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Ahmadi A, Till K, Backe PH, Blicher P, Diekmann R, Schüttpelz M, Glette K, Tørresen J, Bjørås M, Rowe AD, Dalhus B. Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex. Commun Biol 2021; 4:876. [PMID: 34267321 PMCID: PMC8282808 DOI: 10.1038/s42003-021-02400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katharina Till
- FOM Institute AMOLF, Science Park 104, Amsterdam, The Netherlands.,Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Paul Hoff Backe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Kyrre Glette
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.
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Rowe AD, Stoway SD, Åhlman H, Arora V, Caggana M, Fornari A, Hagar A, Hall PL, Marquardt GC, Miller BJ, Nixon C, Norgan AP, Orsini JJ, Pettersen RD, Piazza AL, Schubauer NR, Smith AC, Tang H, Tavakoli NP, Wei S, Zetterström RH, Currier RJ, Mørkrid L, Rinaldo P. A Novel Approach to Improve Newborn Screening for Congenital Hypothyroidism by Integrating Covariate-Adjusted Results of Different Tests into CLIR Customized Interpretive Tools. Int J Neonatal Screen 2021; 7:23. [PMID: 33922835 PMCID: PMC8167643 DOI: 10.3390/ijns7020023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/07/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Newborn screening for congenital hypothyroidism remains challenging decades after broad implementation worldwide. Testing protocols are not uniform in terms of targets (TSH and/or T4) and protocols (parallel vs. sequential testing; one or two specimen collection times), and specificity (with or without collection of a second specimen) is overall poor. The purpose of this retrospective study is to investigate the potential impact of multivariate pattern recognition software (CLIR) to improve the post-analytical interpretation of screening results. Seven programs contributed reference data (N = 1,970,536) and two sets of true (TP, N = 1369 combined) and false (FP, N = 15,201) positive cases for validation and verification purposes, respectively. Data were adjusted for age at collection, birth weight, and location using polynomial regression models of the fifth degree to create three-dimensional regression surfaces. Customized Single Condition Tools and Dual Scatter Plots were created using CLIR to optimize the differential diagnosis between TP and FP cases in the validation set. Verification testing correctly identified 446/454 (98%) of the TP cases, and could have prevented 1931/5447 (35%) of the FP cases, with variable impact among locations (range 4% to 50%). CLIR tools either as made here or preferably standardized to the recommended uniform screening panel could improve performance of newborn screening for congenital hypothyroidism.
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Affiliation(s)
- Alexander D. Rowe
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (A.D.R.); (S.D.S.); (R.D.P.)
| | - Stephanie D. Stoway
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (A.D.R.); (S.D.S.); (R.D.P.)
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.F.); (A.P.N.); (A.L.P.)
| | - Henrik Åhlman
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 17177 Solna, Sweden; (H.Å.); (R.H.Z.)
| | - Vaneet Arora
- Division of Laboratory Services, Kentucky Department for Public Health, Frankfort, KY 40601, USA; (V.A.); (A.C.S.); (S.W.)
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, Albany, NY 12237, USA; (M.C.); (J.J.O.); (N.P.T.)
| | - Anna Fornari
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.F.); (A.P.N.); (A.L.P.)
- Fondazione MBBM/Ospedale San Gerardo, University of Milano-Bicocca, 20900 Monza, Italy
| | - Arthur Hagar
- Georgia Department of Public Health, Atlanta, GA 30303, USA; (A.H.); (P.L.H.)
| | - Patricia L. Hall
- Georgia Department of Public Health, Atlanta, GA 30303, USA; (A.H.); (P.L.H.)
| | - Gregg C. Marquardt
- Division of Laboratory Pathology External Applications, Department of Information Technology, Mayo Clinic, Rochester, MN 55905, USA; (G.C.M.); (B.J.M.); (N.R.S.)
| | - Bobby J. Miller
- Division of Laboratory Pathology External Applications, Department of Information Technology, Mayo Clinic, Rochester, MN 55905, USA; (G.C.M.); (B.J.M.); (N.R.S.)
| | - Christopher Nixon
- Virginia Department of General Services, Division of Consolidated Laboratory Services, Richmond, VA 23219, USA;
| | - Andrew P. Norgan
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.F.); (A.P.N.); (A.L.P.)
| | - Joseph J. Orsini
- Wadsworth Center, New York State Department of Health, Albany, NY 12237, USA; (M.C.); (J.J.O.); (N.P.T.)
| | - Rolf D. Pettersen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (A.D.R.); (S.D.S.); (R.D.P.)
| | - Amy L. Piazza
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.F.); (A.P.N.); (A.L.P.)
| | - Neil R. Schubauer
- Division of Laboratory Pathology External Applications, Department of Information Technology, Mayo Clinic, Rochester, MN 55905, USA; (G.C.M.); (B.J.M.); (N.R.S.)
| | - Amy C. Smith
- Division of Laboratory Services, Kentucky Department for Public Health, Frankfort, KY 40601, USA; (V.A.); (A.C.S.); (S.W.)
| | - Hao Tang
- Genetic Disease Screening Program, California Department of Public Health, Richmond, CA 94804, USA;
| | - Norma P. Tavakoli
- Wadsworth Center, New York State Department of Health, Albany, NY 12237, USA; (M.C.); (J.J.O.); (N.P.T.)
| | - Sainan Wei
- Division of Laboratory Services, Kentucky Department for Public Health, Frankfort, KY 40601, USA; (V.A.); (A.C.S.); (S.W.)
| | - Rolf H. Zetterström
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, 17177 Solna, Sweden; (H.Å.); (R.H.Z.)
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Robert J. Currier
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA;
| | - Lars Mørkrid
- Department of Medical Biochemistry, Division of Laboratory Medicine, Oslo University Hospital HF, 0424 Oslo, Norway;
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, 0130 Oslo, Norway
| | - Piero Rinaldo
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (A.D.R.); (S.D.S.); (R.D.P.)
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.F.); (A.P.N.); (A.L.P.)
