1
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Daiwile AP, McCoy MT, Ladenheim B, Subramaniam J, Cadet JL. Incubation of methamphetamine craving in punishment-resistant individuals is associated with activation of specific gene networks in the rat dorsal striatum. Mol Psychiatry 2024:10.1038/s41380-024-02455-2. [PMID: 38351172 DOI: 10.1038/s41380-024-02455-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Methamphetamine use disorder (MUD) is characterized by loss of control over compulsive drug use. Here, we used a self-administration (SA) model to investigate transcriptional changes associated with the development of early and late compulsivity during contingent footshocks. Punishment initially separated methamphetamine taking rats into always shock-resistant (ASR) rats that continued active lever pressing and shock-sensitive (SS) rats that reduced their lever pressing. At the end of the punishment phase, rats underwent 15 days of forced abstinence at the end of which they were re-introduced to the SA paradigm followed by SA plus contingent shocks. Interestingly, 36 percent of the initial SS rats developed delayed shock-resistance (DSR). Of translational relevance, ASR rats showed more incubation of methamphetamine craving than DSR and always sensitive (AS) rats. RNA sequencing revealed increased striatal Rab37 and Dipk2b mRNA levels that correlated with incubation of methamphetamine craving. Interestingly, Bdnf mRNA levels showed HDAC2-dependent decreased expression in the AS rats. The present SA paradigm should help to elucidate the molecular substrates of early and late addiction-like behaviors.
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Affiliation(s)
- Atul P Daiwile
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224, USA
| | - Michael T McCoy
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224, USA
| | - Bruce Ladenheim
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224, USA
| | - Jayanthi Subramaniam
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224, USA
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224, USA.
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2
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Du S, Zhu C, Ren X, Chen X, Cui X, Guan S. Regulation of secretory pathway kinase or kinase-like proteins in human cancers. Front Immunol 2023; 14:942849. [PMID: 36825005 PMCID: PMC9941534 DOI: 10.3389/fimmu.2023.942849] [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: 05/13/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Secretory pathway kinase or kinase-like proteins (SPKKPs) are effective in the lumen of the endoplasmic reticulum (ER), Golgi apparatus (GA), and extracellular space. These proteins are involved in secretory signaling pathways and are distinctive from typical protein kinases. Various reports have shown that SPKKPs regulate the tumorigenesis and progression of human cancer via the phosphorylation of various substrates, which is essential in physiological and pathological processes. Emerging evidence has revealed that the expression of SPKKPs in human cancers is regulated by multiple factors. This review summarizes the current understanding of the contribution of SPKKPs in tumorigenesis and the progression of immunity. With the epidemic trend of immunotherapy, targeting SPKKPs may be a novel approach to anticancer therapy. This study briefly discusses the recent advances regarding SPKKPs.
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Affiliation(s)
- Shaonan Du
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Xiaolin Ren
- Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, China
| | - Xin Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Cui
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Shu Guan
- Department of Surgical Oncology and Breast Surgery, The First Hospital of China Medical University, Shenyang, China
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3
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Al Dera H. Cellular and molecular mechanisms underlying autism spectrum disorders and associated comorbidities: A pathophysiological review. Biomed Pharmacother 2022; 148:112688. [PMID: 35149383 DOI: 10.1016/j.biopha.2022.112688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/25/2022] [Accepted: 02/01/2022] [Indexed: 12/31/2022] Open
Abstract
Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders that develop in early life due to interaction between several genetic and environmental factors and lead to alterations in brain function and structure. During the last decades, several mechanisms have been placed to explain the pathogenesis of autism. Unfortunately, these are reported in several studies and reviews which make it difficult to follow by the reader. In addition, some recent molecular mechanisms related to ASD have been unrevealed. This paper revises and highlights the major common molecular mechanisms responsible for the clinical symptoms seen in people with ASD, including the roles of common genetic factors and disorders, neuroinflammation, GABAergic signaling, and alterations in Ca+2 signaling. Besides, it covers the major molecular mechanisms and signaling pathways involved in initiating the epileptic seizure, including the alterations in the GABAergic and glutamate signaling, vitamin and mineral deficiency, disorders of metabolism, and autoimmunity. Finally, this review also discusses sleep disorder patterns and the molecular mechanisms underlying them.
