Zebrafish As a Model to Understand the Impact of Inactivity And
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Key Pathways Involved in Prostate Cancer Based on Gene Set Enrichment Analysis and Meta Analysis
Key pathways involved in prostate cancer based on gene set enrichment analysis and meta analysis Q.Y. Ning1, J.Z. Wu1, N. Zang2, J. Liang3, Y.L. Hu2 and Z.N. Mo4 1Department of Infection, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China 2The Medical Scientific Research Centre, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China 3Department of Biology Technology, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region, China 4Department of Urology, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China Corresponding authors: Y.L. Hu / Z.N. Mo E-mail: [email protected] / [email protected] Genet. Mol. Res. 10 (4): 3856-3887 (2011) Received June 7, 2011 Accepted October 14, 2011 Published December 14, 2011 DOI http://dx.doi.org/10.4238/2011.December.14.10 ABSTRACT. Prostate cancer is one of the most common male malignant neoplasms; however, its causes are not completely understood. A few recent studies have used gene expression profiling of prostate cancer to identify differentially expressed genes and possible relevant pathways. However, few studies have examined the genetic mechanics of prostate cancer at the pathway level to search for such pathways. We used gene set enrichment analysis and a meta-analysis of six independent studies after standardized microarray preprocessing, which increased concordance between these gene datasets. Based on gene set enrichment analysis, there were 12 down- and 25 up-regulated mixing pathways in more than two tissue datasets, while there were two down- and two up-regulated mixing pathways in three cell datasets. -
Identification of an FHL1 Protein Complex Containing Gamma-Actin and Non-Muscle Myosin IIB by Analysis of Protein-Protein Interactions
Identification of an FHL1 Protein Complex Containing Gamma-Actin and Non-Muscle Myosin IIB by Analysis of Protein-Protein Interactions Lili Wang1*, Jianing Miao1, Lianyong Li2,DiWu1, Yi Zhang1, Zhaohong Peng1, Lijun Zhang2, Zhengwei Yuan1, Kailai Sun3 1 Key Laboratory of Health ~Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China, 2 Department of Pediatric Surgery, Shengjing Hospital, China Medical University, Shenyang, China, 3 Department of Medical Genetics, China Medical University, Shenyang, China Abstract FHL1 is multifunctional and serves as a modular protein binding interface to mediate protein-protein interactions. In skeletal muscle, FHL1 is involved in sarcomere assembly, differentiation, growth, and biomechanical stress. Muscle abnormalities may play a major role in congenital clubfoot (CCF) deformity during fetal development. Thus, identifying the interactions of FHL1 could provide important new insights into its functional role in both skeletal muscle development and CCF pathogenesis. Using proteins derived from rat L6GNR4 myoblastocytes, we detected FHL1 interacting proteins by immunoprecipitation. Samples were analyzed by liquid chromatography mass spectrometry (LC-MS). Dynamic gene expression of FHL1 was studied. Additionally, the expression of the possible interacting proteins gamma-actin and non- muscle myosin IIB, which were isolated from the lower limbs of E14, E15, E17, E18, E20 rat embryos or from adult skeletal muscle was analyzed. Potential interacting proteins isolated from E17 lower limbs were verified by immunoprecipitation, and co-localization in adult gastrocnemius muscle was visualized by fluorescence microscopy. FHL1 expression was associated with skeletal muscle differentiation. E17 was found to be the critical time-point for skeletal muscle differentiation in the lower limbs of rat embryos. -
Removal of Abnormal Myofilament O-Glcnacylation Restores Ca
