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Nicholson L, Piras IS, DeBoth MD, Siniard A, Heras-Garvin A, Stefanova N, Huentelman MJ. Transcriptomic insights into multiple system atrophy from a PLP-α-synuclein transgenic mouse model. Brain Res 2024; 1834:148912. [PMID: 38575106 DOI: 10.1016/j.brainres.2024.148912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024]
Abstract
Multiple system atrophy (MSA) is a rare, neurodegenerative disorder with rapid motor and non-motor symptom progression. MSA is characterized by protein aggregations of α-synuclein found in the cytoplasm of oligodendrocytes. Despite this pathological hallmark, there is still little known about the cause of this disease, resulting in poor treatment options and quality of life post-diagnosis. In this study, we investigated differentially expressed genes (DEGs) via RNA-sequencing of brain samples from a validated PLP-α-synuclein transgenic mouse model, identifying a total of 40 DEGs in the PLP group compared to wild-type (WT), with top detected genes being Gm15446, Mcm6, Aldh7a1 and Gm3435. We observed a significant enrichment of immune pathways and endothelial cell genes among the upregulated genes, whereas downregulated genes were significantly enriched for oligodendrocyte and neuronal genes. We then calculated possible overlap of these DEGs with previously profiled human MSA RNA, resulting in the identification of significant downregulation of the Tsr2 gene. Identifying key gene expression profiles specific to MSA patients is crucial to further understanding the cause, and possible prevention, of this rapidly progressive neurodegenerative disorder.
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Affiliation(s)
- L Nicholson
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - I S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M D DeBoth
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - A Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - A Heras-Garvin
- Laboratory for Translational Neurodegeneration Research, Department of Neurology, Medical University of Innsbruck, Austria
| | - N Stefanova
- Laboratory for Translational Neurodegeneration Research, Department of Neurology, Medical University of Innsbruck, Austria.
| | - M J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
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Van Etten EJ, Bharadwaj PK, Grilli MD, Raichlen DA, Hishaw GA, Huentelman MJ, Trouard TP, Alexander GE. Impact of age and apolipoprotein E ε4 status on regional white matter hyperintensity volume and cognition in healthy aging. J Int Neuropsychol Soc 2024:1-11. [PMID: 38515367 DOI: 10.1017/s1355617724000122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
OBJECTIVE White matter hyperintensity (WMH) volume is a neuroimaging marker of lesion load related to small vessel disease that has been associated with cognitive aging and Alzheimer's disease (AD) risk. METHOD The present study sought to examine whether regional WMH volume mediates the relationship between APOE ε4 status, a strong genetic risk factor for AD, and cognition and if this association is moderated by age group differences within a sample of 187 healthy older adults (APOE ε4 status [carrier/non-carrier] = 56/131). RESULTS After we controlled for sex, education, and vascular risk factors, ANCOVA analyses revealed significant age group by APOE ε4 status interactions for right parietal and left temporal WMH volumes. Within the young-old group (50-69 years), ε4 carriers had greater right parietal and left temporal WMH volumes than non-carriers. However, in the old-old group (70-89 years), right parietal and left temporal WMH volumes were comparable across APOE ε4 groups. Further, within ε4 non-carriers, old-old adults had greater right parietal and left temporal WMH volumes than young-old adults, but there were no significant differences across age groups in ε4 carriers. Follow-up moderated mediation analyses revealed that, in the young-old, but not the old-old group, there were significant indirect effects of ε4 status on memory and executive functions through left temporal WMH volume. CONCLUSIONS These findings suggest that, among healthy young-old adults, increased left temporal WMH volume, in the context of the ε4 allele, may represent an early marker of cognitive aging with the potential to lead to greater risk for AD.
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Affiliation(s)
- Emily J Van Etten
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - Pradyumna K Bharadwaj
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - Matthew D Grilli
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
- Department of Neurology, University of Arizona, Tucson, AZ, USA
| | - David A Raichlen
- Human and Evolutionary Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Georg A Hishaw
- Department of Neurology, University of Arizona, Tucson, AZ, USA
| | - Matthew J Huentelman
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Theodore P Trouard
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA
| | - Gene E Alexander
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Department of Psychiatry, University of Arizona, Tucson, AZ, USA
- Neuroscience Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
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Van Etten EJ, Bharadwaj PK, Grilli MD, Raichlen DA, Hishaw GA, Huentelman MJ, Trouard TP, Alexander GE. Regional covariance of white matter hyperintensity volume patterns associated with hippocampal volume in healthy aging. Front Aging Neurosci 2024; 16:1349449. [PMID: 38524117 PMCID: PMC10957632 DOI: 10.3389/fnagi.2024.1349449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Hippocampal volume is particularly sensitive to the accumulation of total brain white matter hyperintensity volume (WMH) in aging, but how the regional distribution of WMH volume differentially impacts the hippocampus has been less studied. In a cohort of 194 healthy older adults ages 50-89, we used a multivariate statistical method, the Scaled Subprofile Model (SSM), to (1) identify patterns of regional WMH differences related to left and right hippocampal volumes, (2) examine associations between the multimodal neuroimaging covariance patterns and demographic characteristics, and (3) investigate the relation of the patterns to subjective and objective memory in healthy aging. We established network covariance patterns of regional WMH volume differences associated with greater left and right hippocampal volumes, which were characterized by reductions in left temporal and right parietal WMH volumes and relative increases in bilateral occipital WMH volumes. Additionally, we observed lower expression of these hippocampal-related regional WMH patterns were significantly associated with increasing age and greater subjective memory complaints, but not objective memory performance in this healthy older adult cohort. Our findings indicate that, in cognitively healthy older adults, left and right hippocampal volume reductions were associated with differences in the regional distribution of WMH volumes, which were exacerbated by advancing age and related to greater subjective memory complaints. Multivariate network analyses, like SSM, may help elucidate important early effects of regional WMH volume on brain and cognitive aging in healthy older adults.
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Affiliation(s)
- Emily J. Van Etten
- Department of Psychology, University of Arizona, Tucson, AZ, United States
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
| | - Pradyumna K. Bharadwaj
- Department of Psychology, University of Arizona, Tucson, AZ, United States
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
| | - Matthew D. Grilli
- Department of Psychology, University of Arizona, Tucson, AZ, United States
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
- Department of Neurology, University of Arizona, Tucson, AZ, United States
| | - David A. Raichlen
- Human and Evolutionary Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Anthropology, University of Southern California, Los Angeles, CA, United States
| | - Georg A. Hishaw
- Department of Neurology, University of Arizona, Tucson, AZ, United States
| | - Matthew J. Huentelman
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
- Arizona Alzheimer’s Consortium, Phoenix, AZ, United States
| | - Theodore P. Trouard
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
- Arizona Alzheimer’s Consortium, Phoenix, AZ, United States
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, United States
| | - Gene E. Alexander
- Department of Psychology, University of Arizona, Tucson, AZ, United States
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, United States
- Arizona Alzheimer’s Consortium, Phoenix, AZ, United States
- Department of Psychiatry, University of Arizona, Tucson, AZ, United States
- Neuroscience Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, United States
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Floris G, Godar SC, Braccagni G, Piras IS, Ravens A, Zanda MT, Huentelman MJ, Bortolato M. The sinking platform test: a novel paradigm to measure persistence in animal models. Neuropsychopharmacology 2024:10.1038/s41386-024-01827-0. [PMID: 38396257 DOI: 10.1038/s41386-024-01827-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024]
Abstract
Persistence is the propensity to maintain goal-directed actions despite adversities. While this temperamental trait is crucial to mitigate depression risk, its neurobiological foundations remain elusive. Developing behavioral tasks to capture persistence in animal models is crucial for understanding its molecular underpinnings. Here, we introduce the Sinking Platform Test (SPT), a novel high-throughput paradigm to measure persistence. Mice were trained to exit a water-filled tank by ascending onto a platform above water level. Throughout the training, mice were also occasionally exposed to "failure trials," during which an operator would submerge a platform right after the mouse climbed onto it, requiring the mouse to reach and ascend a newly introduced platform. Following training, mice were subjected to a 5-min test exclusively consisting of failure trials. Male and female mice exhibited comparable persistence, measured by the number of climbed platforms during the test. Furthermore, this index was increased by chronic administration of fluoxetine or imipramine; conversely, it was reduced by acute and chronic haloperidol. Notably, six weeks of social isolation reduced SPT performance, and this effect was rescued by imipramine treatment over the last two weeks. A 4-week regimen of voluntary wheel running also improved persistence in socially isolated mice. Finally, comparing transcriptomic profiles of the prefrontal cortex of mice with high and low SPT performance revealed significant enrichment of immediate-early genes known to shape susceptibility for chronic stress. These findings highlight the potential of SPT as a promising method to uncover the biological mechanisms of persistence and evaluate novel interventions to enhance this response.
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Affiliation(s)
- Gabriele Floris
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA
- Department of Neural Sciences, Temple University, Philadelphia, PA, USA
| | - Sean C Godar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Giulia Braccagni
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Alicia Ravens
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Mary T Zanda
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Marco Bortolato
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
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Winstone JK, Pathak KV, Winslow W, Piras IS, White J, Sharma R, Huentelman MJ, Pirrotte P, Velazquez R. Correction: Glyphosate infiltrates the brain and increases pro-inflammatory cytokine TNFα: implications for neurodegenerative disorders. J Neuroinflammation 2024; 21:20. [PMID: 38233859 PMCID: PMC10792902 DOI: 10.1186/s12974-023-02990-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Affiliation(s)
- Joanna K Winstone
- Arizona State University‑Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Khyatiben V Pathak
- Integrated Mass Spectrometry Shared Resources (IMS-SR), City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Wendy Winslow
- Arizona State University‑Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA
| | - Ignazio S Piras
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jennifer White
- Arizona State University‑Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA
| | - Ritin Sharma
- Integrated Mass Spectrometry Shared Resources (IMS-SR), City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Matthew J Huentelman
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resources (IMS-SR), City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Ramon Velazquez
- Arizona State University‑Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA.
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6
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Thapaliya G, Kundu P, Jansen E, Naymik MA, Lee R, Bruchhage MMK, D’Sa V, Huentelman MJ, Lewis CR, Müller HG, Deoni SCL, Carnell S. FTO variation and early frontostriatal brain development in children. Obesity (Silver Spring) 2024; 32:156-165. [PMID: 37817330 PMCID: PMC10840826 DOI: 10.1002/oby.23926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 10/12/2023]
Abstract
OBJECTIVE Common obesity-associated genetic variants at the fat mass and obesity-associated (FTO) locus have been associated with appetitive behaviors and altered structure and function of frontostriatal brain regions. The authors aimed to investigate the influence of FTO variation on frontostriatal appetite circuits in early life. METHODS Data were drawn from RESONANCE, a longitudinal study of early brain development. Growth trajectories of nucleus accumbens and frontal lobe volumes, as well as total gray matter and white matter volume, by risk allele (AA) carrier status on FTO single-nucleotide polymorphism rs9939609 were examined in 228 children (102 female, 126 male) using magnetic resonance imaging assessments obtained from infancy through middle childhood. The authors fit functional concurrent regression models with brain volume outcomes over age as functional responses, and FTO genotype, sex, BMI z score, and maternal education were included as predictors. RESULTS Bootstrap pointwise 95% CI for regression coefficient functions in the functional concurrent regression models showed that the AA group versus the group with no risk allele (TT) had greater nucleus accumbens volume (adjusted for total brain volume) in the interval of 750 to 2250 days (2-6 years). CONCLUSIONS These findings suggest that common genetic risk for obesity is associated with differences in early development of brain reward circuitry and argue for investigating dynamic relationships among genotype, brain, behavior, and weight throughout development.
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Affiliation(s)
- Gita Thapaliya
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Poorbita Kundu
- Department of Statistics, University of California, Davis, Davis, CA, USA
| | - Elena Jansen
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | | | - Richard Lee
- Department of Psychiatry, and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore MD, USA
| | - Muriel Marisa Katharina Bruchhage
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence, RI, USA
- Department of Psychology, Social Sciences, University of Stavanger, Norway
| | - Viren D’Sa
- Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence, RI, USA
| | | | - Candace R Lewis
- Neurogenomics Division, TGen, Phoenix, AZ, USA
- School of Life Sciences, Arizona State University, Phoenix, AZ, United States
| | - Hans-Georg Müller
- Department of Statistics, University of California, Davis, Davis, CA, USA
| | - Sean C. L. Deoni
- Maternal, Newborn and Child Health Discovery & Tools, Bill & Melinda Gates Foundation, Seattle, WA
| | | | - Susan Carnell
- Division of Child and Adolescent Psychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore MD, USA
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Telpoukhovskaia MA, Murdy TJ, Marola OJ, Charland K, MacLean M, Luquez T, Lish AM, Neuner S, Dunn A, Onos KD, Wiley J, Archer D, Huentelman MJ, Arnold M, Menon V, Goate A, Van Eldik LJ, Territo PR, Howell GR, Carter GW, O'Connell KMS, Kaczorowski CC. New directions for Alzheimer's disease research from the Jackson Laboratory Center for Alzheimer's and Dementia Research 2022 workshop. Alzheimers Dement (N Y) 2024; 10:e12458. [PMID: 38469553 PMCID: PMC10925728 DOI: 10.1002/trc2.12458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION In September 2022, The Jackson Laboratory Center for Alzheimer's and Dementia Research (JAX CADR) hosted a workshop with leading researchers in the Alzheimer's disease and related dementias (ADRD) field. METHODS During the workshop, the participants brainstormed new directions to overcome current barriers to providing patients with effective ADRD therapeutics. The participants outlined specific areas of focus. Following the workshop, each group used standard literature search methods to provide background for each topic. RESULTS The team of invited experts identified four key areas that can be collectively addressed to make a significant impact in the field: (1) Prioritize the diversification of disease targets, (2) enhance factors promoting resilience, (3) de-risk clinical pipeline, and (4) centralize data management. DISCUSSION In this report, we review these four objectives and propose innovations to expedite ADRD therapeutic pipelines.
