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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Shekhar S, Moehlman AT, Park B, Ewnetu M, Tracy C, Titos I, Pawłowski K, Tagliabracci VS, Krämer H. Allnighter pseudokinase-mediated feedback links proteostasis and sleep in Drosophila. Nat Commun 2023; 14:2932. [PMID: 37217484 DOI: 10.1038/s41467-023-38485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
In nervous systems, retrograde signals are key for organizing circuit activity and maintaining neuronal homeostasis. We identify the conserved Allnighter (Aln) pseudokinase as a cell non-autonomous regulator of proteostasis responses necessary for normal sleep and structural plasticity of Drosophila photoreceptors. In aln mutants exposed to extended ambient light, proteostasis is dysregulated and photoreceptors develop striking, but reversible, dysmorphology. The aln gene is widely expressed in different neurons, but not photoreceptors. However, secreted Aln protein is retrogradely endocytosed by photoreceptors. Inhibition of photoreceptor synaptic release reduces Aln levels in lamina neurons, consistent with secreted Aln acting in a feedback loop. In addition, aln mutants exhibit reduced night time sleep, providing a molecular link between dysregulated proteostasis and sleep, two characteristics of ageing and neurodegenerative diseases.
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Affiliation(s)
- Shashank Shekhar
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
| | - Andrew T Moehlman
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Brenden Park
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
| | - Michael Ewnetu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Charles Tracy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Iris Titos
- Molecular Medicine Program, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Maryland, USA
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
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3
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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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4
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Görtler F, Schön M, Simeth J, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M. Loss-Function Learning for Digital Tissue Deconvolution. J Comput Biol 2020; 27:342-355. [DOI: 10.1089/cmb.2019.0462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Franziska Görtler
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Marian Schön
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Jakob Simeth
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Stefan Solbrig
- Department of Physics, University of Regensburg, Regensburg, Germany
| | - Tilo Wettig
- Department of Physics, University of Regensburg, Regensburg, Germany
| | - Peter J. Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Michael Altenbuchinger
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
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5
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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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6
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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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7
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The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases. Biochem Soc Trans 2017; 45:665-681. [PMID: 28620028 DOI: 10.1042/bst20160331] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/31/2022]
Abstract
Over the past decade, our understanding of the mechanisms by which pseudokinases, which comprise ∼10% of the human and mouse kinomes, mediate signal transduction has advanced rapidly with increasing structural, biochemical, cellular and genetic studies. Pseudokinases are the catalytically defective counterparts of conventional, active protein kinases and have been attributed functions as protein interaction domains acting variously as allosteric modulators of conventional protein kinases and other enzymes, as regulators of protein trafficking or localisation, as hubs to nucleate assembly of signalling complexes, and as transmembrane effectors of such functions. Here, by categorising mammalian pseudokinases based on their known functions, we illustrate the mechanistic diversity among these proteins, which can be viewed as a window into understanding the non-catalytic functions that can be exerted by conventional protein kinases.
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8
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Bennett TM, Zhou Y, Shiels A. Lens transcriptome profile during cataract development in Mip-null mice. Biochem Biophys Res Commun 2016; 478:988-93. [PMID: 27524245 DOI: 10.1016/j.bbrc.2016.08.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/10/2016] [Indexed: 01/08/2023]
Abstract
Major intrinsic protein or aquaporin-0 (MIP/AQP0) functions as a water channel and a cell-junction molecule in the vertebrate eye lens. Loss of MIP function in the lens leads to degraded optical quality and cataract formation by pathogenic mechanisms that are unclear. Here we have used microarray-hybridization analysis to detect lens transcriptome changes during cataract formation in mice that are functionally null for MIP (Mip-/-). In newborn Mip-/- lenses (P1) 11 genes were up-regulated and 18 were down-regulated (>2-fold, p=<0.05) and a similar number of genes was differentially regulated at P7. The most up-regulated genes (>6-fold) in the Mip-/- lens at P1 included those coding for a mitochondrial translocase (Timmdc1), a matrix metallopeptidase (Mmp2), a Rho GTPase-interacting protein (Ubxn11) and a transcription factor (Twist2). Apart from Mip, the most down-regulated genes (>4-fold) in the Mip-/- lens at P1 included those coding for a proteasome sub-unit (Psmd8), a ribonuclease (Pop4), and a heat-shock protein (Hspb1). Lens fiber cell degeneration in the Mip-/- lens was associated with increased numbers of TUNEL-positive cell nuclei and dramatically elevated levels of calpain-mediated proteolysis of αII-spectrin. However red-ox status, measured by glutathione and free-radical levels, was similar to that of wild-type. These data suggest that while relatively few genes (∼1.5% of the transcriptome) were differentially regulated >2-fold in the Mip-/- lens, calpain hyper-activation acts as a terminal pathogenic event during lens fiber cell death and cataract formation.
