1
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Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular determinants and signaling effects of PKA RIα phase separation. Mol Cell 2024; 84:1570-1584.e7. [PMID: 38537638 PMCID: PMC11031308 DOI: 10.1016/j.molcel.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/07/2023] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures proper cellular function. Liquid-liquid phase separation (LLPS) of the ubiquitous PKA regulatory subunit RIα promotes cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces, combined with the cAMP-induced unleashing of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence, drive RIα condensate formation in the cytosol of mammalian cells, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in forming a non-canonical R:C complex, which recruits active PKA-C to RIα condensates to maintain low basal PKA activity in the cytosol. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
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Affiliation(s)
- Julia C Hardy
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily H Pool
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica G H Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingrong Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daojia R Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Max Palay
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gerald Tan
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lisa Chen
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jaclyn L C Choi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ha Neul Lee
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stefan Strack
- Department of Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Dong Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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2
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Do QB, Noor H, Marquez-Gomez R, Cramb KML, Ng B, Abbey A, Ibarra-Aizpurua N, Caiazza MC, Sharifi P, Lang C, Beccano-Kelly D, Baleriola J, Bengoa-Vergniory N, Wade-Martins R. Early deficits in an in vitro striatal microcircuit model carrying the Parkinson's GBA-N370S mutation. NPJ Parkinsons Dis 2024; 10:82. [PMID: 38609392 PMCID: PMC11014935 DOI: 10.1038/s41531-024-00694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Understanding medium spiny neuron (MSN) physiology is essential to understand motor impairments in Parkinson's disease (PD) given the architecture of the basal ganglia. Here, we developed a custom three-chambered microfluidic platform and established a cortico-striato-nigral microcircuit partially recapitulating the striatal presynaptic landscape in vitro using induced pluripotent stem cell (iPSC)-derived neurons. We found that, cortical glutamatergic projections facilitated MSN synaptic activity, and dopaminergic transmission enhanced maturation of MSNs in vitro. Replacement of wild-type iPSC-derived dopamine neurons (iPSC-DaNs) in the striatal microcircuit with those carrying the PD-related GBA-N370S mutation led to a depolarisation of resting membrane potential and an increase in rheobase in iPSC-MSNs, as well as a reduction in both voltage-gated sodium and potassium currents. Such deficits were resolved in late microcircuit cultures, and could be reversed in younger cultures with antagonism of protein kinase A activity in iPSC-MSNs. Taken together, our results highlight the unique utility of modelling striatal neurons in a modular physiological circuit to reveal mechanistic insights into GBA1 mutations in PD.
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Affiliation(s)
- Quyen B Do
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Humaira Noor
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Nuffield Department of Medicine (NDM), University of Oxford, Henry Wellcome Building for Molecular Physiology, Old Road, Oxford, OX3 7BN, UK
| | - Ricardo Marquez-Gomez
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Kaitlyn M L Cramb
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Bryan Ng
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Ajantha Abbey
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Naroa Ibarra-Aizpurua
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Parnaz Sharifi
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
| | - Charmaine Lang
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Dayne Beccano-Kelly
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK
| | - Jimena Baleriola
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- Ikerbasque-Basque Foundation for Science, Bilbao, Spain
| | - Nora Bengoa-Vergniory
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK.
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Achucarro Basque Center for Neuroscience, Leioa, Spain.
- Ikerbasque-Basque Foundation for Science, Bilbao, Spain.
- University of the Basque Country (UPV/EHU), Department of Neuroscience, Leioa, Spain.
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford, OX1 3QU, UK.
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford, OX1 3QU, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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Glebov-McCloud AGP, Saide WS, Gaine ME, Strack S. Protein Kinase A in neurological disorders. J Neurodev Disord 2024; 16:9. [PMID: 38481146 PMCID: PMC10936040 DOI: 10.1186/s11689-024-09525-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Cyclic adenosine 3', 5' monophosphate (cAMP)-dependent Protein Kinase A (PKA) is a multi-functional serine/threonine kinase that regulates a wide variety of physiological processes including gene transcription, metabolism, and synaptic plasticity. Genomic sequencing studies have identified both germline and somatic variants of the catalytic and regulatory subunits of PKA in patients with metabolic and neurodevelopmental disorders. In this review we discuss the classical cAMP/PKA signaling pathway and the disease phenotypes that result from PKA variants. This review highlights distinct isoform-specific cognitive deficits that occur in both PKA catalytic and regulatory subunits, and how tissue-specific distribution of these isoforms may contribute to neurodevelopmental disorders in comparison to more generalized endocrine dysfunction.
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Affiliation(s)
- Alexander G P Glebov-McCloud
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Walter S Saide
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Marie E Gaine
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy Building, College of Pharmacy, University of Iowa, 180 S. Grand Ave, Iowa City, IA, 52242, USA
- Iowa Neuroscience Institute, Intellectual and Developmental Disabilities Research Center, Iowa City, IA, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA.
- Iowa Neuroscience Institute, Intellectual and Developmental Disabilities Research Center, Iowa City, IA, USA.
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4
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Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
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Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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5
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Hardy JC, Pool EH, Bruystens JGH, Zhou X, Li Q, Zhou DR, Palay M, Tan G, Chen L, Choi JLC, Lee HN, Strack S, Wang D, Taylor SS, Mehta S, Zhang J. Molecular Determinants and Signaling Effects of PKA RIα Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570836. [PMID: 38168176 PMCID: PMC10760030 DOI: 10.1101/2023.12.10.570836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures the specific execution of various cellular functions. Liquid-liquid phase separation (LLPS) of the ubiquitously expressed PKA regulatory subunit RIα was recently identified as a major driver of cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces combined with the cAMP-induced release of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence are required to drive RIα condensate formation in cytosol, which is antagonized by docking to A-kinase anchoring proteins. Strikingly, we find that the RIα pseudosubstrate region is critically involved in the formation of a non-canonical R:C complex, which serves to maintain low basal PKA activity in the cytosol by enabling the recruitment of active PKA-C to RIα condensates. Our results suggest that RIα LLPS not only facilitates cAMP compartmentation but also spatially restrains active PKA-C, thus highlighting the functional versatility of biomolecular condensates in driving signaling specificity.
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6
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Ortiz GG, Ramírez-Jirano J, Arizaga RL, Delgado-Lara DLC, Torres-Sánchez ED. Frontotemporal-TDP and LATE Neurocognitive Disorders: A Pathophysiological and Genetic Approach. Brain Sci 2023; 13:1474. [PMID: 37891841 PMCID: PMC10605418 DOI: 10.3390/brainsci13101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Frontotemporal lobar degeneration (FTLD) belongs to a heterogeneous group of highly complex neurodegenerative diseases and represents the second cause of presenile dementia in individuals under 65. Frontotemporal-TDP is a subgroup of frontotemporal dementia characterized by the aggregation of abnormal protein deposits, predominantly transactive response DNA-binding protein 43 (TDP-43), in the frontal and temporal brain regions. These deposits lead to progressive degeneration of neurons resulting in cognitive and behavioral impairments. Limbic age-related encephalopathy (LATE) pertains to age-related cognitive decline primarily affecting the limbic system, which is crucial for memory, emotions, and learning. However, distinct, emerging research suggests a potential overlap in pathogenic processes, with some cases of limbic encephalopathy displaying TDP-43 pathology. Genetic factors play a pivotal role in both disorders. Mutations in various genes, such as progranulin (GRN) and chromosome 9 open reading frame 72 (C9orf72), have been identified as causative in frontotemporal-TDP. Similarly, specific genetic variants have been associated with an increased risk of developing LATE. Understanding these genetic links provides crucial insights into disease mechanisms and the potential for targeted therapies.