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Affiliation(s)
| | - Thomas J. Murdy
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | | | - Kevin Charland
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Michael MacLean
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Tain Luquez
- Center for Translational and Computational NeuroimmunologyDepartment of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Alexandra M. Lish
- Ann Romney Center for Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Sarah Neuner
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Amy Dunn
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Kristen D. Onos
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | | | - Derek Archer
- Vanderbilt Memory and Alzheimer's CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of NeurologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Matthew J. Huentelman
- Neurogenomics DivisionTranslational Genomics Research Institute (TGen)PhoenixArizonaUSA
| | - Matthias Arnold
- Institute of Computational BiologyHelmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNorth CarolinaUSA
| | - Vilas Menon
- Center for Translational and Computational NeuroimmunologyDepartment of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Alison Goate
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | | | - Paul R. Territo
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
- Stark Neuroscience Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
| | - Gareth R. Howell
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Graduate School of Biomedical Science and EngineeringUniversity of MaineOronoMaineUSA
- Neuroscience Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
- Genetics Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
| | - Gregory W. Carter
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Graduate School of Biomedical Science and EngineeringUniversity of MaineOronoMaineUSA
- Neuroscience Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
- Genetics Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
| | - Kristen M. S. O'Connell
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Graduate School of Biomedical Science and EngineeringUniversity of MaineOronoMaineUSA
- Neuroscience Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
- Genetics Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
| | - Catherine C. Kaczorowski
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Department of NeurologyUniversity of MichiganAnn ArborMichiganUSA
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Harker SA, Al-Hassan L, Huentelman MJ, Braden BB, Lewis CR. APOE ε4-Allele in Middle-Aged and Older Autistic Adults: Associations with Verbal Learning and Memory. Int J Mol Sci 2023; 24:15988. [PMID: 37958971 PMCID: PMC10650864 DOI: 10.3390/ijms242115988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disability and recent evidence suggests that autistic adults are more likely to develop Alzheimer's disease (Alz) and other dementias compared to neurotypical (NT) adults. The ε4-allele of the Apolipoprotein E (APOE) gene is the strongest genetic risk factor for Alz and negatively impacts cognition in middle-aged and older (MA+) adults. This study aimed to determine the impact of the APOE ε4-allele on verbal learning and memory in MA+ autistic adults (ages 40-71 years) compared to matched NT adults. Using the Auditory Verbal Learning Test (AVLT), we found that ε4 carriers performed worse on short-term memory and verbal learning across diagnosis groups, but there was no interaction with diagnosis. In exploratory analyses within sex and diagnosis groups, only autistic men carrying APOE ε4 showed worse verbal learning (p = 0.02), compared to autistic men who were not carriers. Finally, the APOE ε4-allele did not significantly affect long-term memory in this sample. These findings replicate previous work indicating that the APOE ε4-allele negatively impacts short-term memory and verbal learning in MA+ adults and presents new preliminary findings that MA+ autistic men may be vulnerable to the effects of APOE ε4 on verbal learning. Future work with a larger sample is needed to determine if autistic women may also be vulnerable.
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Affiliation(s)
- Samantha A. Harker
- School of Life Sciences and Psychology, Arizona State University, Tempe, AZ 85287, USA;
- College of Health Solutions, Arizona State University, Tempe, AZ 85287, USA; (L.A.-H.); (B.B.B.)
| | - Lamees Al-Hassan
- College of Health Solutions, Arizona State University, Tempe, AZ 85287, USA; (L.A.-H.); (B.B.B.)
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA;
| | - B. Blair Braden
- College of Health Solutions, Arizona State University, Tempe, AZ 85287, USA; (L.A.-H.); (B.B.B.)
| | - Candace R. Lewis
- School of Life Sciences and Psychology, Arizona State University, Tempe, AZ 85287, USA;
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA;
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Piras IS, Braccagni G, Huentelman MJ, Bortolato M. A preliminary transcriptomic analysis of the orbitofrontal cortex of antisocial individuals. CNS Neurosci Ther 2023; 29:3173-3182. [PMID: 37269073 PMCID: PMC10580340 DOI: 10.1111/cns.14283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
AIMS Antisocial personality disorder (ASPD) and conduct disorder (CD) are characterized by a persistent pattern of violations of societal norms and others' rights. Ample evidence shows that the pathophysiology of these disorders is contributed by orbitofrontal cortex (OFC) alterations, yet the underlying molecular mechanisms remain elusive. To address this knowledge gap, we performed the first-ever RNA sequencing study of postmortem OFC samples from subjects with a lifetime diagnosis of ASPD and/or CD. METHODS The transcriptomic profiles of OFC samples from subjects with ASPD and/or CD were compared to those of unaffected age-matched controls (n = 9/group). RESULTS The OFC of ASPD/CD-affected subjects displayed significant differences in the expression of 328 genes. Further gene-ontology analyses revealed an extensive downregulation of excitatory neuron transcripts and upregulation of astrocyte transcripts. These alterations were paralleled by significant modifications in synaptic regulation and glutamatergic neurotransmission pathways. CONCLUSION These preliminary findings suggest that ASPD and CD feature a complex array of functional deficits in the pyramidal neurons and astrocytes of the OFC. In turn, these aberrances may contribute to the reduced OFC connectivity observed in antisocial subjects. Future analyses on larger cohorts are needed to validate these results.
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Affiliation(s)
- Ignazio S. Piras
- Neurogenomics DivisionTranslational Genomics Research Institute (TGen)PhoenixArizonaUSA
| | - Giulia Braccagni
- Department of Pharmacology and ToxicologyCollege of PharmacyUniversity of UtahSalt Lake CityUtahUSA
| | - Matthew J. Huentelman
- Neurogenomics DivisionTranslational Genomics Research Institute (TGen)PhoenixArizonaUSA
| | - Marco Bortolato
- Department of Pharmacology and ToxicologyCollege of PharmacyUniversity of UtahSalt Lake CityUtahUSA
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10
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Belnap N, Price-Smith A, Ramsey K, Leka K, Abraham A, Lieberman E, Hassett K, Potu S, Rudy N, Smith K, Mikhail FM, Monaghan KG, Hendershot A, Mourmans J, Descartes M, Huentelman MJ, Sills J, Rangasamy S, Narayanan V. Inherited CSNK2A1 variants in families with Okur-Chung neurodevelopmental syndrome. Clin Genet 2023; 104:607-609. [PMID: 37491870 DOI: 10.1111/cge.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023]
Abstract
Pedigree showing the autosomal dominant inheritance pattern of CSNK21 variants in families presenting with OCNDS. (A) Maternal inheritance to two daughters in Family 1, (B) Paternal inheritance to a daughter in Family 2, and (C) Maternal inheritance to two sons in Family 3.
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Affiliation(s)
- Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Aiai Price-Smith
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Keri Ramsey
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Kamawela Leka
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Anna Abraham
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Emma Lieberman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Katie Hassett
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Sai Potu
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Natasha Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kirstin Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | | | | | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | | | - Sampath Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
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11
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Rajabli F, Benchek P, Tosto G, Kushch N, Sha J, Bazemore K, Zhu C, Lee WP, Haut J, Hamilton-Nelson KL, Wheeler NR, Zhao Y, Farrell JJ, Grunin MA, Leung YY, Kuksa PP, Li D, Lucio da Fonseca E, Mez JB, Palmer EL, Pillai J, Sherva RM, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Abner E, Adams PM, Aguirre A, Albert MS, Albin RL, Allen M, Alvarez L, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Ayres G, Baldwin CT, Barber RC, Barnes LL, Barral S, Beach TG, Becker JT, Beecham GW, Beekly D, Benitez BA, Bennett D, Bertelson J, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Brewer J, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Chasse S, Chesselet MF, Chin NA, Chui HC, Chung J, Craft S, Crane PK, Cribbs DH, Crocco EA, Cruchaga C, Cuccaro ML, Cullum M, Darby E, Davis B, De Jager PL, DeCarli C, DeToledo J, Dick M, Dickson DW, Dombroski BA, Doody RS, Duara R, Ertekin-Taner NI, Evans DA, Faber KM, Fairchild TJ, Fallon KB, Fardo DW, Farlow MR, Fernandez-Hernandez V, Ferris S, Foroud TM, Frosch MP, Fulton-Howard B, Galasko DR, Gamboa A, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Goate AM, Grabowski TJ, Graff-Radford NR, Green RC, Growdon JH, Hakonarson H, Hall J, Hamilton RL, Harari O, Hardy J, Harrell LE, Head E, Henderson VW, Hernandez M, Hohman T, Honig LS, Huebinger RM, Huentelman MJ, Hulette CM, Hyman BT, Hynan LS, Ibanez L, Jarvik GP, Jayadev S, Jin LW, Johnson K, Johnson L, Kamboh MI, Karydas AM, Katz MJ, Kauwe JS, Kaye JA, Keene CD, Khaleeq A, Kim R, Knebl J, Kowall NW, Kramer JH, Kukull WA, LaFerla FM, Lah JJ, Larson EB, Lerner A, Leverenz JB, Levey AI, Lieberman AP, Lipton RB, Logue M, Lopez OL, Lunetta KL, Lyketsos CG, Mains D, Margaret FE, Marson DC, Martin ERR, Martiniuk F, Mash DC, Masliah E, Massman P, Masurkar A, McCormick WC, McCurry SM, McDavid AN, McDonough S, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Monuki ES, Morris JC, Mukherjee S, Myers AJ, Nguyen T, O'Bryant S, Olichney JM, Ory M, Palmer R, Parisi JE, Paulson HL, Pavlik V, Paydarfar D, Perez V, Peskind E, Petersen RC, Pierce A, Polk M, Poon WW, Potter H, Qu L, Quiceno M, Quinn JF, Raj A, Raskind M, Reiman EM, Reisberg B, Reisch JS, Ringman JM, Roberson ED, Rodriguear M, Rogaeva E, Rosen HJ, Rosenberg RN, Royall DR, Sager MA, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Slifer SH, Small S, Smith AG, Smith JP, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Stevens AB, Strittmatter SM, Sultzer D, Swerdlow RH, Tanzi RE, Tilson JL, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, van Eldik LJ, Vance JM, Vardarajan BN, Vassar R, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Whitehead PL, Wijsman EM, Wilhelmsen KC, Williams B, Williamson J, Wilms H, Wingo TS, Wisniewski T, Woltjer RL, Woon M, Wright CB, Wu CK, Younkin SG, Yu CE, Yu L, Zhu X, Kunkle BW, Bush WS, Wang LS, Farrer LA, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Jun GR, Reitz C, Naj AC. Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK , GRB14 , and KIAA0825 as novel risk loci for Alzheimer's disease: the Alzheimer's Disease Genetics Consortium. medRxiv 2023:2023.07.06.23292311. [PMID: 37461624 PMCID: PMC10350126 DOI: 10.1101/2023.07.06.23292311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer's Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/near CR1 , BIN1 , TREM2 , CD2AP , PTK2B , CLU , SHARPIN , MS4A6A , PICALM , ABCA7 , APOE and two novel loci not previously reported at 11p12 ( LRRC4C ) and 12q24.13 ( LHX5-AS1 ). Reflecting the power of diverse ancestry in GWAS, we observed the SHARPIN locus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near ( PTPRK ( P =2.4×10 -8 ) and GRB14 ( P =1.7×10 -8 ) in HIS), and KIAA0825 ( P =2.9×10 -8 in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest with P adjusted =1.6×10 -4 ) and the classical complement pathway ( P adjusted =1.3×10 -3 ). Genes at/near our novel loci have known roles in neuronal development ( LRRC4C, LHX5-AS1 , and PTPRK ) and insulin receptor activity regulation ( GRB14 ). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.
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12
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Frankel E, Podder A, Sharifi M, Pillai R, Belnap N, Ramsey K, Dodson J, Venugopal P, Brzezinski M, Llaci L, Gerald B, Mills G, Sanchez-Castillo M, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Naymik M, Schrauwen I, Craig DW, Piras IS, Huentelman MJ, Schork NJ, Narayanan V, Rangasamy S. Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders. Cells 2023; 12:1437. [PMID: 37408271 DOI: 10.3390/cells12101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. A subset of patients who are recognized to have an overlapping neurological phenotype with RTT but are lacking a mutation in a gene that causes classical or atypical RTT can be described as having a 'Rett-syndrome-like phenotype (RTT-L). Here, we report eight patients from our cohort diagnosed as having RTT-L who carry mutations in genes unrelated to RTT. We annotated the list of genes associated with RTT-L from our patient cohort, considered them in the light of peer-reviewed articles on the genetics of RTT-L, and constructed an integrated protein-protein interaction network (PPIN) consisting of 2871 interactions connecting 2192 neighboring proteins among RTT- and RTT-L-associated genes. Functional enrichment analysis of RTT and RTT-L genes identified a number of intuitive biological processes. We also identified transcription factors (TFs) whose binding sites are common across the set of RTT and RTT-L genes and appear as important regulatory motifs for them. Investigation of the most significant over-represented pathway analysis suggests that HDAC1 and CHD4 likely play a central role in the interactome between RTT and RTT-L genes.