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Affiliation(s)
- Hussain Al Dera
- Department of Basic Medical Sciences, College of Medicine at King Saud, Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia.
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4
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You K, Wang L, Chou CH, Liu K, Nakata T, Jaiswal A, Yao J, Lefkovith A, Omar A, Perrigoue JG, Towne JE, Regev A, Graham DB, Xavier RJ. QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis. Science 2021; 371:371/6524/eabb6896. [PMID: 33384352 DOI: 10.1126/science.abb6896] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/17/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Tissue homeostasis is perturbed in a diversity of inflammatory pathologies. These changes can elicit endoplasmic reticulum (ER) stress, protein misfolding, and cell death. ER stress triggers the unfolded protein response (UPR), which can promote recovery of ER proteostasis and cell survival or trigger programmed cell death. Here, we leveraged single-cell RNA sequencing to define dynamic transcriptional states associated with the adaptive versus terminal UPR in the mouse intestinal epithelium. We integrated these transcriptional programs with genome-scale CRISPR screening to dissect the UPR pathway functionally. We identified QRICH1 as a key effector of the PERK-eIF2α axis of the UPR. QRICH1 controlled a transcriptional program associated with translation and secretory networks that were specifically up-regulated in inflammatory pathologies. Thus, QRICH1 dictates cell fate in response to pathological ER stress.
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Affiliation(s)
- Kwontae You
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lingfei Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Kai Liu
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Toru Nakata
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alok Jaiswal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Junmei Yao
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Abdifatah Omar
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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5
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Lin CZ, Qi BR, Hu JS, Huang XQ. A fetus with Kabuki syndrome 2 detected by chromosomal microarray analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:302-306. [PMID: 32211113 PMCID: PMC7061791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Kabuki syndrome is a rare multiple congenital anomaly syndrome characterized by distinct facial features, intellectual disability, cardiovascular and musculoskeletal abnormalities, persistence of fetal fingertip pads, and postnatal growth deficiency. Currently, the diagnosis mainly depends on clinical manifestations and genetic testing. To date, there is no report on the identification Kabuki syndrome in fetuses using chromosomal microarray analysis (CMA). CASE PRESENTATION A fetus was identified with growth retardation and cardiovascular abnormality on color Doppler ultrasonography; however, non-invasive prenatal testing (NIPT) revealed a low risk and G-banding karyotyping revealed no abnormal karyotype detected. CMA identified a 1.3 Mb deletion on the X chromosome (Xp11.3) containing KDM6A, DUSP21, MIR222, MIR221 and CXorf36 genes. The fetus was diagnosed with Kabuki syndrome 2, and labor was induced. In addition, CMA detected a 1.3 Mb deletion in the chromosome Xp11.3 in the mother, which contains 5 genes namely KDM6A, DUSP21, MIR222, MIR221 and CXorf36, while no chromosomal abnormality was identified in the father. CONCLUSIONS We report a fetus with Kabuki syndrome 2 detected using CMA. It is strongly recommended that CMA be included in prenatal diagnosis in fetuses with growth retardation, cardiovascular and musculoskeletal abnormalities revealed by routine Color Doppler ultrasonography.
