An Integrated Approach to Comprehensively Map the Molecular Context of Proteins

Total Page:16

File Type:pdf, Size:1020Kb

An Integrated Approach to Comprehensively Map the Molecular Context of Proteins bioRxiv preprint doi: https://doi.org/10.1101/264788; this version posted February 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Liu et al. An integrated approach to comprehensively map the molecular context of proteins Xiaonan Liu1,2, Kari Salokas1,2, Fitsum Tamene1,2,3 and Markku Varjosalo1,2,3* 1Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland 2Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland 3Proteomics Unit, University of Helsinki, Helsinki 00014, Finland *Corresponding author Abstract: Protein-protein interactions underlie almost all cellular functions. The comprehensive mapping of these complex cellular networks of stable and transient associations has been made available by affi nity purifi cation mass spectrometry (AP-MS) and more recently by proximity based labelling methods such as BioID. Due the advancements in both methods and MS instrumentation, an in-depth analysis of the whole human proteome is at grasps. In order to facilitate this, we designed and optimized an integrated approach utilizing MAC-tag combining both AP-MS and BioID in a single construct. We systematically applied this approach to 18 subcellular localization markers and generated a molecular context database, which can be used to defi ne molecular locations for any protein of interest. In addition, we show that by combining the AP-MS and BioID results we can also obtain interaction distances within a complex. Taken together, our combined strategy off ers comprehensive approach for mapping physical and functional protein interactions. Introduction: Majority of proteins do not function in isolation geting the endogenous bait protein, allowing and their interactions with other proteins defi ne purifi cation of the bait protein together with the their cellular functions. Therefore, detailed under- associating proteins (preys). This approach has standing of protein-protein interactions (PPIs) is been proven well suited for even large-scale high- the key for deciphering regulation of cellular net- throughput studies, and to yield highly repro- works and pathways. During the last decade, the ducible data in both intra- and inter-laboratory versatile combination of affi nity purifi cation and usage2. The most commonly used epitope tags in mass spectrometry (AP-MS) revolutionized the medium to large-scale studies include FLAG3, His4, detailed characterization of protein complexes MYC5, HA6, GFP7and Strep8, of which the Strep-tag and protein-interaction networks1. The AP-MS has become the gold-standard in affi nity purifi - approach relies on expression of a bait protein cation proteomics due to unparalleled protein coupled with an epitope tag or antibodies tar- purity in physiological purifi cation conditions as 1 bioRxiv preprint doi: https://doi.org/10.1101/264788; this version posted February 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. An integrated approach to comprehensively map the molecular context of proteins well as the possibility for native competitive elu- we included as well a nine amino acid hemagglu- tion using biotin. tinin (HA)-epitope. The HA-epitope also facilitates AP-MS can also be combined with quantitative additional follow-up approaches such as ChIP- proteomics approaches to better understand the Seq17 and purifi cation of the crosslinked proteins protein complex stoichiometry9 and the dynamics for cross-linking coupled with mass spectrometry of protein–complex (dis)assembly1,10. The combi- (XL-MS)18, making the MAC-tag almost as versatile nation of AP-MS with other techniques, such as as the Swiss Army knife. biochemical fractionation, intact mass measure- To benchmark the usability and performance of ment and chemical crosslinking11,12, has been used the MAC-tag we applied it to 18 bona fi de subcel- to characterize supramolecular organization of lular localization marker proteins. This allowed us protein complexes. to validate the correct localization of the MAC- Although AP-MS remains the most used tagged marker proteins as well as to monitor the method for