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Tangeraas T, Sæves I, Klingenberg C, Jørgensen J, Kristensen E, Gunnarsdottir G, Hansen EV, Strand J, Lundman E, Ferdinandusse S, Salvador CL, Woldseth B, Bliksrud YT, Sagredo C, Olsen ØE, Berge MC, Trømborg AK, Ziegler A, Zhang JH, Sørgjerd LK, Ytre-Arne M, Hogner S, Løvoll SM, Kløvstad Olavsen MR, Navarrete D, Gaup HJ, Lilje R, Zetterström RH, Stray-Pedersen A, Rootwelt T, Rinaldo P, Rowe AD, Pettersen RD. Performance of Expanded Newborn Screening in Norway Supported by Post-Analytical Bioinformatics Tools and Rapid Second-Tier DNA Analyses. Int J Neonatal Screen 2020; 6:51. [PMID: 33123633 PMCID: PMC7570219 DOI: 10.3390/ijns6030051] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
In 2012, the Norwegian newborn screening program (NBS) was expanded (eNBS) from screening for two diseases to that for 23 diseases (20 inborn errors of metabolism, IEMs) and again in 2018, to include a total of 25 conditions (21 IEMs). Between 1 March 2012 and 29 February 2020, 461,369 newborns were screened for 20 IEMs in addition to phenylketonuria (PKU). Excluding PKU, there were 75 true-positive (TP) (1:6151) and 107 (1:4311) false-positive IEM cases. Twenty-one percent of the TP cases were symptomatic at the time of the NBS results, but in two-thirds, the screening result directed the exact diagnosis. Eighty-two percent of the TP cases had good health outcomes, evaluated in 2020. The yearly positive predictive value was increased from 26% to 54% by the use of the Region 4 Stork post-analytical interpretive tool (R4S)/Collaborative Laboratory Integrated Reports 2.0 (CLIR), second-tier biochemical testing and genetic confirmation using DNA extracted from the original dried blood spots. The incidence of IEMs increased by 46% after eNBS was introduced, predominantly due to the finding of attenuated phenotypes. The next step is defining which newborns would truly benefit from screening at the milder end of the disease spectrum. This will require coordinated international collaboration, including proper case definitions and outcome studies.
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Affiliation(s)
- Trine Tangeraas
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Ingjerd Sæves
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Claus Klingenberg
- Department of Paediatrics, University Hospital of North Norway, 9019 Tromsø, Norway;
- Paediatric Research Group, Department of Clinical Medicine, UiT The Artic University of Norway, 9019 Tromsø, Norway
| | - Jens Jørgensen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Erle Kristensen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
- Paediatric Research Group, Department of Clinical Medicine, UiT The Artic University of Norway, 9019 Tromsø, Norway
| | - Gunnþórunn Gunnarsdottir
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (G.G.); (R.L.); (T.R.)
| | | | - Janne Strand
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Emma Lundman
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Centers, University of Amsterdam, AZ 1105 Amsterdam, The Netherlands;
| | - Cathrin Lytomt Salvador
- Norwegian National Unit for Diagnostics of Congenital Metabolic Disorders, Department of Medical Biochemistry, Oslo University Hospital, 0424 Oslo, Norway; (C.L.S.); (B.W.); (Y.T.B.)
| | - Berit Woldseth
- Norwegian National Unit for Diagnostics of Congenital Metabolic Disorders, Department of Medical Biochemistry, Oslo University Hospital, 0424 Oslo, Norway; (C.L.S.); (B.W.); (Y.T.B.)
| | - Yngve T Bliksrud
- Norwegian National Unit for Diagnostics of Congenital Metabolic Disorders, Department of Medical Biochemistry, Oslo University Hospital, 0424 Oslo, Norway; (C.L.S.); (B.W.); (Y.T.B.)
| | - Carlos Sagredo
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Øyvind E Olsen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Mona C Berge
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Anette Kjoshagen Trømborg
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Anders Ziegler
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Jin Hui Zhang
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Linda Karlsen Sørgjerd
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Mari Ytre-Arne
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Silje Hogner
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Siv M Løvoll
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Mette R Kløvstad Olavsen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Dionne Navarrete
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Hege J Gaup
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Rina Lilje
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (G.G.); (R.L.); (T.R.)
| | - Rolf H Zetterström
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Solna, Sweden, Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden;
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Terje Rootwelt
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (G.G.); (R.L.); (T.R.)
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Piero Rinaldo
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, NY 55902, USA;
| | - Alexander D Rowe
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
| | - Rolf D Pettersen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Oslo, Norway; (I.S.); (J.J.); (E.K.); (J.S.); (E.L.); (C.S.); (Ø.E.O.); (M.C.B.); (A.K.T.); (A.Z.); (J.H.Z.); (L.K.S.); (M.Y.-A.); (S.H.); (S.M.L.); (M.R.K.O.); (D.N.); (H.J.G.); (A.S.-P.); (A.D.R.); (R.D.P.)
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Villanger GD, Ystrom E, Engel SM, Longnecker MP, Pettersen R, Rowe AD, Reichborn-Kjennerud T, Aase H. Neonatal thyroid-stimulating hormone and association with attention-deficit/hyperactivity disorder. Paediatr Perinat Epidemiol 2020; 34:590-596. [PMID: 32072662 PMCID: PMC7431377 DOI: 10.1111/ppe.12643] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/26/2019] [Accepted: 12/04/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Normal brain development is dependent on maternal, fetal and neonatal thyroid function. Measuring neonatal thyroid-stimulating hormone (TSH) 48-72 hours after birth screens for congenital hypothyroidism, allowing early treatment to avoid serious impairment. However, even within sub-clinical ranges, disrupted thyroid homeostasis during brain development has been linked to adverse neurodevelopmental outcomes, including attention-deficit/hyperactivity disorder (ADHD). OBJECTIVES To estimate the association between neonatal TSH below threshold for potential congenital hypothyroidism and subsequent ADHD diagnosis using a population-based birth cohort. METHODS Children with a diagnosis of ADHD in the Norwegian Mother, Father and Child Cohort Study (MoBa) were identified through linkage with the Norwegian Patient Registry using ICD-10 codes for hyperkinetic disorders. The study included 405 ADHD cases and 1,092 controls (born 2003-2008) with available neonatal TSH concentrations below 10 mU/L (cut-off for potential congenital hypothyroidism) measured in dried blood spots sampled 48-72 hours after birth. RESULTS In multivariable, quintile models the relationship appeared to follow a U-shaped pattern with elevated odds ratios (OR) at lower and higher TSH levels. Among children with TSH in the lowest quintile, odds of ADHD was approximately 1.5-fold higher than children in the middle quintile (OR 1.60, 95% CI 1.09, 2.34), which was driven by substantially elevated risk among girls, with no association among boys (Pinteraction = 0.02; girls OR 3.10, 95% CI 1.53, 6.30; boys OR 1.16, 95% CI 0.73, 1.84). CONCLUSIONS ADHD risk appeared to be elevated among newborns with low TSH levels (i.e. with hyperthyroid status), and this association was mainly found among girls. Because our findings are suggestive of increased risk at very low TSH concentrations, where analytical accuracy is low, future studies should employ highly sensitive assays capable of accurate quantitation at very low concentrations. Also, larger studies are needed to investigate these associations at higher neonatal TSH concentrations where data are more widely distributed.
