear envelope, the rough ER, and the smooth ER. The ER has multiple critical functions and a characteristic structure. In this study, we identified a new protein of the ER, TMCC1 (transmembrane and coiled-coil domain family 1). The TMCC family consists of at least 3 putative proteins (TMCC1-3) that are conserved from nematode to human. We show that TMCC1 is an ER protein that is expressed in diverse human cell lines. TMCC1 contains 2 adjacent transmembrane domains near the C-terminus, in addition to coiled-coil domains. TMCC1 was targeted to the rough ER through the transmembrane domains, whereas the N-terminal region and C-terminal tail of TMCC1 were found to reside in the cytoplasm. Moreover, the cytosolic region of TMCC1 formed homo- or hetero-dimers or oligomers with other TMCC proteins and interacted with ribosomal proteins. Notably, overexpression of TMCC1 or its transmembrane domains caused defects in ER morphology. Our results suggest roles of TMCC1 in ER organization.
Collapse
Affiliation(s)
- Chao Zhang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yik-Shing Kho
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhe Wang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yan Ting Chiang
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Department of Experimental Therapeutics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Gary K. H. Ng
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Pang-Chui Shaw
- Biochemistry Programme and Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert Z. Qi
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- * E-mail:
| |
Collapse
|
20
|
Yamasaki R. Anti-neurofascin antibody in combined central and peripheral demyelination. ACTA ACUST UNITED AC 2013. [DOI: 10.1111/cen3.12061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ryo Yamasaki
- Department of Neurological Therapeutics; Graduate School of Medical Sciences; Kyushu University; Fukuoka Japan
| |
Collapse
|
21
|
Huang Q, Zhang L, Wang Y, Zhang C, Zhou S, Yang G, Li Z, Gao X, Chen Z, Zhang Z. Depletion of PHF14, a novel histone-binding protein gene, causes neonatal lethality in mice due to respiratory failure. Acta Biochim Biophys Sin (Shanghai) 2013; 45:622-33. [PMID: 23688586 DOI: 10.1093/abbs/gmt055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The plant homeodomain (PHD) finger is identified in many chromatin-binding proteins, and functions as a 'reader' that recognizes specific epigenetic marks on histone tails, bridging transcription factors and their associated complexes to chromatin, and regulating gene expression. PHD finger-containing proteins perform many biological functions and are involved in many human diseases including cancer. PHF14 is predicted to code for a protein with multiple PHD fingers. However, its function is unidentified. The aim of this study is to characterize PHF14 and investigate its biological significance by employing multiple approaches including mouse gene-targeting knockout, and molecular cloning and characterization. Three transcripts of PHF14 in human cell lines were identified by reverse transcriptase polymerase chain reaction. Two isoforms of PHF14 (PHF14α and PHF14β) were cloned in this study. It was found that PHF14 was ubiquitously expressed in mouse tissues and human cell lines. PHF14α, the major isoform of PHF14, was localized in the nucleus and also bound to chromatin during cell division. Interestingly, co-immunoprecipitation results suggested that PHF14α bound to histones via its PHD fingers. Strikingly, gene-targeting knockout of PHF14 in mice resulted in a neonatal lethality due to respiratory failure. Pathological analysis revealed severe disorders of tissue and cell structures in multiple organs, particularly in the lungs. These results indicated that PHF14 might be an epigenetic regulator and play an important role in the development of multiple organs in mouse.
Collapse
Affiliation(s)
- Qin Huang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Parker MD, Boron WF. The divergence, actions, roles, and relatives of sodium-coupled bicarbonate transporters. Physiol Rev 2013; 93:803-959. [PMID: 23589833 PMCID: PMC3768104 DOI: 10.1152/physrev.00023.2012] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mammalian Slc4 (Solute carrier 4) family of transporters is a functionally diverse group of 10 multi-spanning membrane proteins that includes three Cl-HCO3 exchangers (AE1-3), five Na(+)-coupled HCO3(-) transporters (NCBTs), and two other unusual members (AE4, BTR1). In this review, we mainly focus on the five mammalian NCBTs-NBCe1, NBCe2, NBCn1, NDCBE, and NBCn2. Each plays a specialized role in maintaining intracellular pH and, by contributing to the movement of HCO3(-) across epithelia, in maintaining whole-body pH and otherwise contributing to epithelial transport. Disruptions involving NCBT genes are linked to blindness, deafness, proximal renal tubular acidosis, mental retardation, and epilepsy. We also review AE1-3, AE4, and BTR1, addressing their relevance to the study of NCBTs. This review draws together recent advances in our understanding of the phylogenetic origins and physiological relevance of NCBTs and their progenitors. Underlying these advances is progress in such diverse disciplines as physiology, molecular biology, genetics, immunocytochemistry, proteomics, and structural biology. This review highlights the key similarities and differences between individual NCBTs and the genes that encode them and also clarifies the sometimes confusing NCBT nomenclature.
Collapse
Affiliation(s)
- Mark D Parker
- Dept. of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106-4970, USA.
| | | |
Collapse
|
23
|
Coleman JA, Quazi F, Molday RS. Mammalian P4-ATPases and ABC transporters and their role in phospholipid transport. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:555-74. [PMID: 23103747 DOI: 10.1016/j.bbalip.2012.10.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 02/08/2023]
Abstract
Transport of phospholipids across cell membranes plays a key role in a wide variety of biological processes. These include membrane biosynthesis, generation and maintenance of membrane asymmetry, cell and organelle shape determination, phagocytosis, vesicle trafficking, blood coagulation, lipid homeostasis, regulation of membrane protein function, apoptosis, etc. P(4)-ATPases and ATP binding cassette (ABC) transporters are the two principal classes of membrane proteins that actively transport phospholipids across cellular membranes. P(4)-ATPases utilize the energy from ATP hydrolysis to flip aminophospholipids from the exocytoplasmic (extracellular/lumen) to the cytoplasmic leaflet of cell membranes generating membrane lipid asymmetry and lipid imbalance which can induce membrane curvature. Many ABC transporters play crucial roles in lipid homeostasis by actively transporting phospholipids from the cytoplasmic to the exocytoplasmic leaflet of cell membranes or exporting phospholipids to protein acceptors or micelles. Recent studies indicate that some ABC proteins can also transport phospholipids in the opposite direction. The importance of P(4)-ATPases and ABC transporters is evident from the findings that mutations in many of these transporters are responsible for severe human genetic diseases linked to defective phospholipid transport. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
Collapse
Affiliation(s)
- Jonathan A Coleman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | | |
Collapse
|
24
|
Wilson GN. Maternal genetic effect in DNA analysis: Egg on your traits. Am J Med Genet A 2012; 158A:1589-93. [DOI: 10.1002/ajmg.a.35407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 03/12/2012] [Indexed: 11/11/2022]
|
25
|
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. Mob DNA 2012; 3:8. [PMID: 22541534 PMCID: PMC3357318 DOI: 10.1186/1759-8753-3-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 04/30/2012] [Indexed: 01/25/2023] Open
Abstract
Background Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. Results Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. Conclusions This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.
