1
|
Vandebergh M, Ramos EM, Corriveau-Lecavalier N, Ramanan VK, Kornak J, Mester C, Kolander T, Brushaber D, Staffaroni AM, Geschwind D, Wolf A, Kantarci K, Gendron TF, Petrucelli L, Van den Broeck M, Wynants S, Baker MC, Borrego – Écija S, Appleby B, Barmada S, Bozoki A, Clark D, Darby RR, Dickerson BC, Domoto-Reilly K, Fields JA, Galasko DR, Ghoshal N, Graff-Radford N, Grant IM, Honig LS, Hsiung GYR, Huey ED, Irwin D, Knopman DS, Kwan JY, Léger GC, Litvan I, Masdeu JC, Mendez MF, Onyike C, Pascual B, Pressman P, Ritter A, Roberson ED, Snyder A, Sullivan AC, Tartaglia MC, Wint D, Heuer HW, Forsberg LK, Boxer AL, Rosen HJ, Boeve BF, Rademakers R. Gene specific effects on brain volume and cognition of TMEM106B in frontotemporal lobar degeneration. medRxiv 2024:2024.04.05.24305253. [PMID: 38633784 PMCID: PMC11023674 DOI: 10.1101/2024.04.05.24305253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Background and Objectives TMEM106B has been proposed as a modifier of disease risk in FTLD-TDP, particularly in GRN mutation carriers. Furthermore, TMEM106B has been investigated as a disease modifier in the context of healthy aging and across multiple neurodegenerative diseases. The objective of this study is to evaluate and compare the effect of TMEM106B on gray matter volume and cognition in each of the common genetic FTD groups and in sporadic FTD patients. Methods Participants were enrolled through the ARTFL/LEFFTDS Longitudinal Frontotemporal Lobar Degeneration (ALLFTD) study, which includes symptomatic and presymptomatic individuals with a pathogenic mutation in C9orf72, GRN, MAPT, VCP, TBK1, TARDBP, symptomatic non-mutation carriers, and non-carrier family controls. All participants were genotyped for the TMEM106B rs1990622 SNP. Cross-sectionally, linear mixed-effects models were fitted to assess an association between TMEM106B and genetic group interaction with each outcome measure (gray matter volume and UDS3-EF for cognition), adjusting for education, age, sex and CDR®+NACC-FTLD sum of boxes. Subsequently, associations between TMEM106B and each outcome measure were investigated within the genetic group. For longitudinal modeling, linear mixed-effects models with time by TMEM106B predictor interactions were fitted. Results The minor allele of TMEM106B rs1990622, linked to a decreased risk of FTD, associated with greater gray matter volume in GRN mutation carriers under the recessive dosage model. This was most pronounced in the thalamus in the left hemisphere, with a retained association when considering presymptomatic GRN mutation carriers only. The minor allele of TMEM106B rs1990622 also associated with greater cognitive scores among all C9orf72 mutation carriers and in presymptomatic C9orf72 mutation carriers, under the recessive dosage model. Discussion We identified associations of TMEM106B with gray matter volume and cognition in the presence of GRN and C9orf72 mutations. This further supports TMEM106B as modifier of TDP-43 pathology. The association of TMEM106B with outcomes of interest in presymptomatic GRN and C9orf72 mutation carriers could additionally reflect TMEM106B's impact on divergent pathophysiological changes before the appearance of clinical symptoms.