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Affiliation(s)
- Genaro Gabriel Ortiz
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico;
- Postgraduate Gerontology Program, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Javier Ramírez-Jirano
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute, IMSS, Guadalajara 44340, Jalisco, Mexico;
| | - Raul L. Arizaga
- Public Health Department, School of Medicine, University of Buenos Aires, Buenos Aires C1121ABG, Argentina;
| | - Daniela L. C. Delgado-Lara
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico;
- Departamento Académico de Formación Universitaria, Ciencias de la Salud, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
| | - Erandis D. Torres-Sánchez
- Department of Medical and Life Sciences, University Center of la Cienega, University of Guadalajara, Ocotlan 47820, Jalisco, Mexico
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7
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Ondičová M, Irwin RE, Thursby SJ, Hilman L, Caffrey A, Cassidy T, McLaughlin M, Lees-Murdock DJ, Ward M, Murphy M, Lamers Y, Pentieva K, McNulty H, Walsh CP. Folic acid intervention during pregnancy alters DNA methylation, affecting neural target genes through two distinct mechanisms. Clin Epigenetics 2022; 14:63. [PMID: 35578268 PMCID: PMC9112484 DOI: 10.1186/s13148-022-01282-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/29/2022] [Indexed: 12/22/2022] Open
Abstract
Background We previously showed that continued folic acid (FA) supplementation beyond the first trimester of pregnancy appears to have beneficial effects on neurocognitive performance in children followed for up to 11 years, but the biological mechanism for this effect has remained unclear. Using samples from our randomized controlled trial of folic acid supplementation in second and third trimester (FASSTT), where significant improvements in cognitive and psychosocial performance were demonstrated in children from mothers supplemented in pregnancy with 400 µg/day FA compared with placebo, we examined methylation patterns from cord blood (CB) using the EPIC array which covers approximately 850,000 cytosine–guanine (CG) sites across the genome. Genes showing significant differences were verified using pyrosequencing and mechanistic approaches used in vitro to determine effects on transcription. Results FA supplementation resulted in significant differences in methylation, particularly at brain-related genes. Further analysis showed these genes split into two groups. In one group, which included the CES1 gene, methylation changes at the promoters were important for regulating transcription. We also identified a second group which had a characteristic bimodal profile, with low promoter and high gene body (GB) methylation. In the latter, loss of methylation in the GB is linked to decreases in transcription: this group included the PRKAR1B/HEATR2 genes and the dopamine receptor regulator PDE4C. Overall, methylation in CB also showed good correlation with methylation profiles seen in a published data set of late gestation foetal brain samples. Conclusion We show here clear alterations in DNA methylation at specific classes of neurodevelopmental genes in the same cohort of children, born to FA-supplemented mothers, who previously showed improved cognitive and psychosocial performance. Our results show measurable differences at neural genes which are important for transcriptional regulation and add to the supporting evidence for continued FA supplementation throughout later gestation. This trial was registered on 15 May 2013 at www.isrctn.com as ISRCTN19917787. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01282-y.
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Affiliation(s)
- Miroslava Ondičová
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Rachelle E Irwin
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Sara-Jayne Thursby
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK.,The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Luke Hilman
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Aoife Caffrey
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Tony Cassidy
- Psychology Institute, Ulster University, Coleraine, Northern Ireland, UK
| | - Marian McLaughlin
- Psychology Institute, Ulster University, Coleraine, Northern Ireland, UK
| | - Diane J Lees-Murdock
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Michelle Murphy
- Unitat de Medicina Preventiva i Salut Pública, Facultat de Medicina i Ciències de La Salut, Universitat Rovira i Virgili, Reus, Spain
| | - Yvonne Lamers
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, The University of British Columbia, and British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK. .,Centre for Research and Development, Region Gävleborg/Uppsala University, Gävle, Sweden.
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8
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Papale LA, Madrid A, Zhang Q, Chen K, Sak L, Keleş S, Alisch RS. Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders. Genome Res 2022; 32:266-279. [PMID: 34949667 PMCID: PMC8805724 DOI: 10.1101/gr.276137.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/22/2021] [Indexed: 11/25/2022]
Abstract
Mouse knockouts of Cntnap2 show altered neurodevelopmental behavior, deficits in striatal GABAergic signaling, and a genome-wide disruption of an environmentally sensitive DNA methylation modification (5-hydroxymethylcytosine [5hmC]) in the orthologs of a significant number of genes implicated in human neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2 +/-; lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2 +/- female mice show repetitive behaviors and altered sociability, similar to the homozygote phenotype. Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull-down data indicated that 5hmC abundance alters the binding of the transcription factor CLOCK near the promoters of these genes (e.g., Palld, Gigyf1, and Fry), providing a mechanistic role for 5hmC in gene regulation. Together, these data support gene-by-environment hypotheses for the origins of mental illness and provide a means to identify the elusive factors contributing to complex human diseases.
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Affiliation(s)
- Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Qi Zhang
- Department Mathematics and Statistics, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Kailei Chen
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Lara Sak
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Sündüz Keleş
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
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9
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Ramms DJ, Raimondi F, Arang N, Herberg FW, Taylor SS, Gutkind JS. G αs-Protein Kinase A (PKA) Pathway Signalopathies: The Emerging Genetic Landscape and Therapeutic Potential of Human Diseases Driven by Aberrant G αs-PKA Signaling. Pharmacol Rev 2021; 73:155-197. [PMID: 34663687 PMCID: PMC11060502 DOI: 10.1124/pharmrev.120.000269] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many of the fundamental concepts of signal transduction and kinase activity are attributed to the discovery and crystallization of cAMP-dependent protein kinase, or protein kinase A. PKA is one of the best-studied kinases in human biology, with emphasis in biochemistry and biophysics, all the way to metabolism, hormone action, and gene expression regulation. It is surprising, however, that our understanding of PKA's role in disease is largely underappreciated. Although genetic mutations in the PKA holoenzyme are known to cause diseases such as Carney complex, Cushing syndrome, and acrodysostosis, the story largely stops there. With the recent explosion of genomic medicine, we can finally appreciate the broader role of the Gαs-PKA pathway in disease, with contributions from aberrant functioning G proteins and G protein-coupled receptors, as well as multiple alterations in other pathway components and negative regulators. Together, these represent a broad family of diseases we term the Gαs-PKA pathway signalopathies. The Gαs-PKA pathway signalopathies encompass diseases caused by germline, postzygotic, and somatic mutations in the Gαs-PKA pathway, with largely endocrine and neoplastic phenotypes. Here, we present a signaling-centric review of Gαs-PKA-driven pathophysiology and integrate computational and structural analysis to identify mutational themes commonly exploited by the Gαs-PKA pathway signalopathies. Major mutational themes include hotspot activating mutations in Gαs, encoded by GNAS, and mutations that destabilize the PKA holoenzyme. With this review, we hope to incite further study and ultimately the development of new therapeutic strategies in the treatment of a wide range of human diseases. SIGNIFICANCE STATEMENT: Little recognition is given to the causative role of Gαs-PKA pathway dysregulation in disease, with effects ranging from infectious disease, endocrine syndromes, and many cancers, yet these disparate diseases can all be understood by common genetic themes and biochemical signaling connections. By highlighting these common pathogenic mechanisms and bridging multiple disciplines, important progress can be made toward therapeutic advances in treating Gαs-PKA pathway-driven disease.
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Affiliation(s)
- Dana J Ramms
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Francesco Raimondi
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Nadia Arang
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Friedrich W Herberg
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Susan S Taylor
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - J Silvio Gutkind
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
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10
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Molecular Pathways Involved in Frontotemporal Lobar Degeneration with TDP-43 Proteinopathy: What Can We Learn from Proteomics? Int J Mol Sci 2021; 22:ijms221910298. [PMID: 34638637 PMCID: PMC8508653 DOI: 10.3390/ijms221910298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) is a neurodegenerative disorder clinically characterized by behavioral, language, and motor symptoms, with major impact on the lives of patients and their families. TDP-43 proteinopathy is the underlying neuropathological substrate in the majority of cases, referred to as FTLD-TDP. Several genetic causes have been identified, which have revealed some components of its pathophysiology. However, the exact mechanisms driving FTLD-TDP remain largely unknown, forestalling the development of therapies. Proteomic approaches, in particular high-throughput mass spectrometry, hold promise to help elucidate the pathogenic molecular and cellular alterations. In this review, we describe the main findings of the proteomic profiling studies performed on human FTLD-TDP brain tissue. Subsequently, we address the major biological pathways implicated in FTLD-TDP, by reviewing these data together with knowledge derived from genomic and transcriptomic literature. We illustrate that an integrated perspective, encompassing both proteomic, genetic, and transcriptomic discoveries, is vital to unravel core disease processes, and to enable the identification of disease biomarkers and therapeutic targets for this devastating disorder.