Collapse
|
26
|
Lier N, Gresko N, Chiara M, Loffing-Cueni D, Loffing J. Immunofluorescent localization of the Rab-GAP protein TBC1D4 (AS160) in mouse kidney. Histochem Cell Biol 2012; 138:101-12. [DOI: 10.1007/s00418-012-0944-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2012] [Indexed: 10/28/2022]
|
27
|
Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms. J Neural Transm (Vienna) 2011; 119:425-33. [PMID: 22072270 DOI: 10.1007/s00702-011-0729-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 10/24/2011] [Indexed: 12/31/2022]
Abstract
Several genome-wide association (GWA) studies of alcohol dependence (AD) and alcohol-related phenotypes have been conducted; however, little is known about genetic variants influencing alcohol withdrawal symptoms (AWS). We conducted the first GWA study of AWS using 461 cases of AD with AWS and 408 controls in Caucasian population in the Collaborative Study on the Genetics of Alcoholism (COGA) sample. Logistic regression analysis of AWS as a binary trait, adjusted for age and sex, was performed using PLINK. We identified 51 SNPs associated with AWS with p < 10(-4). The first best signal was rs770182 (p = 3.65 × 10(-6)) at 5q21 near EFNA5 gene which was replicated in the Australian twin-family study of 273 families (p = 0.0172). Furthermore, three SNPs (rs10975990, rs10758821 and rs1407862) within KDM4C gene at 9p24.1 showed p < 10(-4) (p = 7.15 × 10(-6), 2.79 × 10(-5) and 4.93 × 10(-5), respectively) in the COGA sample while one SNP rs12001158 within KDM4C with p = 1.97 × 10(-4) in the COGA sample was replicated in the family sample (p = 0.01). Haplotype analysis further supported the associations of single-marker analyses of KDM4C in the COGA sample. Moreover, two SNPs (rs2046593 and rs10497668) near FSIP2 at 2q32.1 with moderate associations with AWS in the COGA sample (p = 2.66 × 10(-4) and 9.48 × 10(-5), respectively) were replicated in the family sample (p = 0.0013 and 0.0162, respectively). In addition, several SNPs in GABRA1, GABRG1, and GABRG3 were associated with AWS (p < 10(-2)) in the COGA sample. In conclusion, we identified several loci associated with AWS. These findings offer the potential for new insights into the pathogenesis of AD and AWS.
Collapse
|
28
|
Lauridsen JB, Johansen JL, Rekling JC, Thirstrup K, Moerk A, Sager TN. Regulation of the Bcas1 and Baiap3 transcripts in the subthalamic nucleus in mice recovering from MPTP toxicity. Neurosci Res 2011; 70:269-76. [PMID: 21514331 DOI: 10.1016/j.neures.2011.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/25/2011] [Accepted: 03/28/2011] [Indexed: 12/20/2022]
Abstract
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) exposure leads to significant and irreversible damage to dopaminergic neurons in both mice and humans. While MPTP exposure in humans causes permanent symptoms of Parkinson's disease, MPTP treated mice will recover behaviorally over a 3-week period. This mouse specific recovery might be linked to transcriptional changes in the basal ganglia enabling mice to maintain normal motor function in spite of low striatal dopamine levels. Laser microdissection was used to isolate the subthalamic nucleus from mice 7 and 28 days following MPTP exposure. High quality RNA was recovered and expressional analysis was performed on whole mouse genome microarrays. Identified regulated transcripts were validated in a separate batch of animals using quantitative PCR. Two transcripts with a significant regulation from days 7 to 28 in the MPTP treated groups, were identified: the brain specific angiogenesis inhibitor associated protein 3 (Baiap3) and the breast carcinoma amplified sequence 1 (Bcas1). Further studies of the molecular pathways involving these two transcripts may uncover processes in the subthalamic nucleus associated with the behavioral recovery observed after MPTP exposure.
Collapse
Affiliation(s)
- J B Lauridsen
- Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.
| | | | | | | | | | | |
Collapse
|
29
|
Ricco R, Kanduc D. Hepatitis B virus and Homo sapiens proteome-wide analysis: A profusion of viral peptide overlaps in neuron-specific human proteins. Biologics 2010; 4:75-81. [PMID: 20531967 PMCID: PMC2880343 DOI: 10.2147/btt.s8890] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Indexed: 01/09/2023]
Abstract
The primary amino acid sequence of the hepatitis B virus (HBV) proteome was searched for identity spots in the human proteome by using the Protein Information Resource database. We find that the HBV polyprotein shares sixty-five heptapeptides, one octapeptide, and one nonapeptide with the human proteins. The viral matches are disseminated among fundamental human proteins such as adhesion molecules, leukocyte differentiation antigens, enzymes, proteins associated with spermatogenesis, and transcription factors. As a datum of special interest, a number of peptide motifs are shared between the virus- and brain-specific antigens involved in neuronal protection. This study may help to evaluate the potential cross reactions and side effects of HBV antigen-based vaccines.