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Affiliation(s)
- Eric Frankel
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Avijit Podder
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Megan Sharifi
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Roshan Pillai
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Julius Dodson
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Pooja Venugopal
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Molly Brzezinski
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Lorida Llaci
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Brittany Gerald
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Gabrielle Mills
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Chris D Balak
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Szabolcs Szelinger
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ryan Richholt
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Nicholas J Schork
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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13
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Hooyman A, Huentelman MJ, De Both M, Ryan L, Schaefer SY. Establishing the Validity and Reliability of an Online Motor Learning Game: Applications for Alzheimer's Disease Research Within MindCrowd. Games Health J 2023; 12:132-139. [PMID: 36745382 PMCID: PMC10066776 DOI: 10.1089/g4h.2022.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objective: Motor practice effects (i.e., improvements in motor task performance with practice) are emerging as a unique variable that can predict Alzheimer's disease (AD) progression and biomarker positivity. However, the tasks used to study motor practice effects have involved face-to-face assessment, making them difficult to integrate into large internet-based cohorts that represent the next generation of AD research. The purpose of this study was to validate an online computer game against its in-lab version, which has been shown previously to characterize motor practice effects. Materials and Methods: This study leveraged young adult participants within the MindCrowd electronic cohort, a large nationwide cohort for AD research collected entirely through the internet. Validation compared performance on the online version among MindCrowd users against an age-matched cohort's performance on an in-lab version using a different controller (Xbox 360 controller joystick for in-lab sample versus keyboard arrow keys for online sample). Results: Data indicated that the rate of skill acquisition among MindCrowd users were not significantly different from those of the in-lab cohort. Furthermore, the contact-to-consent rate observed in this study (although low) was similar to that of other online AD cohorts. Conclusion: Overall, this study demonstrates that implementing online games designed to study and measure motor practice effects into online research cohorts is feasible and valid. Future research will explore how online game performance is associated with age and dementia risk factors that may help further an understanding of AD.
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Affiliation(s)
- Andrew Hooyman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- The Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Matthew J. Huentelman
- The Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Matt De Both
- The Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Lee Ryan
- The Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Psychology Department, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - Sydney Y. Schaefer
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- The Arizona Alzheimer's Consortium, Phoenix, AZ, USA
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14
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Lavin KM, Graham ZA, McAdam JS, O'Bryan SM, Drummer D, Bell MB, Kelley CJ, Lixandrão ME, Peoples B, Tuggle SC, Seay RS, Van Keuren-Jensen K, Huentelman MJ, Pirrotte P, Reiman R, Alsop E, Hutchins E, Antone J, Bonfitto A, Meechoovet B, Palade J, Talboom JS, Sullivan A, Aban I, Peri K, Broderick TJ, Bamman MM. Dynamic transcriptomic responses to divergent acute exercise stimuli in young adults. Physiol Genomics 2023; 55:194-212. [PMID: 36939205 PMCID: PMC10110731 DOI: 10.1152/physiolgenomics.00144.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/08/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2023] Open
Abstract
Acute exercise elicits dynamic transcriptional changes that, when repeated, form the fundamental basis of health, resilience, and performance adaptations. While moderate-intensity endurance training combined with conventional resistance training (traditional, TRAD) is often prescribed and recommended by public health guidance, high-intensity training combining maximal-effort intervals with intensive, limited-rest resistance training is a time-efficient alternative that may be used tactically (HITT) to confer similar benefits. Mechanisms of action of these distinct stimuli are incompletely characterized and have not been directly compared. We assessed transcriptome-wide responses in skeletal muscle and circulating extracellular vesicles (EVs) to a single exercise bout in young adults randomized to TRAD (n = 21, 12 M/9 F, 22 ± 3 yr) or HITT (n = 19, 11 M/8 F, 22 ± 2 yr). Next-generation sequencing captured small, long, and circular RNA in muscle and EVs. Analysis identified differentially expressed transcripts (|log2FC|>1, FDR ≤ 0.05) immediately (h0, EVs only), h3, and h24 postexercise within and between exercise protocols. In aaddition, all apparently responsive transcripts (FDR < 0.2) underwent singular value decomposition to summarize data structures into latent variables (LVs) to deconvolve molecular expression circuits and interregulatory relationships. LVs were compared across time and exercise protocol. TRAD, a longer but less intense stimulus, generally elicited a stronger transcriptional response than HITT, but considerable overlap and key differences existed. Findings reveal shared and unique molecular responses to the exercise stimuli and lay groundwork toward establishing relationships between protein-coding genes and lesser-understood transcripts that serve regulatory roles following exercise. Future work should advance the understanding of these circuits and whether they repeat in other populations or following other types of exercise/stress.NEW & NOTEWORTHY We examined small and long transcriptomics in skeletal muscle and serum-derived extracellular vesicles before and after a single exposure to traditional combined exercise (TRAD) and high-intensity tactical training (HITT). Across 40 young adults, we found more consistent protein-coding gene responses to TRAD, whereas HITT elicited differential expression of microRNA enriched in brain regions. Follow-up analysis revealed relationships and temporal dynamics across transcript networks, highlighting potential avenues for research into mechanisms of exercise response and adaptation.
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Affiliation(s)
- Kaleen M Lavin
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Zachary A Graham
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, United States
| | - Jeremy S McAdam
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Samia M O'Bryan
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Devin Drummer
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Margaret B Bell
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Christian J Kelley
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Manoel E Lixandrão
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Brandon Peoples
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - S Craig Tuggle
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Regina S Seay
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Matthew J Huentelman
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Patrick Pirrotte
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, California, United States
| | - Rebecca Reiman
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Eric Alsop
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Elizabeth Hutchins
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Jerry Antone
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Anna Bonfitto
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Bessie Meechoovet
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Joanna Palade
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Joshua S Talboom
- Cancer & Cell Biology, Translational Genomics Research Institute, Phoenix, Arizona, United States
| | - Amber Sullivan
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Inmaculada Aban
- Department of Biostatistics, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Kalyani Peri
- Department of Biostatistics, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Timothy J Broderick
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
| | - Marcas M Bamman
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
- UAB Center for Exercise Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States
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15
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Deoni SCL, Burton P, Beauchemin J, Cano-Lorente R, De Both MD, Johnson M, Ryan L, Huentelman MJ. Neuroimaging and verbal memory assessment in healthy aging adults using a portable low-field MRI scanner and a web-based platform: results from a proof-of-concept population-based cross-section study. Brain Struct Funct 2023; 228:493-509. [PMID: 36352153 PMCID: PMC9646260 DOI: 10.1007/s00429-022-02595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/01/2022] [Indexed: 11/10/2022]
Abstract
Consumer wearables and health monitors, internet-based health and cognitive assessments, and at-home biosample (e.g., saliva and capillary blood) collection kits are increasingly used by public health researchers for large population-based studies without requiring intensive in-person visits. Alongside reduced participant time burden, remote and virtual data collection allows the participation of individuals who live long distances from hospital or university research centers, or who lack access to transportation. Unfortunately, studies that include magnetic resonance neuroimaging are challenging to perform remotely given the infrastructure requirements of MRI scanners, and, as a result, they often omit socially, economically, and educationally disadvantaged individuals. Lower field strength systems (< 100 mT) offer the potential to perform neuroimaging at a participant's home, enabling more accessible and equitable research. Here we report the first use of a low-field MRI "scan van" with an online assessment of paired-associate learning (PAL) to examine associations between brain morphometry and verbal memory performance. In a sample of 67 individuals, 18-93 years of age, imaged at or near their home, we show expected white and gray matter volume trends with age and find significant (p < 0.05 FWE) associations between PAL performance and hippocampus, amygdala, caudate, and thalamic volumes. High-quality data were acquired in 93% of individuals, and at-home scanning was preferred by all individuals with prior MRI at a hospital or research setting. Results demonstrate the feasibility of remote neuroimaging and cognitive data collection, with important implications for engaging traditionally under-represented communities in neuroimaging research.
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Affiliation(s)
- Sean C L Deoni
- Maternal, Newborn, and Child Health Discovery & Tools, Bill & Melinda Gates Foundation, 500 5th Ave, Seattle, WA, 98109, USA.
| | - Phoebe Burton
- Advanced Baby Imaging Lab, Rhode Island Hospital, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence, RI, USA
| | - Jennifer Beauchemin
- Advanced Baby Imaging Lab, Rhode Island Hospital, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence, RI, USA
| | - Rosa Cano-Lorente
- Advanced Baby Imaging Lab, Rhode Island Hospital, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence, RI, USA
| | | | | | - Lee Ryan
- Department of Psychology, University of Arizona, Tucson, AZ, USA
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16
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Piras IS, Brokaw D, Kong Y, Weisenberger DJ, Krate J, Delvaux E, Mahurkar S, Blattler A, Siegmund KD, Sue L, Serrano GE, Beach TG, Laird PW, Huentelman MJ, Coleman PD. Integrated DNA Methylation/RNA Profiling in Middle Temporal Gyrus of Alzheimer's Disease. Cell Mol Neurobiol 2023:10.1007/s10571-022-01307-3. [PMID: 36596913 DOI: 10.1007/s10571-022-01307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/08/2022] [Indexed: 01/05/2023]
Abstract
Alzheimer's disease is a neurodegenerative disorder clinically defined by gradual cognitive impairment and alteration in executive function. We conducted an epigenome-wide association study (EWAS) of a clinically and neuropathologically characterized cohort of 296 brains, including Alzheimer's disease (AD) and non-demented controls (ND), exploring the relationship with the RNA expression from matched donors. We detected 5246 CpGs and 832 regions differentially methylated, finding overlap with previous EWAS but also new associations. CpGs previously identified in ANK1, MYOC, and RHBDF2 were differentially methylated, and one of our top hits (GPR56) was not previously detected. ANK1 was differentially methylated at the region level, along with APOE and RHBDF2. Only a small number of genes showed a correlation between DNA methylation and RNA expression statistically significant. Multiblock partial least-squares discriminant analysis showed several CpG sites and RNAs discriminating AD and ND (AUC = 0.908) and strongly correlated with each other. Furthermore, the CpG site cg25038311 was negatively correlated with the expression of 22 genes. Finally, with the functional epigenetic module analysis, we identified a protein-protein network characterized by inverse RNA/DNA methylation correlation and enriched for "Regulation of insulin-like growth factor transport", with IGF1 as the hub gene. Our results confirm and extend the previous EWAS, providing new information about a brain region not previously explored in AD DNA methylation studies. The relationship between DNA methylation and gene expression is not significant for most of the genes in our sample, consistently with the complexities in the gene expression regulation.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Danielle Brokaw
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Yinfei Kong
- Department of Information Systems and Decision Sciences, California State University Fullerton, Fullerton, CA, 92831, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Biology, University of South California, Los Angeles, CA, 90033, USA
| | - Jonida Krate
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
- UnityPoint Clinic, Waterloo, IA, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Swapna Mahurkar
- UCLA Division of Digestive Diseases, University of California, Los Angeles, CA, 90024, USA
| | - Adam Blattler
- Department of Biochemistry and Molecular Biology, University of South California, Los Angeles, CA, 90033, USA
- Genetics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Kimberly D Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089-9175, USA
| | - Lucia Sue
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Geidy E Serrano
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Paul D Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287, USA.
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17
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Song H, Bharadwaj PK, Raichlen DA, Habeck CG, Huentelman MJ, Hishaw GA, Trouard TP, Alexander GE. Association of homocysteine-related subcortical brain atrophy with white matter lesion volume and cognition in healthy aging. Neurobiol Aging 2023; 121:129-138. [PMID: 36436304 PMCID: PMC10002471 DOI: 10.1016/j.neurobiolaging.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/16/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Homocysteine (Hcy) is a vascular risk factor associated with cognitive impairment and cerebrovascular disease but has also been implicated in Alzheimer's disease (AD). Using multivariate Scaled Subprofile Model (SSM) analysis, we sought to identify a network pattern in structural neuroimaging reflecting the regionally distributed association of plasma Hcy with subcortical gray matter (SGM) volumes and its relation to other health risk factors and cognition in 160 healthy older adults, ages 50-89. We identified an SSM Hcy-SGM pattern that was characterized by bilateral hippocampal and nucleus accumbens volume reductions with relative volume increases in bilateral caudate, pallidum, and putamen. Greater Hcy-SGM pattern expression was associated with greater white matter hyperintensity (WMH) volume, older age, and male sex, but not with other vascular and AD-related risk factors. Mediation analyses revealed that age predicted WMH volume, which predicted Hcy-SGM pattern expression, which, in turn, predicted cognitive processing speed performance. These findings suggest that the multivariate SSM Hcy-SGM pattern may be indicative of cognitive aging, reflecting a potential link between vascular health and cognitive dysfunction in healthy older adults.
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Affiliation(s)
- Hyun Song
- Department of Psychology, University of Arizona, Tucson, AZ, USA; Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - Pradyumna K Bharadwaj
- Department of Psychology, University of Arizona, Tucson, AZ, USA; Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - David A Raichlen
- Human and Evolutionary Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christian G Habeck
- Cognitive Neuroscience Division, Department of Neurology and Taub Institute, Columbia University, New York, NY, USA
| | - Matthew J Huentelman
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA; Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Georg A Hishaw
- Department of Neurology, University of Arizona, Tucson, AZ, USA
| | - Theodore P Trouard
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Gene E Alexander
- Department of Psychology, University of Arizona, Tucson, AZ, USA; Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA; Arizona Alzheimer's Consortium, Phoenix, AZ, USA; Department of Psychiatry, University of Arizona, Tucson, AZ, USA; Neuroscience and Physiological Sciences Graduate Interdisciplinary Programs, University of Arizona, Tucson, AZ, USA.
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18
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Green JM, Barry F, Burton P, Beauchemin J, Huentelman MJ, Deoni SCL, Lewis CR. At-home dried blood spot (DBS) collection to increase population heterogeneity representation in pediatric research: An ECHO study. Front Pediatr 2023; 11:1059107. [PMID: 36937973 PMCID: PMC10020170 DOI: 10.3389/fped.2023.1059107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/31/2023] [Indexed: 03/06/2023] Open
Abstract
Self-collection of dried blood samples (DBS) in the participant's home provides an alternative to university/hospital visits for research and has the potential to improve the representation of population heterogeneity in research. This study aimed to assess the feasibility of guardian and/or self-DBS collection in healthy youth in the lab and home. Guardians/youth [N = 140; females = 63; M age = 8.73, SD age = 3.56] who enrolled in a longitudinal study of typical development were asked during a lab visit to provide a DBS. Upon providing a sample, the participants were asked if they would be willing to self-collect in the home and return the sample via the post office. Of those asked to provide a sample in the lab, 82% consented and 18% declined, with a significant difference in age but no significant difference in sex, ethnicity, race, or family income. Of those who provided a sample in the lab, 75% were willing to self-collect DBS in the home, with no significant difference in demographic variables between them. We report a quality assessment and DNA extraction results from a subset of samples. The results demonstrate a high feasibility of DBS collection from healthy youth for research purposes both in the laboratory and in the home across different demographic variables. Developmental researchers should consider including this approach in their studies to increase population heterogeneity representation.