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11
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Ghantous A, Novoloaca A, Bouaoun L, Cuenin C, Cros MP, Xu Y, Hernandez-Vargas H, Darboe MK, Prentice AM, Moore SE, Gong YY, Herceg Z, Routledge MN. Aflatoxin Exposure during Early Life Is Associated with Differential DNA Methylation in Two-Year-Old Gambian Children. Int J Mol Sci 2021; 22:8967. [PMID: 34445674 PMCID: PMC8396526 DOI: 10.3390/ijms22168967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
Background: DNA methylation is an epigenetic control mechanism that may be altered by environmental exposures. We have previously reported that in utero exposure to the mycotoxin and liver carcinogen aflatoxin B1 from the maternal diet, as measured using biomarkers in the mothers' blood, was associated with differential DNA methylation in white blood cells of 6-month-old infants from The Gambia. Methods: Here we examined aflatoxin B1-associated differential DNA methylation in white blood cells of 24-month-old children from the same population (n = 244), in relation to the child's dietary exposure assessed using aflatoxin albumin biomarkers in blood samples collected at 6, 12 and 18 months of age. HM450 BeadChip arrays were used to assess DNA methylation, with data compared to aflatoxin albumin adduct levels using two approaches; a continuous model comparing aflatoxin adducts measured in samples collected at 18 months to DNA methylation at 24 months, and a categorical time-dose model that took into account aflatoxin adduct levels at 6, 12 and 18 months, for comparison to DNA methylation at 24 months. Results: Geometric mean (95% confidence intervals) for aflatoxin albumin levels were 3.78 (3.29, 4.34) at 6 months, 25.1 (21.67, 29.13) at 12 months and 49.48 (43.34, 56.49) at 18 months of age. A number of differentially methylated CpG positions and regions were associated with aflatoxin exposure, some of which affected gene expression. Pathway analysis highlighted effects on genes involved with with inflammatory, signalling and growth pathways. Conclusions: This study provides further evidence that exposure to aflatoxin in early childhood may impact on DNA methylation.
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Affiliation(s)
- Akram Ghantous
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Alexei Novoloaca
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Liacine Bouaoun
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Cyrille Cuenin
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Marie-Pierre Cros
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Ya Xu
- School of Medicine, University of Leeds, Leeds LS2 9JT, UK;
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun-Yat Sen University, Guangzhou 510006, China
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
- Cancer Research Centre of Lyon (CRCL), Université de Lyon, 69008 Lyon, France
| | - Momodou K. Darboe
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia; (M.K.D.); (A.M.P.); (S.E.M.)
| | - Andrew M. Prentice
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia; (M.K.D.); (A.M.P.); (S.E.M.)
| | - Sophie E. Moore
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, Banjul P.O. Box 273, The Gambia; (M.K.D.); (A.M.P.); (S.E.M.)
- Department of Women and Children’s Health, King’s College London, St Thomas’ Hospital, London SE1 7EH, UK
| | - Yun Yun Gong
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK;
| | - Zdenko Herceg
- International Agency for Research on Cancer, 150, Cours Albert Thomas, 69372 Lyon, France; (A.G.); (A.N.); (L.B.); (C.C.); (M.-P.C.); (H.H.-V.); (Z.H.)
| | - Michael N. Routledge
- School of Medicine, University of Leeds, Leeds LS2 9JT, UK;
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
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12
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Marbach F, Stoyanov G, Erger F, Stratakis CA, Settas N, London E, Rosenfeld JA, Torti E, Haldeman-Englert C, Sklirou E, Kessler E, Ceulemans S, Nelson SF, Martinez-Agosto JA, Palmer CGS, Signer RH, Andrews MV, Grange DK, Willaert R, Person R, Telegrafi A, Sievers A, Laugsch M, Theiß S, Cheng Y, Lichtarge O, Katsonis P, Stocco A, Schaaf CP. Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain. Genet Med 2021; 23:1465-1473. [PMID: 33833410 PMCID: PMC8354857 DOI: 10.1038/s41436-021-01152-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022] Open
Abstract
PURPOSE We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1β subunit of the cyclic AMP-dependent protein kinase A (PKA). METHODS Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development. RESULTS Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs. CONCLUSION Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.
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Affiliation(s)
- Felix Marbach
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Georgi Stoyanov
- Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Florian Erger
- Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Nikolaos Settas
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Edra London
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | | | | | - Evgenia Sklirou
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elena Kessler
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sophia Ceulemans
- Genetics/Dysmorphology, Rady Children's Hospital, San Diego, CA, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Institute for Society and Genetics, UCLA, Los Angeles, CA, USA
| | - Rebecca H Signer
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marisa V Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | | | | | | | - Aaron Sievers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Magdalena Laugsch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Susanne Theiß
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - YuZhu Cheng
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Biomedicine West Wing, International Centre for Life, Times Square, Newcastle upon Tyne, UK
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amber Stocco
- INTEGRIS Pediatric Neurology, Oklahoma City, OK, USA
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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13
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The role of frontotemporal dementia associated genes in patients with Alzheimer's disease. Neurobiol Aging 2021; 107:153-158. [PMID: 34172279 DOI: 10.1016/j.neurobiolaging.2021.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) and frontotemporal dementia (FTD) overlap clinically and pathologically. However, the role of FTD-associated genes in patients with AD remained unclear. To explore the relationship between FTD-associated genes and AD risk, we investigated 14 FTD-associated genes via targeted next-generation sequencing panel or whole-genome sequencing in a total of 721 AD patients and 1391 controls. Common variant-based association analysis and gene-based association test of rare variants were performed by PLINK 1.9 and Sequence Kernel Association Test-Optimal (SKAT-O test) respectively. As a result, 2 common variants, UBQLN1 rs1044175 (p value = 2.76 × 10-4) and MAPT rs2258689 (p value = 5.71 × 10-4), differed significantly between AD patients and controls. Additionally, gene-based analysis aggregating rare variants demonstrated that HNRNPA1 reached statistical significance in the SKAT-O test (p value = 2.24 × 10-3). Protein-protein interaction analysis showed that UBQLN1, MAPT, and HNRNPA1 interacted with proteins encoded by well-recognized AD-associated genes. Our study indicated that UBQLN1, MAPT, and HNRNPA1 are implicated in the pathogenesis of AD in the mainland Chinese population.
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14
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Hoang Trung H, Yoshihara T, Nakao A, Hayashida K, Hirata Y, Shirasuna K, Kuwamura M, Nakagawa Y, Kaneko T, Mori Y, Asano M, Kuramoto T. Deficiency of the RIβ subunit of protein kinase A causes body tremor and impaired fear conditioning memory in rats. Sci Rep 2021; 11:2039. [PMID: 33479380 PMCID: PMC7820254 DOI: 10.1038/s41598-021-81515-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/06/2021] [Indexed: 11/09/2022] Open
Abstract
The RIβ subunit of cAMP-dependent protein kinase (PKA), encoded by Prkar1b, is a neuronal isoform of the type I regulatory subunit of PKA. Mice lacking the RIβ subunit exhibit normal long-term potentiation (LTP) in the Schaffer collateral pathway of the hippocampus and normal behavior in the open-field and fear conditioning tests. Here, we combined genetic, electrophysiological, and behavioral approaches to demonstrate that the RIβ subunit was involved in body tremor, LTP in the Schaffer collateral pathway, and fear conditioning memory in rats. Genetic analysis of WTC-furue, a mutant strain with spontaneous tremors, revealed a deletion in the Prkar1b gene of the WTC-furue genome. Prkar1b-deficient rats created by the CRISPR/Cas9 system exhibited body tremor. Hippocampal slices from mutant rats showed deficient LTP in the Schaffer collateral-CA1 synapse. Mutant rats also exhibited decreased freezing time following contextual and cued fear conditioning, as well as increased exploratory behavior in the open field. These findings indicate the roles of the RIβ subunit in tremor pathogenesis and contextual and cued fear memory, and suggest that the hippocampal and amygdala roles of this subunit differ between mice and rats and that rats are therefore beneficial for exploring RIβ function.
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Affiliation(s)
- Hieu Hoang Trung
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Toru Yoshihara
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Akito Nakao
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Katsumi Hayashida
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Yoshiki Hirata
- Laboratory of Animal Reproduction, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Koumei Shirasuna
- Laboratory of Animal Reproduction, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Mitsuru Kuwamura
- Laboratory of Veterinary Pathology, Graduate School of Life and Environmental Science, Osaka Prefecture University, 1-58 Rinkuuourai-kita, Izumisano, Osaka, 598-8531, Japan
| | - Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Takehito Kaneko
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Takashi Kuramoto
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan. .,Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
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15
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Mastrangelo M, Torres B, De Vita G, Goldoni M, De Giorgi A, Bernardini L, Leuzzi V. Neurodevelopmental Impairment As the Main Phenotypic Hallmark Associated with the Translocation t(7;10)(7p22.3;q26.11). J Pediatr Genet 2020; 11:68-73. [PMID: 35186394 DOI: 10.1055/s-0040-1715479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Reported here is a novel patient carrying an unbalanced t (10q26.11-q26.3; 7p22.3) and presenting with a severe intellectual disability with autistic features, abnormalities of muscle tone, and a drug-responsive epilepsy. The prominence of neurological and neurodevelopmental abnormalities in the clinical phenotype highlights a possible pathogenic role for different genes in the involved regions. Hypothetical mechanisms may include a possible gene dosage effect for DOCK1 and/or haploinsufficiency of PRKAR1B SUN1, ADAP1 , and GPER1 .