mapping protein-protein inter- localization of the in vivo biotinylated interactors. actions, the recently developed proximity Additionally the interactions provide new infor- labeling approaches, such as BioID13 and APEX14, mation about these 18 marker proteins and their have become complementary and somewhat cellular functions. Furthermore the 18 localization competing methods. BioID involves expression markers and their 1911 interactions, form a basis of the protein of interest fused with a prokary- of the reference molecular context repository, otic biotin ligase (BirA) and the subsequent which we show can be used for “mass spectrom- biotinylation of the amine groups of the neigh- etry (MS) microscopy” analysis of any protein of boring proteins when excess of biotin is added interest. The combinatory analysis with AP-MS and to the cells. Whereas the wild-type BirA from E. BioID also provided information, which effi ciently Coli is capable of transferring the biotin only to a could be used to derive relative spatial distances substrate bearing a specifi c recognition sequence, for proteins in a complex. Taken together, our the generation of a promiscuous BirA* (Arg118Gly devised combinatory MAC-tag and analysis mutant) allows the biotinylation of any protein approaches around it provide a plethora of infor- found within a 10 nm labeling radius13,15. While mation of the cellular functions and the molecular BioID has the abilities to capture weak and/or context of any studied protein. transient protein-protein interactions, the identi- fi ed interactions are not limited to direct binders RESULTS but can include proximate proteins as well. MAC- tag AP-MS and BioID pipeline for In order to avoid artefactual interactions detection of physical and functional caused by overexpression of the bait proteins, interactions majority of the large-scale interaction proteomic studies employ the Flp-In™ T-REx 293 cell line To generate a versatile approach for identifi- allowing moderate and inducible bait protein cation of both stable physical and transient expression from isogenic cell clones16. Although functional protein-protein interactions we inte- the system allows rapid generation of transgene grated and optimized the BioID approach with 10,23 stably expressing cell lines, comprehensive our single-strep Strep AP-MS pipeline . Both analyses utilizing complementarily both AP-MS of these approaches have become the method and BioID is resource-intense in the respect of cell of choice for interactomics analyses. We have line generation. To address this caveat and allow recently shown the eff ectiveness of using these 10,23 high-throughput comprehensive interactome approached complimentarily . However, the analyses, we generated a Gateway®-compatible complementary use of the two techniques has MAC (Multiple Approaches Combined) -tag been labor-intense, involving tagging of the bait enabling both the single-step Strep AP-MS as well proteins with BirA* and Strep-tag individually, as the BioID analysis with a single construct, which as well as generation of two set of cell lines per decreases the number of required individual cell bait. To overcome the major limitations, we have lines by 50%. In addition to allow visualization of developed an integrated experimental workfl ow tagged bait protein by immunohistochemistry, utilizing a MAC-tag containing both StrepIII-tag 2 bioRxiv preprint doi: https://doi.org/10.1101/264788; this version posted February 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Liu et al. and BirA* (Supplementary Fig. 1a). In addition to included: mitochondria (Apoptosis-inducing fac- optimizing the experimental steps, we focused tor 1, AIFM1); endoplasmic reticulum (Calnexin, on the compatibility of the two methods and to CALX); peroxisome (Catalase, CATA); early endo- the simplicity of the analysis pipelines to gener- some (Early endosome antigen 1, EEA1); cytoplas- ate a process with improved performance and mic peripheral plasma membrane marker (Ezrin, reproducibility on detecting protein-protein EZRI); nucleolus marker (rRNA 2’-O-methyltrans- interactions. The two pipelines diff er only in the ferase fi brillarin, FBRL); cis-Golgi marker (Golgin activation of the BirA* by