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Affiliation(s)
- Joseph M. Green
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Fatoumata Barry
- Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Phoebe Burton
- Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Jennifer Beauchemin
- Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Matthew J. Huentelman
- Neurogenomics, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Sean C. L. Deoni
- Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, United States
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Candace R. Lewis
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Neurogenomics, Translational Genomics Research Institute, Phoenix, AZ, United States
- Correspondence: Candace R. Lewis
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19
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Rogalski EJ, Huentelman MJ, Roberts AC, Maher AC, McIlroy B, Van Ooteghem K, Finger E, Lim A, Okonkwo OC, Goldstein FC, Hajjar I, Parrish T, Scholtens D, Gutierrez S, Weintraub S, Geula C, Mesulam M. The SuperAging Research Initiative: A multisite consortium focused on identifying factors promoting extraordinary cognitive aging. Alzheimers Dement 2022. [DOI: 10.1002/alz.066407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Matthew J Huentelman
- The Translational Genomics Research Institute (TGen‐ an Affiliate of City of Hope) Phoenix AZ USA
| | | | | | | | | | - Elizabeth Finger
- Department of Clinical Neurological Sciences, University of Western Ontario London ON Canada
| | - Andrew Lim
- Sunnybrook Health Sciences Centre Toronto ON Canada
| | - Ozioma C. Okonkwo
- Alzheimer’s Disease Research Center, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
| | - Felicia C Goldstein
- Emory University Goizueta Alzheimer’s Disease Research Center Atlanta GA USA
| | - Ihab Hajjar
- Emory University School of Medicine Atlanta GA USA
| | | | | | | | | | - Changiz Geula
- Northwestern University Feinberg School of Medicine Chicago IL USA
| | - M.‐Marsel Mesulam
- Northwestern University Feinberg School of Medicine Chicago IL USA
- Northwestern University Chicago IL USA
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20
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Bergamino M, Burke A, Baxter LC, Caselli RJ, Sabbagh MN, Talboom JS, Huentelman MJ, Stokes AM. Longitudinal Assessment of Intravoxel Incoherent Motion Diffusion-Weighted MRI Metrics in Cognitive Decline. J Magn Reson Imaging 2022; 56:1845-1862. [PMID: 35319142 DOI: 10.1002/jmri.28172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Advanced diffusion-based MRI biomarkers may provide insight into microstructural and perfusion changes associated with neurodegeneration and cognitive decline. PURPOSE To assess longitudinal microstructural and perfusion changes using apparent diffusion coefficient (ADC) and intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) parameters in cognitively impaired (CI) and healthy control (HC) groups. STUDY TYPE Prospective/longitudinal. POPULATION Twelve CI patients (75% female) and 13 HC subjects (69% female). FIELD STRENGTH/SEQUENCE 3 T; Spin-Echo-IVIM-DWI. ASSESSMENT Two MRI scans were performed with a 12-month interval. ADC and IVIM-DWI metrics (diffusion coefficient [D] and perfusion fraction [f]) were generated from monoexponential and biexponential fits, respectively. Additionally, voxel-based correlations were evaluated between change in Montreal Cognitive Assessment (ΔMoCA) and baseline imaging parameters. STATISTICAL TESTS Analysis of covariance with sex and age as covariates was performed for main effects of group and time (false discovery rate [FDR] corrected) with post hoc comparisons using Bonferroni correction. Partial-η2 and Hedges' g were used for effect-size analysis. Spearman's correlations (FDR corrected) were used for the relationship between ΔMoCA score and imaging. P < 0.05 was considered statistically significant. RESULTS Significant differences were found for the main effects of group (HC vs. CI) and time. For group effects, higher ADC, IVIM-D, and IVIM-f were observed in the CI group compared to HC (ADC: 1.23 ± 0.08. 10-3 vs. 1.09 ± 0.07. 10-3 mm2 /sec; IVIM-D: 0.82 ± 0.01. 10-3 vs. 0.73 ± 0.01. 10-3 mm2 /sec; and IVIM-f: 0.317 ± 0.008 vs. 0.253 ± 0.009). Significantly higher ADC, IVIM-D, and IVIM-f values were observed in the CI group after 12 months (ADC: 1.45 ± 0.05. 10-3 vs. 1.50 ± 0.07. 10-3 mm2 /sec; IVIM-D: 0.87 ± 0.01. 10-3 vs. 0.94 ± 0.02. 10-3 mm2 /sec; and IVIM-f: 0.303 ± 0.007 vs. 0.332 ± 0.008), but not in the HC group at large effect size. ADC, IVIM-D, and IVIM-f negatively correlated with ΔMoCA score (ρ = -0.49, -0.51, and -0.50, respectively). DATA CONCLUSION These findings demonstrate that longitudinal differences between CI and HC cohorts can be measured using IVIM-based metrics. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY STAGE: 2.
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Affiliation(s)
- Maurizio Bergamino
- Barrow Neuroimaging Innovation Center, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Anna Burke
- Department of Neurology, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Leslie C Baxter
- Department of Neurology, Mayo Clinic Arizona, Phoenix, Arizona, USA
| | - Richard J Caselli
- Department of Psychiatry and Psychology, Mayo Clinic Arizona, Phoenix, Arizona, USA
| | - Marwan N Sabbagh
- Department of Neurology, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Joshua S Talboom
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Ashley M Stokes
- Barrow Neuroimaging Innovation Center, Barrow Neurological Institute, Phoenix, Arizona, USA
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21
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Nassan M, Piras I, Rogalski EJ, Geula C, Mesulam M, Dashti H, Saxena R, Huentelman MJ. Genetically Proxied Angiotensin‐Converting‐Enzyme Inhibition is Potentially Causal for Alzheimer Disease: A Mendelian Randomization Study. Alzheimers Dement 2022. [DOI: 10.1002/alz.069349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Ignazio Piras
- The Translational Genomics Research Institute (TGen‐ an Affiliate of City of Hope) Phoenix AZ USA
| | | | - Changiz Geula
- Northwestern University Feinberg School of Medicine Chicago IL USA
| | | | | | | | - Matthew J Huentelman
- The Translational Genomics Research Institute (TGen‐ an Affiliate of City of Hope) Phoenix AZ USA
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22
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Winstone JK, Pathak KV, Winslow W, Piras IS, White J, Sharma R, Huentelman MJ, Pirrotte P, Velazquez R. Glyphosate infiltrates the brain and increases pro-inflammatory cytokine TNFα: implications for neurodegenerative disorders. J Neuroinflammation 2022; 19:193. [PMID: 35897073 PMCID: PMC9331154 DOI: 10.1186/s12974-022-02544-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/05/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Herbicides are environmental contaminants that have gained much attention due to the potential hazards they pose to human health. Glyphosate, the active ingredient in many commercial herbicides, is the most heavily applied herbicide worldwide. The recent rise in glyphosate application to corn and soy crops correlates positively with increased death rates due to Alzheimer's disease and other neurodegenerative disorders. Glyphosate has been shown to cross the blood-brain barrier in in vitro models, but has yet to be verified in vivo. Additionally, reports have shown that glyphosate exposure increases pro-inflammatory cytokines in blood plasma, particularly TNFα. METHODS Here, we examined whether glyphosate infiltrates the brain and elevates TNFα levels in 4-month-old C57BL/6J mice. Mice received either 125, 250, or 500 mg/kg/day of glyphosate, or a vehicle via oral gavage for 14 days. Urine, plasma, and brain samples were collected on the final day of dosing for analysis via UPLC-MS and ELISAs. Primary cortical neurons were derived from amyloidogenic APP/PS1 pups to evaluate in vitro changes in Aβ40-42 burden and cytotoxicity. RNA sequencing was performed on C57BL/6J brain samples to determine changes in the transcriptome. RESULTS Our analysis revealed that glyphosate infiltrated the brain in a dose-dependent manner and upregulated TNFα in both plasma and brain tissue post-exposure. Notably, glyphosate measures correlated positively with TNFα levels. Glyphosate exposure in APP/PS1 primary cortical neurons increases levels of soluble Aβ40-42 and cytotoxicity. RNAseq revealed over 200 differentially expressed genes in a dose-dependent manner and cell-type-specific deconvolution analysis showed enrichment of key biological processes in oligodendrocytes including myelination, axon ensheathment, glial cell development, and oligodendrocyte development. CONCLUSIONS Collectively, these results show for the first time that glyphosate infiltrates the brain, elevates both the expression of TNFα and soluble Aβ, and disrupts the transcriptome in a dose-dependent manner, suggesting that exposure to this herbicide may have detrimental outcomes regarding the health of the general population.
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Affiliation(s)
- Joanna K Winstone
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Khyatiben V Pathak
- Integrated Mass Spectrometry Shared Resources (IMS-SR), City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Wendy Winslow
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA
| | - Ignazio S Piras
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jennifer White
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA
| | - Ritin Sharma
- Integrated Mass Spectrometry Shared Resources (IMS-SR), City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Matthew J Huentelman
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resources (IMS-SR), City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Ramon Velazquez
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, 797 E Tyler St, Tempe, AZ, 85287, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA.
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23
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Serrano GE, Walker JE, Tremblay C, Piras IS, Huentelman MJ, Belden CM, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Caselli R, Woodruff BK, Haarer CF, Ruhlen T, Torres M, Nguyen S, Schmitt D, Rapscak SZ, Bime C, Peters JL, Alevritis E, Arce RA, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Russell A, Suszczewicz KE, Borja CI, Cline MP, Hemmingsen SJ, Qiji S, Hobgood HM, Mizgerd JP, Sahoo MK, Zhang H, Solis D, Montine TJ, Berry GJ, Reiman EM, Röltgen K, Boyd SD, Pinsky BA, Zehnder JL, Talbot P, Desforges M, DeTure M, Dickson DW, Beach TG. SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19. J Neuropathol Exp Neurol 2022; 81:666-695. [PMID: 35818336 PMCID: PMC9278252 DOI: 10.1093/jnen/nlac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.
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Affiliation(s)
- Geidy E Serrano
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Jessica E Walker
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Cécilia Tremblay
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - Danielle Goldfarb
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - David Shprecher
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alireza Atri
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA.,Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Charles H Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Holly A Shill
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | | | - Shyamal H Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Richard Caselli
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Bryan K Woodruff
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | | | - Thomas Ruhlen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Maria Torres
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Steve Nguyen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Dasan Schmitt
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | | | | | | | | | - Richard A Arce
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Michael J Glass
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Daisy Vargas
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Lucia I Sue
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Courtney M Nelson
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Javon Oliver
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Aryck Russell
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Claryssa I Borja
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Madison P Cline
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Sanaria Qiji
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Holly M Hobgood
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Daniel Solis
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, California, USA.,From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, California, USA.,Division of Infectious Disease & Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pierre Talbot
- Laboratory of Neuroimmunology, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Marc Desforges
- Laboratory of Virology, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Michael DeTure
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Dennis W Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Thomas G Beach
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
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Alsop E, Meechoovet B, Kitchen R, Sweeney T, Beach TG, Serrano GE, Hutchins E, Ghiran I, Reiman R, Syring M, Hsieh M, Courtright-Lim A, Valkov N, Whitsett TG, Rakela J, Pockros P, Rozowsky J, Gallego J, Huentelman MJ, Shah R, Nakaji P, Kalani MYS, Laurent L, Das S, Van Keuren-Jensen K. A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids. Front Cell Dev Biol 2022; 10:804164. [PMID: 35317387 PMCID: PMC8934391 DOI: 10.3389/fcell.2022.804164] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/28/2022] [Indexed: 12/20/2022] Open
Abstract
One promising goal for utilizing the molecular information circulating in biofluids is the discovery of clinically useful biomarkers. Extracellular RNAs (exRNAs) are one of the most diverse classes of molecular cargo, easily assayed by sequencing and with expressions that rapidly change in response to subject status. Despite diverse exRNA cargo, most evaluations from biofluids have focused on small RNA sequencing and analysis, specifically on microRNAs (miRNAs). Another goal of characterizing circulating molecular information, is to correlate expression to injuries associated with specific tissues of origin. Biomarker candidates are often described as being specific, enriched in a particular tissue or associated with a disease process. Likewise, miRNA data is often reported to be specific, enriched for a tissue, without rigorous testing to support the claim. Here we provide a tissue atlas of small RNAs from 30 different tissues and three different blood cell types. We analyzed the tissues for enrichment of small RNA sequences and assessed their expression in biofluids: plasma, cerebrospinal fluid, urine, and saliva. We employed published data sets representing physiological (resting vs. acute exercise) and pathologic states (early- vs. late-stage liver fibrosis, and differential subtypes of stroke) to determine differential tissue-enriched small RNAs. We also developed an online tool that provides information about exRNA sequences found in different biofluids and tissues. The data can be used to better understand the various types of small RNA sequences in different tissues as well as their potential release into biofluids, which should help in the validation or design of biomarker studies.