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Affiliation(s)
- Mario Mastrangelo
- Division of Child Neurology and Infantile Psychiatry, Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | - Barbara Torres
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Gloria De Vita
- Division of Child Neurology and Infantile Psychiatry, Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | - Marina Goldoni
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Agnese De Giorgi
- Division of Child Neurology and Infantile Psychiatry, Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | - Laura Bernardini
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Vincenzo Leuzzi
- Division of Child Neurology and Infantile Psychiatry, Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
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16
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Neumann M, Mackenzie IRA. Review: Neuropathology of non-tau frontotemporal lobar degeneration. Neuropathol Appl Neurobiol 2020; 45:19-40. [PMID: 30357887 DOI: 10.1111/nan.12526] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/29/2018] [Indexed: 12/12/2022]
Abstract
Frontotemporal dementia (FTD) is a heterogeneous clinical syndrome associated with frontotemporal lobar degeneration (FTLD) as a relatively consistent neuropathological hallmark feature. However, the discoveries in the past decade of many of the relevant pathological proteins aggregating in human FTD brains in addition to several new FTD causing gene mutations underlined that FTD is a diverse condition on the neuropathological and genetic basis. This resulted in a novel molecular classification of these conditions based on the predominant protein abnormality and allows most cases of FTD to be placed now into one of three broad molecular subgroups; FTLD with tau, TAR DNA-binding protein 43 or FET protein accumulation (FTLD-tau, FTLD-TDP and FTLD-FET respectively). This review will provide an overview of the molecular neuropathology of non-tau FTLD, insights into disease mechanisms gained from the study of human post mortem tissue as well as discussion of current controversies in the field.
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Affiliation(s)
- M Neumann
- Department of Neuropathology, University Hospital of Tübingen, Tübingen, Germany.,Molecular Neuropathology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - I R A Mackenzie
- Department of Pathology, University of British Columbia and Vancouver General Hospital, Vancouver, BC, Canada
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17
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Guerreiro R, Gibbons E, Tábuas-Pereira M, Kun-Rodrigues C, Santo GC, Bras J. Genetic architecture of common non-Alzheimer's disease dementias. Neurobiol Dis 2020; 142:104946. [PMID: 32439597 PMCID: PMC8207829 DOI: 10.1016/j.nbd.2020.104946] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
Frontotemporal dementia (FTD), dementia with Lewy bodies (DLB) and vascular dementia (VaD) are the most common forms of dementia after Alzheimer’s disease (AD). The heterogeneity of these disorders and/or the clinical overlap with other diseases hinder the study of their genetic components. Even though Mendelian dementias are rare, the study of these forms of disease can have a significant impact in the lives of patients and families and have successfully brought to the fore many of the genes currently known to be involved in FTD and VaD, starting to give us a glimpse of the molecular mechanisms underlying these phenotypes. More recently, genome-wide association studies have also pointed to disease risk-associated loci. This has been particularly important for DLB where familial forms of disease are very rarely described. In this review we systematically describe the Mendelian and risk genes involved in these non-AD dementias in an effort to contribute to a better understanding of their genetic architecture, find differences and commonalities between different dementia phenotypes, and uncover areas that would benefit from more intense research endeavors.
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Affiliation(s)
- Rita Guerreiro
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA; Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA.
| | - Elizabeth Gibbons
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Miguel Tábuas-Pereira
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Celia Kun-Rodrigues
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Gustavo C Santo
- Department of Neurology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal; Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jose Bras
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA; Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
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18
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Charo LM, Burgoyne AM, Fanta PT, Patel H, Chmielecki J, Sicklick JK, McHale MT. A Novel PRKAR1B-BRAF Fusion in Gastrointestinal Stromal Tumor Guides Adjuvant Treatment Decision-Making During Pregnancy. J Natl Compr Canc Netw 2019. [PMID: 29523662 DOI: 10.6004/jnccn.2017.7039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Gastrointestinal stromal tumors (GISTs) are rare in pregnancy, with only 11 reported cases. Adjuvant imatinib therapy, which targets the most common driver mutations in GIST (KIT and PDGFRA), is recommended for patients with high-risk GIST, but it has known teratogenicity in the first trimester. A 34-year-old G3P2 woman underwent exploratory laparotomy at 16 weeks' gestation for a presumed adnexal mass. Surgical findings included normal adnexa and a 14-cm solid small bowel mass. The mass was resected en bloc with a segment of jejunum followed by a primary anastomosis. Histopathology and genomic analyses demonstrated a GIST with high-risk features but lack of KIT/PDGFRA mutations and identified the presence of a previously unreported, pathogenic PRKAR1B-BRAF gene fusion. Given her tumor profile, adjuvant therapy with imatinib was not recommended. GIST is rare in pregnancy, but can masquerade as an adnexal mass in women of childbearing age. Because neoadjuvant/adjuvant imatinib has risks of teratogenicity, tumor molecular profiling is critical as we identified a previously unreported gene fusion of PRKAR1B with BRAF that is predicted to be imatinib-resistant. In this case, testing provided the rationale for not offering adjuvant imatinib to avoid unnecessary toxicity to the patient and fetus.
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Affiliation(s)
- Lindsey M Charo
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
| | - Adam M Burgoyne
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
| | - Paul T Fanta
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
| | - Hitendra Patel
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
| | - Juliann Chmielecki
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
| | - Jason K Sicklick
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
| | - Michael T McHale
- From the Division of Gynecologic Oncology, Department of Reproductive Medicine, and Division of Hematology-Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California; Foundation Medicine, Inc., Cambridge, Massachusetts; and Division of Surgical Oncology, Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, California
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19
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de Vries M, van der Plaat DA, Nedeljkovic I, Verkaik-Schakel RN, Kooistra W, Amin N, van Duijn CM, Brandsma CA, van Diemen CC, Vonk JM, Marike Boezen H. From blood to lung tissue: effect of cigarette smoke on DNA methylation and lung function. Respir Res 2018; 19:212. [PMID: 30390659 PMCID: PMC6215675 DOI: 10.1186/s12931-018-0904-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/28/2018] [Indexed: 01/07/2023] Open
Abstract
Background Genetic and environmental factors play a role in the development of COPD. The epigenome, and more specifically DNA methylation, is recognized as important link between these factors. We postulate that DNA methylation is one of the routes by which cigarette smoke influences the development of COPD. In this study, we aim to identify CpG-sites that are associated with cigarette smoke exposure and lung function levels in whole blood and validate these CpG-sites in lung tissue. Methods The association between pack years and DNA methylation was studied genome-wide in 658 current smokers with >5 pack years using robust linear regression analysis. Using mediation analysis, we subsequently selected the CpG-sites that were also associated with lung function levels. Significant CpG-sites were validated in lung tissue with pyrosequencing and expression quantitative trait methylation (eQTM) analysis was performed to investigate the association between DNA methylation and gene expression. Results 15 CpG-sites were significantly associated with pack years and 10 of these were additionally associated with lung function levels. We validated 5 CpG-sites in lung tissue and found several associations between DNA methylation and gene expression. Conclusion This study is the first to validate a panel of CpG-sites that are associated with cigarette smoking and lung function levels in whole blood in the tissue of interest: lung tissue. Electronic supplementary material The online version of this article (10.1186/s12931-018-0904-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, Groningen, 9713, GZ, The Netherlands. .,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, Groningen, 9713, GZ, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rikst Nynke Verkaik-Schakel
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynaecology, Groningen, The Netherlands
| | - Wierd Kooistra