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Affiliation(s)
- Gro D. Villanger
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway,Corresponding author: Gro Dehli Villanger, Norwegian Institute of Public Health, Division of Mental and Physical Health, Department of Child Health and Development, PO Box 222 Skøyen, N-0213 Oslo, Norway. Phone no. +47 91605784.
| | - Eivind Ystrom
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway,Department of Psychology, University of Oslo, Norway,PharmacoEpidemiology and Drug Safety Research Group, School of Pharmacy, & PharmaTox Strategic Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway
| | - Stephanie M. Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew P. Longnecker
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Ramboll, Research Triangle Park, North Carolina, USA
| | - Rolf Pettersen
- Department of Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Alexander D. Rowe
- Department of Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Ted Reichborn-Kjennerud
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Heidi Aase
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
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Strand J, Gul KA, Erichsen HC, Lundman E, Berge MC, Trømborg AK, Sørgjerd LK, Ytre-Arne M, Hogner S, Halsne R, Gaup HJ, Osnes LT, Kro GAB, Sorte HS, Mørkrid L, Rowe AD, Tangeraas T, Jørgensen JV, Alme C, Bjørndalen TEH, Rønnestad AE, Lang AM, Rootwelt T, Buechner J, Øverland T, Abrahamsen TG, Pettersen RD, Stray-Pedersen A. Second-Tier Next Generation Sequencing Integrated in Nationwide Newborn Screening Provides Rapid Molecular Diagnostics of Severe Combined Immunodeficiency. Front Immunol 2020; 11:1417. [PMID: 32754152 PMCID: PMC7381310 DOI: 10.3389/fimmu.2020.01417] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
Severe combined immunodeficiency (SCID) and other T cell lymphopenias can be detected during newborn screening (NBS) by measuring T cell receptor excision circles (TRECs) in dried blood spot (DBS) DNA. Second tier next generation sequencing (NGS) with an amplicon based targeted gene panel using the same DBS DNA was introduced as part of our prospective pilot research project in 2015. With written parental consent, 21 000 newborns were TREC-tested in the pilot. Three newborns were identified with SCID, and disease-causing variants in IL2RG, RAG2, and RMRP were confirmed by NGS on the initial DBS DNA. The molecular findings directed follow-up and therapy: the IL2RG-SCID underwent early hematopoietic stem cell transplantation (HSCT) without any complications; the leaky RAG2-SCID received prophylactic antibiotics, antifungals, and immunoglobulin infusions, and underwent HSCT at 1 year of age. The child with RMRP-SCID had complete Hirschsprung disease and died at 1 month of age. Since January 2018, all newborns in Norway have been offered NBS for SCID using 1st tier TRECs and 2nd tier gene panel NGS on DBS DNA. During the first 20 months of nationwide SCID screening an additional 88 000 newborns were TREC tested, and four new SCID cases were identified. Disease-causing variants in DCLRE1C, JAK3, NBN, and IL2RG were molecularly confirmed on day 8, 15, 8 and 6, respectively after birth, using the initial NBS blood spot. Targeted gene panel NGS integrated into the NBS algorithm rapidly delineated the specific molecular diagnoses and provided information useful for management, targeted therapy and follow-up i.e., X rays and CT scans were avoided in the radiosensitive SCID. Second tier targeted NGS on the same DBS DNA as the TREC test provided instant confirmation or exclusion of SCID, and made it possible to use a less stringent TREC cut-off value. This allowed for the detection of leaky SCIDs, and simultaneously reduced the number of control samples, recalls and false positives. Mothers were instructed to stop breastfeeding until maternal cytomegalovirus (CMV) status was determined. Our limited data suggest that shorter time-interval from birth to intervention, may prevent breast milk transmitted CMV infection in classical SCID.
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Affiliation(s)
- Janne Strand
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Kiran Aftab Gul
- Paediatric Research Institute, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Hans Christian Erichsen
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Emma Lundman
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Mona C. Berge
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Anette K. Trømborg
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Linda K. Sørgjerd
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Mari Ytre-Arne
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Silje Hogner
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Ruth Halsne
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Department of Forensic Biology, Oslo University Hospital, Oslo, Norway
| | - Hege Junita Gaup
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Liv T. Osnes
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Grete A. B. Kro
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Hanne S. Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Alexander D. Rowe
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Trine Tangeraas
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Jens V. Jørgensen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Charlotte Alme
- Department of Paediatric Haematology, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Arild E. Rønnestad
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Astri M. Lang
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Terje Rootwelt
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jochen Buechner
- Department of Paediatric Haematology, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Torstein Øverland
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Tore G. Abrahamsen
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rolf D. Pettersen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Department of Paediatrics, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
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Zhang B, Ayuda-Durán P, Piechaczyk L, Fløisand Y, Safont MM, Karlsen IT, Fandalyuk Z, Tadele D, van Mierlo P, Rowe AD, Robertson JM, Gjertsen BT, McCormack E, Enserink JM. GRP94 rewires and buffers the FLT3-ITD signaling network and promotes survival of acute myeloid leukemic stem cells. Haematologica 2019; 104:e229. [PMID: 31040234 DOI: 10.3324/haematol.2019.220533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Beibei Zhang
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello
| | - Laure Piechaczyk
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello.,Institute of Clinical Medicine, University of Oslo
| | - Yngvar Fløisand
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello.,Department of Hematology, Oslo University Hospital, Rikshospitalet, Oslo
| | | | - Ida Tveit Karlsen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen
| | - Zina Fandalyuk
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen
| | - Dagim Tadele
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello.,Institute of Clinical Medicine, University of Oslo
| | - Pepijn van Mierlo
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello
| | - Alexander D Rowe
- Norwegian National Unit for Newborn Screening, Woman and Children's Division, Oslo University Hospital, Rikshospitalet