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Affiliation(s)
- Chen-Zhao Lin
- Department of Obstetrics and Gynecology, Fuzhou Municipal First Hospital Affiliated to Fujian Medical UniversityFuzhou 350009, Fujian Province, The People’s Republic of China
| | - Bi-Ru Qi
- Department of Obstetrics and Gynecology, Fuzhou Municipal First Hospital Affiliated to Fujian Medical UniversityFuzhou 350009, Fujian Province, The People’s Republic of China
| | - Jian-Su Hu
- Department of Ultrasound, Fuzhou Municipal First Hospital Affiliated to Fujian Medical UniversityFuzhou 350009, Fujian Province, The People’s Republic of China
| | - Xiu-Qiong Huang
- Department of Laboratory Medicine, Fuzhou Municipal First Hospital Affiliated to Fujian Medical UniversityFuzhou 350009, Fujian Province, The People’s Republic of China
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6
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Kanduc D. The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity. Biol Chem 2019; 400:629-638. [PMID: 30504522 DOI: 10.1515/hsz-2018-0271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/07/2018] [Indexed: 11/15/2022]
Abstract
Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, I-70124 Bari, Italy
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7
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Tian X, Zheng P, Zhou C, Wang X, Ma H, Ma W, Zhou X, Teng J, Chen J. DIPK2A promotes STX17- and VAMP7-mediated autophagosome-lysosome fusion by binding to VAMP7B. Autophagy 2019; 16:797-810. [PMID: 31251111 DOI: 10.1080/15548627.2019.1637199] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Autophagosome and lysosome fusion is an important macroautophagy/autophagy process for cargo degradation, and SNARE proteins, including STX17, SNAP29, VAMP7 and VAMP8, are key players in this process. However, the manner in which this process is precisely regulated is poorly understood. Here, we show that VAMP7B, a SNARE domain-disrupted isoform of R-SNARE protein VAMP7, competes with SNARE domain functional isoform VAMP7A to bind to STX17 and inhibits autophagosome-lysosome fusion. Moreover, we show that DIPK2A, a late endosome- and lysosome-localized protein, binds to VAMP7B, which inhibits the interaction of VAMP7B with STX17 and enhances the binding of STX17 to VAMP7A, thus enhancing autophagosome-lysosome fusion. Furthermore, DIPK2A participates in autophagic degradation of mitochondria proteins and alleviates apoptosis. Thus, we reveal a new aspect of autophagosome-lysosome fusion in which different isoforms of VAMP7 compete with STX17 and their regulation by DIPK2A.Abbreviations: DIPK2A: divergent protein kinase domain 2A; EEA1: early endosome antigen 1; GOLGA2: golgin A2; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MFN2: mitofusin 2; MT-CO2: mitochondrially encoded cytochrome c oxidase II; PARP1: poly(ADP-ribose) polymerase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RAB5A: RAB5A, member RAS oncogene family; RAB7A: RAB7A, member RAS oncogene family; REEP: receptor accessory protein; RTN4: reticulon 4; SNARE: SNAP receptor; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TOMM20: translocase of outer mitochondrial membrane 20; VAMP7: vesicle associated membrane protein 7; VAMP8: vesicle associated membrane protein 8.
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Affiliation(s)
- Xiaoyu Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Pengli Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Chenqian Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Xurui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Hua Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Wei Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xiaokai Zhou
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
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8
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Park BC, Reese M, Tagliabracci VS. Thinking outside of the cell: Secreted protein kinases in bacteria, parasites, and mammals. IUBMB Life 2019; 71:749-759. [PMID: 30941842 DOI: 10.1002/iub.2040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 01/02/2023]
Abstract
Previous decades have seen an explosion in our understanding of protein kinase function in human health and disease. Hundreds of unique kinase structures have been solved, allowing us to create generalized rules for catalysis, assign roles of communities within the catalytic core, and develop specific drugs for targeting various pathways. Although our understanding of intracellular kinases has developed at a fast rate, our exploration into extracellular kinases has just begun. In this review, we will cover the secreted protein kinase families found in humans, bacteria, and parasites. © 2019 IUBMB Life, 71(6):749-759, 2019.
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Affiliation(s)
- Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Reese
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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9
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Hareza A, Bakun M, Świderska B, Dudkiewicz M, Koscielny A, Bajur A, Jaworski J, Dadlez M, Pawłowski K. Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58. PeerJ 2018; 6:e4599. [PMID: 29666759 PMCID: PMC5896498 DOI: 10.7717/peerj.4599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography–tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.