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Cleo C van Diemen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, Groningen, 9713, GZ, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Hanzeplein 1, Groningen, 9713, GZ, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
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20
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Bartoletti-Stella A, Baiardi S, Stanzani-Maserati M, Piras S, Caffarra P, Raggi A, Pantieri R, Baldassari S, Caporali L, Abu-Rumeileh S, Linarello S, Liguori R, Parchi P, Capellari S. Identification of rare genetic variants in Italian patients with dementia by targeted gene sequencing. Neurobiol Aging 2018. [DOI: 10.1016/j.neurobiolaging.2018.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Wang PQ, Liu Q, Xu WJ, Yu YN, Zhang YY, Li B, Liu J, Wang Z. Pure mechanistic analysis of additive neuroprotective effects between baicalin and jasminoidin in ischemic stroke mice. Acta Pharmacol Sin 2018; 39:961-974. [PMID: 29345255 PMCID: PMC6256271 DOI: 10.1038/aps.2017.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
Both baicalin (BA) and jasminoidin (JA) are active ingredients in Chinese herb medicine Scutellaria baicalensis and Fructus gardeniae, respectively. They have been shown to exert additive neuroprotective action in ischemic stroke models. In this study we used transcriptome analysis to explore the pure therapeutic mechanisms of BA, JA and their combination (BJ) contributing to phenotype variation and reversal of pathological processes. Mice with middle cerebral artery obstruction were treated with BA, JA, their combination (BJ), or concha margaritifera (CM). Cerebral infarct volume was examined to determine the effect of these compounds on phenotype. Using the hippocampus microarray and ingenuity pathway analysis (IPA) software, we exacted the differentially expressed genes, networks, pathways, and functions in positive-phenotype groups (BA, JA and BJ) by comparing with the negative-phenotype group (CM). In the BA, JA, and BJ groups, a total of 7, 4, and 11 specific target molecules, 1, 1, and 4 networks, 51, 59, and 18 canonical pathways and 70, 53, and 64 biological functions, respectively, were identified. Pure therapeutic mechanisms of BA and JA were mainly overlapped in specific target molecules, functions and pathways, which were related to the nervous system, inflammation and immune response. The specific mechanisms of BA and JA were associated with apoptosis and cancer-related signaling and endocrine and hormone regulation, respectively. In the BJ group, novel target profiles distinct from mono-therapies were revealed, including 11 specific target molecules, 10 functions, and 10 pathways, the majority of which were related to a virus-mediated immune response. The pure additive effects between BA and JA were based on enhanced action in virus-mediated immune response. This pure mechanistic analysis may provide a clearer outline of the target profiles of multi-target compounds and combination therapies.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- Disease Models, Animal
- Drug Synergism
- Drug Therapy, Combination
- Flavonoids/pharmacology
- Gene Expression Profiling/methods
- Gene Expression Regulation
- Gene Regulatory Networks/drug effects
- Hippocampus/drug effects
- Hippocampus/immunology
- Hippocampus/metabolism
- Hippocampus/pathology
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Infarction, Middle Cerebral Artery/drug therapy
- Infarction, Middle Cerebral Artery/genetics
- Infarction, Middle Cerebral Artery/metabolism
- Infarction, Middle Cerebral Artery/pathology
- Iridoids/pharmacology
- Male
- Mice
- Neuroprotective Agents/pharmacology
- Oligonucleotide Array Sequence Analysis
- Phenotype
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Systems Biology/methods
- Transcriptome/drug effects
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Affiliation(s)
- Peng-qian Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiong Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wen-juan Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ya-nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ying-ying Zhang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
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22
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Carbajosa G, Malki K, Lawless N, Wang H, Ryder JW, Wozniak E, Wood K, Mein CA, Dobson RJB, Collier DA, O'Neill MJ, Hodges AK, Newhouse SJ. Loss of Trem2 in microglia leads to widespread disruption of cell coexpression networks in mouse brain. Neurobiol Aging 2018; 69:151-166. [PMID: 29906661 PMCID: PMC6075941 DOI: 10.1016/j.neurobiolaging.2018.04.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/26/2018] [Accepted: 04/28/2018] [Indexed: 12/19/2022]
Abstract
Rare heterozygous coding variants in the triggering receptor expressed in myeloid cells 2 (TREM2) gene, conferring increased risk of developing late-onset Alzheimer's disease, have been identified. We examined the transcriptional consequences of the loss of Trem2 in mouse brain to better understand its role in disease using differential expression and coexpression network analysis of Trem2 knockout and wild-type mice. We generated RNA-Seq data from cortex and hippocampus sampled at 4 and 8 months. Using brain cell-type markers and ontology enrichment, we found subnetworks with cell type and/or functional identity. We primarily discovered changes in an endothelial gene-enriched subnetwork at 4 months, including a shift toward a more central role for the amyloid precursor protein gene, coupled with widespread disruption of other cell-type subnetworks, including a subnetwork with neuronal identity. We reveal an unexpected potential role of Trem2 in the homeostasis of endothelial cells that goes beyond its known functions as a microglial receptor and signaling hub, suggesting an underlying link between immune response and vascular disease in dementia.
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Affiliation(s)
- Guillermo Carbajosa
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK.
| | | | | | - Hong Wang
- Eli Lilly and Company, Indianapolis, IN, USA
| | | | - Eva Wozniak
- Barts and the London Genome Centre, John Vane Science Centre, Barts and the London School of Medicine and Dentistry, London, UK
| | - Kristie Wood
- Barts and the London Genome Centre, John Vane Science Centre, Barts and the London School of Medicine and Dentistry, London, UK
| | - Charles A Mein
- Barts and the London Genome Centre, John Vane Science Centre, Barts and the London School of Medicine and Dentistry, London, UK
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | | | | | - Angela K Hodges
- Maurice Wohl Clinical Neuroscience Institute James Black Centre Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Stephen J Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
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23
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Klioueva N, Bovenberg J, Huitinga I. Banking brain tissue for research. HANDBOOK OF CLINICAL NEUROLOGY 2018; 145:9-12. [PMID: 28987198 DOI: 10.1016/b978-0-12-802395-2.00002-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Well-characterized human brain tissue is crucial for scientific breakthroughs in research of the human brain and brain diseases. However, the collection, characterization, management, and accessibility of brain human tissue are rather complex. Well-characterized human brain tissue is often provided from private, sometimes small, brain tissue collections by (neuro)pathologic experts. However, to meet the increasing demand for human brain tissue from the scientific community, many professional brain-banking activities aiming at both neurologic and psychiatric diseases as well as healthy controls are currently being initiated worldwide. Professional biobanks are open-access and in many cases run donor programs. They are therefore costly and need effective business plans to guarantee long-term sustainability. Here we discuss the ethical, legal, managerial, and financial aspects of professional brain banks.
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Affiliation(s)
- Natasja Klioueva
- Netherlands Brain Bank, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
| | | | - Inge Huitinga
- Netherlands Brain Bank, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands.
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24
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Hondius DC, Hoozemans JJM, Rozemuller AJM, Li KW, Smit AB. A Laser Microdissection-Liquid Chromatography-Tandem Mass Spectrometry Workflow for Post-mortem Analysis of Brain Tissue. Methods Mol Biol 2018; 1723:371-383. [PMID: 29344872 DOI: 10.1007/978-1-4939-7558-7_21] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Improved speed and sensitivity of mass spectrometry allow the simultaneous quantification of high numbers of proteins from increasingly smaller quantities of tissue sample. Quantitative data of the proteome is highly valuable for providing unbiased information on, for example, protein expression changes related to disease or identifying related biomarkers. In brain diseases the affected area can be small and pathogenic events can be related to a specific cell type in an otherwise heterogeneous tissue type. An emerging approach dedicated to analyzing this type of samples is laser micro-dissection (LMD) combined with LC-MS/MS into a single workflow. In this chapter, we describe different options for isolating tissue suitable for LC-MS/MS analysis.
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Affiliation(s)
- David C Hondius
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands. .,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands.