addition of biotin to the subfamily A member 2, GOGA2); chromatin (His- cell culture media and harsher lysis condition in tone H3.1, H31); exosome (Heat shock cognate 71 the BioID pipeline (Fig. 1, Supplementary Fig. 1). kDa protein, HSP7C); lysosome (Lysosome-associ- Without biotin addition the BirA* in the MAC-tag ated membrane glycoprotein 1, LAMP1); nuclear remains inactive (Supplementary Fig. 1b, c), result- envelope marker (Prelamin-A/C, LMNA); protea- ing in identical (cor=0.88-0.99) single-step affi nity some (Proteasome subunit alpha type-1, PSA1); purifi cation results as vector with only StrepIII-tag recycling endosome (Ras-related protein Rab-11A, (Supplementary Fig. 1d, e). Similarly, when biotin RAB11A); late endosome (Ras-related protein Rab- was added the results compare (cor=0.95-0.97) to 9A, RAB9A); microtubule (Tubulin alpha-1A chain, that of a
Recommended publications
  • AP2A2 Antibody Cat
    AP2A2 Antibody Cat. No.: 63-513 AP2A2 Antibody Formalin-fixed and paraffin-embedded human Flow cytometric analysis of HepG2 cells using AP2A2 hepatocarcinoma with AP2A2 Antibody , which was Antibody (bottom histogram) compared to a negative peroxidase-conjugated to the secondary antibody, control cell (top histogram). FITC-conjugated goat-anti- followed by DAB staining. rabbit secondary antibodies were used for the analysis. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human This AP2A2 antibody is generated from rabbits immunized with a KLH conjugated IMMUNOGEN: synthetic peptide between 610-637 amino acids from the Central region of human AP2A2. TESTED APPLICATIONS: Flow, IHC-P, WB For WB starting dilution is: 1:1000 APPLICATIONS: For IHC-P starting dilution is: 1:10~50 For FACS starting dilution is: 1:10~50 September 25, 2021 1 https://www.prosci-inc.com/ap2a2-antibody-63-513.html PREDICTED MOLECULAR 104 kDa WEIGHT: Properties This antibody is purified through a protein A column, followed by peptide affinity PURIFICATION: purification. CLONALITY: Polyclonal ISOTYPE: Rabbit Ig CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: Supplied in PBS with 0.09% (W/V) sodium azide. CONCENTRATION: batch dependent Store at 4˚C for three months and -20˚C, stable for up to one year. As with all antibodies STORAGE CONDITIONS: care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: AP2A2 AP-2 complex subunit alpha-2, 100 kDa coated vesicle
    [Show full text]
  • Global-Scale Analysis of the Dynamic Transcriptional Adaptations Within Skeletal Muscle During Hypertrophic Growth
    University of Kentucky UKnowledge Theses and Dissertations--Physiology Physiology 2015 GLOBAL-SCALE ANALYSIS OF THE DYNAMIC TRANSCRIPTIONAL ADAPTATIONS WITHIN SKELETAL MUSCLE DURING HYPERTROPHIC GROWTH Tyler Kirby University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Kirby, Tyler, "GLOBAL-SCALE ANALYSIS OF THE DYNAMIC TRANSCRIPTIONAL ADAPTATIONS WITHIN SKELETAL MUSCLE DURING HYPERTROPHIC GROWTH" (2015). Theses and Dissertations--Physiology. 22. https://uknowledge.uky.edu/physiology_etds/22 This Doctoral Dissertation is brought to you for free and open access by the Physiology at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Physiology by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. I agree that the document mentioned above may be made available immediately for worldwide access unless an embargo applies.
    [Show full text]
  • Protein Interaction Network of Alternatively Spliced Isoforms from Brain Links Genetic Risk Factors for Autism
    ARTICLE Received 24 Aug 2013 | Accepted 14 Mar 2014 | Published 11 Apr 2014 DOI: 10.1038/ncomms4650 OPEN Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Roser Corominas1,*, Xinping Yang2,3,*, Guan Ning Lin1,*, Shuli Kang1,*, Yun Shen2,3, Lila Ghamsari2,3,w, Martin Broly2,3, Maria Rodriguez2,3, Stanley Tam2,3, Shelly A. Trigg2,3,w, Changyu Fan2,3, Song Yi2,3, Murat Tasan4, Irma Lemmens5, Xingyan Kuang6, Nan Zhao6, Dheeraj Malhotra7, Jacob J. Michaelson7,w, Vladimir Vacic8, Michael A. Calderwood2,3, Frederick P. Roth2,3,4, Jan Tavernier5, Steve Horvath9, Kourosh Salehi-Ashtiani2,3,w, Dmitry Korkin6, Jonathan Sebat7, David E. Hill2,3, Tong Hao2,3, Marc Vidal2,3 & Lilia M. Iakoucheva1 Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases.