Diabetes Volume 64, October 2015 3573 Genaro A. Ramirez-Correa,1 Junfeng Ma,2 Chad Slawson,3 Quira Zeidan,2 Nahyr S. Lugo-Fagundo,1 Mingguo Xu,1 Xiaoxu Shen,4 Wei Dong Gao,4 Viviane Caceres,5 Khalid Chakir,5 Lauren DeVine,2 Robert N. Cole,2 Luigi Marchionni,6 Nazareno Paolocci,5 Gerald W. Hart,2 and Anne M. Murphy1 Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle Diabetes 2015;64:3573–3587 | DOI: 10.2337/db14-1107 Contractile dysfunction and increased deposition of In diabetic cardiomyopathy, the contractile and electro- O-linked b-N-acetyl-D-glucosamine (O-GlcNAc) in car- physiological properties of the cardiac muscle are altered diac proteins are a hallmark of the diabetic heart. How- (1). Prior studies have mainly focused on alterations in ever, whether and how this posttranslational alteration Ca2+ handling (2–4). However, these perturbations alone contributes to lower cardiac function remains unclear. unlikely account for lower force production and altered COMPLICATIONS fi b Using a re ned -elimination/Michael addition with tan- relaxation typically found in the heart of patients with dem mass tags (TMT)–labeling proteomic technique, we diabetes (5,6). Indeed, the intrinsic properties of cardiac show that CpOGA, a bacterial analog of O-GlcNAcase myofilaments appear to be altered too (7,8). More specif- (OGA) that cleaves O-GlcNAc in vivo, removes site- 2+ 2+ fi specific O-GlcNAcylation from myofilaments, restoring ically, Ca sensitivity (ECa 50), a measure of myo la- 2+ Ca2+ sensitivity in streptozotocin (STZ) diabetic cardiac ment force production at near physiological Ca levels, – muscles. -
Profiling of the Muscle-Specific Dystroglycan Interactome Reveals the Role of Hippo Signaling in Muscular Dystrophy and Age-Dependent Muscle Atrophy Andriy S
Yatsenko et al. BMC Medicine (2020) 18:8 https://doi.org/10.1186/s12916-019-1478-3 RESEARCH ARTICLE Open Access Profiling of the muscle-specific dystroglycan interactome reveals the role of Hippo signaling in muscular dystrophy and age-dependent muscle atrophy Andriy S. Yatsenko1†, Mariya M. Kucherenko2,3,4†, Yuanbin Xie2,5†, Dina Aweida6, Henning Urlaub7,8, Renate J. Scheibe1, Shenhav Cohen6 and Halyna R. Shcherbata1,2* Abstract Background: Dystroglycanopathies are a group of inherited disorders characterized by vast clinical and genetic heterogeneity and caused by abnormal functioning of the ECM receptor dystroglycan (Dg). Remarkably, among many cases of diagnosed dystroglycanopathies, only a small fraction can be linked directly to mutations in Dg or its regulatory enzymes, implying the involvement of other, not-yet-characterized, Dg-regulating factors. To advance disease diagnostics and develop new treatment strategies, new approaches to find dystroglycanopathy-related factors should be considered. The Dg complex is highly evolutionarily conserved; therefore, model genetic organisms provide excellent systems to address this challenge. In particular, Drosophila is amenable to experiments not feasible in any other system, allowing original insights about the functional interactors of the Dg complex. Methods: To identify new players contributing to dystroglycanopathies, we used Drosophila as a genetic muscular dystrophy model. Using mass spectrometry, we searched for muscle-specific Dg interactors. Next, in silico analyses allowed us to determine their association with diseases and pathological conditions in humans. Using immunohistochemical, biochemical, and genetic interaction approaches followed by the detailed analysis of the muscle tissue architecture, we verified Dg interaction with some of the discovered factors. -
CANDIDATE GENES in the FIELD of EXERCISE GENOMICS Abstract
EXERCISE AND QUALITY OF LIFE Review article Volume 3, No. 1, 2011, 23-29 575.113:612.74 UDC CANDIDATE GENES IN THE FIELD OF EXERCISE GENOMICS ã Vladimir Gali Department of Physiology Medical faculty Novi Sad Abstract Skeletal muscle is extremely adaptable to various stresses which can be placed upon it. In spite of importance of skeletal muscles, little is known about genetic factors which demonstrate high influence to muscle size, function, strength and adaptation to various environmental factors. Because endurance performance is a multifactorial trait, the list of candidate genes which could account for human variation in related phenotypes is extensive. One of the first characterized and most frequently studied genetic variant is a polymorphism in the angiotensin converting enzyme I gene. The ACTN3 gene is the first structural skeletal muscle gene with a relation between its ’ performance. N genotype and elite sprinter evertheless, current genetic testing cannot provide an extra advantage over existing testing methods in determining sports selection in young athletes. The main challenge still remains to identify other, complex polygenetic variants and their interactions with environmental factors which could provide benefit in the sports selection and existing talent identification. Keywords: exercise genomics, genetic polymorphism, muscle tissue Introduction Muscle tissue constitutes approximately 30% of body mass, it is metabolically very active with high turnover of energy and is capable of efficient response to different environmental stimuli. Skeletal muscle is extremely adaptable to various stresses which can be placed upon it. These adaptations can be either positive, such as tissue growth, extreme athletic performance or reparation of an injury, or negative, such as decline in mass and function over the ’s years of disuse or disease. -