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Affiliation(s)
- Agnieszka Hareza
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Magda Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Bianka Świderska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Alicja Koscielny
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Anna Bajur
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland.,Current affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jacek Jaworski
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
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10
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Kuroda T, Mizutani Y. Response acquisition by zebrafish (Danio rerio) with delayed reinforcement. J Exp Anal Behav 2018; 109:520-532. [PMID: 29624678 DOI: 10.1002/jeab.324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/13/2018] [Indexed: 11/07/2022]
Abstract
Zebrafish (Danio rerio) is a common vertebrate animal model in biomedical research and is a promising species for studying how genes interact with environmental factors in determining behavior. The present study investigated how reinforcement parameters affect zebrafish behavior by assessing response acquisition with delayed reinforcement, which has been studied with other species (e.g., rats, pigeons, humans, etc.) but not with zebrafish. Twenty-four experimentally naïve subjects were exposed to a tandem fixed-ratio 1 differential-reinforcement-of-other-behavior x-s schedule of reinforcement, where x varied across subjects. There were six different delay-to-reinforcement durations and sets of four fish were assigned to each delay duration. All of the fish assigned to a 0-, 0.5-, or 1-s delay acquired responding. Two fish acquired responding with a 3-s delay and one fish appeared to have acquired it with a 6-s delay although the latter result was less clear. None acquired responding with a 12-s delay. These results suggest that zebrafish behavior is sensitive to delays to reinforcement and the time frame over which reinforcement is effective may be limited approximately to 6 s. This time frame is shorter than that found with other species. Practical and theoretical implications of the present finding are discussed.
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11
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Identification of Novel Hemangioblast Genes in the Early Chick Embryo. Cells 2018; 7:cells7020009. [PMID: 29385069 PMCID: PMC5850097 DOI: 10.3390/cells7020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/17/2018] [Accepted: 01/27/2018] [Indexed: 12/20/2022] Open
Abstract
During early vertebrate embryogenesis, both hematopoietic and endothelial lineages derive from a common progenitor known as the hemangioblast. Hemangioblasts derive from mesodermal cells that migrate from the posterior primitive streak into the extraembryonic yolk sac. In addition to primitive hematopoietic cells, recent evidence revealed that yolk sac hemangioblasts also give rise to tissue-resident macrophages and to definitive hematopoietic stem/progenitor cells. In our previous work, we used a novel hemangioblast-specific reporter to isolate the population of chick yolk sac hemangioblasts and characterize its gene expression profile using microarrays. Here we report the microarray profile analysis and the identification of upregulated genes not yet described in hemangioblasts. These include the solute carrier transporters SLC15A1 and SCL32A1, the cytoskeletal protein RhoGap6, the serine protease CTSG, the transmembrane receptor MRC1, the transcription factors LHX8, CITED4 and PITX1, and the previously uncharacterized gene DIA1R. Expression analysis by in situ hybridization showed that chick DIA1R is expressed not only in yolk sac hemangioblasts but also in particular intraembryonic populations of hemogenic endothelial cells, suggesting a potential role in the hemangioblast-derived hemogenic lineage. Future research into the function of these newly identified genes may reveal novel important regulators of hemangioblast development.
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12
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Zebrafish models of autism spectrum disorder. Exp Neurol 2018; 299:207-216. [DOI: 10.1016/j.expneurol.2017.02.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/23/2017] [Accepted: 02/01/2017] [Indexed: 11/19/2022]
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13
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HASF (C3orf58) is a novel ligand of the insulin-like growth factor 1 receptor. Biochem J 2017; 474:771-780. [PMID: 28096202 DOI: 10.1042/bcj20160976] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 11/17/2022]
Abstract
We have recently shown that hypoxia and Akt-induced stem cell factor (HASF) protects the heart from ischemia-induced damage and promotes cardiomyocyte proliferation. While we have identified certain signaling pathways responsible for these protective effects, the receptor mediating these effects was unknown. Here, we undertook studies to identify the HASF receptor. A yeast two-hybrid screen identified a partial fragment of insulin-like growth factor 1 receptor (IGF1R) as a binding partner of HASF. Subsequent co-immunoprecipitation experiments showed that HASF bound to full-length IGF1R. Binding assays revealed a high affinity of HASF for IGF1R. The treatment of neonatal ventricular cardiomyocytes with HASF resulted in the phosphorylation of IGF1R and other proteins known to be involved in IGF1R-mediated signaling pathways. HASF-mediated ERK activation was abrogated by IGF1R pharmacological inhibitors and siRNAs that targeted IGF1R. However, siRNA-mediated knockdown of either IGF2R or the insulin receptor had no effect on HASF-induced cell signaling. Additionally, pharmacologic inhibition of IGF1R impeded HASF's ability to induce cardiomyocyte proliferation. Finally, we documented that in vivo deletion of the IGF1R completely abolished the ability of HASF to promote cardiomyocyte proliferation in an overexpression mouse model providing further evidence in vivo that the IGF1R is the functional receptor for HASF.