    [Show full text]
  • Seq2pathway Vignette
    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
    [Show full text]
  • Transcriptomic Analysis of the Aquaporin (AQP) Gene Family
    Pancreatology 19 (2019) 436e442 Contents lists available at ScienceDirect Pancreatology journal homepage: www.elsevier.com/locate/pan Transcriptomic analysis of the Aquaporin (AQP) gene family interactome identifies a molecular panel of four prognostic markers in patients with pancreatic ductal adenocarcinoma Dimitrios E. Magouliotis a, b, Vasiliki S. Tasiopoulou c, Konstantinos Dimas d, * Nikos Sakellaridis d, Konstantina A. Svokos e, Alexis A. Svokos f, Dimitris Zacharoulis b, a Division of Surgery and Interventional Science, Faculty of Medical Sciences, UCL, London, UK b Department of Surgery, University of Thessaly, Biopolis, Larissa, Greece c Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, Greece d Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, Greece e The Warren Alpert Medical School of Brown University, Providence, RI, USA f Riverside Regional Medical Center, Newport News, VA, USA article info abstract Article history: Background: This study aimed to assess the differential gene expression of aquaporin (AQP) gene family Received 14 October 2018 interactome in pancreatic ductal adenocarcinoma (PDAC) using data mining techniques to identify novel Received in revised form candidate genes intervening in the pathogenicity of PDAC. 29 January 2019 Method: Transcriptome data mining techniques were used in order to construct the interactome of the Accepted 9 February 2019 AQP gene family and to determine which genes members are differentially expressed in PDAC as Available online 11 February 2019 compared to controls. The same techniques were used in order to evaluate the potential prognostic role of the differentially expressed genes. Keywords: PDAC Results: Transcriptome microarray data of four GEO datasets were incorporated, including 142 primary Aquaporin tumor samples and 104 normal pancreatic tissue samples.
    [Show full text]
  • The Interplay Between Dysregulated Ion Transport and Mitochondrial Architecture As a Dangerous Liaison in Cancer
    International Journal of Molecular Sciences Review The Interplay between Dysregulated Ion Transport and Mitochondrial Architecture as a Dangerous Liaison in Cancer Stine F. Pedersen 1,* , Mette Flinck 1 and Luis A. Pardo 2,* 1 Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark; mette.fl[email protected] 2 Oncophysiology Group, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany * Correspondence: [email protected] (S.F.P.); [email protected] (L.A.P.) Abstract: Transport of ions and nutrients is a core mitochondrial function, without which there would be no mitochondrial metabolism and ATP production. Both ion homeostasis and mitochondrial phenotype undergo pervasive changes during cancer development, and both play key roles in driving the malignancy. However, the link between these events has been largely ignored. This review comprehensively summarizes and critically discusses the role of the reciprocal relationship between ion transport and mitochondria in crucial cellular functions, including metabolism, signaling, and cell fate decisions. We focus on Ca2+,H+, and K+, which play essential and highly interconnected roles in mitochondrial function and are profoundly dysregulated in cancer. We describe the transport and roles of these ions in normal mitochondria, summarize the changes occurring during cancer development, and discuss how they might impact tumorigenesis. Keywords: mitochondrial fission; mitochondrial fusion; calcium; pH; potassium; membrane potential; metabolism; apoptosis; cell cycle; metastasis Citation: Pedersen, S.F.; Flinck, M.; Pardo, L.A. The Interplay between Dysregulated Ion Transport and Mitochondrial Architecture as a 1. Introduction Dangerous Liaison in Cancer. Int. J. Since the first observation of mitochondria in the 1840s, a century had to pass until it Mol.