Hypertrophic Cardiomyopathy- Associated Mutations in Genes That Encode Calcium-Handling Proteins
Current Molecular Medicine 2012, 12, 507-518 507 Beyond the Cardiac Myofilament: Hypertrophic Cardiomyopathy- Associated Mutations in Genes that Encode Calcium-Handling Proteins A.P. Landstrom and M.J. Ackerman* Departments of Medicine, Pediatrics, and Molecular Pharmacology & Experimental Therapeutics, Divisions of Cardiovascular Diseases and Pediatric Cardiology, and the Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota, USA Abstract: Traditionally regarded as a genetic disease of the cardiac sarcomere, hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disease and a significant cause of sudden cardiac death. While the most common etiologies of this phenotypically diverse disease lie in a handful of genes encoding critical contractile myofilament proteins, approximately 50% of patients diagnosed with HCM worldwide do not host sarcomeric gene mutations. Recently, mutations in genes encoding calcium-sensitive and calcium- handling proteins have been implicated in the pathogenesis of HCM. Among these are mutations in TNNC1- encoded cardiac troponin C, PLN-encoded phospholamban, and JPH2-encoded junctophilin 2 which have each been associated with HCM in multiple studies. In addition, mutations in RYR2-encoded ryanodine receptor 2, CASQ2-encoded calsequestrin 2, CALR3-encoded calreticulin 3, and SRI-encoded sorcin have been associated with HCM, although more studies are required to validate initial findings. While a relatively uncommon cause of HCM, mutations in genes that encode calcium-handling proteins represent an emerging genetic subset of HCM. Furthermore, these naturally occurring disease-associated mutations have provided useful molecular tools for uncovering novel mechanisms of disease pathogenesis, increasing our understanding of basic cardiac physiology, and dissecting important structure-function relationships within these proteins. -
Myofilament Dynamics Modulate Cellular Drivers of Arrhythmogenesis in Human Cardiac Disease
MYOFILAMENT DYNAMICS MODULATE CELLULAR DRIVERS OF ARRHYTHMOGENESIS IN HUMAN CARDIAC DISEASE by Melanie Anne Zile A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland October, 2017 © Melanie Anne Zile 2017 All rights reserved Abstract Cardiac arrhythmia is common in cardiac disease, but our understanding of the cellular mechanisms underlying arrhythmia is incomplete. Alternans, the beat-to-beat alteration in cardiac electrical or mechanical signals, has been linked to susceptibility to lethal arrhythmias in human heart failure (HF) as well as in human chronic atrial fibrillation (cAF). In addition, early afterdepolarizations (EADs), a type of aberrant cellular behavior that causes spontaneous slowing or reversal of normal repolarization, have been implicated as an arrhythmogenic trigger in human hypertrophic cardiomyopathy (HCM). Abnormal myofilament dynamics has been observed in human HF, HCM, and cAF, but whether this aberrant behavior alters the formation of alternans or EADs remains unknown. To address this gap in understanding, a computational modeling approach was taken. Three mechanistically-based bidirectionally coupled human electromechanical myocyte models were constructed, under the conditions of HF, HCM, or cAF. Our goal was to elucidate whether aberrant myofilament dynamics modulate the cellular drivers of arrhythmogenesis in human cardiac disease. In simulations with our human HF ventricular myocyte model, we found that the magnitudes of force, calcium, and action potential voltage alternans were modulated by heart failure induced-remodeling of mechanical parameters and sarcomere length due to the presence of myofilament feedback (MEF) at clinically-relevant pacing rates. In simulations with our human HCM ventricular myocyte model, we found that incorporating MEF diminished the degree of repolarization reserve reduction necessary for EADs to emerge and increased the frequency of EAD occurrence, especially at faster pacing rates. -
Transcriptional Adaptation in Caenorhabditis Elegans