Collapse
|
30
|
Yamazaki T, Takata N, Uemura M, Kawamura Y. Arabidopsis synaptotagmin SYT1, a type I signal-anchor protein, requires tandem C2 domains for delivery to the plasma membrane. J Biol Chem 2010; 285:23165-76. [PMID: 20498364 DOI: 10.1074/jbc.m109.084046] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The correct localization of integral membrane proteins to subcellular compartments is important for their functions. Synaptotagmin contains a single transmembrane domain that functions as a type I signal-anchor sequence in its N terminus and two calcium-binding domains (C(2)A and C(2)B) in its C terminus. Here, we demonstrate that the localization of an Arabidopsis synaptotagmin homolog, SYT1, to the plasma membrane (PM) is modulated by tandem C2 domains. An analysis of the roots of a transformant-expressing green fluorescent protein-tagged SYT1 driven by native SYT1 promoter suggested that SYT1 is synthesized in the endoplasmic reticulum, and then delivered to the PM via the exocytotic pathway. We transiently expressed a series of truncated proteins in protoplasts, and determined that tandem C(2)A-C(2)B domains were necessary for the localization of SYT1 to the PM. The PM localization of SYT1 was greatly reduced following mutation of the calcium-binding motifs of the C(2)B domain, based on sequence comparisons with other homologs, such as endomembrane-localized SYT5. The localization of SYT1 to the PM may have been required for the functional divergence that occurred in the molecular evolution of plant synaptotagmins.
Collapse
Affiliation(s)
- Tomokazu Yamazaki
- 21st Century Center of Excellence Program, Iwate University, Morioka, Iwate 020-8550, Japan
| | | | | | | |
Collapse
|
31
|
Garriock HA, Kraft JB, Shyn SI, Peters EJ, Yokoyama JS, Jenkins GD, Reinalda MS, Slager SL, McGrath PJ, Hamilton SP. A genomewide association study of citalopram response in major depressive disorder. Biol Psychiatry 2010; 67:133-8. [PMID: 19846067 PMCID: PMC2794921 DOI: 10.1016/j.biopsych.2009.08.029] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 08/20/2009] [Accepted: 08/21/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND Antidepressant response is likely influenced by genetic constitution, but the actual genes involved have yet to be determined. We have carried out a genomewide association study to determine whether common DNA variation influences antidepressant response. METHODS Our sample is derived from Level 1 participants in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, all treated with citalopram. Association for the response phenotype included 883 responders and 608 nonresponders. For the remission phenotype, 743 subjects that achieved remission were compared with 608 nonresponders. We used a subset of single nucleotide polymorphisms (SNPs; n = 430,198) from the Affymetrix 500K and 5.0 Human SNP Arrays, and association analysis was carried out after correcting for population stratification. RESULTS We identified three SNPs associated with response with p values less than 1 x 10(-5) near the UBE3C gene (rs6966038, p = 4.65 x 10(-7)), another 100 kb away from BMP7 (rs6127921, p = 3.45 x 10(-6)), and a third that is intronic in the RORA gene (rs809736, p = 8.19 x 10(-6)). These same SNPs were also associated with remission. Thirty-nine additional SNPs are of interest with p values < or = .0001 for the response and remission phenotypes. CONCLUSIONS Although the findings reported here do not meet a genomewide threshold for significance, the regions identified from this study provide targets for independent replication and novel pathways to investigate mechanisms of antidepressant response. This study was not placebo controlled, making it possible that we are also observing associations to nonspecific aspects of drug treatment of depression.
Collapse
Affiliation(s)
- Holly A. Garriock
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA
| | - Jeffrey B. Kraft
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA
| | - Stanley I. Shyn
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA
| | - Eric J. Peters
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA
| | - Jennifer S. Yokoyama
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA
| | | | - Megan S. Reinalda
- Department of Health Sciences Research, Mayo Clinic College of Medicine
| | - Susan L. Slager
- Department of Health Sciences Research, Mayo Clinic College of Medicine
| | - Patrick J. McGrath
- Department of Psychiatry, Columbia University College of Physicians and Surgeons and New York State Psychiatric Institute
| | - Steven P. Hamilton
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA,corresponding author Steven P. Hamilton, MD, PhD, Carol Cochran Schaffner Endowed Chair in Mental Health, University of California, San Francisco, Department of Psychiatry, 401 Parnassus Ave, Box NGL-0984, San Francisco, CA, 94143-0984,
| |
Collapse
|
32
|
Folmer DE, Elferink RPJO, Paulusma CC. P4 ATPases - lipid flippases and their role in disease. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:628-35. [PMID: 19254779 DOI: 10.1016/j.bbalip.2009.02.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/12/2009] [Accepted: 02/12/2009] [Indexed: 12/11/2022]
Abstract
P4 ATPases (type 4 P-type ATPases) are multispan transmembrane proteins that have been implicated in phospholipid translocation from the exoplasmic to the cytoplasmic leaflet of biological membranes. Studies in Saccharomyces cerevisiae have indicated that P4 ATPases are important in vesicle biogenesis and are required for vesicular trafficking along several intracellular vesicular transport routes. Although little is known about mammalian P4 ATPases, some members of this subfamily appear to be associated with human disease or mouse pathophysiology. ATP8B1, a phosphatidylserine translocase, is the most extensively studied mammalian P4 ATPase. This protein is important for maintaining the detergent resistant properties of the apical membrane of the hepatocyte. Mutations in ATP8B1 give rise to severe liver disease. Furthermore, a role for Atp8b3 in mouse sperm cell capacitation has been suggested, whereas deficiency of Atp10a and Atp10d leads to insulin resistance and obesity in mice. Here we review the present status on the pathophysiological consequences of P4 ATPase deficiency.
Collapse
Affiliation(s)
- Dineke E Folmer
- AMC Liver Center, Academic Medical Center, University of Amsterdam, Meibergdreef 69-71, 1105BK Amsterdam, The Netherlands
| | | | | |
Collapse
|
33
|
Yamakawa H. High-throughput construction of ORF clones for production of the recombinant proteins. Methods Mol Biol 2009; 577:25-39. [PMID: 19718506 DOI: 10.1007/978-1-60761-232-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Expression-ready cDNA clones, where the open reading frame (ORF) of the gene of interest is placed under the control of an appropriate promoter, are critical for functional characterization of the gene products. To create a resource of human gene products, we attempted to systematically convert original cDNA clones to expression-ready forms for recombinant proteins. For this purpose, we adopted a rare-cutting restriction enzyme-based system, the Flexi cloning system, to construct ORF clones. Taking advantage of the fully sequenced cDNA clones we accumulated to date, a number of sets of Flexi ORF clones in a 96-well format have been prepared. In this section, two methods for the preparation of Flexi ORF clones in a 96-well format are described. A protocol for transferring ORFs between Flexi vectors in a 96-well format is also described. We believe that the resultant clone set could be successfully used as a versatile reagent for functional characterization of human proteins.