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14
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Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen J, Xiao J, Cui J, Nguyen KB, Engel JL, Coon JJ, Grishin N, Pinna LA, Pagliarini DJ, Dixon JE. A Single Kinase Generates the Majority of the Secreted Phosphoproteome. Cell 2015; 161:1619-32. [PMID: 26091039 DOI: 10.1016/j.cell.2015.05.028] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/05/2015] [Accepted: 05/06/2015] [Indexed: 01/12/2023]
Abstract
The existence of extracellular phosphoproteins has been acknowledged for over a century. However, research in this area has been undeveloped largely because the kinases that phosphorylate secreted proteins have escaped identification. Fam20C is a kinase that phosphorylates S-x-E/pS motifs on proteins in milk and in the extracellular matrix of bones and teeth. Here, we show that Fam20C generates the majority of the extracellular phosphoproteome. Using CRISPR/Cas9 genome editing, mass spectrometry, and biochemistry, we identify more than 100 secreted phosphoproteins as genuine Fam20C substrates. Further, we show that Fam20C exhibits broader substrate specificity than previously appreciated. Functional annotations of Fam20C substrates suggest roles for the kinase beyond biomineralization, including lipid homeostasis, wound healing, and cell migration and adhesion. Our results establish Fam20C as the major secretory pathway protein kinase and serve as a foundation for new areas of investigation into the role of secreted protein phosphorylation in human biology and disease.
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Affiliation(s)
- Vincent S Tagliabracci
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sandra E Wiley
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiao Guo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lisa N Kinch
- Department of Biophysics, University of Texas, Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | - Eric Durrant
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jianzhong Wen
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Junyu Xiao
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jixin Cui
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kim B Nguyen
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - James L Engel
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nick Grishin
- Department of Biophysics, University of Texas, Southwestern Medical Center, Dallas, TX 75390-9050, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy; Venetian Institute of Molecular Medicine, 35129 Padova, Italy
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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15
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Namba T, Funahashi Y, Nakamuta S, Xu C, Takano T, Kaibuchi K. Extracellular and Intracellular Signaling for Neuronal Polarity. Physiol Rev 2015; 95:995-1024. [PMID: 26133936 DOI: 10.1152/physrev.00025.2014] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neurons are one of the highly polarized cells in the body. One of the fundamental issues in neuroscience is how neurons establish their polarity; therefore, this issue fascinates many scientists. Cultured neurons are useful tools for analyzing the mechanisms of neuronal polarization, and indeed, most of the molecules important in their polarization were identified using culture systems. However, we now know that the process of neuronal polarization in vivo differs in some respects from that in cultured neurons. One of the major differences is their surrounding microenvironment; neurons in vivo can be influenced by extrinsic factors from the microenvironment. Therefore, a major question remains: How are neurons polarized in vivo? Here, we begin by reviewing the process of neuronal polarization in culture conditions and in vivo. We also survey the molecular mechanisms underlying neuronal polarization. Finally, we introduce the theoretical basis of neuronal polarization and the possible involvement of neuronal polarity in disease and traumatic brain injury.
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Affiliation(s)
- Takashi Namba
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Funahashi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichi Nakamuta
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chundi Xu
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Takano
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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16
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Yavarna T, Al-Dewik N, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, Lakhani S, AlMulla M, Nawaz Z, Vitazka P, Alkuraya FS, Ben-Omran T. High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders. Hum Genet 2015; 134:967-80. [PMID: 26077850 DOI: 10.1007/s00439-015-1575-0] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 05/30/2015] [Indexed: 12/16/2022]
Abstract
Clinical exome sequencing (CES) has become an increasingly popular diagnostic tool in patients with heterogeneous genetic disorders, especially in those with neurocognitive phenotypes. Utility of CES in consanguineous populations has not yet been determined on a large scale. A clinical cohort of 149 probands from Qatar with suspected Mendelian, mainly neurocognitive phenotypes, underwent CES from July 2012 to June 2014. Intellectual disability and global developmental delay were the most common clinical presentations but our cohort displayed other phenotypes, such as epilepsy, dysmorphism, microcephaly and other structural brain anomalies and autism. A pathogenic or likely pathogenic mutation, including pathogenic CNVs, was identified in 89 probands for a diagnostic yield of 60%. Consanguinity and positive family history predicted a higher diagnostic yield. In 5% (7/149) of cases, CES implicated novel candidate disease genes (MANF, GJA9, GLG1, COL15A1, SLC35F5, MAGE4, NEUROG1). CES uncovered two coexisting genetic disorders in 4% (6/149) and actionable incidental findings in 2% (3/149) of cases. Average time to diagnosis was reduced from 27 to 5 months. CES, which already has the highest diagnostic yield among all available diagnostic tools in the setting of Mendelian disorders, appears to be particularly helpful diagnostically in the highly consanguineous Middle Eastern population.