RESEARCH ARTICLE Transcriptional adaptation in Caenorhabditis elegans Vahan Serobyan1*, Zacharias Kontarakis1†, Mohamed A El-Brolosy1, Jordan M Welker1, Oleg Tolstenkov2,3‡, Amr M Saadeldein1, Nicholas Retzer1, Alexander Gottschalk2,3,4, Ann M Wehman5, Didier YR Stainier1* 1Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; 2Institute for Biophysical Chemistry, Goethe University, Frankfurt Am Main, Germany; 3Cluster of Excellence Frankfurt - Macromolecular Complexes (CEF-MC), Goethe University, Frankfurt Am Main, Germany; 4Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt Am Main, Germany; 5Rudolf Virchow Center, University of Wu¨ rzburg, Wu¨ rzburg, Germany Abstract Transcriptional adaptation is a recently described phenomenon by which a mutation in *For correspondence: one gene leads to the transcriptional modulation of related genes, termed adapting genes. At the [email protected] molecular level, it has been proposed that the mutant mRNA, rather than the loss of protein (VS); function, activates this response. While several examples of transcriptional adaptation have been [email protected] (DYRS) reported in zebrafish embryos and in mouse cell lines, it is not known whether this phenomenon is observed across metazoans. Here we report transcriptional adaptation in C. elegans, and find that † Present address: Genome this process requires factors involved in mutant mRNA decay, as in zebrafish and mouse. We Engineering and Measurement further uncover a requirement for Argonaute proteins and Dicer, factors involved in small RNA Lab, ETH Zurich, Functional maturation and transport into the nucleus. Altogether, these results provide evidence for Genomics Center Zurich of ETH transcriptional adaptation in C. -
Inhibition of a New Differentiation Pathway in Neuroblastoma by Copy Number Defects of N-Myc, Cdc42, and Nm23 Genes
Research Article Inhibition of a New Differentiation Pathway in Neuroblastoma by Copy Number Defects of N-myc, Cdc42, and nm23 Genes Linda J. Valentijn, Arjen Koppen, Ronald van Asperen, Heather A. Root, Franciska Haneveld, and Rogier Versteeg Department of Human Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands Abstract are of variable length as well, but can be smaller with a more The best studied oncogenic mechanisms are inactivating telomeric SRO (3, 4). The different SROs in N-myc-amplified defects in both alleles of tumor suppressor genes and neuroblastomas have raised the idea that more than one tumor suppressor gene maps on distal chromosome 1p (5). activating mutations in oncogenes. Chromosomal gains and losses are frequent in human tumors, but for many regions, N-myc-amplified neuroblastomas follow a very aggressive course like 1p36 and 17q in neuroblastoma, no mutated tumor (6). Overexpression of transfected N-myc genes in neuroblastoma suppressor genes or oncogenes were identified. Amplification cell lines strongly increased proliferation rates (7, 8). Recent mRNA of N-myc in neuroblastoma is strongly correlated with loss of expression profiling experiments, serial analysis of gene expression 1p36 and gain of 17q. Here we report that N-myc down- (SAGE) and microarray analysis, identified many myc-regulated regulates the mRNA expression of many genes with a role in genes (9–13). We used SAGE to identify genes regulated by N-myc cell architecture. One of them is the 1p36 gene Cdc42. in neuroblastoma. Genes up-regulated by N-myc were involved in Restoring the Cdc42 expression in neuroblastoma cells rRNA processing and protein synthesis (9). -
Neuronal Dystroglycan Is Necessary for Formation and Maintenance of Functional CCK-Positive Basket Cell Terminals on Pyramidal Cells
10296 • The Journal of Neuroscience, October 5, 2016 • 36(40):10296–10313 Cellular/Molecular Neuronal Dystroglycan Is Necessary for Formation and Maintenance of Functional CCK-Positive Basket Cell Terminals on Pyramidal Cells Simon Fru¨h,1,5 Jennifer Romanos,1,5 Patrizia Panzanelli,2 XDaniela Bu¨rgisser,3 XShiva K. Tyagarajan,1,5 X Kevin P. Campbell,4 XMirko Santello,1,5 and XJean-Marc Fritschy1,5 1Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland, 2Department of Neuroscience Rita Levi Montalcini, University of Turin, 10124 Turin, Italy, 3ETH Zurich, 8092 Zurich, Switzerland, 4Howard Hughes Medical Institute, Department of Molecular Physiology and Biophysics, Department of Neurology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa 52242, and 5Neuroscience Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland Distinct types of GABAergic interneurons target different