| | - Joseph M Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello
| | - Bjørn Tore Gjertsen
- Department of Hematology, Oslo University Hospital, Rikshospitalet, Oslo.,Hematology Section, Department of Internal Medicine, Haukeland University Hospital, Bergen
| | - Emmet McCormack
- Department of Hematology, Oslo University Hospital, Rikshospitalet, Oslo.,Hematology Section, Department of Internal Medicine, Haukeland University Hospital, Bergen
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello .,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, Montebello.,Section for Biochemistry and Molecular Biology, The Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway
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Ahmadi A, Rosnes I, Blicher P, Diekmann R, Schüttpelz M, Glette K, Tørresen J, Bjørås M, Dalhus B, Rowe AD. Publisher Correction: Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V. Nat Commun 2019; 10:1991. [PMID: 31024006 PMCID: PMC6484037 DOI: 10.1038/s41467-019-10070-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article was updated shortly after publication to add a link to the Peer Review file, which was inadvertently omitted. The Peer Review file is available to download as a Supplementary File from the HTML version of the Article.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway
| | - Ida Rosnes
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway
| | - Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany.,European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße 1, DE-69117, Heidelberg, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany
| | - Kyrre Glette
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), PO Box 8905, NO-7491, Trondheim, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. .,Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
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8
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Salvador CL, Tøndel C, Rowe AD, Bjerre A, Brun A, Brackman D, Mørkrid L. Estimating glomerular filtration rate in children: evaluation of creatinine- and cystatin C-based equations. Pediatr Nephrol 2019; 34:301-311. [PMID: 30171354 DOI: 10.1007/s00467-018-4067-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND Glomerular filtration rate (GFR) estimated by creatinine- and/or cystatin C-based equations (eGFR) is widely used in daily practice. The purpose of our study was to compare new and old eGFR equations with measured GFR (mGFR) by iohexol clearance in a cohort of children with chronic kidney disease (CKD). METHODS We examined 96 children (median age 9.2 years (range 0.25-17.5)) with CKD stages 1-5. A 7-point iohexol clearance (GFR7p) was defined as the reference method (median mGFR 66 mL/min/1.73 m2, range 6-153). Ten different eGFR equations, with or without body height, were evaluated: Schwartzbedside, SchwartzCKiD, SchwartzcysC, CAPA, LMREV, (LMREV + CAPA) / 2, FAScrea, FAScysC, FAScombi, FASheight. The accuracy was evaluated with percentage within 10 and 30% of GFR7p (P10 and P30). RESULTS In the group with mGFR below 60 mL/min/1.73 m2, the SchwartzcysC equation had the lowest median bias (interquartile range; IQR) 3.27 (4.80) mL/min/1.73 m2 and the highest accuracy with P10 of 44% and P30 of 85%. In the group with mGFR above 60 mL/min/1.73 m2, the SchwartzCKiD presented with the lowest bias 3.41 (13.1) mL/min/1.73 m2 and P10 of 62% and P30 of 98%. Overall, the SchwartzcysC had the lowest bias - 1.49 (13.5) mL/min/1.73 m2 and both SchwartzcysC and SchwartzCKiD showed P30 of 90%. P10 was 44 and 48%, respectively. CONCLUSIONS The SchwartzcysC and the combined SchwartzCKiD present with lower bias and higher accuracy as compared to the other equations. The SchwartzcysC equation is a good height-independent alternative to the SchwartzCKiD equation in children and can be reported directly by the laboratory information system. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov , Identifier NCT01092260, https://clinicaltrials.gov/ct2/show/NCT01092260?term=tondel&rank=2.
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Affiliation(s)
- Cathrin L Salvador
- Department of Medical Biochemistry, Oslo University Hospital, PB 4950 Nydalen, 0424, Oslo, Norway. .,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Camilla Tøndel
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Alexander D Rowe
- Department of Newborn screening, Oslo University Hospital, Oslo, Norway
| | - Anna Bjerre
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Atle Brun
- Laboratory for Clinical Biochemistry, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Damien Brackman
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, PB 4950 Nydalen, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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9
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Lång A, Øye A, Eriksson J, Rowe AD, Lång E, Bøe SO. Influence of acute promyelocytic leukemia therapeutic drugs on nuclear pore complex density and integrity. Biochem Biophys Res Commun 2018; 499:570-576. [PMID: 29596829 DOI: 10.1016/j.bbrc.2018.03.191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/25/2018] [Indexed: 11/16/2022]
Abstract
During cell division, a large number of nuclear proteins are released into the cytoplasm due to nuclear envelope breakdown. Timely nuclear import of these proteins following exit from mitosis is critical for establishment of the G1 nuclear environment. Dysregulation of post-mitotic nuclear import may affect the fate of newly divided stem or progenitor cells and may lead to cancer. Acute promyelocytic leukemia (APL) is a malignant disorder that involves a defect in blood cell differentiation at the promyelocytic stage. Recent studies suggest that pharmacological concentrations of the APL therapeutic drugs, all-trans retinoic acid (ATRA) and arsenic trioxide (ATO), affect post-mitotic nuclear import of the APL-associated oncoprotein PML/RARA. In the present study, we have investigated the possibility that ATRA and ATO affect post-mitotic nuclear import through interference with components of the nuclear import machinery. We observe reduced density and impaired integrity of nuclear pore complexes after ATRA and/or ATO exposure. Using a post-mitotic nuclear import assay, we demonstrate distinct import kinetics among different nuclear import pathways while nuclear import rates were similar in the presence or absence of APL therapeutic drugs.
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Affiliation(s)
- Anna Lång
- Department of Medical Biochemistry and Department of Microbiology, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Postboks 1171 Blindern, 0318 Oslo, Norway.
| | - Alexander Øye
- Department of Medical Biochemistry and Department of Microbiology, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway.
| | - Jens Eriksson
- Department of Medical Biochemistry and Department of Microbiology, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway.
| | - Alexander D Rowe
- Department of Medical Biochemistry and Department of Microbiology, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway; Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway.
| | - Emma Lång
- Department of Medical Biochemistry and Department of Microbiology, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway.
| | - Stig Ove Bøe
- Department of Medical Biochemistry and Department of Microbiology, Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway.