Collapse
Affiliation(s)
- Hisashi Yamakawa
- Department of Human Genome Research, Kazusa DNA Research Institute, Laboratory of Human Gene Research, Chiba, Japan
| |
Collapse
|
34
|
Abstract
RhoBTB proteins constitute a subfamily of atypical members within the Rho family of small guanosine triphosphatases (GTPases). Their most salient feature is their domain architecture: a GTPase domain (in most cases, non-functional) is followed by a prolinerich region, a tandem of 2 broadcomplex, tramtrack, bric a brac (BTB) domains, and a conserved Cterminal region. In humans, the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophila and Dictyostelium, but have been lost in plants and fungi. Interest in RhoBTB arose when RHOBTB2 was identified as the gene homozygously deleted in breast cancer samples and was proposed as a candidate tumor suppressor gene, a property that has been extended to RHOBTB1. The functions of RhoBTB proteins have not been defined yet, but may be related to the roles of BTB domains in the recruitment of cullin3, a component of a family of ubiquitin ligases. A model emerges in which RhoBTB proteins are required to maintain constant levels of putative substrates involved in cell cycle regulation or vesicle transport through targeting for degradation in the 26S proteasome. RhoBTB proteins are engrossing the list of Rho GTPases involved in tumorigenesis. Unlike typical Rho GTPases (usually overexpressed or hyperactive), RhoBTB proteins appear to play a part in the carcinogenic process through a mechanism that involves the decreased or abolished expression of the corresponding genes, or more rarely, mutations that result in impaired functioning of the protein, presumably leading to the accumulation of RhoBTB substrates and alterations of the cellular homeostasis.
Collapse
Affiliation(s)
- Jessica Berthold
- Centers for Biochemistry and Molecular Medicine, University of Cologne, Cologne, Germany
| | | | | |
Collapse
|
35
|
Bernardo AA, Bernardo CM, Espiritu DJ, Arruda JAL. The sodium bicarbonate cotransporter: structure, function, and regulation. Semin Nephrol 2007; 26:352-60. [PMID: 17071329 DOI: 10.1016/j.semnephrol.2006.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The role of the Na(+)-coupled HCO(3)(-) transporter (NBC) family is indispensable in acid-base homeostasis. Almost all tissues express a member of the NBC family. NBC has been studied extensively in the kidney and plays a role in proximal tubule HCO(3)(-) reabsorption. Although the exact function of this transporter family on other tissues is not very clear, the ubiquitous expression of NBC family suggests a role in cell pH regulation. Altered NBC activity caused by mutations of the gene responsible for NBC protein expression results in pathophysiologic conditions. Mutations of NBC resulting in important clinical disorders have been reported extensively on one member of the NBC family, the kidney NBC (NBC1). These mutations have led to several structural studies to understand the mechanism of the abnormal NBC1 activity.
Collapse
Affiliation(s)
- Angelito A Bernardo
- Department of Medicine, Section of Nephrology, University of Illinois at Chicago, 820 S. Wood Street, Chicago, IL 60612, USA
| | | | | | | |
Collapse
|
36
|
Ohnuma K, Kaneko H, Noguchi J, Kikuchi K, Ozawa M, Hasegawa Y. Isolation and Identification of F-Spondin in the Boar Testis and Its Production During Testis Growth. J Reprod Dev 2007; 53:151-8. [PMID: 17043384 DOI: 10.1262/jrd.18090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
F-spondin/vascular smooth muscle cell growth-promoting factor (VSGP), purified from the follicular fluid of adult bovine ovaries, has been identified as a promoter of neuronal differentiation and vascular smooth muscle growth. The objectives of the present study were (1) to clarify whether F-spondin is also produced in the testis, which is ontogenically equivalent to the ovary, and (2) to examine whether production of this protein changes with testicular growth. To isolate F-spondin from the testis, testicular homogenates obtained from 8-week-old boars were sequentially subjected to heparin-Sepharose chromatography, diethylaminoethyl (DEAE)-Sepharose chromatography, and reverse-phase high-performance liquid chromatography (RP-HPLC). The isolated protein had a molecular mass of approximately 110 kDa and was cross-reactive with anti-F-spondin antibody by Western blotting. The purified protein was further characterized by amino acid sequence analysis of its internal peptide. The sequence obtained was GEQCNIVPDN VD, and a homology search indicated that the purified protein is a homologue of rat, human, and bovine F-spondin. By fractionation of the same amounts of testis tissue obtained from 1-, 8-, 16-, and 40-week-old boars, we analyzed age-related production of F-spondin in the testis. Western blotting of the fractions obtained from RP-HPLC revealed the presence of a band at approximately 110 kDa, corresponding to F-spondin, in the testes obtained from boars between 1 and 16 weeks old, but this band was not detected at 40 weeks. These results clearly indicate that (1) the porcine testis produces F-spondin and that (2) production of this protein is evident in the immature porcine testis, but not the adult testis.
Collapse
Affiliation(s)
- Katsuhiko Ohnuma
- Reproductive Biology Research Unit (Kannondai), National Institute of Agrobiological Science, Ibaraki, Japan
| | | | | | | | | | | |
Collapse
|
37
|
Wang Q, Du X, Cai Z, Greene MI. Characterization of the structures involved in localization of the SUN proteins to the nuclear envelope and the centrosome. DNA Cell Biol 2006; 25:554-62. [PMID: 17132086 DOI: 10.1089/dna.2006.25.554] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nuclear envelope forms a selective barrier that separates the cytoplasm from the nucleus. During mitosis the nuclear envelope breaks down so that the microtubule network can form contacts with the kinetochore and guide chromosome segregation. Previous studies have suggested a model in which the centrosome and the microtubule network may play a role in nuclear envelope breakdown through as yet unidentified interactions with proteins localized to the nuclear envelope. In the current study we characterized a nuclear envelope protein SUN2 and identified a substructure involved in its localization to the nuclear envelope. We found that a structurally related protein, SUN1, may be localized to the nuclear envelope through a different mechanism. Furthermore, the SUN2 protein can form different assemblies, including homodimers and heterodimers with SUN1. Finally, we provide evidence indicating that SUN1 and SUN2 may form a physical interaction between the nuclear envelope and the centrosome.