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
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25
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An update on the genetics of dementia with Lewy bodies. Parkinsonism Relat Disord 2017; 43:1-8. [DOI: 10.1016/j.parkreldis.2017.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/12/2017] [Indexed: 02/06/2023]
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26
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Gelpi E, Carrato C, Grau-López L, Becerra JL, Garcia-Armengol R, Massuet A, Cervera-Carles L, Clarimon J, Beyer K, Álvarez R. Incidental neuronal intermediate filament inclusion pathology: unexpected biopsy findings in a 37-year-old woman with epilepsy. Neuropathol Appl Neurobiol 2017; 43:636-640. [PMID: 28880406 DOI: 10.1111/nan.12441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/23/2017] [Indexed: 11/27/2022]
Affiliation(s)
- E Gelpi
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-Insitut d'Investigacions Biomèdiques August Pi I Sunyer, Barcelona, Spain
| | - C Carrato
- Pathology Department and Research Institute, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
| | - L Grau-López
- Neurology Department, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
| | - J L Becerra
- Neurology Department, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
| | - R Garcia-Armengol
- Neurosurgery, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
| | - A Massuet
- IDI-Magnetic Resonance Imaging Unit, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
| | - L Cervera-Carles
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - J Clarimon
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - K Beyer
- Pathology Department and Research Institute, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
| | - R Álvarez
- Neurology Department, Hospital Germans Trias i Pujol, Universitat de Barcelona, Badalona, Spain
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27
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Stefan E, Troppmair J, Bister K. Targeting the Architecture of Deregulated Protein Complexes in Cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 111:101-132. [PMID: 29459029 DOI: 10.1016/bs.apcsb.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The architectures of central signaling hubs are precisely organized by static and dynamic protein-protein interactions (PPIs). Upon deregulation, these PPI platforms are capable to propagate or initiate pathophysiological signaling events. This causes the acquisition of molecular features contributing to the etiology or progression of many diseases, including cancer, where deregulated molecular interactions of signaling proteins have been best studied. The reasons for PPI-dependent reprogramming of cancer-initiating cells are manifold; in many cases, mutations perturb PPIs, enzyme activities, protein abundance, or protein localization. Consequently, the pharmaceutical targeting of PPIs promises to be of remarkable therapeutic value. For this review we have selected three key players of oncogenic signaling which are differently affected by PPI deregulation: two (the small G proteins of the RAS family and the transcription factor MYC) are considered "undruggable" using classical drug discovery approaches and in the case of the third protein discussed here, PKA, standard kinase inhibitors, may be unsuitable in the clinic. These circumstances require alternative strategies, which may lie in pharmaceutical drug interference of critical PPIs accountable for oncogenic signaling.
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Affiliation(s)
- Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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28
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Pottier C, Ravenscroft TA, Sanchez-Contreras M, Rademakers R. Genetics of FTLD: overview and what else we can expect from genetic studies. J Neurochem 2017; 138 Suppl 1:32-53. [PMID: 27009575 DOI: 10.1111/jnc.13622] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/26/2016] [Accepted: 03/18/2016] [Indexed: 12/11/2022]
Abstract
Frontotemporal lobar degeneration (FTLD) comprises a highly heterogeneous group of disorders clinically associated with behavioral and personality changes, language impairment, and deficits in executive functioning, and pathologically associated with degeneration of frontal and temporal lobes. Some patients present with motor symptoms including amyotrophic lateral sclerosis. Genetic research over the past two decades in FTLD families led to the identification of three common FTLD genes (microtubule-associated protein tau, progranulin, and chromosome 9 open reading frame 72) and a small number of rare FTLD genes, explaining the disease in almost all autosomal dominant FTLD families but only a minority of apparently sporadic patients or patients in whom the family history is less clear. Identification of additional FTLD (risk) genes is therefore highly anticipated, especially with the emerging use of next-generation sequencing. Common variants in the transmembrane protein 106 B were identified as a genetic risk factor of FTLD and disease modifier in patients with known mutations. This review summarizes for each FTLD gene what we know about the type and frequency of mutations, their associated clinical and pathological features, and potential disease mechanisms. We also provide an overview of emerging disease pathways encompassing multiple FTLD genes. We further discuss how FTLD specific issues, such as disease heterogeneity, the presence of an unclear family history and the possible role of an oligogenic basis of FTLD, can pose challenges for future FTLD gene identification and risk assessment of specific variants. Finally, we highlight emerging clinical, genetic, and translational research opportunities that lie ahead. Genetic research led to the identification of three common FTLD genes with rare variants (MAPT, GRN, and C9orf72) and a small number of rare genes. Efforts are now ongoing, which aimed at the identification of rare variants with high risk and/or low frequency variants with intermediate effect. Common risk variants have also been identified, such as TMEM106B. This review discusses the current knowledge on FTLD genes and the emerging disease pathways encompassing multiple FTLD genes.
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Affiliation(s)
- Cyril Pottier
- Mayo Clinic Jacksonville, Department of Neuroscience, Jacksonville, FL, USA
| | | | | | - Rosa Rademakers
- Mayo Clinic Jacksonville, Department of Neuroscience, Jacksonville, FL, USA
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Yuan A, Rao MV, Veeranna, Nixon RA. Neurofilaments and Neurofilament Proteins in Health and Disease. Cold Spring Harb Perspect Biol 2017; 9:9/4/a018309. [PMID: 28373358 DOI: 10.1101/cshperspect.a018309] [Citation(s) in RCA: 408] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SUMMARYNeurofilaments (NFs) are unique among tissue-specific classes of intermediate filaments (IFs) in being heteropolymers composed of four subunits (NF-L [neurofilament light]; NF-M [neurofilament middle]; NF-H [neurofilament heavy]; and α-internexin or peripherin), each having different domain structures and functions. Here, we review how NFs provide structural support for the highly asymmetric geometries of neurons and, especially, for the marked radial expansion of myelinated axons crucial for effective nerve conduction velocity. NFs in axons extensively cross-bridge and interconnect with other non-IF components of the cytoskeleton, including microtubules, actin filaments, and other fibrous cytoskeletal elements, to establish a regionally specialized network that undergoes exceptionally slow local turnover and serves as a docking platform to organize other organelles and proteins. We also discuss how a small pool of oligomeric and short filamentous precursors in the slow phase of axonal transport maintains this network. A complex pattern of phosphorylation and dephosphorylation events on each subunit modulates filament assembly, turnover, and organization within the axonal cytoskeleton. Multiple factors, and especially turnover rate, determine the size of the network, which can vary substantially along the axon. NF gene mutations cause several neuroaxonal disorders characterized by disrupted subunit assembly and NF aggregation. Additional NF alterations are associated with varied neuropsychiatric disorders. New evidence that subunits of NFs exist within postsynaptic terminal boutons and influence neurotransmission suggests how NF proteins might contribute to normal synaptic function and neuropsychiatric disease states.
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Affiliation(s)
- Aidong Yuan
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York 10962.,Department of Psychiatry, New York University School of Medicine, New York, New York 10016
| | - Mala V Rao
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York 10962.,Department of Psychiatry, New York University School of Medicine, New York, New York 10016
| | - Veeranna
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York 10962.,Department of Psychiatry, New York University School of Medicine, New York, New York 10016
| | - Ralph A Nixon
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York 10962.,Department of Psychiatry, New York University School of Medicine, New York, New York 10016.,Cell Biology, New York University School of Medicine, New York, New York 10016
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30
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Torres-Quesada O, Röck R, Stefan E. Systematic Quantification of GPCR/cAMP-Controlled Protein Kinase A Interactions. Horm Metab Res 2017; 49:240-249. [PMID: 28427097 DOI: 10.1055/s-0042-110791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The diffusible second messenger cyclic AMP (cAMP) originates from multiple G protein-coupled receptor (GPCR) cascades activating the intracellular key effector protein kinase A (PKA). Spatially and temporally restricted cAMP-fluxes are directly sensed by macromolecular PKA complexes. The consequences are alterations of molecular interactions, which lead to activation of compartmentalized PKA phosphotransferase activities, regulating a vast array of cellular functions. To decode cell-type and cell-compartment specific PKA functions, the spatio-temporal dynamics of small molecule:protein interactions, protein:protein interactions (PPIs), cAMP-mobilization, and phosphotransferase activities need to be determined directly in the appropriate cellular context. A collection of cell-based reporters has been developed to either visualize or quantitatively measure kinase activities or PKA complex formation/dissociation. In this review, we list a collection of unimolecular and bimolecular PKA biosensors, followed by the specification of the modular design of a Renilla luciferase based protein-fragment complementation assay (PCA) platform for measuring PKA network interactions. We discuss the application spectrum of the PCA reporter to identify, quantify, and dissect dynamic and transient PKA complexes downstream of specific GPCR activities. We specify the implementation of a PCA PKA platform to systematically quantify the concurrent involvement of receptor-cAMP signaling, post-translational modifications, and kinase subunit mutations/perturbations in PKA activation. The systematic quantification of transient PKA network interactions will contribute to a better understanding how GPCR-recognized input signals are streamlined through the compartmentalized and cAMP-interacting PKA signalosome.