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10
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Zhang B, Durán PA, Piechaczyk L, Fløisand Y, Safont MMS, Karlsen IT, Fandalyuk Z, Tadele D, Mierlo PV, Rowe AD, Robertson JM, Gjertsen BT, McCormack E, Enserink JM. GRP94 rewires and buffers the FLT3-ITD signaling network and promotes survival of acute myeloid leukemic stem cells. Haematologica 2018; Online ahead of print:haematol.2018.189399. [PMID: 29748445 DOI: 10.3324/haematol.2018.189399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/07/2018] [Indexed: 11/09/2022] Open
Abstract
Internal tandem duplications in the tyrosine kinase receptor FLT3 (FLT3-ITD) are among the most common lesions in acute myeloid leukemia and there exists a need for new forms of treatment. Using ex vivo drug sensitivity screening, we found that FLT3-ITD+ patient cells are particularly sensitive to HSP90 inhibitors. While it is well known that HSP90 is important for FLT3-ITD stability, we found that HSP90 family members play a much more complex role in FLT3-ITD signaling than previously appreciated. First, we found that FLT3-ITD activates the unfolded protein response, leading to increased expression of GRP94/HSP90B1. This results in activation of a nefarious feedback loop, in which GRP94 rewires FLT3-ITD signaling by binding and retaining FLT3-ITD in the endoplasmic reticulum, leading to aberrant activation of downstream signaling pathways and further inducing the unfolded protein response. Second, HSP90 family proteins protect FLT3-ITD+ acute myeloid leukemia cells against apoptosis by alleviating proteotoxic stress, and treatment with HSP90 inhibitors results in proteotoxic overload that triggers unfolded protein response-induced apoptosis. Importantly, leukemic stem cells are strongly dependent upon HSP90 for their survival, and the HSP90 inhibitor ganetespib causes leukemic stem cell exhaustion in patient-derived mouse xenograft models. Taken together, our study reveals a molecular basis for HSP90 addiction of FLT3-ITD+ acute myeloid leukemia cells and provides a rationale for including HSP90 inhibitors in the treatment regime for FLT3-ITD+ acute myeloid leukemia.
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Affiliation(s)
- Beibei Zhang
- Oslo University Hospital, Montebello, Oslo, Norway
| | | | | | | | | | | | | | - Dagim Tadele
- Oslo University Hospital, Montebello, Oslo, Norway
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11
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Scheffler K, Rachek L, You P, Rowe AD, Wang W, Kuśnierczyk A, Kittelsen L, Bjørås M, Eide L. 8-oxoguanine DNA glycosylase (Ogg1) controls hepatic gluconeogenesis. DNA Repair (Amst) 2017; 61:56-62. [PMID: 29207315 DOI: 10.1016/j.dnarep.2017.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022]
Abstract
Mitochondrial DNA (mtDNA) resides in close proximity to metabolic reactions, and is maintained by the 8-oxoguanine DNA glycosylase (Ogg1) and other members of the base excision repair pathway. Here, we tested the hypothesis that changes in liver metabolism as under fasting/feeding conditions would be sensed by liver mtDNA, and that Ogg1 deficient mice might unravel a metabolic phenotype. Wild type (WT) and ogg1-/- mice were either fed ad libitum or subjected to fasting for 24h, and the corresponding effects on liver gene expression, DNA damage, as well as serum values were analyzed. Ogg1 deficient mice fed ad libitum exhibited hyperglycemia, elevated insulin levels and higher liver glycogen content as well as increased accumulation of 8oxoG in mtDNA compared to age- and gender matched WT mice. Interestingly, these phenotypes were absent in ogg1-/- mice during fasting. Gene expression and functional analyses suggest that the diabetogenic phenotype in the ogg1-/- mice is due to a failure to suppress gluconeogensis in the fed state. The ogg1-/- mice exhibited reduced mitochondrial electron transport chain (ETC) capacity and a combined low activity of the pyruvate dehydrogenase (PDH), alluding to inefficient channeling of glycolytic products into the citric acid cycle. Our data demonstrate a physiological role of base excision repair that goes beyond DNA maintenance, and implies that DNA repair is involved in regulating metabolism.
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Affiliation(s)
- Katja Scheffler
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Lyudmila Rachek
- University of South Alabama, Mobile, AL, United States of America
| | - Panpan You
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Newborn Screening, Oslo University Hospital, Norway
| | - Wei Wang
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lene Kittelsen
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway
| | - Magnar Bjørås
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway.
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12
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Salvador CL, Tøndel C, Rowe AD, Bjerre A, Brun A, Brackman D, Bolstad N, Mørkrid L. Renal Function Influences Diagnostic Markers in Serum and Urine: A Study of Guanidinoacetate, Creatine, Human Epididymis Protein 4, and Neutrophil Gelatinase–Associated Lipocalin in Children. ACTA ACUST UNITED AC 2017; 2:297-308. [DOI: 10.1373/jalm.2016.022145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/17/2017] [Indexed: 11/06/2022]
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13
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Kvisvik B, Mørkrid L, Røsjø H, Cvancarova M, Rowe AD, Eek C, Bendz B, Edvardsen T, Gravning J. High-Sensitivity Troponin T vs I in Acute Coronary Syndrome: Prediction of Significant Coronary Lesions and Long-term Prognosis. Clin Chem 2016; 63:552-562. [PMID: 27974383 DOI: 10.1373/clinchem.2016.261107] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND High-sensitivity cardiac troponin (hs-cTn) T and I assays are established as crucial tools for the diagnosis of acute myocardial infarction (AMI), as they have been found superior to old troponin assays. However, eventual differences between the assays in prediction of significant coronary lesions and long-term prognosis in patients with acute coronary syndrome (ACS) have not been fully unraveled. METHODS Serum concentrations of hs-cTnT (Roche), hs-cTnI (Abbott), and amino-terminal pro-B-type natriuretic peptide (NT-proBNP; Roche) in 390 non-ST-elevation (NSTE) ACS patients were evaluated in relation to significant coronary lesions on coronary angiography (defined as a stenosis >50% of the luminal diameter, with need for revascularization) and prognostic accuracy for cardiovascular mortality, all-cause mortality, as well as the composite end point of cardiovascular mortality and hospitalizations for AMI or heart failure. RESULTS The mean (SD) follow-up was 2921 (168) days. Absolute hs-cTnI concentrations were significantly higher than the hs-cTnT concentrations. The relationship between analyzed biomarkers and significant coronary lesions on coronary angiography, as quantified by the area under the ROC curve (AUC), revealed no difference between hs-cTnT [AUC, 0.81; 95% CI, 0.77-0.86] and hs-cTnI (AUC, 0.81; 95% CI, 0.76-0.86; P = NS). NT-proBNP was superior to both hs-cTn assays regarding prognostic accuracy for both cardiovascular and all-cause mortality and for the composite end point during follow-up, also in multivariate analyses. CONCLUSIONS The hs-cTnT and hs-cTnI assays displayed a similar ability to predict significant coronary lesions in NSTE-ACS patients. NT-proBNP was superior to both hs-cTn assays as a marker of long-term prognosis in this patient group.