Collapse
Affiliation(s)
- Marijne Vandebergh
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Eliana Marisa Ramos
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nick Corriveau-Lecavalier
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | | | - John Kornak
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Carly Mester
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Tyler Kolander
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Danielle Brushaber
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Adam M Staffaroni
- Department of Neurology, Memory and Aging Center, University of California, San Francisco Weill Institute for Neurosciences, San Francisco, CA, USA
| | - Daniel Geschwind
- Institute for Precision Health, Departments of Neurology, Psychiatry and Human Genetics at David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy Wolf
- Department of Neurology, Memory and Aging Center, University of California, San Francisco Weill Institute for Neurosciences, San Francisco, CA, USA
| | - Kejal Kantarci
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Marleen Van den Broeck
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Wynants
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Sergi Borrego – Écija
- Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona, Barcelona, Spain
| | - Brian Appleby
- Department of Neurology, Case Western Reserve University, Cleveland, OH, USA
| | - Sami Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Bozoki
- Department of Neurology, University of North Carolina, Chapel Hill, NC, USA
| | - David Clark
- Department of Neurology, Indiana University, Indianapolis, IN, USA
| | - R Ryan Darby
- Department of Neurology, Vanderbilt University, Nashville, TN, USA
| | | | | | - Julie A. Fields
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Douglas R. Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Nupur Ghoshal
- Departments of Neurology and Psychiatry, Washington University School of Medicine, Washington University, St. Louis, MO, USA
| | | | - Ian M Grant
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - Lawrence S Honig
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Neurology, Columbia University, New York, NY, USA
| | - Ging-Yuek Robin Hsiung
- Division of Neurology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Edward D Huey
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - David Irwin
- Department of Neurology and Penn Frontotemporal Degeneration Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David S Knopman
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Gabriel C Léger
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Irene Litvan
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Joseph C Masdeu
- Department of Neurology, Houston Methodist, Houston, TX, USA
| | - Mario F Mendez
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chiadi Onyike
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Belen Pascual
- Department of Neurology, Houston Methodist, Houston, TX, USA
| | - Peter Pressman
- Department of Neurology, University of Colorado, Aurora, CO, USA
| | - Aaron Ritter
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, 89106, USA
| | - Erik D Roberson
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Allison Snyder
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anna Campbell Sullivan
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, UT Health San Antonio
| | - M Carmela Tartaglia
- Tanz Centre for Research in Neurodegenerative Diseases, Division of Neurology, University of Toronto, Toronto, Ontario, Canada
| | - Dylan Wint
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, 89106, USA
| | - Hilary W Heuer
- Department of Neurology, Memory and Aging Center, University of California, San Francisco Weill Institute for Neurosciences, San Francisco, CA, USA
| | - Leah K Forsberg
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Adam L Boxer
- Department of Neurology, Memory and Aging Center, University of California, San Francisco Weill Institute for Neurosciences, San Francisco, CA, USA
| | - Howard J Rosen
- Department of Neurology, Memory and Aging Center, University of California, San Francisco Weill Institute for Neurosciences, San Francisco, CA, USA
| | | | - Rosa Rademakers
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| |
Collapse
|
2
|
Morris AC, Ibrahim Z, Heslin M, Moghraby OS, Stringaris A, Grant IM, Zalewski L, Pritchard M, Stewart R, Hotopf M, Pickles A, Dobson RJB, Simonoff E, Downs J. Assessing the feasibility of a web-based outcome measurement system in child and adolescent mental health services - myHealthE a randomised controlled feasibility pilot study. Child Adolesc Ment Health 2023; 28:128-147. [PMID: 35684987 PMCID: PMC10083915 DOI: 10.1111/camh.12571] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/01/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Interest in internet-based patient reported outcome measure (PROM) collection is increasing. The NHS myHealthE (MHE) web-based monitoring system was developed to address the limitations of paper-based PROM completion. MHE provides a simple and secure way for families accessing Child and Adolescent Mental Health Services to report clinical information and track their child's progress. This study aimed to assess whether MHE improves the completion of the Strengths and Difficulties Questionnaire (SDQ) compared with paper collection. Secondary objectives were to explore caregiver satisfaction and application acceptability. METHODS A 12-week single-blinded randomised controlled feasibility pilot trial of MHE was conducted with 196 families accessing neurodevelopmental services in south London to examine whether electronic questionnaires are completed more readily than paper-based questionnaires over a 3-month period. Follow up process evaluation phone calls with a subset (n = 8) of caregivers explored system satisfaction and usability. RESULTS MHE group assignment was significantly associated with an increased probability of completing an SDQ-P in the study period (adjusted hazard ratio (HR) 12.1, 95% CI 4.7-31.0; p = <.001). Of those caregivers' who received the MHE invitation (n = 68) 69.1% completed an SDQ using the platform compared to 8.8% in the control group (n = 68). The system was well received by caregivers, who cited numerous benefits of using MHE, for example, real-time feedback and ease of completion. CONCLUSIONS MHE holds promise for improving PROM completion rates. Research is needed to refine MHE, evaluate large-scale MHE implementation, cost effectiveness and explore factors associated with differences in electronic questionnaire uptake.