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Affiliation(s)
- Thomas M Bennett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuefang Zhou
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.
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9
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Ozantürk A, Davis EE, Sabo A, Weiss MM, Muzny D, Dugan-Perez S, Sistermans EA, Gibbs RA, Özgül KR, Yalnızoglu D, Serdaroglu E, Dursun A, Katsanis N. A t(5;16) translocation is the likely driver of a syndrome with ambiguous genitalia, facial dysmorphism, intellectual disability, and speech delay. Cold Spring Harb Mol Case Stud 2016; 2:a000703. [PMID: 27148584 PMCID: PMC4849851 DOI: 10.1101/mcs.a000703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genetic studies grounded on monogenic paradigms have accelerated both gene discovery and molecular diagnosis. At the same time, complex genomic rearrangements are also appreciated as potent drivers of disease pathology. Here, we report two male siblings with a dysmorphic face, ambiguous genitalia, intellectual disability, and speech delay. Through quad-based whole-exome sequencing and concomitant molecular cytogenetic testing, we identified two copy-number variants (CNVs) in both affected individuals likely arising from a balanced translocation: a 13.5-Mb duplication on Chromosome 16 (16q23.1 → 16qter) and a 7.7-Mb deletion on Chromosome 5 (5p15.31 → 5pter), as well as a hemizygous missense variant in CXorf36 (also known as DIA1R). The 5p terminal deletion has been associated previously with speech delay, whereas craniofacial dysmorphia and genital/urinary anomalies have been reported in patients with a terminal duplication of 16q. However, dosage changes in either genomic region alone could not account for the overall clinical presentation in our family; functional testing of CXorf36 in zebrafish did not induce defects in neurogenesis or the craniofacial skeleton. Notably, literature and database analysis revealed a similar dosage disruption in two siblings with extensive phenotypic overlap with our patients. Taken together, our data suggest that dosage perturbation of genes within the two chromosomal regions likely drives the syndromic manifestations of our patients and highlight how multiple genetic lesions can contribute to complex clinical pathologies.
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Affiliation(s)
- Ayşegül Ozantürk
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey;; Department of Biology, Molecular Biology Section, Hacettepe University, Ankara 06800, Turkey;; Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center (Amsterdam), NL-1081 HV Amsterdam, The Netherlands
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center (Amsterdam), NL-1081 HV Amsterdam, The Netherlands
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Köksal R Özgül
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey
| | - Dilek Yalnızoglu
- Department of Pediatrics, Pediatric Neurology Unit, Hacettepe University, Ankara 06410, Turkey
| | - Esra Serdaroglu
- Department of Pediatrics, Pediatric Neurology Unit, Hacettepe University, Ankara 06410, Turkey
| | - Ali Dursun
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
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10
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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: 236] [Impact Index Per Article: 26.2] [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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11
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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: 147] [Impact Index Per Article: 16.3] [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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12
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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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13
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Schaafsma SM, Pfaff DW. Etiologies underlying sex differences in Autism Spectrum Disorders. Front Neuroendocrinol 2014; 35:255-71. [PMID: 24705124 DOI: 10.1016/j.yfrne.2014.03.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/06/2014] [Accepted: 03/17/2014] [Indexed: 01/09/2023]
Abstract
The male predominance of Autism Spectrum Disorders (ASD) is one of the best-known, and at the same time, one of the least understood characteristics of these disorders. In this paper we review genetic, epigenetic, hormonal, and environmental mechanisms underlying this male preponderance. Sex-specific effects of Y-linked genes (including SRY expression leading to testicular development), balanced and skewed X-inactivation, genes that escape X-inactivation, parent-of-origin allelic imprinting, and the hypothetical heterochromatin sink are reviewed. These mechanisms likely contribute to etiology, instead of being simply causative to ASD. Environments, both internal and external, also play important roles in ASD's etiology. Early exposure to androgenic hormones and early maternal immune activation comprise environmental factors affecting sex-specific susceptibility to ASD. The gene-environment interactions underlying ASD, suggested here, implicate early prenatal stress as being especially detrimental to boys with a vulnerable genotype.