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Affiliation(s)
- Tarunashree Yavarna
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, P.O.BOX. 3050, Doha, Qatar
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17
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Sreelatha A, Kinch LN, Tagliabracci VS. The secretory pathway kinases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1687-93. [PMID: 25862977 DOI: 10.1016/j.bbapap.2015.03.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 03/31/2015] [Indexed: 12/16/2022]
Abstract
Protein phosphorylation is a nearly universal post-translation modification involved in a plethora of cellular events. Even though phosphorylation of extracellular proteins had been observed, the identity of the kinases that phosphorylate secreted proteins remained a mystery until only recently. Advances in genome sequencing and genetic studies have paved the way for the discovery of a new class of kinases that localize within the endoplasmic reticulum, Golgi apparatus and the extracellular space. These novel kinases phosphorylate proteins and proteoglycans in the secretory pathway and appear to regulate various extracellular processes. Mutations in these kinases cause human disease, thus underscoring the biological importance of phosphorylation within the secretory pathway. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Anju Sreelatha
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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18
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Abstract
MOTIVATION Discovering the transcriptional regulatory architecture of the metabolism has been an important topic to understand the implications of transcriptional fluctuations on metabolism. The reporter algorithm (RA) was proposed to determine the hot spots in metabolic networks, around which transcriptional regulation is focused owing to a disease or a genetic perturbation. Using a z-score-based scoring scheme, RA calculates the average statistical change in the expression levels of genes that are neighbors to a target metabolite in the metabolic network. The RA approach has been used in numerous studies to analyze cellular responses to the downstream genetic changes. In this article, we propose a mutual information-based multivariate reporter algorithm (MIRA) with the goal of eliminating the following problems in detecting reporter metabolites: (i) conventional statistical methods suffer from small sample sizes, (ii) as z-score ranges from minus to plus infinity, calculating average scores can lead to canceling out opposite effects and (iii) analyzing genes one by one, then aggregating results can lead to information loss. MIRA is a multivariate and combinatorial algorithm that calculates the aggregate transcriptional response around a metabolite using mutual information. We show that MIRA's results are biologically sound, empirically significant and more reliable than RA. RESULTS We apply MIRA to gene expression analysis of six knockout strains of Escherichia coli and show that MIRA captures the underlying metabolic dynamics of the switch from aerobic to anaerobic respiration. We also apply MIRA to an Autism Spectrum Disorder gene expression dataset. Results indicate that MIRA reports metabolites that highly overlap with recently found metabolic biomarkers in the autism literature. Overall, MIRA is a promising algorithm for detecting metabolic drug targets and understanding the relation between gene expression and metabolic activity. AVAILABILITY AND IMPLEMENTATION The code is implemented in C# language using .NET framework. Project is available upon request.