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Affiliation(s)
- O Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - R Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - E Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
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31
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Ilouz R, Lev-Ram V, Bushong EA, Stiles TL, Friedmann-Morvinski D, Douglas C, Goldberg JL, Ellisman MH, Taylor SS. Isoform-specific subcellular localization and function of protein kinase A identified by mosaic imaging of mouse brain. eLife 2017; 6:17681. [PMID: 28079521 PMCID: PMC5300705 DOI: 10.7554/elife.17681] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 01/03/2017] [Indexed: 01/26/2023] Open
Abstract
Protein kinase A (PKA) plays critical roles in neuronal function that are mediated by different regulatory (R) subunits. Deficiency in either the RIβ or the RIIβ subunit results in distinct neuronal phenotypes. Although RIβ contributes to synaptic plasticity, it is the least studied isoform. Using isoform-specific antibodies, we generated high-resolution large-scale immunohistochemical mosaic images of mouse brain that provided global views of several brain regions, including the hippocampus and cerebellum. The isoforms concentrate in discrete brain regions, and we were able to zoom-in to show distinct patterns of subcellular localization. RIβ is enriched in dendrites and co-localizes with MAP2, whereas RIIβ is concentrated in axons. Using correlated light and electron microscopy, we confirmed the mitochondrial and nuclear localization of RIβ in cultured neurons. To show the functional significance of nuclear localization, we demonstrated that downregulation of RIβ, but not of RIIβ, decreased CREB phosphorylation. Our study reveals how PKA isoform specificity is defined by precise localization. DOI:http://dx.doi.org/10.7554/eLife.17681.001
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Affiliation(s)
- Ronit Ilouz
- Department of Pharmacology, University of California, San Diego, La Jolla, United States
| | - Varda Lev-Ram
- Department of Pharmacology, University of California, San Diego, La Jolla, United States
| | - Eric A Bushong
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, San Diego, United States
| | - Travis L Stiles
- Department of Ophthalmology, Shiley Eye Center, University of California, San Diego, La Jolla, United States
| | - Dinorah Friedmann-Morvinski
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, United States.,Department of Biochemistry and Molecular Biology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Christopher Douglas
- Department of Ophthalmology, Shiley Eye Center, University of California, San Diego, La Jolla, United States
| | - Jeffrey L Goldberg
- Department of Ophthalmology, Shiley Eye Center, University of California, San Diego, La Jolla, United States
| | - Mark H Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California, San Diego, San Diego, United States.,Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, United States
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
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32
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Hortobágyi T, Cairns NJ. Amyotrophic lateral sclerosis and non-tau frontotemporal lobar degeneration. HANDBOOK OF CLINICAL NEUROLOGY 2017; 145:369-381. [PMID: 28987183 DOI: 10.1016/b978-0-12-802395-2.00026-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is the major motor neuron disorder. The hallmark features are progressive, irreversible motor neuron loss leading to denervation atrophy of muscles and death, usually within 5 years of disease onset. The hallmark proteins of the pathognomonic inclusions are SOD-1, TDP-43, or FUS; rarely the disease is caused by mutation of the respective genes. Frontotemporal lobar degeneration (FTLD) is genetically, neuropathologically, and clinically heterogeneous and may present as a dementia with three major clinical syndromes dominated by behavioral, language, and motor disorders, respectively. The characteristic aggregate-forming protein in non-tau FTLD is either TDP-43 or FUS. It has been known for several years that frontotemporal dementia (or less severe forms of cognitive impairment) may coexist with ALS. Recent discoveries in genetics (e.g., C9orf72 mutation) and the subsequent neuropathologic characterization have revealed remarkable overlap between ALS and non-tau FTLD also at a molecular level, indicating common molecular pathways in pathogenesis. After a historic overview we demonstrate and compare the macroscopic and microscopic appearances and molecular characteristics with emphasis on genetic background, neuroanatomic distribution, and morphology of abnormal protein aggregates and their possible association with specific mutations. The clinicopathologic classifications and correlations are also discussed.
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Affiliation(s)
- Tibor Hortobágyi
- Department of Neuropathology, Institute of Pathology, University of Debrecen, Debrecen, Hungary
| | - Nigel J Cairns
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
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33
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Abplanalp WT, Conklin DJ, Cantor JM, Ginsberg MH, Wysoczynski M, Bhatnagar A, O'Toole TE. Enhanced Integrin α4β1-Mediated Adhesion Contributes to a Mobilization Defect of Endothelial Progenitor Cells in Diabetes. Diabetes 2016; 65:3505-3515. [PMID: 27495221 PMCID: PMC5079633 DOI: 10.2337/db16-0634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/26/2016] [Indexed: 12/13/2022]
Abstract
Diabetes is associated with a deficit of circulating endothelial progenitor cells (EPCs), which has been attributed to their defective mobilization from the bone marrow. The basis for this mobilization defect is not completely understood, and we sought to determine if hyperglycemic conditions enhanced EPC adhesion. We found that culturing EPCs in high glucose media increased adhesion to bone marrow stromal cells. This enhanced adhesion was associated with decreased expression of protein kinase A regulatory subunit 1β (PRKAR1β), activation of protein kinase A (PKA), and phosphorylation of α4-integrin on serine 988. This potentiated adhesion was reversed by treatment with a PKA inhibitor, overexpression of PRKAR1β, or expression of a phosphorylation-defective α4-integrin variant (α4[S988A]). Using a model of type 1 diabetes, we showed that α4(S988A)-expressing mice have more circulating EPCs than their wild-type counterparts. Moreover, diabetic α4(S988A) mice demonstrate enhanced revascularization after hind limb ischemia. Thus, we have identified a novel signaling mechanism activating PKA in diabetes (downregulation of an inhibitory regulatory subunit) that leads to deficits of circulating EPCs and impaired vascular repair, which could be reversed by α4-integrin mutation.
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Affiliation(s)
- Wesley T Abplanalp
- Diabetes and Obesity Center, University of Louisville, Louisville, KY
- Department of Physiology, University of Louisville, Louisville, KY
| | - Daniel J Conklin
- Diabetes and Obesity Center, University of Louisville, Louisville, KY
| | - Joseph M Cantor
- Department of Medicine, University of California, San Diego, San Diego, CA
| | - Mark H Ginsberg
- Department of Medicine, University of California, San Diego, San Diego, CA
| | | | - Aruni Bhatnagar
- Diabetes and Obesity Center, University of Louisville, Louisville, KY
- Department of Physiology, University of Louisville, Louisville, KY
| | - Timothy E O'Toole
- Diabetes and Obesity Center, University of Louisville, Louisville, KY
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34
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Gpr161 anchoring of PKA consolidates GPCR and cAMP signaling. Proc Natl Acad Sci U S A 2016; 113:7786-91. [PMID: 27357676 DOI: 10.1073/pnas.1608061113] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Scaffolding proteins organize the information flow from activated G protein-coupled receptors (GPCRs) to intracellular effector cascades both spatially and temporally. By this means, signaling scaffolds, such as A-kinase anchoring proteins (AKAPs), compartmentalize kinase activity and ensure substrate selectivity. Using a phosphoproteomics approach we identified a physical and functional connection between protein kinase A (PKA) and Gpr161 (an orphan GPCR) signaling. We show that Gpr161 functions as a selective high-affinity AKAP for type I PKA regulatory subunits (RI). Using cell-based reporters to map protein-protein interactions, we discovered that RI binds directly and selectively to a hydrophobic protein-protein interaction interface in the cytoplasmic carboxyl-terminal tail of Gpr161. Furthermore, our data demonstrate that a binary complex between Gpr161 and RI promotes the compartmentalization of Gpr161 to the plasma membrane. Moreover, we show that Gpr161, functioning as an AKAP, recruits PKA RI to primary cilia in zebrafish embryos. We also show that Gpr161 is a target of PKA phosphorylation, and that mutation of the PKA phosphorylation site affects ciliary receptor localization. Thus, we propose that Gpr161 is itself an AKAP and that the cAMP-sensing Gpr161:PKA complex acts as cilium-compartmentalized signalosome, a concept that now needs to be considered in the analyzing, interpreting, and pharmaceutical targeting of PKA-associated functions.