Collapse
Affiliation(s)
- Anna C. Morris
- South London and Maudsley NHS Foundation TrustLondonUK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| | - Zina Ibrahim
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Margaret Heslin
- Health Service and Population Research Department, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| | | | - Argyris Stringaris
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- Emotion & Development Branch, National Institute of Mental HealthNational Institutes of HealthBethesdaMDUSA
| | - Ian M. Grant
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| | - Lukasz Zalewski
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| | - Megan Pritchard
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Robert Stewart
- South London and Maudsley NHS Foundation TrustLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Matthew Hotopf
- South London and Maudsley NHS Foundation TrustLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Andrew Pickles
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Richard J. B. Dobson
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Emily Simonoff
- South London and Maudsley NHS Foundation TrustLondonUK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| | - Johnny Downs
- South London and Maudsley NHS Foundation TrustLondonUK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- NIHR South London and Maudsley Biomedical Research CentreLondonUK
| |
Collapse
|
3
|
Morris AC, Ibrahim Z, Moghraby OS, Stringaris A, Grant IM, Zalewski L, McClellan S, Moriarty G, Simonoff E, Dobson RJB, Downs J. Moving from development to implementation of digital innovations within the NHS: myHealthE, a remote monitoring system for tracking patient outcomes in child and adolescent mental health services. Digit Health 2023; 9:20552076231211551. [PMID: 37954687 PMCID: PMC10638880 DOI: 10.1177/20552076231211551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Objective This paper aims to report our experience of developing, implementing, and evaluating myHealthE (MHE), a digital innovation for Child and Adolescents Mental Health Services (CAMHS), which automates the remote collection and reporting of Patient-Reported Outcome Measures (PROMs) into National Health Services (NHS) electronic healthcare records. Methods We describe the logistical and governance issues encountered in developing the MHE interface with patient-identifiable information, and the steps taken to overcome these development barriers. We describe the application's architecture and hosting environment to enable its operability within the NHS, as well as the capabilities needed within the technical team to bridge the gap between academic development and NHS operational teams. Results We present evidence on the feasibility and acceptability of this system within clinical services and the process of iterative development, highlighting additional functions that were incorporated to increase system utility. Conclusion This article provides a framework with which to plan, develop, and implement automated PROM collection from remote devices back to NHS infrastructure. The challenges and solutions described in this paper will be pertinent to other digital health innovation researchers aspiring to deploy interoperable systems within NHS clinical systems.
Collapse
Affiliation(s)
- Anna C Morris
- South London and Maudsley NHS Foundation Trust, London, UK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Zina Ibrahim
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Omer S Moghraby
- South London and Maudsley NHS Foundation Trust, London, UK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Argyris Stringaris
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Emotion & Development Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Ian M Grant
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR South London and Maudsley Biomedical Research Centre, London, UK
| | - Lukasz Zalewski
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR South London and Maudsley Biomedical Research Centre, London, UK
| | | | - Garry Moriarty
- South London and Maudsley NHS Foundation Trust, London, UK
| | - Emily Simonoff
- South London and Maudsley NHS Foundation Trust, London, UK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR South London and Maudsley Biomedical Research Centre, London, UK
| | - Richard JB Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR South London and Maudsley Biomedical Research Centre, London, UK
- Health Data Research UK London, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Johnny Downs
- South London and Maudsley NHS Foundation Trust, London, UK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR South London and Maudsley Biomedical Research Centre, London, UK
| |
Collapse
|
4
|