Collapse
Affiliation(s)
- Qiang Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
| | | | | | | |
Collapse
|
38
|
Carinci F, Piattelli A, Guida L, Perrotti V, Laino G, Oliva A, Annunziata M, Palmieri A, Pezzetti F. Effects of Emdogain on osteoblast gene expression. Oral Dis 2006; 12:329-42. [PMID: 16700745 DOI: 10.1111/j.1601-0825.2005.01204.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Emdogain (EMD) is a protein extract purified from porcine enamel and has been introduced in clinical practice to obtain periodontal regeneration. EMD is composed mainly of amelogenins (90%), while the remaining 10% is composed of non-amelogenin enamel matrix proteins such as enamelins, tuftelin, amelin and ameloblastin. Enamel matrix proteins seem to be involved in root formation. EMD has been reported to promote proliferation, migration, adhesion and differentiation of cells associated with healing periodontal tissues in vivo. DESIGN How this protein acts on osteoblasts is poorly understood. We therefore attempted to address this question by using a microarray technique to identify genes that are differently regulated in osteoblasts exposed to enamel matrix proteins. RESULTS By using DNA microarrays containing 20,000 genes, we identified several upregulated and downregulated genes in the osteoblast-like cell line (MG-63) cultured with enamel matrix proteins (Emd). The differentially expressed genes cover a broad range of functional activities: (i) signaling transduction, (ii) transcription, (iii) translation, (iv) cell cycle regulation, proliferation and apoptosis, (v) immune system, (vi) vesicular transport and lysosome activity, and (vii) cytoskeleton, cell adhesion and extracellular matrix production. CONCLUSIONS The data reported are the first genome-wide scan of the effect of enamel matrix proteins on osteoblast-like cells. These results can contribute to our understanding of the molecular mechanisms of bone regeneration and as a model for comparing other materials with similar clinical effects.
Collapse
Affiliation(s)
- F Carinci
- Department of Maxillofacial Surgery, University of Ferrara, Ferrara, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Liu S, Rauhut R, Vornlocher HP, Lührmann R. The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. RNA (NEW YORK, N.Y.) 2006; 12:1418-30. [PMID: 16723661 PMCID: PMC1484429 DOI: 10.1261/rna.55406] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The human 25S U4/U6.U5 tri-snRNP is a major building block of the U2-type spliceosome and contains, in addition to the U4, U6, and U5 snRNAs, at least 30 distinct proteins. To learn more about the molecular architecture of the tri-snRNP, we have investigated interactions between tri-snRNP proteins using the yeast two-hybrid assay and in vitro binding assays, and, in addition, have identified distinct protein domains that are critical for the connectivity of this protein network in the human tri-snRNP. These studies revealed multiple interactions between distinct domains of the U5 proteins hPrp8, hBrr2 (a DExH/D-box helicase), and hSnu114 (a putative GTPase), which are key players in the catalytic activation of the spliceosome, during which the U4/U6 base-pairing interaction is disrupted and U4 is released from the spliceosome. Both the U5-specific, TPR/HAT-repeat-containing hPrp6 protein and the tri-snRNP-specific hSnu66 protein interact with several U5- and U4/U6-associated proteins, including hBrr2 and hPrp3, which contacts the U6 snRNA. Thus, both proteins are located at the interface between U5 and U4/U6 in the tri-snRNP complex, and likely play an important role in transmitting the activity of hBrr2 and hSnu114 in the U5 snRNP to the U4/U6 duplex during spliceosome activation. A more detailed analysis of these protein interactions revealed that different HAT repeats mediate interactions with specific hPrp6 partners. Taken together, data presented here provide a detailed picture of the network of protein interactions within the human tri-snRNP.
Collapse
Affiliation(s)
- Sunbin Liu
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
| | | | | | | |
Collapse
|
40
|
Kalla C, Mertens D, Lichter P. Response. Genes Chromosomes Cancer 2005. [DOI: 10.1002/gcc.20194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
41
|
Paulusma CC, Oude Elferink RPJ. The type 4 subfamily of P-type ATPases, putative aminophospholipid translocases with a role in human disease. Biochim Biophys Acta Mol Basis Dis 2005; 1741:11-24. [PMID: 15919184 DOI: 10.1016/j.bbadis.2005.04.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 04/21/2005] [Accepted: 04/25/2005] [Indexed: 11/22/2022]
Abstract
The maintenance of phospholipid asymmetry in membrane bilayers is a paradigm in cell biology. However, the mechanisms and proteins involved in phospholipid translocation are still poorly understood. Members of the type 4 subfamily of P-type ATPases have been implicated in the translocation of phospholipids from the outer to the inner leaflet of membrane bilayers. In humans, several inherited disorders have been identified which are associated with loci harboring type 4 P-type ATPase genes. Up to now, one inherited disorder, Byler disease or progressive familial intrahepatic cholestasis type 1 (PFIC1), has been directly linked to mutations in a type 4 P-type ATPase gene. How the absence of an aminophospholipid translocase activity relates to this severe disease is, however, still unclear. Studies in the yeast Saccharomyces cerevisiae have recently identified important roles for type 4 P-type ATPases in intracellular membrane- and protein-trafficking events. These processes require an (amino)phospholipid translocase activity to initiate budding or fusion of membrane vesicles from or with other membranes. The studies in yeast have greatly contributed to our cell biological insight in membrane dynamics and intracellular-trafficking events; if this knowledge can be translated to mammalian cells and organs, it will help to elucidate the molecular mechanisms which underlie severe inherited human diseases such as Byler disease.