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Affiliation(s)
- Eric Alsop
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Bessie Meechoovet
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Robert Kitchen
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Thadryan Sweeney
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Geidy E. Serrano
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Elizabeth Hutchins
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ionita Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Rebecca Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Michael Syring
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Michael Hsieh
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Amanda Courtright-Lim
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Nedyalka Valkov
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Timothy G. Whitsett
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | - Paul Pockros
- Division of Gastroenterology/Hepatology, Scripps Clinic, La Jolla, CA, United States
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Juan Gallego
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, United States
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, United States
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
| | - Matthew J. Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ravi Shah
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Peter Nakaji
- Department of Neurosurgery, Banner Health, Phoenix, AZ, United States
| | - M. Yashar S. Kalani
- Department of Neurosurgery, St. John Medical Center, Tulsa, OK, United States
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, San Diego, CA, United States
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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Piras IS, Huentelman MJ, Pinna F, Paribello P, Solmi M, Murru A, Carpiniello B, Manchia M, Zai CC. A review and meta-analysis of gene expression profiles in suicide. Eur Neuropsychopharmacol 2022; 56:39-49. [PMID: 34923210 DOI: 10.1016/j.euroneuro.2021.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022]
Abstract
Suicide claims over 800,000 deaths worldwide, making it a serious public health problem. The etiopathophysiology of suicide remains unclear and is highly complex, and postmortem gene expression studies can offer insights into the molecular biological mechanism underlying suicide. In the current study, we conducted a meta-analysis of postmortem brain gene expression in relation to suicide. We identified five gene expression datasets for postmortem orbitofrontal, prefrontal, or dorsolateral prefrontal cortical brain regions from the Gene Expression Omnibus repository. After quality control, the total sample size was 380 (141 suicide deaths and 239 deaths from other causes). We performed the analyses using two meta-analytic approaches. We further performed pathway and cell-set enrichment analyses. We found reduced expression of the KCNJ2 (Potassium Inwardly Rectifying Channel Subfamily J Member 2), A2M (Alpha-2-Macroglobulin), AGT (Angiotensinogen), PMP2 (Peripheral Myelin Protein 2), and VEZF1 (Vascular Endothelial Zinc Finger 1) genes (FDR p<0.05). Our findings support the involvement of astrocytes, stress response, immune system, and microglia in suicide. These findings will require further validation in additional large datasets.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Federica Pinna
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy; Unit of Clinical Psychiatry, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Pasquale Paribello
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy; Unit of Clinical Psychiatry, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Marco Solmi
- Department of Psychiatry, University of Ottawa, Ontario, Canada; Department of Mental Health, The Ottawa Hospital, Ontario, Canada; Ottawa Hospital Research Institute (OHRI) Clinical Epidemiology Program University of Ottawa Ottawa Ontario; Early Psychosis: Interventions and Clinical-detection (EPIC) Lab, Institute of Psychiatry, Psychology & Neuroscience, Department of Psychosis Studies, King's College London, London, United Kingdom
| | - Andrea Murru
- Bipolar and Depression Disorders Unit, Institute of Neuroscience, Hospital Clinic, IDIBAPS CIBERSAM, University of Barcelona, Barcelona, Catalonia, Spain
| | - Bernardo Carpiniello
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy; Unit of Clinical Psychiatry, University Hospital Agency of Cagliari, Cagliari, Italy
| | - Mirko Manchia
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy; Unit of Clinical Psychiatry, University Hospital Agency of Cagliari, Cagliari, Italy; Department of Pharmacology, Dalhousie University, Halifax, NS, Canada.
| | - Clement C Zai
- Neurogenetics Section, Molecular Brain Science, Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry, Institute of Medical Science, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, United States
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26
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Ramsey K, Belnap N, Bonfitto A, Jepsen W, Naymik M, Sanchez-Castillo M, Craig DW, Szelinger S, Huentelman MJ, Narayanan V, Rangasamy S. Progressive cerebellar atrophy caused by heterozygous TECPR2 mutations. Mol Genet Genomic Med 2022; 10:e1857. [PMID: 34994087 PMCID: PMC8830808 DOI: 10.1002/mgg3.1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/06/2022] Open
Affiliation(s)
- Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Newell Belnap
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Anna Bonfitto
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Wayne Jepsen
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - David W Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona, USA
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Piras IS, Huentelman MJ, Walker JE, Arce R, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Suszczewicz KE, Borja CL, Desforges M, Deture M, Dickson DW, Beach TG, Serrano GE. Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19. medRxiv 2021:2021.09.12.21263291. [PMID: 34545375 PMCID: PMC8452114 DOI: 10.1101/2021.09.12.21263291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study we conducted RNA sequencing on two brain regions (olfactory bulb and amygdala) from subjects who died from COVID-19 or who died of other causes. We found several-fold more transcriptional changes in the olfactory bulb than in the amygdala, consistent with our own work and that of others indicating that the olfactory bulb may be the initial and most common brain region infected. To some extent our results converge with pseudotime analysis towards common processes shared between the brain regions, possibly induced by the systemic immune reaction following SARS-CoV-2 infection. Changes in amygdala emphasized upregulation of interferon-related neuroinflammation genes, as well as downregulation of synaptic and other neuronal genes, and may represent the substrate of reported acute and subacute COVID-19 neurological effects. Additionally, and only in olfactory bulb, we observed an increase in angiogenesis and platelet activation genes, possibly associated with microvascular damages induced by neuroinflammation. Through coexpression analysis we identified two key genes (CAMK2B for the synaptic neuronal network and COL1A2 for the angiogenesis/platelet network) that might be interesting potential targets to reverse the effects induced by SARS-CoV-2 infection. Finally, in olfactory bulb we detected an upregulation of olfactory and taste genes, possibly as a compensatory response to functional deafferentation caused by viral entry into primary olfactory sensory neurons. In conclusion, we were able to identify transcriptional profiles and key genes involved in neuroinflammation, neuronal reaction and olfaction induced by direct CNS infection and/or the systemic immune response to SARS-CoV-2 infection.
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Affiliation(s)
- Ignazio S. Piras
- Translational Genomics Research Institute, Neurogenomics Division
| | | | | | - Richard Arce
- Banner Sun Health Research Institute, Sun City, AZ
| | | | - Daisy Vargas
- Banner Sun Health Research Institute, Sun City, AZ
| | - Lucia I. Sue
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | | | | | - Marc Desforges
- Centre Hospitalier Universitaire Sainte-Justine, Laboratory of Virology, Montreal, Canada
| | - Michael Deture
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, FL
| | - Dennis W. Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, FL
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28
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Dave N, Vural AS, Piras IS, Winslow W, Surendra L, Winstone JK, Beach TG, Huentelman MJ, Velazquez R. Identification of retinoblastoma binding protein 7 (Rbbp7) as a mediator against tau acetylation and subsequent neuronal loss in Alzheimer's disease and related tauopathies. Acta Neuropathol 2021; 142:279-294. [PMID: 33978814 PMCID: PMC8270842 DOI: 10.1007/s00401-021-02323-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/14/2021] [Accepted: 05/01/2021] [Indexed: 12/14/2022]
Abstract
Evidence indicates that tau hyper-phosphorylation and subsequent neurofibrillary tangle formation contribute to the extensive neuronal death in Alzheimer's disease (AD) and related tauopathies. Recent work has identified that increased tau acetylation can promote tau phosphorylation. Tau acetylation occurs at lysine 280 resulting from increased expression of the lysine acetyltransferase p300. The exact upstream mechanisms mediating p300 expression remain elusive. Additional work highlights the role of the epigenome in tau pathogenesis, suggesting that dysregulation of epigenetic proteins may contribute to acetylation and hyper-phosphorylation of tau. Here, we identify and focus on the histone-binding subunit of the Nucleosome Remodeling and Deacetylase (NuRD) complex: Retinoblastoma-Binding Protein 7 (Rbbp7). Rbbp7 chaperones chromatin remodeling proteins to their nuclear histone substrates, including histone acetylases and deacetylases. Notably, Rbbp7 binds to p300, suggesting that it may play a role in modulating tau acetylation. We interrogated Rbbp7 in post-mortem brain tissue, cell lines and mouse models of AD. We found reduced Rbbp7 mRNA expression in AD cases, a significant negative correlation with CERAD (neuritic plaque density) and Braak Staging (pathogenic tau inclusions) and a significant positive correlation with post-mortem brain weight. We also found a neuron-specific downregulation of Rbbp7 mRNA in AD patients. Rbbp7 protein levels were significantly decreased in 3xTg-AD and PS19 mice compared to NonTg, but no decreases were found in APP/PS1 mice that lack tau pathology. In vitro, Rbbp7 overexpression rescued TauP301L-induced cytotoxicity in immortalized hippocampal cells and primary cortical neurons. In vivo, hippocampal Rbbp7 overexpression rescued neuronal death in the CA1 of PS19 mice. Mechanistically, we found that increased Rbbp7 reduced p300 levels, tau acetylation at lysine 280 and tau phosphorylation at AT8 and AT100 sites. Collectively, these data identify a novel role of Rbbp7, protecting against tau-related pathologies, and highlight its potential as a therapeutic target in AD and related tauopathies.
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Affiliation(s)
- Nikhil Dave
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Austin S Vural
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Wendy Winslow
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Likith Surendra
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joanna K Winstone
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Thomas G Beach
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Ramon Velazquez
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, USA.
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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Lewis CR, Bonham KS, McCann SH, Volpe AR, D’Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL, Klepac-Ceraj V. Family SES Is Associated with the Gut Microbiome in Infants and Children. Microorganisms 2021; 9:1608. [PMID: 34442687 PMCID: PMC8398307 DOI: 10.3390/microorganisms9081608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children. METHODS Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed. RESULTS Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001). CONCLUSIONS Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand.
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Affiliation(s)
- Candace R. Lewis
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Kevin S. Bonham
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
| | - Shelley Hoeft McCann
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
| | - Alexandra R. Volpe
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
| | - Viren D’Sa
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Matt D. De Both
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | - Matthew J. Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA; (M.N.); (M.D.D.B.); (M.J.H.)
| | | | - Sarah K. Highlander
- Pathogen and Microbiome Division, Translational Genomics Research Institute North (TGen), Flagstaff, AZ 86005, USA;
| | - Sean C. L. Deoni
- Advanced Baby Imaging Lab, Hasbro Children’s Hospital, Rhode Island Hospital, Providence, RI 02903, USA; (A.R.V.); (V.D.); (S.C.L.D.)
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- MNCH D&T, Bill and Melinda Gates Foundation, Seattle, WA 98109, USA
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA; (K.S.B.); (S.H.M.)
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30
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Lewis CR, Breitenstein RS, Henderson A, Sowards HA, Piras IS, Huentelman MJ, Doane LD, Lemery-Chalfant K. Harsh Parenting Predicts Novel HPA Receptor Gene Methylation and NR3C1 Methylation Predicts Cortisol Daily Slope in Middle Childhood. Cell Mol Neurobiol 2021; 41:783-793. [PMID: 32472381 DOI: 10.1007/s10571-020-00885-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/23/2020] [Indexed: 01/16/2023]
Abstract
Adverse experiences in childhood are associated with altered hypothalamic-pituitary-adrenal (HPA) axis function and negative health outcomes throughout life. It is now commonly accepted that abuse and neglect can alter epigenetic regulation of HPA genes. Accumulated evidence suggests harsh parenting practices such as spanking are also strong predictors of negative health outcomes. We predicted harsh parenting at 2.5 years old would predict HPA gene DNA methylation similarly to abuse and neglect, and cortisol output at 8.5 years old. Saliva samples were collected three times a day across 3 days to estimate cortisol diurnal slopes. Methylation was quantified using the Illumina Infinium MethylationEPIC array BeadChip (850 K) with DNA collected from buccal cells. We used principal components analysis to compute a summary statistic for CpG sites across candidate genes. The first and second components were used as outcome variables in mixed linear regression analyses with harsh parenting as a predictor variable. We found harsh parenting significantly predicted methylation of several HPA axis genes, including novel gene associations with AVPRB1, CRHR1, CRHR2, and MC2R (FDR corrected p < 0.05). Further, we found NR3C1 methylation predicted a steeper diurnal cortisol slope. Our results extend the current literature by demonstrating harsh parenting may influence DNA methylation similarly to more extreme early life experiences such as abuse and neglect. Further, we show NR3C1 methylation is associated with diurnal HPA function. Elucidating the molecular consequences of harsh parenting on health can inform best parenting practices and provide potential treatment targets for common complex disorders.
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Affiliation(s)
- Candace R Lewis
- Neurogenomics, Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA.
- Psychology, Arizona State University, Tempe, AZ, USA.
| | | | - Adrienne Henderson
- Neurogenomics, Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | | | - Ignazio S Piras
- Neurogenomics, Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Matthew J Huentelman
- Neurogenomics, Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Leah D Doane
- Psychology, Arizona State University, Tempe, AZ, USA
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Henderson AR, Wang Q, Meechoovet B, Siniard AL, Naymik M, De Both M, Huentelman MJ, Caselli RJ, Driver-Dunckley E, Dunckley T. DNA Methylation and Expression Profiles of Whole Blood in Parkinson's Disease. Front Genet 2021; 12:640266. [PMID: 33981329 PMCID: PMC8107387 DOI: 10.3389/fgene.2021.640266] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/16/2021] [Indexed: 12/20/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common age-related neurodegenerative disease. It is presently only accurately diagnosed at an advanced stage by a series of motor deficits, which are predated by a litany of non-motor symptoms manifesting over years or decades. Aberrant epigenetic modifications exist across a range of diseases and are non-invasively detectable in blood as potential markers of disease. We performed comparative analyses of the methylome and transcriptome in blood from PD patients and matched controls. Our aim was to characterize DNA methylation and gene expression patterns in whole blood from PD patients as a foundational step toward the future goal of identifying molecular markers that could predict, accurately diagnose, or track the progression of PD. We found that differentially expressed genes (DEGs) were involved in the processes of transcription and mitochondrial function and that PD methylation profiles were readily distinguishable from healthy controls, even in whole-blood DNA samples. Differentially methylated regions (DMRs) were functionally varied, including near transcription factor nuclear transcription factor Y subunit alpha (NFYA), receptor tyrosine kinase DDR1, RING finger ubiquitin ligase (RNF5), acetyltransferase AGPAT1, and vault RNA VTRNA2-1. Expression quantitative trait methylation sites were found at long non-coding RNA PAX8-AS1 and transcription regulator ZFP57 among others. Functional epigenetic modules were highlighted by IL18R1, PTPRC, and ITGB2. We identified patterns of altered disease-specific DNA methylation and associated gene expression in whole blood. Our combined analyses extended what we learned from the DEG or DMR results alone. These studies provide a foundation to support the characterization of larger sample cohorts, with the goal of building a thorough, accurate, and non-invasive molecular PD biomarker.