    [Show full text]
  • The Endocytic Membrane Trafficking Pathway Plays a Major Role
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Liverpool Repository RESEARCH ARTICLE The Endocytic Membrane Trafficking Pathway Plays a Major Role in the Risk of Parkinson’s Disease Sara Bandres-Ciga, PhD,1,2 Sara Saez-Atienzar, PhD,3 Luis Bonet-Ponce, PhD,4 Kimberley Billingsley, MSc,1,5,6 Dan Vitale, MSc,7 Cornelis Blauwendraat, PhD,1 Jesse Raphael Gibbs, PhD,7 Lasse Pihlstrøm, MD, PhD,8 Ziv Gan-Or, MD, PhD,9,10 The International Parkinson’s Disease Genomics Consortium (IPDGC), Mark R. Cookson, PhD,4 Mike A. Nalls, PhD,1,11 and Andrew B. Singleton, PhD1* 1Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain 3Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 4Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 5Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom 6Department of Pathophysiology, University of Tartu, Tartu, Estonia 7Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA 8Department of Neurology, Oslo University Hospital, Oslo, Norway 9Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montréal, Quebec, Canada 10Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada 11Data Tecnica International, Glen Echo, Maryland, USA ABSTRACT studies, summary-data based Mendelian randomization Background: PD is a complex polygenic disorder.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Familial Multiple Coagulation Factor Deficiencies
    Journal of Clinical Medicine Article Familial Multiple Coagulation Factor Deficiencies (FMCFDs) in a Large Cohort of Patients—A Single-Center Experience in Genetic Diagnosis Barbara Preisler 1,†, Behnaz Pezeshkpoor 1,† , Atanas Banchev 2 , Ronald Fischer 3, Barbara Zieger 4, Ute Scholz 5, Heiko Rühl 1, Bettina Kemkes-Matthes 6, Ursula Schmitt 7, Antje Redlich 8 , Sule Unal 9 , Hans-Jürgen Laws 10, Martin Olivieri 11 , Johannes Oldenburg 1 and Anna Pavlova 1,* 1 Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, 53127 Bonn, Germany; [email protected] (B.P.); [email protected] (B.P.); [email protected] (H.R.); [email protected] (J.O.) 2 Department of Paediatric Haematology and Oncology, University Hospital “Tzaritza Giovanna—ISUL”, 1527 Sofia, Bulgaria; [email protected] 3 Hemophilia Care Center, SRH Kurpfalzkrankenhaus Heidelberg, 69123 Heidelberg, Germany; ronald.fi[email protected] 4 Department of Pediatrics and Adolescent Medicine, University Medical Center–University of Freiburg, 79106 Freiburg, Germany; [email protected] 5 Center of Hemostasis, MVZ Labor Leipzig, 04289 Leipzig, Germany; [email protected] 6 Hemostasis Center, Justus Liebig University Giessen, 35392 Giessen, Germany; [email protected] 7 Center of Hemostasis Berlin, 10789 Berlin-Schöneberg, Germany; [email protected] 8 Pediatric Oncology Department, Otto von Guericke University Children’s Hospital Magdeburg, 39120 Magdeburg, Germany; [email protected] 9 Division of Pediatric Hematology Ankara, Hacettepe University, 06100 Ankara, Turkey; Citation: Preisler, B.; Pezeshkpoor, [email protected] B.; Banchev, A.; Fischer, R.; Zieger, B.; 10 Department of Pediatric Oncology, Hematology and Clinical Immunology, University of Duesseldorf, Scholz, U.; Rühl, H.; Kemkes-Matthes, 40225 Duesseldorf, Germany; [email protected] B.; Schmitt, U.; Redlich, A.; et al.
    [Show full text]
  • Epigenome-Wide Exploratory Study of Monozygotic Twins Suggests Differentially Methylated Regions to Associate with Hand Grip Strength
    Biogerontology (2019) 20:627–647 https://doi.org/10.1007/s10522-019-09818-1 (0123456789().,-volV)( 0123456789().,-volV) RESEARCH ARTICLE Epigenome-wide exploratory study of monozygotic twins suggests differentially methylated regions to associate with hand grip strength Mette Soerensen . Weilong Li . Birgit Debrabant . Marianne Nygaard . Jonas Mengel-From . Morten Frost . Kaare Christensen . Lene Christiansen . Qihua Tan Received: 15 April 2019 / Accepted: 24 June 2019 / Published online: 28 June 2019 Ó The Author(s) 2019 Abstract Hand grip strength is a measure of mus- significant CpG sites or pathways were found, how- cular strength and is used to study age-related loss of ever two of the suggestive top CpG sites were mapped physical capacity. In order to explore the biological to the COL6A1 and CACNA1B genes, known to be mechanisms that influence hand grip strength varia- related to muscular dysfunction. By investigating tion, an epigenome-wide association study (EWAS) of genomic regions using the comb-p algorithm, several hand grip strength in 672 middle-aged and elderly differentially methylated regions in regulatory monozygotic twins (age 55–90 years) was performed, domains were identified as significantly associated to using both individual and twin pair level analyses, the hand grip strength, and pathway analyses of these latter controlling the influence of genetic variation. regions revealed significant pathways related to the Moreover, as measurements of hand grip strength immune system, autoimmune disorders, including performed over 8 years were available in the elderly diabetes type 1 and viral myocarditis, as well as twins (age 73–90 at intake), a longitudinal EWAS was negative regulation of cell differentiation.