Collapse
Affiliation(s)
- C C Paulusma
- Department of Experimental Hepatology, Academic Medical Center/AMC Liver Center, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands.
| | | |
Collapse
|
42
|
Sutherland LC, Rintala-Maki ND, White RD, Morin CD. RNA binding motif (RBM) proteins: a novel family of apoptosis modulators? J Cell Biochem 2005; 94:5-24. [PMID: 15514923 DOI: 10.1002/jcb.20204] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RBM5 is a known modulator of apoptosis, an RNA binding protein, and a putative tumor suppressor. Originally identified as LUCA-15, and subsequently as H37, it was designated "RBM" (for RNA Binding Motif) due to the presence of two RRM (RNA Recognition Motif) domains within the protein coding sequence. Recently, a number of proteins have been attributed with this same RBM designation, based on the presence of one or more RRM consensus sequences. One such protein, RBM3, was also recently found to have apoptotic modulatory capabilities. The high sequence homology at the amino acid level between RBM5, RBM6, and particularly, RBM10 suggests that they, too, may play an important role in regulating apoptosis. It is the intent of this article to ammalgamate the data on the ten originally identified RBM proteins in order to question the existence of a novel family of RNA binding apoptosis regulators.
Collapse
Affiliation(s)
- Leslie C Sutherland
- Tumour Biology Group, Northeastern Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, Ontario P3E 5J1, Canada.
| | | | | | | |
Collapse
|
43
|
Shimada K, Uzawa K, Kato M, Endo Y, Shiiba M, Bukawa H, Yokoe H, Seki N, Tanzawa H. Aberrant expression of RAB1A in human tongue cancer. Br J Cancer 2005; 92:1915-21. [PMID: 15870709 PMCID: PMC2361773 DOI: 10.1038/sj.bjc.6602594] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
This study was designed to identify specific gene expression changes in tongue squamous cell carcinomas (TSCCs) compared with normal tissues using in-house cDNA microarray that comprised of 2304 full-length cDNAs from a cDNA library prepared from normal oral tissues, primary oral cancers, and oral cancer cell lines. The genes identified by our microarray system were further analysed at the mRNA or protein expression level in a series of clinical samples by real-time quantitative reverse transcriptase–polymerase chain reaction (qRT–PCR) analysis and imuunohositochemistry. The microarray analysis identified a total of 16 genes that were significantly upregulated in common among four TSCC specimens. Consistent with the results of the microarray, increased mRNA levels of selected genes with known molecular functions were found in the four TSCCs. Among genes identified, Rab1a, a member of the Ras oncogene family, was further analysed for its protein expression in 54 TSCCs and 13 premalignant lesions. We found a high prevalence of Rab1A-overexpression not only in TSCCs (98%) but also in premalignant lesions (93%). Thus, our results suggest that rapid characterisation of the target gene(s) for TSCCs can be accomplished using our in-house cDNA microarray analysis combined with the qRT–PCR and immunohistochemistry, and that the Rab1A is a potential biomarker of tongue carcinogenesis.
Collapse
Affiliation(s)
- K Shimada
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - K Uzawa
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
- Division of Oral Surgery, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan. E-mail:
| | - M Kato
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Y Endo
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - M Shiiba
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - H Bukawa
- Division of Oral Surgery, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - H Yokoe
- Division of Oral Surgery, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - N Seki
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
- Center of Excellence (COE) Program in the 21st Century, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - H Tanzawa
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
- Division of Oral Surgery, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
- Center of Excellence (COE) Program in the 21st Century, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| |
Collapse
|
44
|
Kalla C, Nentwich H, Schlotter M, Mertens D, Wildenberger K, Döhner H, Stilgenbauer S, Lichter P. Translocation t(X;11)(q13;q23) in B-cell chronic lymphocytic leukemia disrupts two novel genes. Genes Chromosomes Cancer 2004; 42:128-43. [PMID: 15543602 DOI: 10.1002/gcc.20131] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Deletion of chromosome region 11q22-q23 defines a subgroup of patients with B-cell chronic lymphocytic leukemia (B-CLL) characterized by poor survival. Although the tumor-suppressor gene ATM in the consensus deletion region was found to be biallelically inactivated in about one third of B-CLL cases, in the majority of those who have this deletion, inactivation of the remaining ATM allele was not observed. To identify a second disease-associated gene, we investigated two B-CLL cases with translocation breakpoints in the critical 11q23 deletion region. In one case, a t(X;11)(q13;q23) was cloned and two novel genes were isolated. The breakpoint on 11q23 affected the ARHGAP20 gene, which encodes a protein predicted to be involved in the regulation of Rho family GTPases. The breakpoint on Xq13 occurred in BRWD3, which codes for a putative novel transcription factor. The rearrangement of ARHGAP20 and BRWD3 did not result in fusion transcripts, but it disrupted both genes. Mutation analysis of 28 B-CLL samples with monoallelic deletions and two B-CLL samples with 11q23 translocations detected no deleterious mutation in the remaining copy of ARHGAP20. Quantitative expression analysis in 22 B-CLLs revealed significant up-regulation of ARHGAP20 in CLL B cells, whereas BRWD3 was slightly down-regulated. Thus, deregulation of ARHGAP20 by altered gene expression or by gene disruption (but not point mutation) might be a general molecular mechanism of B-CLL leukemogenesis.