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Affiliation(s)
- A Ercument Cicek
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA 15213 and Department of Electrical Engineering and Computer Science, School of Engineering, Case Western Reserve University, Cleveland, OH, USA 44106
| | - Kathryn Roeder
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA 15213 and Department of Electrical Engineering and Computer Science, School of Engineering, Case Western Reserve University, Cleveland, OH, USA 44106
| | - Gultekin Ozsoyoglu
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA 15213 and Department of Electrical Engineering and Computer Science, School of Engineering, Case Western Reserve University, Cleveland, OH, USA 44106
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19
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Hotz A, Hellenbroich Y, Sperner J, Linder-Lucht M, Tacke U, Walter C, Caliebe A, Nagel I, Saunders DE, Wolff G, Martin P, Morris-Rosendahl DJ. Microdeletion 5q14.3 and anomalies of brain development. Am J Med Genet A 2013; 161A:2124-33. [DOI: 10.1002/ajmg.a.36020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/31/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Alrun Hotz
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | | | | | - Michaela Linder-Lucht
- Zentrum für Kinder- und Jugendmedizin; Albert-Ludwigs-Universitätsklinikum Freiburg; Freiburg Germany
| | - Uta Tacke
- Zentrum für Kinder- und Jugendmedizin; Albert-Ludwigs-Universitätsklinikum Freiburg; Freiburg Germany
| | - Caren Walter
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | - Almuth Caliebe
- Institut für Humangenetik; Christian-Albrechts-Universität Kiel; Kiel Germany
| | - Inga Nagel
- Institut für Humangenetik; Christian-Albrechts-Universität Kiel; Kiel Germany
| | - Dawn E. Saunders
- Department of Radiology; Great Ormond Street Hospital; London United Kingdom
| | - Gerhard Wolff
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | - Peter Martin
- Séguin Klinik; Epilepsiezentrum Kehl-Kork; Kork Germany
| | - Deborah J. Morris-Rosendahl
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
- National Heart and Lung Institute; Imperial College, London; London United Kingdom
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20
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A novel predicted calcium-regulated kinase family implicated in neurological disorders. PLoS One 2013; 8:e66427. [PMID: 23840464 PMCID: PMC3696010 DOI: 10.1371/journal.pone.0066427] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/08/2013] [Indexed: 12/03/2022] Open
Abstract
The catalogues of protein kinases, the essential effectors of cellular signaling, have been charted in Metazoan genomes for a decade now. Yet, surprisingly, using bioinformatics tools, we predicted protein kinase structure for proteins coded by five related human genes and their Metazoan homologues, the FAM69 family. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases present in four out of five human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they may function as Ca2+-dependent kinases. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 (DIA1) and CXORF36 (DIA1R), are by large uncharacterised molecularly, yet linked to several neurological disorders in genetics studies. The C3ORF58 gene is found deleted in autism, and resides in the Golgi. Unusually high cysteine content and presence of signal peptides in some of the family members suggest that FAM69 proteins may be involved in phosphorylation of proteins in the secretory pathway and/or of extracellular proteins.
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21
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Aziz A, Harrop SP, Bishop NE. DIA1R is an X-linked gene related to Deleted In Autism-1. PLoS One 2011; 6:e14534. [PMID: 21264219 PMCID: PMC3022024 DOI: 10.1371/journal.pone.0014534] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 12/21/2010] [Indexed: 01/28/2023] Open
Abstract
Background Autism spectrum disorders (ASDs) are frequently occurring disorders diagnosed by deficits in three core functional areas: social skills, communication, and behaviours and/or interests. Mental retardation frequently accompanies the most severe forms of ASDs, while overall ASDs are more commonly diagnosed in males. Most ASDs have a genetic origin and one gene recently implicated in the etiology of autism is the Deleted-In-Autism-1 (DIA1) gene. Methodology/Principal Findings Using a bioinformatics-based approach, we have identified a human gene closely related to DIA1, we term DIA1R (DIA1-Related). While DIA1 is autosomal (chromosome 3, position 3q24), DIA1R localizes to the X chromosome at position Xp11.3 and is known to escape X-inactivation. The gene products are of similar size, with DIA1 encoding 430, and DIA1R 433, residues. At the amino acid level, DIA1 and DIA1R are 62% similar overall (28% identical), and both encode signal peptides for targeting to the secretory pathway. Both genes are ubiquitously expressed, including in fetal and adult brain tissue. Conclusions/Significance Examination of published literature revealed point mutations in DIA1R are associated with X-linked mental retardation (XLMR) and DIA1R deletion is associated with syndromes with ASD-like traits and/or XLMR. Together, these results support a model where the DIA1 and DIA1R gene products regulate molecular traffic through the cellular secretory pathway or affect the function of secreted factors, and functional deficits cause disorders with ASD-like symptoms and/or mental retardation.
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Affiliation(s)
- Azhari Aziz
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Sean P. Harrop
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Naomi E. Bishop
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
- * E-mail:
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