subcellular domains of pyramidal cells, thereby shaping pyramidal cell activity patterns. Whether the presynaptic heterogeneity of GABAergic innervation is mirrored by specific postsynaptic factors is largely unex- plored. Here we show that dystroglycan, a protein responsible for the majority of congenital muscular dystrophies when dysfunctional, has a function at postsynaptic sites restricted to a subset of GABAergic interneurons. Conditional deletion of Dag1, encoding dystrogly- can, in pyramidal cells caused loss of CCK-positive basket cell terminals in hippocampus and neocortex. PV-positive basket cell terminals were unaffected in mutant mice, demonstrating interneuron subtype-specific function of dystroglycan. Loss of dystroglycan in pyrami- dal cells had little influence on clustering of other GABAergic postsynaptic proteins and of glutamatergic synaptic proteins. -
Postmortem Changes in the Myofibrillar and Other Cytoskeletal Proteins in Muscle
BIOCHEMISTRY - IMPACT ON MEAT TENDERNESS Postmortem Changes in the Myofibrillar and Other C'oskeletal Proteins in Muscle RICHARD M. ROBSON*, ELISABETH HUFF-LONERGAN', FREDERICK C. PARRISH, JR., CHIUNG-YING HO, MARVIN H. STROMER, TED W. HUIATT, ROBERT M. BELLIN and SUZANNE W. SERNETT introduction filaments (titin), and integral Z-line region (a-actinin, Cap Z), as well as proteins of the intermediate filaments (desmin, The cytoskeleton of "typical" vertebrate cells contains paranemin, and synemin), Z-line periphery (filamin) and three protein filament systems, namely the -7-nm diameter costameres underlying the cell membrane (filamin, actin-containing microfilaments, the -1 0-nm diameter in- dystrophin, talin, and vinculin) are listed along with an esti- termediate filaments (IFs), and the -23-nm diameter tubu- mate of their abundance, approximate molecular weights, lin-containing microtubules (Robson, 1989, 1995; Robson and number of subunits per molecule. Because the myofibrils et al., 1991 ).The contractile myofibrils, which are by far the are the overwhelming components of the skeletal muscle cell major components of developed skeletal muscle cells and cytoskeleton, the approximate percentages of the cytoskel- are responsible for most of the desirable qualities of muscle eton listed for the myofibrillar proteins (e.g., myosin, actin, foods (Robson et al., 1981,1984, 1991 1, can be considered tropomyosin, a-actinin, etc.) also would represent their ap- the highly expanded corollary of the microfilament system proximate percentages of total myofibrillar protein. of non-muscle cells. The myofibrils, IFs, cell membrane skel- eton (complex protein-lattice subjacent to the sarcolemma), Some Important Characteristics, Possible and attachment sites connecting these elements will be con- Roles, and Postmortem Changes of Key sidered as comprising the muscle cell cytoskeleton in this Cytoskeletal Proteins review. -
Advanced Fiber Type-Specific Protein Profiles Derived from Adult Murine
proteomes Article Advanced Fiber Type-Specific Protein Profiles Derived from Adult Murine Skeletal Muscle Britta Eggers 1,2,* , Karin Schork 1,2, Michael Turewicz 1,2 , Katalin Barkovits 1,2 , Martin Eisenacher 1,2, Rolf Schröder 3, Christoph S. Clemen 4,5 and Katrin Marcus 1,2,* 1 Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany; [email protected] (K.S.); [email protected] (M.T.); [email protected] (K.B.); [email protected] (M.E.) 2 Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801 Bochum, Germany 3 Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany; [email protected] 4 German Aerospace Center, Institute of Aerospace Medicine, 51147 Cologne, Germany; [email protected] 5 Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, 50931 Cologne, Germany * Correspondence: [email protected] (B.E.); [email protected] (K.M.) Abstract: Skeletal muscle is a heterogeneous tissue consisting of blood vessels, connective tissue, and muscle fibers. The last are highly adaptive and can change their molecular composition depending on external and internal factors, such as exercise, age, and disease. Thus, examination of the skeletal muscles at the fiber type level is essential to detect potential alterations. Therefore, we established a protocol in which myosin heavy chain isoform immunolabeled muscle fibers were laser Citation: Eggers, B.; Schork, K.; microdissected and separately investigated by mass spectrometry to develop advanced proteomic Turewicz, M.; Barkovits, K.; profiles of all murine skeletal muscle fiber types.