Collapse
MESH Headings
- Chromosome Banding/methods
- Chromosome Breakage/genetics
- Chromosome Deletion
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, X/genetics
- Cloning, Molecular/methods
- DNA Mutational Analysis/methods
- DNA, Neoplasm/genetics
- Exons/genetics
- GTPase-Activating Proteins
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Molecular Sequence Data
- Oncogene Proteins, Fusion/genetics
- RNA Splice Sites/genetics
- Transcription Factors/genetics
- Transcription Factors/physiology
- Translocation, Genetic/genetics
Collapse
Affiliation(s)
- Claudia Kalla
- Abteilung Molekulare Genetik, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Sitz JH, Tigges M, Baumgärtel K, Khaspekov LG, Lutz B. Dyrk1A potentiates steroid hormone-induced transcription via the chromatin remodeling factor Arip4. Mol Cell Biol 2004; 24:5821-34. [PMID: 15199138 PMCID: PMC480880 DOI: 10.1128/mcb.24.13.5821-5834.2004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2004] [Accepted: 03/26/2004] [Indexed: 11/20/2022] Open
Abstract
Dyrk1A, a mammalian homolog of the Drosophila minibrain gene, encodes a dual-specificity kinase, involved in neuronal development and in adult brain physiology. In humans, a third copy of DYRK1A is present in Down syndrome (trisomy 21) and has been implicated in the etiology of mental retardation. To further understand this pathology, we searched for Dyrk1A-interacting proteins and identified Arip4 (androgen receptor-interacting protein 4), a SNF2-like steroid hormone receptor cofactor. Mouse hippocampal and cerebellar neurons coexpress Dyrk1A and Arip4. In HEK293 cells and hippocampal neurons, both proteins are colocalized in a speckle-like nuclear subcompartment. The functional interaction of Dyrk1A with Arip4 was analyzed in a series of transactivation assays. Either Dyrk1A or Arip4 alone displays an activating effect on androgen receptor- and glucocorticoid receptor-mediated transactivation, and Dyrk1A and Arip4 together act synergistically. These effects are independent of the kinase activity of Dyrk1A. Inhibition of endogenous Dyrk1A and Arip4 expression by RNA interference showed that both proteins are necessary for the efficient activation of androgen receptor- and glucocorticoid receptor-dependent transcription. As Dyrk1A is an activator of steroid hormone-regulated transcription, the overexpression of DYRK1A in persons with Down syndrome may cause rather broad changes in the homeostasis of steroid hormone-controlled cellular events.
Collapse
Affiliation(s)
- Jan Hendrik Sitz
- Molecular Genetics of Behavior, Max Planck Institute of Psychiatry, Munich, Germany
| | | | | | | | | |
Collapse
|
46
|
Hodzic DM, Yeater DB, Bengtsson L, Otto H, Stahl PD. Sun2 Is a Novel Mammalian Inner Nuclear Membrane Protein. J Biol Chem 2004; 279:25805-12. [PMID: 15082709 DOI: 10.1074/jbc.m313157200] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sun protein (Sun1 and Sun2) cDNAs were previously cloned based on the homology of their C-terminal regions (SUN (Sad1 and UNC) domain) with the Caenorhabditis elegans protein UNC-84 whose mutation disrupts nuclear migration/positioning. In this study, we raised an anti-Sun2 serum and identified Sun2 in mammalian cells. In HeLa cells, Sun2 displays a nuclear rim-like pattern typical for a nuclear envelope protein. The Sun2 antibody signal co-localizes with nuclear pore and INM markers signals. The rim-like pattern was also observed with the recombinant full-length Sun2 protein fused to either EGFP or V5 epitopes. In addition, we found that a recombinant truncated form of Sun2, extending from amino acids 26 to 339, is sufficient to specify the nuclear envelope localization. Biochemical analyses show that Sun2 is an 85-kDa protein that is partially insoluble in detergent with high salt concentration and in chaotropic agents. Furthermore, Sun2 is enriched in purified HeLa cell nuclei. Electron microscopy analysis shows that Sun2 localizes in the nuclear envelope with a sub-population present in small clusters. Additionally, we show that the SUN domain of Sun2 is localized to the periplasmic space between the inner and the outer nuclear membranes. From our data, we conclude that Sun2 is a new mammalian inner nuclear membrane protein. Because the SUN domain is conserved from fission yeast to mammals, we suggest that Sun2 belongs to a new class of nuclear envelope proteins with potential relevance to nuclear membrane function in the context of the involvement of its components in an increasing spectrum of human diseases.
Collapse
Affiliation(s)
- Didier M Hodzic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | | | | | | |
Collapse
|
47
|
Miyazaki K, Nagase T, Mesaki M, Narukawa J, Ohara O, Ishida N. Phosphorylation of clock protein PER1 regulates its circadian degradation in normal human fibroblasts. Biochem J 2004; 380:95-103. [PMID: 14750904 PMCID: PMC1224138 DOI: 10.1042/bj20031308] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Revised: 01/05/2004] [Accepted: 01/29/2004] [Indexed: 11/17/2022]
Abstract
Recent advances suggest that the molecular components of the circadian clock generate a self-sustaining transcriptional-translational feedback loop with a period of approx. 24 h. The precise expression profiles of human clock genes and their products have not been elucidated. We cloned human clock genes, including per1, per2, per3, cry2 and clock, and evaluated their circadian mRNA expression profiles in WI-38 fibroblasts stimulated with serum. Transcripts of hPer1, hPer2, hPer3, hBMAL1 and hCry2 (where h is human) underwent circadian oscillation. Serum-stimulation also caused daily oscillations of hPER1 protein and the apparent molecular mass of hPER1 changed. Inhibitor studies indicated that the CKI (casein kinase I) family, including CKIepsilon and CKIdelta, phosphorylated hPER1 and increased the apparent molecular mass of hPER1. The inhibition of hPER1 phosphorylation by CKI-7 [ N -(2-aminoethyl)-5-chloro-isoquinoline-8-sulphonamide], a CKI inhibitor, disturbed hPER1 degradation, delayed the nuclear entry of hPER1 and allowed it to persist for longer in the nucleus. Furthermore, proteasome inhibitors specifically blocked hPER1 degradation. However leptomycin B, an inhibitor of nuclear export, did not alter the degradation state of hPER1 protein. These findings indicate that circadian hPER1 degradation through a proteasomal pathway can be regulated through phosphorylation by CKI, but not by subcellular localization.