Kornak J, Fields J, Kremers W, Farmer S, Heuer HW, Forsberg L, Brushaber D, Rindels A, Dodge H, Weintraub S, Besser L, Appleby B, Bordelon Y, Bove J, Brannelly P, Caso C, Coppola G, Dever R, Dheel C, Dickerson B, Dickinson S, Dominguez S, Domoto-Reilly K, Faber K, Ferrall J, Fishman A, Fong J, Foroud T, Gavrilova R, Gearhart D, Ghazanfari B, Ghoshal N, Goldman J, Graff-Radford J, Graff-Radford N, Grant IM, Grossman M, Haley D, Hsiao J, Hsiung R, Huey ED, Irwin D, Jones D, Jones L, Kantarci K, Karydas A, Kaufer D, Kerwin D, Knopman D, Kraft R, Kramer J, Kukull W, Lapid M, Litvan I, Ljubenkov P, Lucente D, Lungu C, Mackenzie I, Maldonado M, Manoochehri M, McGinnis S, McKinley E, Mendez M, Miller B, Multani N, Onyike C, Padmanabhan J, Pantelyat A, Pearlman R, Petrucelli L, Potter M, Rademakers R, Ramos EM, Rankin K, Rascovsky K, Roberson ED, Rogalski-Miller E, Sengdy P, Shaw L, Staffaroni AM, Sutherland M, Syrjanen J, Tartaglia C, Tatton N, Taylor J, Toga A, Trojanowski J, Wang P, Wong B, Wszolek Z, Boeve B, Boxer A, Rosen H. Nonlinear Z-score modeling for improved detection of cognitive abnormality. Alzheimers Dement (Amst) 2019; 11:797-808. [PMID: 31872042 PMCID: PMC6911910 DOI: 10.1016/j.dadm.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Conventional Z-scores are generated by subtracting the mean and dividing by the standard deviation. More recent methods linearly correct for age, sex, and education, so that these "adjusted" Z-scores better represent whether an individual's cognitive performance is abnormal. Extreme negative Z-scores for individuals relative to this normative distribution are considered indicative of cognitive deficiency. METHODS In this article, we consider nonlinear shape constrained additive models accounting for age, sex, and education (correcting for nonlinearity). Additional shape constrained additive models account for varying standard deviation of the cognitive scores with age (correcting for heterogeneity of variance). RESULTS Corrected Z-scores based on nonlinear shape constrained additive models provide improved adjustment for age, sex, and education, as indicated by higher adjusted-R2. DISCUSSION Nonlinearly corrected Z-scores with respect to age, sex, and education with age-varying residual standard deviation allow for improved detection of non-normative extreme cognitive scores.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Hiroko Dodge
- Oregon Health and Science University, Portland, OR, USA
- University of Michigan, Ann Arbor, MI, USA
| | | | - Lilah Besser
- Florida Atlantic University, Boca Raton, FL, USA
| | | | - Yvette Bordelon
- Department of Psychiatry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jessica Bove
- University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick Brannelly
- Tau Consortium, Rainwater Charitable Foundation, Fort Worth, TX, USA
| | | | - Giovanni Coppola
- Department of Psychiatry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | | | - Susan Dickinson
- Association for Frontotemporal Degeneration, Radnor, PA, USA
| | | | | | - Kelley Faber
- National Cell Repository for Alzheimer's Disease (NCRAD), Indiana University, Indianapolis, IN, USA
| | | | - Ann Fishman
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Tatiana Foroud
- National Cell Repository for Alzheimer's Disease (NCRAD), Indiana University, Indianapolis, IN, USA
| | | | | | | | | | | | | | | | | | | | | | - John Hsiao
- National Institute on Aging (NIA), Bethesda, MD, USA
| | - Robin Hsiung
- University of British Columbia, Vancouver, British Columbia, Canada
| | | | - David Irwin
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | - Ruth Kraft
- Mayo Clinic Rochester, Rochester, MN, USA
| | | | - Walter Kukull
- National Alzheimer Coordinating Center (NACC), University of Washington, Seattle, WA, USA
| | | | | | | | | | - Codrin Lungu
- National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Ian Mackenzie
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Miranda Maldonado
- Department of Psychiatry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | - Emily McKinley
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mario Mendez
- Department of Psychiatry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | - Madeline Potter
- National Cell Repository for Alzheimer's Disease (NCRAD), Indiana University, Indianapolis, IN, USA
| | | | - Eliana Marisa Ramos
- Department of Psychiatry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | | | | | - Pheth Sengdy
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Les Shaw
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Margaret Sutherland
- National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | | | | | - Nadine Tatton
- Association for Frontotemporal Degeneration, Radnor, PA, USA
| | | | - Arthur Toga
- Laboratory of Neuroimaging (LONI), USC, Los Angeles, CA, USA
| | | | | | | | | | - Brad Boeve
- Mayo Clinic Rochester, Rochester, MN, USA
| | | | | | | |
Collapse
|
5
|
Limb MAL, Suardíaz R, Grant IM, Mulholland AJ. Quantum Mechanics/Molecular Mechanics Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme. Chemistry 2019; 25:764-768. [PMID: 30347479 DOI: 10.1002/chem.201805250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 01/07/2023]
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on lysozyme show significant distortion of the bound saccharide is required to facilitate the catalytic reaction.