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35
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Mackenzie IRA, Neumann M. Molecular neuropathology of frontotemporal dementia: insights into disease mechanisms from postmortem studies. J Neurochem 2016; 138 Suppl 1:54-70. [PMID: 27306735 DOI: 10.1111/jnc.13588] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 12/13/2022]
Abstract
Frontotemporal dementia (FTD) is a clinical syndrome with a heterogeneous molecular basis. The past decade has seen the discovery of several new FTD-causing genetic mutations and the identification of many of the relevant pathological proteins. The current neuropathological classification is based on the predominant protein abnormality and allows most cases of FTD to be placed into one of three broad molecular subgroups; frontotemporal lobar degeneration with tau, TDP-43 or FET protein accumulation. This review will describe our current understanding of the molecular basis of FTD, focusing on insights gained from the study of human postmortem tissue, as well as some of the current controversies. Most cases of FTD can be subclassified into one of three broad molecular subgroups based on the predominant protein that accumulates as pathological cellular inclusions. Understanding the associated pathogenic mechanisms and recognizing these FTD molecular subtypes in vivo will likely be crucial for the development and use of targeted therapies. This article is part of the Frontotemporal Dementia special issue.
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Affiliation(s)
- Ian R A Mackenzie
- Department of Pathology, University of British Columbia and Vancouver General Hospital, Vancouver, Canada
| | - Manuela Neumann
- Department of Neuropathology, University of Tübingen and German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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36
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Schizophrenia interactome with 504 novel protein-protein interactions. NPJ SCHIZOPHRENIA 2016; 2:16012. [PMID: 27336055 PMCID: PMC4898894 DOI: 10.1038/npjschz.2016.12] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 11/29/2022]
Abstract
Genome-wide association studies of schizophrenia (GWAS) have revealed the role of rare and common genetic variants, but the functional effects of the risk variants remain to be understood. Protein interactome-based studies can facilitate the study of molecular mechanisms by which the risk genes relate to schizophrenia (SZ) genesis, but protein–protein interactions (PPIs) are unknown for many of the liability genes. We developed a computational model to discover PPIs, which is found to be highly accurate according to computational evaluations and experimental validations of selected PPIs. We present here, 365 novel PPIs of liability genes identified by the SZ Working Group of the Psychiatric Genomics Consortium (PGC). Seventeen genes that had no previously known interactions have 57 novel interactions by our method. Among the new interactors are 19 drug targets that are targeted by 130 drugs. In addition, we computed 147 novel PPIs of 25 candidate genes investigated in the pre-GWAS era. While there is little overlap between the GWAS genes and the pre-GWAS genes, the interactomes reveal that they largely belong to the same pathways, thus reconciling the apparent disparities between the GWAS and prior gene association studies. The interactome including 504 novel PPIs overall, could motivate other systems biology studies and trials with repurposed drugs. The PPIs are made available on a webserver, called Schizo-Pi at http://severus.dbmi.pitt.edu/schizo-pi with advanced search capabilities.
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37
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Abstract
Frontotemporal dementia (FTD) refers to a group of clinically and genetically heterogeneous neurodegenerative disorders that are a common cause of adult-onset behavioural and cognitive impairment. FTD often presents in combination with various hyperkinetic or hypokinetic movement disorders, and evidence suggests that various genetic mutations underlie these different presentations. Here, we review the known syndromatic-genetic correlations in FTD. Although no direct genotype-phenotype correlations have been identified, mutations in multiple genes have been associated with various presentations. Mutations in the genes that encode microtubule-associated protein tau (MAPT) and progranulin (PGRN) can manifest as symmetrical parkinsonism, including the phenotypes of Richardson syndrome and corticobasal syndrome (CBS). Expansions in the C9orf72 gene are most frequently associated with familial FTD, typically combined with motor neuron disease, but other manifestations, such as symmetrical parkinsonism, CBS and multiple system atrophy-like presentations, have been described in patients with these mutations. Less common gene mutations, such as those in TARDBP, CHMP2B, VCP, FUS and TREM2, can also present as atypical parkinsonism. The most common hyperkinetic movement disorders in FTD are motor and vocal stereotypies, which have been observed in up to 78% of patients with autopsy-proven FTD. Other hyperkinetic movements, such as chorea, orofacial dyskinesias, myoclonus and dystonia, are also observed in some patients with FTD.
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38
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Filippi M, Agosta F, Ferraro PM. Charting Frontotemporal Dementia: From Genes to Networks. J Neuroimaging 2015; 26:16-27. [PMID: 26617288 DOI: 10.1111/jon.12316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 12/11/2022] Open
Abstract
Frontotemporal dementia (FTD) is a genetically and clinically heterogeneous syndrome that is characterized by overlapping clinical symptoms involving behavior, personality, language and/or motor functions and degeneration of the frontal and temporal lobes. The term frontotemporal lobar degeneration (FTLD) is used to describe the proteinopathies associated with clinical FTD. Emerging evidence from network-based neuroimaging studies, such as resting state functional MRI and diffusion tensor MRI studies, have implicated specific large-scale brain networks in the pathogenesis of FTD syndromes, suggesting a new paradigm for explaining the distributed and heterogeneous spreading patterns of pathological proteins in FTLD. In this review, we overview recent research on the study of FTD syndromes as connectivity disorders in symptomatic patients as well as genotype-specific changes in asymptomatic FTD-related gene mutation carriers. Characterizing brain network breakdown in these subjects using neuroimaging may help anticipate the diagnosis and perhaps prevent the devastating impact of FTD.
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Affiliation(s)
- Massimo Filippi
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy.,Department of Neurology, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Agosta
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Pilar M Ferraro
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
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39
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Abstract
cAMP-dependent protein kinase (PKA) was the second protein kinase to be discovered and the PKA catalytic (C) subunit serves as a prototype for the large protein kinase superfamily that contains over 500 gene products. The protein kinases regulate much of biology in eukaryotic cells and they are now also a major therapeutic target. Although PKA was discovered nearly 50 years ago and the subsequent discovery of the regulatory subunits that bind cAMP and release the catalytic activity from the holoenzyme followed quickly. Thus in PKA we see the convergence of two major signaling mechanisms - protein phosphorylation and second messenger signaling through cAMP. Crystallography provides a foundation for understanding function, and the structure of the isolated regulatory (R) and C-subunits have been extremely informative. Yet it is the R2C2 holoenzyme that predominates in cells, and one can only appreciate the allosteric features of PKA signaling by seeing the full length protein. The symmetry and the quaternary constraints that one R:C hetero-dimer exerts on the other in the holoenzyme simply are not present in the isolated subunits or even in the R:C hetero-dimer.
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Affiliation(s)
- Ping Zhang
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Jian Wu
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093 ; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
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40
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Wong TH, Verkerk AJMH, Rozemuller AJ, Willemsen R, Neumann M, Bonifati V, van Swieten J. Reply: PRKAR1B mutations are a rare cause of FUS negative neuronal intermediate filament inclusion disease. Brain 2014; 138:e358. [PMID: 25414040 DOI: 10.1093/brain/awu333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tsz Hang Wong
- 1 Department of Neurology, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands
| | - Annemieke J M H Verkerk
- 2 Department of Internal Medicine, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands
| | - Annemieke J Rozemuller
- 3 Department of Pathology, VU University Medical Centre, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Rob Willemsen
- 4 Department of Clinical Genetics, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands
| | - Manuela Neumann
- 5 DZNE, German Centre for Neurodegenerative Disease, 72076 Tübingen, Germany 6 Department of Neuropathology, University of Tübingen, 72076 Tübingen, Germany
| | - Vincenzo Bonifati
- 4 Department of Clinical Genetics, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands
| | - John van Swieten
- 1 Department of Neurology, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands 7 Alzheimer Centre, Neuroscience Campus Amsterdam, 1007 MB Amsterdam, The Netherlands 8 Department of Neurology, Neuroscience Campus Amsterdam, 1007 MB Amsterdam, The Netherlands
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41
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Pottier C, Baker M, Dickson DW, Rademakers R. PRKAR1B mutations are a rare cause of FUS negative neuronal intermediate filament inclusion disease. Brain 2014; 138:e357. [PMID: 25414037 DOI: 10.1093/brain/awu332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cyril Pottier
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Matt Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
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42
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Cohn-Hokke PE, Wong TH, Rizzu P, Breedveld G, van der Flier WM, Scheltens P, Baas F, Heutink P, Meijers-Heijboer EJ, van Swieten JC, Pijnenburg YAL. Mutation frequency of PRKAR1B and the major familial dementia genes in a Dutch early onset dementia cohort. J Neurol 2014; 261:2085-92. [DOI: 10.1007/s00415-014-7456-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/25/2014] [Accepted: 07/27/2014] [Indexed: 12/11/2022]
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