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Affiliation(s)
- Adrienne R Henderson
- Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Qi Wang
- Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Bessie Meechoovet
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Matthew De Both
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | | | - Travis Dunckley
- Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, United States
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Garvin AM, De Both MD, Talboom JS, Lindsey ML, Huentelman MJ, Hale TM. Transient ACE (Angiotensin-Converting Enzyme) Inhibition Suppresses Future Fibrogenic Capacity and Heterogeneity of Cardiac Fibroblast Subpopulations. Hypertension 2021; 77:904-918. [PMID: 33486989 PMCID: PMC7878436 DOI: 10.1161/hypertensionaha.120.16352] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transient ACE (angiotensin-converting enzyme) inhibition in spontaneously hypertensive rats is known to protect against future injury-induced cardiac inflammation, fibrosis, and dysfunction; however, the mechanisms of protection have not been delineated. Here, we used single-cell RNA sequencing to test the hypothesis that transient ACE inhibitor treatment would induce a persistent shift in cardiac fibroblast subpopulations. Adult male spontaneously hypertensive rats (11 weeks old, hypertensive with cardiac hypertrophy) were treated for 2 weeks with an ACE inhibitor, enalapril (30 mg/kg per day, PO), or water (untreated spontaneously hypertensive rats) followed by a 2-week washout period (n=7/group). Cardiac fibroblasts were isolated from the left ventricle and subjected to single-cell RNA sequencing. Nine clusters of fibroblasts were identified, with 98% of cells in clusters 0 to 6. The transient treatment produced significant changes both within and across clusters. Cluster 1 depicted a highly fibrogenic gene profile, with cluster 6 serving as a gateway to cluster 1. Transient ACE inhibition depleted the gateway and expanded cluster 0, which was the least fibrogenic profile. Moreover, within cluster 1 fibroblasts, ACE inhibition reduced expression of individual fibrosis genes (eg, COL1A1, COL3A1, and FN1; all P<1×10-35). Clusters 2 to 5 reflected proliferative, moderately fibrogenic, translationally active, and less inflammatory subsets of fibroblasts, all of which exhibited attenuated fibrogenic gene expression after transient ACE inhibition. In conclusion, transient ACE inhibition shifts cardiac fibroblast subpopulations and degree of activation resulting in an overall reduced fibrogenic phenotype.
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Affiliation(s)
- Alexandra M Garvin
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Matthew D De Both
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Joshua S Talboom
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Merry L Lindsey
- Department of Cellular and Integrative Physiology, Center for Heart and Vascular Research, University of Nebraska Medical Center, and Research Service, Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Taben M Hale
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA
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33
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Serrano GE, Walker JE, Arce R, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Papa J, Russell A, Suszczewicz KE, Borja CI, Belden C, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Readhead B, Huentelman MJ, Peters JL, Alevritis E, Bimi C, Mizgerd JP, Reiman EM, Montine TJ, Desforges M, Zehnder JL, Sahoo MK, Zhang H, Solis D, Pinsky BA, Deture M, Dickson DW, Beach TG. Mapping of SARS-CoV-2 Brain Invasion and Histopathology in COVID-19 Disease. medRxiv 2021:2021.02.15.21251511. [PMID: 33619496 PMCID: PMC7899461 DOI: 10.1101/2021.02.15.21251511] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The coronavirus SARS-CoV-2 (SCV2) causes acute respiratory distress, termed COVID-19 disease, with substantial morbidity and mortality. As SCV2 is related to previously-studied coronaviruses that have been shown to have the capability for brain invasion, it seems likely that SCV2 may be able to do so as well. To date, although there have been many clinical and autopsy-based reports that describe a broad range of SCV2-associated neurological conditions, it is unclear what fraction of these have been due to direct CNS invasion versus indirect effects caused by systemic reactions to critical illness. Still critically lacking is a comprehensive tissue-based survey of the CNS presence and specific neuropathology of SCV2 in humans. We conducted an extensive neuroanatomical survey of RT-PCR-detected SCV2 in 16 brain regions from 20 subjects who died of COVID-19 disease. Targeted areas were those with cranial nerve nuclei, including the olfactory bulb, medullary dorsal motor nucleus of the vagus nerve and the pontine trigeminal nerve nuclei, as well as areas possibly exposed to hematogenous entry, including the choroid plexus, leptomeninges, median eminence of the hypothalamus and area postrema of the medulla. Subjects ranged in age from 38 to 97 (mean 77) with 9 females and 11 males. Most subjects had typical age-related neuropathological findings. Two subjects had severe neuropathology, one with a large acute cerebral infarction and one with hemorrhagic encephalitis, that was unequivocally related to their COVID-19 disease while most of the 18 other subjects had non-specific histopathology including focal β-amyloid precursor protein white matter immunoreactivity and sparse perivascular mononuclear cell cuffing. Four subjects (20%) had SCV2 RNA in one or more brain regions including the olfactory bulb, amygdala, entorhinal area, temporal and frontal neocortex, dorsal medulla and leptomeninges. The subject with encephalitis was SCV2-positive in a histopathologically-affected area, the entorhinal cortex, while the subject with the large acute cerebral infarct was SCV2-negative in all brain regions. Like other human coronaviruses, SCV2 can inflict acute neuropathology in susceptible patients. Much remains to be understood, including what viral and host factors influence SCV2 brain invasion and whether it is cleared from the brain subsequent to the acute illness.
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Affiliation(s)
| | | | - Richard Arce
- Banner Sun Health Research Institute, Sun City, AZ
| | | | - Daisy Vargas
- Banner Sun Health Research Institute, Sun City, AZ
| | - Lucia I. Sue
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | - Javon Oliver
- Banner Sun Health Research Institute, Sun City, AZ
| | - Jaclyn Papa
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | | | | | | | | | - Alireza Atri
- Banner Sun Health Research Institute, Sun City, AZ
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles H. Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ
| | | | | | - Shyamal H. Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ
| | - Benjamin Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Tempe, AZ
| | | | | | | | | | | | | | - Thomas J. Montine
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Marc Desforges
- Centre Hospitalier Universitaire Sainte-Justine, Laboratory of Virology, Montreal, Canada
| | - James L. Zehnder
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Malaya K. Sahoo
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Haiyu Zhang
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Daniel Solis
- Stanford University School of Medicine, Department of Pathology, Stanford, CA
| | - Benjamin A. Pinsky
- Stanford University Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford, CA
| | - Michael Deture
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville FL
| | - Dennis W. Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville FL
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34
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Van Etten EJ, Bharadwaj PK, Hishaw GA, Huentelman MJ, Trouard TP, Grilli MD, Alexander GE. Influence of regional white matter hyperintensity volume and apolipoprotein E ε4 status on hippocampal volume in healthy older adults. Hippocampus 2021; 31:469-480. [PMID: 33586848 PMCID: PMC9119498 DOI: 10.1002/hipo.23308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/22/2020] [Accepted: 01/23/2021] [Indexed: 11/08/2022]
Abstract
While total white matter hyperintensity (WMH) volume on magnetic resonance imaging (MRI) has been associated with hippocampal atrophy, less is known about how the regional distribution of WMH volume may differentially affect the hippocampus in healthy aging. Additionally, apolipoprotein E (APOE) ε4 carriers may be at an increased risk for greater WMH volumes and hippocampal atrophy in aging. The present study sought to investigate whether regional WMH volume mediates the relationship between age and hippocampal volume and if this association is moderated by APOE ε4 status in a group of 190 cognitively healthy adults (APOE ε4 status [carrier/non-carrier] = 59/131), ages 50-89. Analyses revealed that temporal lobe WMH volume significantly mediated the relationship between age and average bilateral hippocampal volume, and this effect was moderated by APOE ε4 status (-0.020 (SE = 0.009), 95% CI, [-0.039, -0.003]). APOE ε4 carriers, but not non-carriers, showed negative indirect effects of age on hippocampal volume through temporal lobe WMH volume (APOE ε4 carriers: -0.016 (SE = 0.007), 95% CI, [-0.030, -0.003]; APOE ε4 non-carriers: .005 (SE = 0.006), 95% CI, [-0.006, 0.017]). These findings remained significant after additionally adjusting for sex, years of education, hypertension status and duration, cholesterol status, diabetes status, Body Mass Index, history of smoking, and the Wechsler Adult Intelligence Scale-IV Full Scale IQ. There were no significant moderated mediation effects for frontal, parietal, and occipital lobe WMH volumes, with or without covariates. Our findings indicate that in cognitively healthy older adults, elevated WMH volume regionally localized to the temporal lobes in APOE ε4 carriers is associated with reduced hippocampal volume, suggesting greater vulnerability to brain aging and the risk for Alzheimer's disease.
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Affiliation(s)
- Emily J Van Etten
- Department of Psychology, University of Arizona, Tucson, Arizona, USA.,Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, USA
| | - Pradyumna K Bharadwaj
- Department of Psychology, University of Arizona, Tucson, Arizona, USA.,Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, USA
| | - Georg A Hishaw
- Department of Neurology, University of Arizona, Tucson, Arizona, USA
| | - Matthew J Huentelman
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, USA.,Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA.,Arizona Alzheimer's Consortium, Phoenix, Arizona, USA
| | - Theodore P Trouard
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, USA.,Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,Arizona Alzheimer's Consortium, Phoenix, Arizona, USA
| | - Matthew D Grilli
- Department of Psychology, University of Arizona, Tucson, Arizona, USA.,Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, USA.,Department of Neurology, University of Arizona, Tucson, Arizona, USA
| | - Gene E Alexander
- Department of Psychology, University of Arizona, Tucson, Arizona, USA.,Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, Arizona, USA.,Department of Psychiatry, University of Arizona, Tucson, Arizona, USA.,Neuroscience Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA.,Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA.,Arizona Alzheimer's Consortium, Phoenix, Arizona, USA
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35
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Jepsen WM, De Both M, Siniard AL, Ramsey K, Piras IS, Naymik M, Henderson A, Huentelman MJ. Adenosine triphosphate binding cassette subfamily C member 1 ( ABCC1) overexpression reduces APP processing and increases alpha- versus beta-secretase activity, in vitro. Biol Open 2021; 10:bio.054627. [PMID: 32878879 PMCID: PMC7860133 DOI: 10.1242/bio.054627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organic anion transporter Adenosine triphosphate binding cassette subfamily C member 1 (ABCC1), also known as MRP1, has been demonstrated in murine models of Alzheimer's disease (AD) to export amyloid beta (Abeta) from the endothelial cells of the blood–brain barrier to the periphery, and that pharmaceutical activation of ABCC1 can reduce amyloid plaque deposition in the brain. Here, we show that ABCC1 is not only capable of exporting Abeta from the cytoplasm of human cells, but also that its overexpression significantly reduces Abeta production and increases the ratio of alpha- versus beta-secretase mediated cleavage of the amyloid precursor protein (APP), likely via indirect modulation of alpha-, beta- and gamma-secretase activity. Summary:Adenosine triphosphate binding cassette subfamily C member 1 (ABCC1) overexpression skews APP processing towards the non-amyloidogenic pathway. Increasing ABCC1 expression or activity may prevent or attenuate Alzheimer's disease symptoms.
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Affiliation(s)
- Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA.,School of Life Sciences, Arizona State University, 427 E. Tyler Mall Tempe, AZ, 85281 USA.,Arizona Alzheimer's Consortium, 4745 N. 7th St., Ste. 105 Phoenix, AZ, 85014 USA
| | - Matthew De Both
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA
| | - Keri Ramsey
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Arizona Alzheimer's Consortium, 4745 N. 7th St., Ste. 105 Phoenix, AZ, 85014 USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA.,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA
| | - Adrienne Henderson
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004 USA .,Center for Rare Childhood Disorders, Translational Genomics Research Institute, 3330 N. 2nd St., Ste. 402 Phoenix, AZ, 85012 USA.,School of Life Sciences, Arizona State University, 427 E. Tyler Mall Tempe, AZ, 85281 USA.,Arizona Alzheimer's Consortium, 4745 N. 7th St., Ste. 105 Phoenix, AZ, 85014 USA
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36
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Piras IS, Krate J, Delvaux E, Nolz J, Mastroeni DF, Persico AM, Jepsen WM, Beach TG, Huentelman MJ, Coleman PD. Transcriptome Changes in the Alzheimer's Disease Middle Temporal Gyrus: Importance of RNA Metabolism and Mitochondria-Associated Membrane Genes. J Alzheimers Dis 2020; 70:691-713. [PMID: 31256118 DOI: 10.3233/jad-181113] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We used Illumina Human HT-12 v4 arrays to compare RNA expression of middle temporal gyrus (MTG; BA21) in Alzheimer's disease (AD = 97) and non-demented controls (ND = 98). A total of 938 transcripts were highly differentially expressed (adj p < 0.01; log2 FC ≥ |0.500|, with 411 overexpressed and 527 underexpressed in AD. Our results correlated with expression profiling in neurons from AD and ND obtained by laser capture microscopy in MTG from an independent dataset (log2 FC correlation: r = 0.504; p = 2.2e-16). Additionally, selected effects were validated by qPCR. ANOVA analysis yielded no difference between genders in response to AD, but some gender specific genes were detected (e.g., IL8 and AGRN in males, and HSPH1 and GRM1 in females). Several transcripts were associated with Braak staging (e.g., AEBP1 and DNALI1), antemortem MMSE (e.g., AEBP1 and GFAP), and tangle density (e.g., RNU1G2, and DNALI1). At the pathway level, we detected enrichment of synaptic vesicle processes and GABAergic transmission genes. Finally, applying the Weighted Correlation Network Analysis, we identified four expression modules enriched for neuronal and synaptic genes, mitochondria-associated membrane, chemical stimulus and olfactory receptor and non-coding RNA metabolism genes. Our results represent an extensive description of MTG mRNA profiling in a large sample of AD and ND. These data provide a list of genes associated with AD, and correlated to neurofibrillary tangles density. In addition, these data emphasize the importance of mitochondrial membranes and transcripts related to olfactory receptors in AD.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonida Krate
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Jennifer Nolz
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Diego F Mastroeni
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Antonio M Persico
- Unit of Child and Adolescent Neuropsychiatry, "Gaetano Martino" University Hospital, University of Messina, Messina, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Thomas G Beach
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, AZ, US
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Paul D Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
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37
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Ouellette AR, Neuner SM, Dumitrescu L, Anderson LC, Gatti DM, Mahoney ER, Bubier JA, Churchill G, Peters L, Huentelman MJ, Herskowitz JH, Yang HS, Smith AN, Reitz C, Kunkle BW, White CC, De Jager PL, Schneider JA, Bennett DA, Seyfried NT, Chesler EJ, Hadad N, Hohman TJ, Kaczorowski CC. Cross-Species Analyses Identify Dlgap2 as a Regulator of Age-Related Cognitive Decline and Alzheimer's Dementia. Cell Rep 2020; 32:108091. [PMID: 32877673 PMCID: PMC7502175 DOI: 10.1016/j.celrep.2020.108091] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 02/10/2020] [Accepted: 08/07/2020] [Indexed: 11/27/2022] Open
Abstract
Genetic mechanisms underlying age-related cognitive decline and dementia remain poorly understood. Here, we take advantage of the Diversity Outbred mouse population to utilize quantitative trait loci mapping and identify Dlgap2 as a positional candidate responsible for modifying working memory decline. To evaluate the translational relevance of this finding, we utilize longitudinal cognitive measures from human patients, RNA expression from post-mortem brain tissue, data from a genome-wide association study (GWAS) of Alzheimer's dementia (AD), and GWAS results in African Americans. We find an association between Dlgap2 and AD phenotypes at the variant, gene and protein expression, and methylation levels. Lower cortical DLGAP2 expression is observed in AD and is associated with more plaques and tangles at autopsy and faster cognitive decline. Results will inform future studies aimed at investigating the cross-species role of Dlgap2 in regulating cognitive decline and highlight the benefit of using genetically diverse mice to prioritize novel candidates.