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Affiliation(s)
- Sara M Schaafsma
- Laboratory of Neurobiology and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Donald W Pfaff
- Laboratory of Neurobiology and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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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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15
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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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16
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Spooren W, Lindemann L, Ghosh A, Santarelli L. Synapse dysfunction in autism: a molecular medicine approach to drug discovery in neurodevelopmental disorders. Trends Pharmacol Sci 2012; 33:669-84. [PMID: 23084458 DOI: 10.1016/j.tips.2012.09.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/04/2012] [Accepted: 09/14/2012] [Indexed: 11/24/2022]
Abstract
Autism and autism spectrum disorders (ASDs) affect millions of individuals worldwide. Despite increased autism diagnoses over the past 30 years, therapeutic intervention is often 'trial and error'. This approach has identified some beneficial agents, but complex heterogeneous disorders require a more personalized treatment regimen. Many ASD risk factors are genetic, implicating impaired synaptic development and function. Monogenetic disorders (e.g., fragile X syndrome, Rett syndrome, and neurofibromatosis) that have phenotypic overlap with autism provide insights into ASD pathology through the identification novel drug targets (e.g., glutamatergic receptors). Encouragingly, some of these novel drug targets provide symptomatic improvement, even in patients who have lived with ASDs for protracted periods of time. Consequently, a targeted drug discovery approach is expected to deliver improved agents for the treatment and management of ASDs. Here, we review the opportunities and challenges in drug development for autism and provide insight into the neurobiology of ASDs.
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Affiliation(s)
- Will Spooren
- CNS Research and Early Clinical Development, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
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17
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Lederer D, Grisart B, Digilio MC, Benoit V, Crespin M, Ghariani SC, Maystadt I, Dallapiccola B, Verellen-Dumoulin C. Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. Am J Hum Genet 2012; 90:119-24. [PMID: 22197486 DOI: 10.1016/j.ajhg.2011.11.021] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/13/2011] [Accepted: 11/21/2011] [Indexed: 12/23/2022] Open
Abstract
Kabuki syndrome (KS) is a rare genetic disease that causes developmental delay and congenital anomalies. Since the identification of MLL2 mutations as the primary cause of KS, such mutations have been identified in 56%-76% of affected individuals, suggesting that there may be additional genes associated with KS. Here, we describe three KS individuals with de novo partial or complete deletions of an X chromosome gene, KDM6A, that encodes a histone demethylase that interacts with MLL2. Although KDM6A escapes X inactivation, we found a skewed X inactivation pattern, in which the deleted X chromosome was inactivated in the majority of the cells. This study identifies KDM6A mutations as another cause of KS and highlights the growing role of histone methylases and histone demethylases in multiple-congenital-anomaly and intellectual-disability syndromes.
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Affiliation(s)
- Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium.
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Characterization of the deleted in autism 1 protein family: implications for studying cognitive disorders. PLoS One 2011; 6:e14547. [PMID: 21283809 PMCID: PMC3023760 DOI: 10.1371/journal.pone.0014547] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/21/2010] [Indexed: 12/21/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a group of commonly occurring, highly-heritable developmental disabilities. Human genes c3orf58 or Deleted In Autism-1 (DIA1) and cXorf36 or Deleted in Autism-1 Related (DIA1R) are implicated in ASD and mental retardation. Both gene products encode signal peptides for targeting to the secretory pathway. As evolutionary medicine has emerged as a key tool for understanding increasing numbers of human diseases, we have used an evolutionary approach to study DIA1 and DIA1R. We found DIA1 conserved from cnidarians to humans, indicating DIA1 evolution coincided with the development of the first primitive synapses. Nematodes lack a DIA1 homologue, indicating Caenorhabditis elegans is not suitable for studying all aspects of ASD etiology, while zebrafish encode two DIA1 paralogues. By contrast to DIA1, DIA1R was found exclusively in vertebrates, with an origin coinciding with the whole-genome duplication events occurring early in the vertebrate lineage, and the evolution of the more complex vertebrate nervous system. Strikingly, DIA1R was present in schooling fish but absent in fish that have adopted a more solitary lifestyle. An additional DIA1-related gene we named DIA1-Like (DIA1L), lacks a signal peptide and is restricted to the genomes of the echinoderm Strongylocentrotus purpuratus and cephalochordate Branchiostoma floridae. Evidence for remarkable DIA1L gene expansion was found in B. floridae. Amino acid alignments of DIA1 family gene products revealed a potential Golgi-retention motif and a number of conserved motifs with unknown function. Furthermore, a glycine and three cysteine residues were absolutely conserved in all DIA1-family proteins, indicating a critical role in protein structure and/or function. We have therefore identified a new metazoan protein family, the DIA1-family, and understanding the biological roles of DIA1-family members will have implications for our understanding of autism and mental retardation.
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