    [Show full text]
  • Dissecting the Genomic Complexity Underlying Medulloblastoma
    LETTER doi:10.1038/nature11284 Dissecting the genomic complexity underlying medulloblastoma A list of authors and their affiliations appears at the end of the paper Medulloblastoma is an aggressively growing tumour, arising in Some cases probably went through even higher polyploidy states the cerebellum or medulla/brain stem. It is the most common before reaching an approximately 4n baseline (for example malignant brain tumour in children, and shows tremendous bio- ICGC_MB45, displaying 4n chromosomes with 4:0 or 3:1 allele ratios; logical and clinical heterogeneity1. Despite recent treatment Supplementary Fig. 2). Across the discovery set, tetraploidy was most advances, approximately 40% of children experience tumour commonly observed in Group 3 (7 out of 13, 54%) and Group 4 recurrence, and 30% will die from their disease. Those who survive tumours (8 out of 20, 40%), followed by SHH (4 out of 14, 29%) and often have a significantly reduced quality of life. Four tumour WNT tumours (1 out of 7, 14%). Interestingly, the four tetraploid SHH subgroups with distinct clinical, biological and genetic profiles tumours all harboured TP53 mutations and also displayed chromo- are currently identified2,3. WNT tumours, showing activated thripsis6. Tetraploid Group 3 and 4 tumours showed significantly wingless pathway signalling, carry a favourable prognosis under more large-scale copy number alterations compared with diploid cases current treatment regimens4. SHH tumours show hedgehog (median 10 changes per tumour in tetraploid versus 4 per tumour in pathway activation, and have an intermediate prognosis2. Group 3 diploid cases, P 5 0.008, two-tailed Mann–Whitney U-test; Supplemen- and 4 tumours are molecularly less well characterized, and also tary Fig.
    [Show full text]
  • KIF1A-Related Autosomal Dominant Spastic Paraplegias (SPG30) in Russian Families G
    Rudenskaya et al. BMC Neurology (2020) 20:290 https://doi.org/10.1186/s12883-020-01872-4 RESEARCH ARTICLE Open Access KIF1A-related autosomal dominant spastic paraplegias (SPG30) in Russian families G. E. Rudenskaya1 , V. A. Kadnikova1* , O. P. Ryzhkova1 , L. A. Bessonova1, E. L. Dadali1 , D. S. Guseva1 , T. V. Markova1 , D. N. Khmelkova2 and A. V. Polyakov1 Abstract Background: Spastic paraplegia type 30 (SPG30) caused by KIF1A mutations was first reported in 2011 and was initially considered a very rare autosomal recessive (AR) form. In the last years, thanks to the development of massive parallel sequencing, SPG30 proved to be a rather common autosomal dominant (AD) form of familial or sporadic spastic paraplegia (SPG),, with a wide range of phenotypes: pure and complicated. The aim of our study is to detect AD SPG30 cases and to examine their molecular and clinical characteristics for the first time in the Russian population. Methods: Clinical, genealogical and molecular methods were used. Molecular methods included massive parallel sequencing (MPS) of custom panel ‘spastic paraplegias’ with 62 target genes complemented by familial Sanger sequencing. One case was detected by the whole -exome sequencing. Results: AD SPG30 was detected in 10 unrelated families, making it the 3rd (8.4%) most common SPG form in the cohort of 118 families. No AR SPG30 cases were detected. In total, 9 heterozygous KIF1A mutations were detected, with 4 novel and 5 known mutations. All the mutations were located within KIF1A motor domain. Six cases had pure phenotypes, of which 5 were familial, where 2 familial cases demonstrated incomplete penetrance, early onset and slow relatively benign SPG course.
    [Show full text]