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Affiliation(s)
- Andrew R Ouellette
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, ME 04469, USA
| | - Sarah M Neuner
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | | | | | - Emily R Mahoney
- Vanderbilt Memory and Alzheimer's Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | | | | | | | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Jeremy H Herskowitz
- Center for Neurodegeneration and Experimental Therapeutics and Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hyun-Sik Yang
- Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alexandra N Smith
- Vanderbilt Memory and Alzheimer's Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, and Departments of Neurology and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brian W Kunkle
- Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Charles C White
- Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Philip L De Jager
- Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Niran Hadad
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37240, USA.
| | - Catherine C Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, ME 04469, USA.
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38
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Remer J, Dean DC, Chen K, Reiman RA, Huentelman MJ, Reiman EM, Deoni SCL. Longitudinal white matter and cognitive development in pediatric carriers of the apolipoprotein ε4 allele. Neuroimage 2020; 222:117243. [PMID: 32822813 PMCID: PMC7779366 DOI: 10.1016/j.neuroimage.2020.117243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/01/2020] [Accepted: 08/05/2020] [Indexed: 01/14/2023] Open
Abstract
We have previously demonstrated cross-sectional differences in magnetic resonance imaging (MRI) measurements of white matter myelin and gray matter in infants with or without the apolipoprotein ε4 allele, a major genetic risk factor for late-onset Alzheimer's disease (AD). In this study, we sought to compare longitudinal MRI white matter myelin and cognitive-behavioral changes in infants and young children with and without this allele. Serial MRI and cognitive tests were obtained on 223 infants and young children, including 74 ε4 carriers and 149 non-carriers, 2–68 months of age, matched for age, gestational duration, birth weight, sex ratio, maternal age, education, and socioeconomic status. Automated brain mapping algorithms and non-linear mixed models were used to characterize and compare trajectories of white matter myelin and cognitive-behavioral test scores. The APOE ε4 carriers had statistically significant differences in white matter myelin development, in the uncinate fasciculus, temporal lobe, internal capsule and occipital lobe. Additionally, ε4 carriers had a slightly greater rate of development in early learning composite a surrogate measure of IQ representative of expressive language, receptive language, fine motor, and visual skills, but displayed slightly lower non verbal development quotient scores a composite measure of fine motor and visual skills across the entire age range. This study supports the possibility that ε4 carriers have slightly altered rates of white matter and cognitive development in childhood. It continues to raise questions about the role of APOE in human brain development and the relevance of these developmental differences to the predisposition to AD.
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Affiliation(s)
- Justin Remer
- Advanced Baby Imaging Lab, Rhode Island Hospital, Providence, RI, USA; Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence RI, USA.
| | - Douglas C Dean
- Department of Pediatrics, University of Wisconsin-Madison, Madison WI 53705 USA; Department of Medical Physics, University of Wisconsin-Madison, Madison WI 5305 USA; Waisman Center, University of Wisconsin-Madison, Madison WI 53705 USA
| | - Kewei Chen
- Arizona Alzheimer's Consortium, University of Arizona School of Medicine, Tucson and Phoenix AZ, USA; Banner Alzheimer's Institute, Phoenix, AZ, USA; University of Arizona College of Medicine, Phoenix, AZ, USA; Arizona State University, Phoenix, AZ, USA
| | - Rebecca A Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, USA; Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Matthew J Huentelman
- Banner Alzheimer's Institute, Phoenix, AZ, USA; Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Eric M Reiman
- Arizona Alzheimer's Consortium, University of Arizona School of Medicine, Tucson and Phoenix AZ, USA; Banner Alzheimer's Institute, Phoenix, AZ, USA; University of Arizona College of Medicine, Phoenix, AZ, USA; Arizona State University, Phoenix, AZ, USA; Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Sean C L Deoni
- Advanced Baby Imaging Lab, Rhode Island Hospital, Providence, RI, USA; Department of Pediatrics, Warren Alpert Medical School at Brown University, Providence RI, USA; Maternal, Newborn, and Child Health Discovery and Tools, Bill and Melinda Gates Foundation; Seattle WA, USA
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39
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Brokaw DL, Piras IS, Mastroeni D, Weisenberger DJ, Nolz J, Delvaux E, Serrano GE, Beach TG, Huentelman MJ, Coleman PD. Cell death and survival pathways in Alzheimer's disease: an integrative hypothesis testing approach utilizing -omic data sets. Neurobiol Aging 2020; 95:15-25. [PMID: 32745806 DOI: 10.1016/j.neurobiolaging.2020.06.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/28/2020] [Accepted: 06/27/2020] [Indexed: 01/01/2023]
Abstract
Whether a cell lives or dies is controlled by an array of intercepting and dynamic molecular pathways. Although there is evidence of neuronal loss in Alzheimer's disease (AD) and multiple programmed cell death (PCD) pathways have been implicated in this process, there has been no comprehensive evaluation of the dominant pathway responsible for cell death in AD. Likewise, the relative dominance of survival and PCD pathways in AD remains unclear. Here, we present the results of hypothesis-driven bioinformatic analysis of PCD and survival pathway activation in paired methylation and expression data from the middle temporal gyrus (MTG) as well as expression from laser-captured cells from the MTG and hippocampus. The results not only indicate activation of cell death pathways in AD-of which apoptosis is responsible for the largest fraction of upregulated genes-but also of cell survival pathways. These results are indicative of a complex balance between survival and death pathways in AD that future studies should work to delineate at a single cell level.
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Affiliation(s)
- Danielle L Brokaw
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA.
| | - Ignazio S Piras
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ, USA
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | | | - Jennifer Nolz
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Elaine Delvaux
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Matthew J Huentelman
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ, USA
| | - Paul D Coleman
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
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Serrano N, D'Lugos AC, Ormsby JC, Thomas NT, Sweeney KR, Carroll CC, Marvasti FF, Naymik MA, Huentelman MJ, Dickinson JM. The Impact Of Age On The Transcriptional And Morphological Profile Of Skeletal Muscle. Med Sci Sports Exerc 2020. [DOI: 10.1249/01.mss.0000677520.70903.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Szelinger S, Krate J, Ramsey K, Strom SP, Shieh PB, Lee H, Belnap N, Balak C, Siniard AL, Russell M, Richholt R, Both MD, Claasen AM, Schrauwen I, Nelson SF, Huentelman MJ, Craig DW, Yang SP, Moore SA, Sivakumar K, Narayanan V, Rangasamy S. Congenital myasthenic syndrome caused by a frameshift insertion mutation in GFPT1. Neurol Genet 2020; 6:e468. [PMID: 32754643 PMCID: PMC7357421 DOI: 10.1212/nxg.0000000000000468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Objective Description of a new variant of the glutamine-fructose-6-phosphate transaminase 1 (GFPT1) gene causing congenital myasthenic syndrome (CMS) in 3 children from 2 unrelated families. Methods Muscle biopsies, EMG, and whole-exome sequencing were performed. Results All 3 patients presented with congenital hypotonia, muscle weakness, respiratory insufficiency, head lag, areflexia, and gastrointestinal dysfunction. Genetic analysis identified a homozygous frameshift insertion in the GFPT1 gene (NM_001244710.1: c.686dupC; p.Arg230Ter) that was shared by all 3 patients. In one of the patients, inheritance of the variant was through uniparental disomy (UPD) with maternal origin. Repetitive nerve stimulation and single-fiber EMG was consistent with the clinical diagnosis of CMS with a postjunctional defect. Ultrastructural evaluation of the muscle biopsy from one of the patients showed extremely attenuated postsynaptic folds at neuromuscular junctions and extensive autophagic vacuolar pathology. Conclusions These results expand on the spectrum of known loss-of-function GFPT1 mutations in CMS12 and in one family demonstrate a novel mode of inheritance due to UPD.
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Affiliation(s)
- Szabolcs Szelinger
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Jonida Krate
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Keri Ramsey
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Samuel P Strom
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Perry B Shieh
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Hane Lee
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Newell Belnap
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Chris Balak
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ashley L Siniard
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Megan Russell
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ryan Richholt
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Matt De Both
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ana M Claasen
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Isabelle Schrauwen
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Stanley F Nelson
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Matthew J Huentelman
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - David W Craig
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Samuel P Yang
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Steven A Moore
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Kumaraswamy Sivakumar
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Vinodh Narayanan
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Sampathkumar Rangasamy
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
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Piras IS, Costa A, Tirindelli MC, Stoccoro A, Huentelman MJ, Sacco R, Coppedè F, Lintas C. Genetic and epigenetic MTHFR gene variants in the mothers of attention-deficit/hyperactivity disorder affected children as possible risk factors for neurodevelopmental disorders. Epigenomics 2020; 12:813-823. [PMID: 32485115 DOI: 10.2217/epi-2019-0356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: To assess promoter methylation levels, gene expression levels and 677C>T/1298A>C genotype and allele frequencies of the MTHFR gene in 45 mothers of attention-deficit/hyperactivity disorder affected child/children (ADHDM) and compare it with age matched healthy control mothers (HCM). Materials & methods: High resolution melting analysis, quantitative real time PCR and PCR-RFLP were performed to assess methylation, gene expression and genotyping, respectively. Significance between ADHDM and HCM was assessed by linear (methylation and gene expression) and logistic regression (genotypes). Results: MTHFR gene expression levels were significantly higher in the ADHDM compared with the HCM group (adj-p < 7.7E-04). No differences in MTHFR promoter methylation level and 677C>T/1298A>C genotype frequencies were detected between ADHDM and HCM. Conclusion: We observed increased MTHFR expression levels not resulting from promoter methylation changes in ADHDM respect to HMC, potentially contributing to the ADHD condition in their children and deserving further investigation.
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Affiliation(s)
- Ignazio Stefano Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Anna Costa
- Service for Neurodevelopmental Disorders, University Campus Bio-Medico, Rome, Italy
| | | | - Andrea Stoccoro
- Medical Genetics Laboratory, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa, Italy
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Roberto Sacco
- Service for Neurodevelopmental Disorders, University Campus Bio-Medico, Rome, Italy
| | - Fabio Coppedè
- Medical Genetics Laboratory, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa, Italy
| | - Carla Lintas
- Service for Neurodevelopmental Disorders, University Campus Bio-Medico, Rome, Italy
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Piras IS, Bleul C, Schrauwen I, Talboom J, Llaci L, De Both MD, Naymik MA, Halliday G, Bettencourt C, Holton JL, Serrano GE, Sue LI, Beach TG, Stefanova N, Huentelman MJ. Transcriptional profiling of multiple system atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease. Acta Neuropathol Commun 2020; 8:76. [PMID: 32493431 PMCID: PMC7268362 DOI: 10.1186/s40478-020-00950-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/19/2020] [Indexed: 01/04/2023] Open
Abstract
Multiple system atrophy (MSA) is a rare adult-onset neurodegenerative disease of unknown cause, with no effective therapeutic options, and no cure. Limited work to date has attempted to characterize the transcriptional changes associated with the disease, which presents as either predominating parkinsonian (MSA-P) or cerebellar (MSC-C) symptoms. We report here the results of RNA expression profiling of cerebellar white matter (CWM) tissue from two independent cohorts of MSA patients (n = 66) and healthy controls (HC; n = 66). RNA samples from bulk brain tissue and from oligodendrocytes obtained by laser capture microdissection (LCM) were sequenced. Differentially expressed genes (DEGs) were obtained and were examined before and after stratifying by MSA clinical sub-type.We detected the highest number of DEGs in the MSA-C group (n = 747) while only one gene was noted in MSA-P, highlighting the larger dysregulation of the transcriptome in the MSA-C CWM. Results from both bulk tissue and LCM analysis showed a downregulation of oligodendrocyte genes and an enrichment for myelination processes with a key role noted for the QKI gene. Additionally, we observed a significant upregulation of neuron-specific gene expression in MSA-C and enrichment for synaptic processes. A third cluster of genes was associated with the upregulation of astrocyte and endothelial genes, two cell types with a key role in inflammation processes. Finally, network analysis in MSA-C showed enrichment for β-amyloid related functional classes, including the known Alzheimer's disease (AD) genes, APP and PSEN1.This is the largest RNA profiling study ever conducted on post-mortem brain tissue from MSA patients. We were able to define specific gene expression signatures for MSA-C highlighting the different stages of the complex neurodegenerative cascade of the disease that included alterations in several cell-specific transcriptional programs. Finally, several results suggest a common transcriptional dysregulation between MSA and AD-related genes despite the clinical and neuropathological distinctions between the two diseases.