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Affiliation(s)
- Brede Kvisvik
- Department of Cardiology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway.,Center for Heart Failure Research, University of Oslo, Norway
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, and Institute for Clinical Medicine, University of Oslo, Norway
| | - Helge Røsjø
- Department of Cardiology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway.,Center for Heart Failure Research, University of Oslo, Norway
| | - Milada Cvancarova
- Department of Cardiology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, and Institute for Clinical Medicine, University of Oslo, Norway.,Norwegian National Unit for newborn screening, Woman and Children's division, Oslo University Hospital, Rikshospitalet, Norway
| | - Christian Eek
- Department of Cardiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Bjørn Bendz
- Department of Cardiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Thor Edvardsen
- Center for Heart Failure Research, University of Oslo, Norway.,Department of Cardiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Jørgen Gravning
- Department of Cardiology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway. .,Center for Heart Failure Research, University of Oslo, Norway
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14
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Møllersen L, Moldestad O, Rowe AD, Bjølgerud A, Holm I, Tveterås L, Klungland A, Retterstøl L. Effects of Anthocyanins on CAG Repeat Instability and Behaviour in Huntington's Disease R6/1 Mice. PLoS Curr 2016; 8. [PMID: 27540492 PMCID: PMC4973517 DOI: 10.1371/currents.hd.58d04209ab6d5de0844db7ef5628ff67] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: Huntington’s disease (HD) is a progressive neurodegenerative disorder caused by CAG repeat expansions in the HTT gene. Somatic repeat expansion in the R6/1 mouse model of HD depends on mismatch repair and is worsened by base excision repair initiated by the 7,8-dihydroxy-8-oxoguanine-DNA glycosylase (Ogg1) or Nei-like 1 (Neil1). Ogg1 and Neil1 repairs common oxidative lesions. Methods: We investigated whether anthocyanin antioxidants added daily to the drinking water could affect CAG repeat instability in several organs and behaviour in R6/1 HD mice. In addition, anthocyanin-treated and untreated R6/1 HD mice at 22 weeks of age were tested in the open field test and on the rotarod. Results: Anthocyanin-treated R6/1 HD mice showed reduced instability index in the ears and in the cortex compared to untreated R6/1 mice, and no difference in liver and kidney. There were no significant differences in any of the parameters tested in the behavioural tests among anthocyanin-treated and untreated R6/1 HD mice. Conclusions: Our results indicate that continuous anthocyanin-treatment may have modest effects on CAG repeat instability in the ears and the cortex of R6/1 mice. More studies are required to investigate if anthocyanin-treatment could affect behaviour earlier in the disease course.
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Affiliation(s)
- Linda Møllersen
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Olve Moldestad
- Centre for Rare Disorders, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Alexander D Rowe
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Anja Bjølgerud
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ingunn Holm
- Department of Medical Genetics, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Linda Tveterås
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lars Retterstøl
- Department of Medical Genetics, Oslo University Hospital, Ullevål, Oslo, Norway
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15
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Frye SA, Lång E, Beyene GT, Balasingham SV, Homberset H, Rowe AD, Ambur OH, Tønjum T. The Inner Membrane Protein PilG Interacts with DNA and the Secretin PilQ in Transformation. PLoS One 2015; 10:e0134954. [PMID: 26248334 PMCID: PMC4527729 DOI: 10.1371/journal.pone.0134954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/15/2015] [Indexed: 11/19/2022] Open
Abstract
Expression of type IV pili (Tfp), filamentous appendages emanating from the bacterial surface, is indispensable for efficient neisserial transformation. Tfp pass through the secretin pore consisting of the membrane protein PilQ. PilG is a polytopic membrane protein, conserved in Gram-positive and Gram-negative bacteria, that is required for the biogenesis of neisserial Tfp. PilG null mutants are devoid of pili and non-competent for transformation. Here, recombinant full-length, truncated and mutated variants of meningococcal PilG were overexpressed, purified and characterized. We report that meningococcal PilG directly binds DNA in vitro, detected by both an electromobility shift analysis and a solid phase overlay assay. PilG DNA binding activity was independent of the presence of the consensus DNA uptake sequence. PilG-mediated DNA binding affinity was mapped to the N-terminus and was inactivated by mutation of residues 43 to 45. Notably, reduced meningococcal transformation of DNA in vivo was observed when PilG residues 43 to 45 were substituted by alanine in situ, defining a biologically significant DNA binding domain. N-terminal PilG also interacted with the N-terminal region of PilQ, which previously was shown to bind DNA. Collectively, these data suggest that PilG and PilQ in concert bind DNA during Tfp-mediated transformation.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Emma Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | | | - Ole Herman Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
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16
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Mørkrid L, Rowe AD, Elgstoen KBP, Olesen JH, Ruijter G, Hall PL, Tortorelli S, Schulze A, Kyriakopoulou L, Wamelink MMC, van de Kamp JM, Salomons GS, Rinaldo P. Continuous Age- and Sex-Adjusted Reference Intervals of Urinary Markers for Cerebral Creatine Deficiency Syndromes: A Novel Approach to the Definition of Reference Intervals. Clin Chem 2015; 61:760-8. [DOI: 10.1373/clinchem.2014.235564] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/12/2015] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Urinary concentrations of creatine and guanidinoacetic acid divided by creatinine are informative markers for cerebral creatine deficiency syndromes (CDSs). The renal excretion of these substances varies substantially with age and sex, challenging the sensitivity and specificity of postanalytical interpretation.
METHODS
Results from 155 patients with CDS and 12 507 reference individuals were contributed by 5 diagnostic laboratories. They were binned into 104 adjacent age intervals and renormalized with Box–Cox transforms (Ξ). Estimates for central tendency (μ) and dispersion (σ) of Ξ were obtained for each bin. Polynomial regression analysis was used to establish the age dependence of both μ[log(age)] and σ[log(age)]. The regression residuals were then calculated as z-scores = {Ξ − μ[log(age)]}/σ[log(age)]. The process was iterated until all z-scores outside Tukey fences ±3.372 were identified and removed. Continuous percentile charts were then calculated and plotted by retransformation.
RESULTS
Statistically significant and biologically relevant subgroups of z-scores were identified. Significantly higher marker values were seen in females than males, necessitating separate reference intervals in both adolescents and adults. Comparison between our reconstructed reference percentiles and current standard age-matched reference intervals highlights an underlying risk of false-positive and false-negative events at certain ages.
CONCLUSIONS
Disease markers depending strongly on covariates such as age and sex require large numbers of reference individuals to establish peripheral percentiles with sufficient precision. This is feasible only through collaborative data sharing and the use of appropriate statistical methods. Broad application of this approach can be implemented through freely available Web-based software.