Collapse
Affiliation(s)
- Koyomi Miyazaki
- Clock Cell Biology Group, IBRF (Institute for Biological Resource and Function), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba central 6, 1-1-1, Higashi, Tsukuba, 305-8566, Japan
| | | | | | | | | | | |
Collapse
|
48
|
Hutcheson HB, Olson LM, Bradford Y, Folstein SE, Santangelo SL, Sutcliffe JS, Haines JL. Examination of NRCAM, LRRN3, KIAA0716, and LAMB1 as autism candidate genes. BMC MEDICAL GENETICS 2004; 5:12. [PMID: 15128462 PMCID: PMC420465 DOI: 10.1186/1471-2350-5-12] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Accepted: 05/05/2004] [Indexed: 11/10/2022]
Abstract
BACKGROUND A substantial body of research supports a genetic involvement in autism. Furthermore, results from various genomic screens implicate a region on chromosome 7q31 as harboring an autism susceptibility variant. We previously narrowed this 34 cM region to a 3 cM critical region (located between D7S496 and D7S2418) using the Collaborative Linkage Study of Autism (CLSA) chromosome 7 linked families. This interval encompasses about 4.5 Mb of genomic DNA and encodes over fifty known and predicted genes. Four candidate genes (NRCAM, LRRN3, KIAA0716, and LAMB1) in this region were chosen for examination based on their proximity to the marker most consistently cosegregating with autism in these families (D7S1817), their tissue expression patterns, and likely biological relevance to autism. METHODS Thirty-six intronic and exonic single nucleotide polymorphisms (SNPs) and one microsatellite marker within and around these four candidate genes were genotyped in 30 chromosome 7q31 linked families. Multiple SNPs were used to provide as complete coverage as possible since linkage disequilibrium can vary dramatically across even very short distances within a gene. Analyses of these data used the Pedigree Disequilibrium Test for single markers and a multilocus likelihood ratio test. RESULTS As expected, linkage disequilibrium occurred within each of these genes but we did not observe significant LD across genes. None of the polymorphisms in NRCAM, LRRN3, or KIAA0716 gave p < 0.05 suggesting that none of these genes is associated with autism susceptibility in this subset of chromosome 7-linked families. However, with LAMB1, the allelic association analysis revealed suggestive evidence for a positive association, including one individual SNP (p = 0.02) and three separate two-SNP haplotypes across the gene (p = 0.007, 0.012, and 0.012). CONCLUSIONS NRCAM, LRRN3, KIAA0716 are unlikely to be involved in autism. There is some evidence that variation in or near the LAMB1 gene may be involved in autism.
Collapse
Affiliation(s)
- Holli B Hutcheson
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37027, U.S.A
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, MD, 21702, U.S.A
| | - Lana M Olson
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37027, U.S.A
| | - Yuki Bradford
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37027, U.S.A
| | - Susan E Folstein
- Department of Psychiatry, New England Medical Center/Tufts University School of Medicine, Boston, MA, 02111, U.S.A
| | - Susan L Santangelo
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02129, U.S.A
| | - James S Sutcliffe
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37027, U.S.A
| | - Jonathan L Haines
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37027, U.S.A
| |
Collapse
|
49
|
Coyle IP, Koh YH, Lee WCM, Slind J, Fergestad T, Littleton JT, Ganetzky B. Nervous Wreck, an SH3 Adaptor Protein that Interacts with Wsp, Regulates Synaptic Growth in Drosophila. Neuron 2004; 41:521-34. [PMID: 14980202 DOI: 10.1016/s0896-6273(04)00016-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2003] [Revised: 11/13/2003] [Accepted: 01/07/2004] [Indexed: 10/26/2022]
Abstract
We describe the isolation and characterization of nwk (nervous wreck), a temperature-sensitive paralytic mutant that causes excessive growth of larval neuromuscular junctions (NMJs), resulting in increased synaptic bouton number and branch formation. Ultrastructurally, mutant boutons have reduced size and fewer active zones, associated with a reduction in synaptic transmission. nwk encodes an FCH and SH3 domain-containing adaptor protein that localizes to the periactive zone of presynaptic terminals and binds to the Drosophila ortholog of Wasp (Wsp), a key regulator of actin polymerization. wsp null mutants display synaptic overgrowth similar to nwk and enhance the nwk morphological phenotype in a dose-dependent manner. Evolutionarily, Nwk belongs to a previously undescribed family of adaptor proteins that includes the human srGAPs, which regulate Rho activity downstream of Robo receptors. We propose that Nwk controls synapse morphology by regulating actin dynamics downstream of growth signals in presynaptic terminals.
Collapse
Affiliation(s)
- Ian P Coyle
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Gisler SM, Pribanic S, Bacic D, Forrer P, Gantenbein A, Sabourin LA, Tsuji A, Zhao ZS, Manser E, Biber J, Murer H. PDZK1: I. A major scaffolder in brush borders of proximal tubular cells11See Editorial by Moe, p. 1916. Kidney Int 2003; 64:1733-45. [PMID: 14531806 DOI: 10.1046/j.1523-1755.2003.00266.x] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND In proximal tubular cells, PDZK1 (NaPi-Cap1) has been implicated in apical expression of the Na+-dependent phosphate cotransporter (NaPi-IIa) via interaction with its C-terminus. PDZK1 represents a multidomain protein consisting of four PDZ domains and thus is believed to have a broader specificity besides NaPi-IIa. METHODS We subjected single PDZ domains derived from PDZK1 either to yeast two-hybrid screens or yeast trap assays. Different pull-down assays and blot overlays were applied to corroborate the PDZK1-mediated interactions in vitro. Co-localization of interacting proteins with PDZK1 in proximal tubular cells was assessed by immunohistochemistry. RESULTS In the yeast screens, the most abundant candidate protein to interact with PDZK1 was the membrane-associated protein of 17 kD (MAP17). Besides MAP17, C-terminal parts of following transporters were also identified: NaPi-IIa, solute carrier SLC17A1 (NaPi-I), Na+/H+ exchanger (NHE-3), organic cation transporter (OCTN1), chloride-formate exchanger (CFEX), and urate-anion exchanger (URAT1). In addition, other regulatory factors were found among the clones, such as a protein kinase A (PKA)-anchoring protein (D-AKAP2) and N+/H+ exchanger regulator factor (NHERF-1). All interactions of itemized proteins with PDZK1 were affirmed by in vitro techniques. Apart from PDZK1, strong in vitro interactions of NHERF-1 were also observed with the solute transporters (excluding MAP17) and D-AKAP2. All identified proteins were immunolocalized in proximal tubular cells, wherein all membrane proteins co-localized with PDZK1 in brush borders. CONCLUSION We hypothesize that PDZK1 and NHERF-1 establish an extended network beneath the apical membrane to which membrane proteins and regulatory components are anchored.
Collapse
Affiliation(s)
- Serge M Gisler
- Department of Physiology and Biochemistry, University of Zürich, Zürich, Switzerland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|