Collapse
Affiliation(s)
- Michael A L Limb
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS81TS, UK
| | - Reynier Suardíaz
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS81TS, UK
| | - Ian M Grant
- Present address: Institute of Psychiatry, Psychology & Neuroscience, King's College London, Denmark Hill, London, SE5 8AF, UK
| | - Adrian J Mulholland
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS81TS, UK
| |
Collapse
|
6
|
Ivanov SD, Grant IM, Marx D. Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated. J Chem Phys 2016; 143:124304. [PMID: 26429008 DOI: 10.1063/1.4931052] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.
Collapse
Affiliation(s)
- Sergei D Ivanov
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Ian M Grant
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| |
Collapse
|
7
|
De Domenico E, Owens NDL, Grant IM, Gomes-Faria R, Gilchrist MJ. Molecular asymmetry in the 8-cell stage Xenopus tropicalis embryo described by single blastomere transcript sequencing. Dev Biol 2015; 408:252-68. [PMID: 26100918 PMCID: PMC4684228 DOI: 10.1016/j.ydbio.2015.06.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 12/17/2022]
Abstract
Correct development of the vertebrate body plan requires the early definition of two asymmetric, perpendicular axes. The first axis is established during oocyte maturation, and the second is established by symmetry breaking shortly after fertilization. The physical processes generating the second asymmetric, or dorsal-ventral, axis are well understood, but the specific molecular determinants, presumed to be maternal gene products, are poorly characterized. Whilst enrichment of maternal mRNAs at the animal and vegetal poles in both the oocyte and the early embryo has been studied, little is known about the distribution of maternal mRNAs along either the dorsal-ventral or left-right axes during the early cleavage stages. Here we report an unbiased analysis of the distribution of maternal mRNA on all axes of the Xenopus tropicalis 8-cell stage embryo, based on sequencing of single blastomeres whose positions within the embryo are known. Analysis of pooled data from complete sets of blastomeres from four embryos has identified 908 mRNAs enriched in either the animal or vegetal blastomeres, of which 793 are not previously reported as enriched. In contrast, we find no evidence for asymmetric distribution along either the dorsal-ventral or left-right axes. We confirm that animal pole enrichment is on average distinctly lower than vegetal pole enrichment, and that considerable variation is found between reported enrichment levels in different studies. We use publicly available data to show that there is a significant association between genes with human disease annotation and enrichment at the animal pole. Mutations in the human ortholog of the most animally enriched novel gene, Slc35d1, are causative for Schneckenbecken dysplasia, and we show that a similar phenotype is produced by depletion of the orthologous protein in Xenopus embryos.
Collapse
Affiliation(s)
- Elena De Domenico
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Nick D L Owens
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Ian M Grant
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Rosa Gomes-Faria
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
| |
Collapse
|
8
|
Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 2015; 408:345-57. [PMID: 26391338 PMCID: PMC4684507 DOI: 10.1016/j.ydbio.2015.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 08/18/2015] [Accepted: 09/09/2015] [Indexed: 12/18/2022]
Abstract
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
Collapse
Affiliation(s)
- Ian M Grant
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prasad Trivedi
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Karpinka
- Xenbase, Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Limin Liu
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Aaron M Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - P Todd Stukenberg
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
| |
Collapse
|
9
|
Bowman AL, Grant IM, Mulholland AJ. QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate. Chem Commun (Camb) 2008:4425-7. [PMID: 18802578 DOI: 10.1039/b810099c] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations indicate that the reaction of native HEWL with its natural substrate involves a covalent intermediate, in contrast to the 'textbook' mechanism for this seminal enzyme.
Collapse
Affiliation(s)
- Anna L Bowman
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK BS8 1TS
| | | | | |
Collapse
|
10
|
Grant IM, Watts TJ, Allworth MB, Morley FHW, Caple IW. Sheep flock health and production: The Mackinnon project of the University of Melbourne Veterinary School. Aust Vet J 1985. [DOI: 10.1111/j.1751-0813.1985.tb13921.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|