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Affiliation(s)
- Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Katja B P Elgstoen
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jess H Olesen
- Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - George Ruijter
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Silvia Tortorelli
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Lianna Kyriakopoulou
- Division of Clinical Biochemistry, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | | | - Jiddeke M van de Kamp
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Piero Rinaldo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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17
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Abstract
During mitosis the nuclear envelope breaks down, leading to potential interactions between cytoplasmic and nuclear components. PML bodies are nuclear structures with tumor suppressor and antiviral functions. Early endosomes, on the other hand, are cytoplasmic vesicles involved in transport and growth factor signaling. Here we demonstrate that PML bodies form stable interactions with early endosomes immediately following entry into mitosis. The 2 compartments remain stably associated throughout mitosis and dissociate in the cytoplasm of newly divided daughter cells. We also show that a minor subset of PML bodies becomes anchored to the mitotic spindle poles during cell division. The study demonstrates a stable mitosis-specific interaction between a cytoplasmic and a nuclear compartment.
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Affiliation(s)
- Vuk Palibrk
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Emma Lång
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Anna Lång
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Kay Oliver Schink
- Department of Biochemistry; Institute for Cancer Research; The Norwegian Radium Hospital; Oslo University Hospital; Oslo, Norway
| | - Alexander D Rowe
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Stig Ove Bøe
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
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18
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Booth JA, Thomassen GOS, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T, Lindvall JM. Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Sci Rep 2013; 3:3053. [PMID: 24157950 PMCID: PMC6505713 DOI: 10.1038/srep03053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022] Open
Abstract
The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.
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Affiliation(s)
- James A Booth
- 1] Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [2] Department of Microbiology, University of Oslo, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [3]
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19
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Rosnes I, Rowe AD, Vik ES, Forstrøm RJ, Alseth I, Bjørås M, Dalhus B. Structural basis of DNA loop recognition by endonuclease V. Structure 2013; 21:257-65. [PMID: 23313664 DOI: 10.1016/j.str.2012.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 11/19/2012] [Accepted: 12/02/2012] [Indexed: 12/25/2022]
Abstract
The DNA repair enzyme endonuclease V (EndoV) recognizes and cleaves DNA at deaminated adenine lesions (hypoxanthine). In addition, EndoV cleaves DNA containing various helical distortions such as loops, hairpins, and flaps. To understand the molecular basis of EndoV's ability to recognize and incise DNA structures with helical distortions, we solved the crystal structure of Thermotoga maritima EndoV in complex with DNA containing a one-nucleotide loop. The structure shows that a strand-separating wedge is crucial for DNA loop recognition, with DNA strands separated precisely at the helical distortion. The additional nucleotide forming the loop rests on the surface of the wedge, while the normal adenine opposite the loop is flipped into a base recognition pocket. Our data show a different principle for DNA loop recognition and cleavage by EndoV, in which a coordinated action of a DNA-intercalating wedge and a base pocket accommodating a flipped normal base facilitate strand incision.
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Affiliation(s)
- Ida Rosnes
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, P.O. Box 4950, Nydalen, N-0424 Oslo, Norway
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20
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Møllersen L, Rowe AD, Illuzzi JL, Hildrestrand GA, Gerhold KJ, Tveterås L, Bjølgerud A, Wilson DM, Bjørås M, Klungland A. Neil1 is a genetic modifier of somatic and germline CAG trinucleotide repeat instability in R6/1 mice. Hum Mol Genet 2012; 21:4939-47. [PMID: 22914735 PMCID: PMC3607484 DOI: 10.1093/hmg/dds337] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by trinucleotide repeat (TNR) expansions. We show here that somatic TNR expansions are significantly reduced in several organs of R6/1 mice lacking exon 2 of Nei-like 1 (Neil1) (R6/1/Neil1−/−), when compared with R6/1/Neil1+/+ mice. Somatic TNR expansion is measured by two different methods, namely mean repeat change and instability index. Reduced somatic expansions are more pronounced in male R6/1/Neil1−/− mice, although expansions are also significantly reduced in brain regions of female R6/1/Neil1−/− mice. In addition, we show that the lack of functional Neil1 significantly reduces germline expansion in R6/1 male mice. In vitro, purified human NEIL1 protein binds and excises 5-hydroxycytosine in duplex DNA more efficiently than in hairpin substrates. NEIL1 excision of cytosine-derived oxidative lesions could therefore be involved in initiating the process of TNR expansion, although other DNA modifications might also contribute. Altogether, these results imply that Neil1 contributes to germline and somatic HD CAG repeat expansion.
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Affiliation(s)
- Linda Møllersen
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo, Norway
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21
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Benam AV, Lång E, Alfsnes K, Fleckenstein B, Rowe AD, Hovland E, Ambur OH, Frye SA, Tønjum T. Structure-function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation. Microbiology (Reading) 2011; 157:1329-1342. [PMID: 21330432 PMCID: PMC3140584 DOI: 10.1099/mic.0.046896-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neisseria meningitidis, the meningococcus, is naturally competent for transformation throughout its growth cycle. The uptake of exogenous DNA into the meningococcus cell during transformation is a multi-step process. Beyond the requirement for type IV pilus expression for efficient transformation, little is known about the neisserial proteins involved in DNA binding, uptake and genome integration. This study aimed to identify and characterize neisserial DNA binding proteins in order to further elucidate the multi-factorial transformation machinery. The meningococcus inner membrane and soluble cell fractions were searched for DNA binding components by employing 1D and 2D gel electrophoresis approaches in combination with a solid-phase overlay assay with DNA substrates. Proteins that bound DNA were identified by MS analysis. In the membrane fraction, multiple components bound DNA, including the neisserial competence lipoprotein ComL. In the soluble fraction, the meningococcus orthologue of the single-stranded DNA binding protein SSB was predominant. The DNA binding activity of the recombinant ComL and SSB proteins purified to homogeneity was verified by electromobility shift assay, and the ComL-DNA interaction was shown to be Mg²+-dependent. In 3D models of the meningococcus ComL and SSB predicted structures, potential DNA binding sites were suggested. ComL was found to co-purify with the outer membrane, directly interacting with the secretin PilQ. The combined use of 1D/2D solid-phase overlay assays with MS analysis was a useful strategy for identifying DNA binding components. The ComL DNA binding properties and outer membrane localization suggest that this lipoprotein plays a direct role in neisserial transformation, while neisserial SSB is a DNA binding protein that contributes to the terminal part of the transformation process.