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Lewis CR, Sowards HA, Huentelman MJ, Doane LD, Lemery-Chalfant K. Epigenetic differences in inflammation genes of monozygotic twins are related to parent-child emotional availability and health. Brain Behav Immun Health 2020; 5:100084. [PMID: 34589859 PMCID: PMC8474531 DOI: 10.1016/j.bbih.2020.100084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 01/03/2023] Open
Abstract
The inflammatory response is an immune defense engaged immediately after injury or infection. Chronic inflammation can be deleterious for various health outcomes and is characterized by high levels of pro-inflammatory markers such as C-reactive protein (CRP), interleukin 6 (IL-6), and tumor necrosis factor alpha (TNF-α). A large body of research demonstrates these inflammatory markers are responsive to stress and quality of social relationships throughout the lifespan. For example, the quality of the early parental bond predicts various health outcomes and may be driven by changes in immune function. Epigenetic processes, such as DNA methylation, may be one mechanism by which early social experiences shape immune functioning. The present study used a monozygotic twin difference design to assess if mother-reported emotional availability at 1 year and 2.5 years predicted immune gene methylation at 8 years of age. Further, we assessed if inflammation gene methylation was related to general health problems (e.g. infections, allergies, etc.). We found that mother-reported emotional availability at 1 year, but not 2.5 years, was related to methylation of various immune genes in monozygotic twins. Furthermore, twin pairs discordant in health problems have more difference in immune gene methylation compared to twin pairs concordant for health problems, suggesting that methylation of immune genes may have functional consequences for general health. These results suggest that the emotional component of attachment quality during infancy contributes to immune epigenetic profiles in childhood, which may influence general health.
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Affiliation(s)
- Candace R Lewis
- Translational Genomics Research Institute, Neurogenomics Division, United States.,Arizona State University, Psychology Department, United States
| | | | - Matthew J Huentelman
- Translational Genomics Research Institute, Neurogenomics Division, United States
| | - Leah D Doane
- Arizona State University, Psychology Department, United States
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Lewis CR, Taguinod F, Jepsen WM, Cohen J, Agrawal K, Huentelman MJ, Smith CJ, Ringenbach SDR, Braden BB. Telomere Length and Autism Spectrum Disorder Within the Family: Relationships With Cognition and Sensory Symptoms. Autism Res 2020; 13:1094-1101. [PMID: 32323911 DOI: 10.1002/aur.2307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/03/2020] [Accepted: 04/01/2020] [Indexed: 12/30/2022]
Abstract
Telomeres are repetitive noncoding deoxynucleotide sequences that cap chromosomes to protect DNA. Telomere length (TL) is affected by both genetic and environmental factors, and shortening of telomeres is associated with multiple neuropsychiatric disorders, early life stress, and age-related cognitive dysfunction. Two previous studies associated shorter TL with autism spectrum disorder (ASD). We aimed to replicate this finding, describe TL in unaffected siblings, and explore novel relationships with symptoms and cognitive function in families with ASD. Participants were 212 male children and adolescents ages 1-17 years (86 with ASD, 57 unaffected siblings, and 69 typically developing [TD]) and 64 parents. TL was measured from blood leukocytes with quantitative real-time polymerase chain reaction and results are expressed by relative ratios with a single copy gene. We replicated that children and adolescents with ASD have shorter TL, compared to TD, and show that unaffected siblings have TL in between those of TD and ASD. We present novel associations between TL and sensory symptoms in ASD. Finally, we demonstrate cognitive functions, but not autistic traits, are related to TL in parents of children with ASD. Cognitive function and TL were not related in children and adolescents. As the third replication, our results elicit confidence in the finding that ASD is associated with shorter TL. Our novel sensory investigation suggests that shortened TL may be a biological mechanism of sensory symptoms in ASD. Furthermore, results highlight the need to better understand relationships between cognition, aging, and TL in families with ASD. Autism Res 2020, 13: 1094-1101. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Telomeres cap chromosomes to protect DNA. They progressively shorten as people age and are related to health outcomes. We replicated previous findings that children and adolescents with autism spectrum disorder (ASD) have shorter telomeres, compared to typically developing (TD), and show that unaffected siblings have telomere length (TL) in between those of TD and ASD. We find shortened TL is related to more severe sensory symptoms. This may mean families with ASD, especially those with elevated sensory symptoms, are at risk for worse age-related health outcomes.
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Affiliation(s)
- Candace R Lewis
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Francis Taguinod
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Jorey Cohen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Komal Agrawal
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | | | - B Blair Braden
- Arizona State University, College of Health Solutions, Tempe, Arizona, USA
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Piras IS, Bleul C, Talboom JS, De Both MD, Schrauwen I, Halliday G, Myers AJ, Serrano GE, Beach TG, Huentelman MJ. ESHRD: deconvolution of brain homogenate RNA expression data to identify cell-type-specific alterations in Alzheimer's disease. Aging (Albany NY) 2020; 12:4124-4162. [PMID: 32125278 PMCID: PMC7093163 DOI: 10.18632/aging.102840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022]
Abstract
Objective: We describe herein a bioinformatics approach that leverages gene expression data from brain homogenates to derive cell-type specific differential expression results. Results: We found that differentially expressed (DE) cell-specific genes were mostly identified as neuronal, microglial, or endothelial in origin. However, a large proportion (75.7%) was not attributable to specific cells due to the heterogeneity in expression among brain cell types. Neuronal DE genes were consistently downregulated and associated with synaptic and neuronal processes as described previously in the field thereby validating this approach. We detected several DE genes related to angiogenesis (endothelial cells) and proteoglycans (oligodendrocytes). Conclusions: We present a cost- and time-effective method exploiting brain homogenate DE data to obtain insights about cell-specific expression. Using this approach we identify novel findings in AD in endothelial cells and oligodendrocytes that were previously not reported. Methods: We derived an enrichment score for each gene using a publicly available RNA profiling database generated from seven different cell types isolated from mouse cerebral cortex. We then classified the differential expression results from 3 publicly accessible Late-Onset Alzheimer’s disease (AD) studies including seven different brain regions.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Christiane Bleul
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Joshua S Talboom
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Matthew D De Both
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Glenda Halliday
- The University of Sydney School of Medicine, Sydney, Camperdown NSW 2050, Australia
| | | | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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McCullough CG, Szelinger S, Belnap N, Ramsey K, Schrauwen I, Claasen AM, Burke LW, Siniard AL, Huentelman MJ, Narayanan V, Craig DW. Front Cover, Volume 41, Issue 2. Hum Mutat 2020. [DOI: 10.1002/humu.23982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Carmel G. McCullough
- Department of Translational GenomicsUniversity of Southern CaliforniaLos Angeles California
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Newell Belnap
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Ana M. Claasen
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Leah W. Burke
- Department of Pediatrics, Larner College of MedicineUniversity of VermontBurlington Vermont
| | - Ashley L. Siniard
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Matthew J. Huentelman
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos Angeles California
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Kalani MYS, Alsop E, Meechoovet B, Beecroft T, Agrawal K, Whitsett TG, Huentelman MJ, Spetzler RF, Nakaji P, Kim S, Van Keuren-Jensen K. Extracellular microRNAs in blood differentiate between ischaemic and haemorrhagic stroke subtypes. J Extracell Vesicles 2020; 9:1713540. [PMID: 32128071 PMCID: PMC7034450 DOI: 10.1080/20013078.2020.1713540] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Rapid identification of patients suffering from cerebral ischaemia, while excluding intracerebral haemorrhage, can assist with patient triage and expand patient access to chemical and mechanical revascularization. We sought to identify blood-based, extracellular microRNAs 15 (ex-miRNAs) derived from extracellular vesicles associated with major stroke subtypes using clinical samples from subjects with spontaneous intraparenchymal haemorrhage (IPH), aneurysmal subarachnoid haemorrhage (SAH) and ischaemic stroke due to cerebral vessel occlusion. We collected blood from patients presenting with IPH (n = 19), SAH (n = 17) and ischaemic stroke (n = 21). We isolated extracellular vesicles from plasma, extracted RNA cargo, 20 sequenced the small RNAs and performed bioinformatic analyses to identify ex-miRNA biomarkers predictive of the stroke subtypes. Sixty-seven miRNAs were significantly variant across the stroke subtypes. A subset of exmiRNAs differed between haemorrhagic and ischaemic strokes, and LASSO analysis could distinguish SAH from the other subtypes with an accuracy of 0.972 ± 0.002. Further analyses predicted 25 miRNA classifiers that stratify IPH from ischaemic stroke with an accuracy of 0.811 ± 0.004 and distinguish haemorrhagic from ischaemic stroke with an accuracy of 0.813 ± 0.003. Blood-based, ex-miRNAs have predictive value, and could be capable of distinguishing between major stroke subtypes with refinement and validation. Such a biomarker could one day aid in the triage of patients to expand the pool eligible for effective treatment.
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Affiliation(s)
- M Yashar S Kalani
- Departments of Neurological Surgery and Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Bessie Meechoovet
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Taylor Beecroft
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Komal Agrawal
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Matthew J Huentelman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Robert F Spetzler
- Department of Neurological Surgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Peter Nakaji
- Department of Neurosurgery, Banner Heath and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Seungchan Kim
- Center for Computational Systems Biology, Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A & M University, Prairie View, TX, USA
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Llaci L, Ramsey K, Belnap N, Claasen AM, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Izat T, Naymik M, De Both M, Piras IS, Craig DW, Huentelman MJ, Narayanan V, Schrauwen I, Rangasamy S. Compound heterozygous mutations in SNAP29 is associated with Pelizaeus-Merzbacher-like disorder (PMLD). Hum Genet 2019; 138:1409-1417. [DOI: 10.1007/s00439-019-02077-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
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50
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Arboleda-Velasquez JF, Lopera F, O'Hare M, Delgado-Tirado S, Marino C, Chmielewska N, Saez-Torres KL, Amarnani D, Schultz AP, Sperling RA, Leyton-Cifuentes D, Chen K, Baena A, Aguillon D, Rios-Romenets S, Giraldo M, Guzmán-Vélez E, Norton DJ, Pardilla-Delgado E, Artola A, Sanchez JS, Acosta-Uribe J, Lalli M, Kosik KS, Huentelman MJ, Zetterberg H, Blennow K, Reiman RA, Luo J, Chen Y, Thiyyagura P, Su Y, Jun GR, Naymik M, Gai X, Bootwalla M, Ji J, Shen L, Miller JB, Kim LA, Tariot PN, Johnson KA, Reiman EM, Quiroz YT. Resistance to autosomal dominant Alzheimer's disease in an APOE3 Christchurch homozygote: a case report. Nat Med 2019; 25:1680-1683. [PMID: 31686034 PMCID: PMC6898984 DOI: 10.1038/s41591-019-0611-3] [Citation(s) in RCA: 279] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
We identified a PSEN1 mutation carrier from the world’s largest autosomal dominant Alzheimer’s disease kindred who did not develop mild cognitive impairment until her seventies, three decades after the expected age of clinical onset. She had two copies of the APOE3 Christchurch (R136S) mutation, unusually high brain amyloid, and limited tau/tangle and neurodegenerative measurements. Our findings have implications for APOE’s role in the pathogenesis, treatment, and prevention of Alzheimer’s disease.
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Affiliation(s)
- Joseph F Arboleda-Velasquez
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Michael O'Hare
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Santiago Delgado-Tirado
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Claudia Marino
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Natalia Chmielewska
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.,Boston College, Boston, MA, USA
| | - Kahira L Saez-Torres
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Dhanesh Amarnani
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Aaron P Schultz
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Reisa A Sperling
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital and the Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - David Leyton-Cifuentes
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.,Universidad Escuela de Ingenieria de Antioquia-EIA, Medellin, Colombia
| | - Kewei Chen
- The Banner Alzheimer's Institute, Phoenix, AZ, USA.,University of Arizona, Tucson, AZ, USA.,Arizona State University, Tempe, AZ, USA
| | - Ana Baena
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - David Aguillon
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Silvia Rios-Romenets
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Margarita Giraldo
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia
| | - Edmarie Guzmán-Vélez
- Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Daniel J Norton
- Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA.,Department of Psychology, Gordon College, Wenham, MA, USA
| | | | - Arabiye Artola
- Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Justin S Sanchez
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Juliana Acosta-Uribe
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia.,Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Matthew Lalli
- Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden
| | - Rebecca A Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Ji Luo
- The Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Yinghua Chen
- The Banner Alzheimer's Institute, Phoenix, AZ, USA
| | | | - Yi Su
- The Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Gyungah R Jun
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Marcus Naymik
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Moiz Bootwalla
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - John B Miller
- Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Leo A Kim
- Schepens Eye Research Institute of Mass Eye and Ear and Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Pierre N Tariot
- The Banner Alzheimer's Institute, Phoenix, AZ, USA.,University of Arizona, Tucson, AZ, USA
| | - Keith A Johnson
- Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital and the Department of Neurology, Harvard Medical School, Boston, MA, USA.,Massachusetts General Hospital and Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Eric M Reiman
- The Banner Alzheimer's Institute, Phoenix, AZ, USA. .,University of Arizona, Tucson, AZ, USA. .,Arizona State University, Tempe, AZ, USA. .,Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Yakeel T Quiroz
- Grupo de Neurociencias de Antioquia de la Universidad de Antioquia, Medellin, Colombia. .,Massachusetts General Hospital and Department of Neurology, Harvard Medical School, Boston, MA, USA. .,Massachusetts General Hospital and the Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
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