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Affiliation(s)
- Afsaneh V Benam
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Emma Lång
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Kristian Alfsnes
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Burkhard Fleckenstein
- Centre for Immune Regulation, Institute of Immunology, University of Oslo, NO-0027 Oslo, Norway
| | - Alexander D Rowe
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
| | - Eirik Hovland
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Stephan A Frye
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
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22
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Thomassen GOS, Weel-Sneve R, Rowe AD, Booth JA, Lindvall JM, Lagesen K, Kristiansen KI, Bjørås M, Rognes T. Tiling array analysis of UV treated Escherichia coli predicts novel differentially expressed small peptides. PLoS One 2010; 5:e15356. [PMID: 21203457 PMCID: PMC3009722 DOI: 10.1371/journal.pone.0015356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/09/2010] [Indexed: 11/19/2022] Open
Abstract
Background Despite comprehensive investigation, the Escherichia coli SOS response system is not yet fully understood. We have applied custom designed whole genome tiling arrays to measure UV invoked transcriptional changes in E. coli. This study provides a more complete insight into the transcriptome and the UV irradiation response of this microorganism. Results We detected a number of novel differentially expressed transcripts in addition to the expected SOS response genes (such as sulA, recN, uvrA, lexA, umuC and umuD) in the UV treated cells. Several of the differentially expressed transcripts might play important roles in regulation of the cellular response to UV damage. We have predicted 23 novel small peptides from our set of detected non-gene transcripts. Further, three of the predicted peptides were cloned into protein expression vectors to test the biological activity. All three constructs expressed the predicted peptides, in which two of them were highly toxic to the cell. Additionally, a remarkably high overlap with previously in-silico predicted non-coding RNAs (ncRNAs) was detected. Generally we detected a far higher transcriptional activity than the annotation suggests, and these findings correspond with previous transcription mappings from E. coli and other organisms. Conclusions Here we demonstrate that the E. coli transcriptome consists of far more transcripts than the present annotation suggests, of which many transcripts seem important to the bacterial stress response. Sequence alignment of promoter regions suggest novel regulatory consensus sequences for some of the upregulated genes. Finally, several of the novel transcripts identified in this study encode putative small peptides, which are biologically active.
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Affiliation(s)
- Gard O. S. Thomassen
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ragnhild Weel-Sneve
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Alexander D. Rowe
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - James A. Booth
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | | | - Karin Lagesen
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Knut I. Kristiansen
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Magnar Bjørås
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
- Institute of Clinical Biochemistry, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
- * E-mail:
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23
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Thomassen GOS, Rowe AD, Lagesen K, Lindvall JM, Rognes T. Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays. PLoS One 2009; 4:e5943. [PMID: 19536279 PMCID: PMC2691959 DOI: 10.1371/journal.pone.0005943] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 05/18/2009] [Indexed: 11/21/2022] Open
Abstract
Background High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, several genome dependent variables, such as the genome's complexity and sequence composition, need to be considered in the design to ensure a high quality microarray. Secondly, since tiling projects today very often exceed the limits of conventional array-experiments, researchers cannot use established computer tools designed for commercial arrays, and instead have to redesign previous methods or create novel tools. Principal Findings Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays. We introduce a novel design method to make two 280,000 feature microarrays covering the entire genome of the bacterial species Escherichia coli and Neisseria meningitidis, respectively, as well as the use of multiple copies of control probe-sets on tiling microarrays. Furthermore, a novel normalisation and background estimation procedure for tiling arrays is presented along with a method for array analysis focused on detection of short transcripts. The design, normalisation and analysis methods have been applied in various experiments and several of the detected novel short transcripts have been biologically confirmed by Northern blot tests. Conclusions Tiling-arrays are becoming increasingly applicable in genomic research, but researchers still lack both the tools for custom design of arrays, as well as the systems and procedures for analysis of the vast amount of data resulting from such experiments. We believe that the methods described herein will be a useful contribution and resource for researchers designing and analysing custom tiling arrays for both bacteria and higher organisms.
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Affiliation(s)
- Gard O. S. Thomassen
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Alexander D. Rowe
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Karin Lagesen
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | | | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
- * E-mail:
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Sowa Y, Rowe AD, Leake MC, Yakushi T, Homma M, Ishijima A, Berry RM. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 2005; 437:916-9. [PMID: 16208378 DOI: 10.1038/nature04003] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 07/11/2005] [Indexed: 11/09/2022]
Abstract
The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel many species of swimming bacteria. The rotor is a set of rings up to 45 nm in diameter in the cytoplasmic membrane; the stator contains about ten torque-generating units anchored to the cell wall at the perimeter of the rotor. The free-energy source for the motor is an inward-directed electrochemical gradient of ions across the cytoplasmic membrane, the protonmotive force or sodium-motive force for H+-driven and Na+-driven motors, respectively. Here we demonstrate a stepping motion of a Na+-driven chimaeric flagellar motor in Escherichia coli at low sodium-motive force and with controlled expression of a small number of torque-generating units. We observe 26 steps per revolution, which is consistent with the periodicity of the ring of FliG protein, the proposed site of torque generation on the rotor. Backwards steps despite the absence of the flagellar switching protein CheY indicate a small change in free energy per step, similar to that of a single ion transit.
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Affiliation(s)
- Yoshiyuki Sowa
- Department of Applied Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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Rowe AD, Bullock PR, Polkey CE, Morris RG. "Theory of mind" impairments and their relationship to executive functioning following frontal lobe excisions. Brain 2001; 124:600-16. [PMID: 11222459 DOI: 10.1093/brain/124.3.600] [Citation(s) in RCA: 232] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has been suggested that mental states play an important role in determining behaviour and that mental state attributions ("theory of mind") underlie the ability to understand and predict other peoples' behaviour. Theory of mind was investigated in 31 patients with unilateral frontal lobe lesions (15 right-sided and 16 left-sided) by comparing their performance with that of 31 matched control subjects. The ability to infer first- and second-order beliefs was tested by requiring subjects to listen to stories in which a protagonist acted upon a false belief. Both patient groups exhibited significantly impaired performance on the two theory of mind measures. Both frontal lobe groups also exhibited a range of deficits in tests of executive functions, but analyses revealed that these seemed to be independent of theory of mind impairments. These findings are discussed in terms of the hypothesis of a specialized, adaptive brain system underlying theory of mind reasoning ability, and are related to observed difficulties in social functioning among patients with frontal lobe damage.
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Affiliation(s)
- A D Rowe
- Department of Psychology, Institute of Psychiatry, De Crespigny Park, King's College Neuroscience Centre, London SE5 8AF, UK.
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