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Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Van Keuren-Jensen K, Mastroeni D, Reiman EM, Readhead BP. Single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. Nat Commun 2024; 15:5815. [PMID: 38987616 PMCID: PMC11237088 DOI: 10.1038/s41467-024-49790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
The emergence of single nucleus RNA sequencing (snRNA-seq) offers to revolutionize the study of Alzheimer's disease (AD). Integration with complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link cell subpopulations and molecular networks with a broader disease-relevant context. We report snRNA-seq profiles from superior frontal gyrus samples from 101 well characterized subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in hematological parameters. We observed an AD-associated CD83(+) microglial subtype with unique molecular networks and which is associated with immunoglobulin IgG4 production in the transverse colon. Our major observations were replicated in two additional, independent snRNA-seq data sets. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal disease biology.
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Affiliation(s)
- Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Winnie S Liang
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Timothy L Karr
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | | | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, 85006, USA
| | - Benjamin P Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA.
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Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Keuren-Jensen KV, Mastroeni D, Reiman EM, Readhead BP. A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563319. [PMID: 37961404 PMCID: PMC10634692 DOI: 10.1101/2023.10.20.563319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The emergence of technologies that can support high-throughput profiling of single cell transcriptomes offers to revolutionize the study of brain tissue from persons with and without Alzheimer's disease (AD). Integration of these data with additional complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link observed cell subpopulations and molecular network features within a broader disease-relevant context. We report here single nucleus RNA sequencing (snRNA-seq) profiles generated from superior frontal gyrus cortical tissue samples from 101 exceptionally well characterized, aged subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in peripheral hematological lab parameters, with these observations replicated in an independent, prospective cohort study of ageing and dementia. We also observed an AD-associated CD83(+) microglial subtype with unique molecular networks that encompass many known regulators of AD-relevant microglial biology, and which are associated with immunoglobulin IgG4 production in the transverse colon. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal novel disease biology. The transcriptomic, genetic, phenotypic, and network data resources described within this study are available for access and utilization by the scientific community.
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Lineros R, Fernández-Delgado L, Vega-Rioja A, Chacón P, Doukkali B, Monteseirin J, Ribas-Pérez D. Associated Factors of Pneumonia in Individuals with Chronic Obstructive Pulmonary Disease (COPD) Apart from the Use of Inhaled Corticosteroids. Biomedicines 2023; 11:biomedicines11051243. [PMID: 37238914 DOI: 10.3390/biomedicines11051243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/09/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Inhaled corticosteroids (ICSs) are widely used in chronic obstructive pulmonary disease (COPD) and in combination with long-acting β2 agonists (LABAs) to reduce exacerbations and improve patient lung function and quality of life. However, ICSs have been associated with an increased risk of pneumonia in individuals with COPD, although the magnitude of this risk remains unclear. Therefore, it is difficult to make informed clinical decisions that balance the benefits and adverse effects of ICSs in people with COPD. There may be other causes of pneumonia in patients with COPD, and these causes are not always considered in studies on the risks of using ICSs in COPD. We consider it very useful to clarify these aspects in assessing the influence of ICSs on the incidence of pneumonia and their role in the treatment of COPD. This issue has important implications for current practice and the evaluation and management of COPD, since COPD patients may benefit from specific ICS-based treatment strategies. Many of the potential causes of pneumonia in patients with COPD can act synergistically, so they can be included in more than one section.
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Affiliation(s)
- Rosario Lineros
- Unidad Salud Mental, Hospital Vázquez Díaz, 21080 Huelva, Spain
| | | | - Antonio Vega-Rioja
- UGC de Alergología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
| | - Pedro Chacón
- UGC de Alergología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
| | - Bouchra Doukkali
- UGC de Alergología, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain
| | | | - David Ribas-Pérez
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41004 Seville, Spain
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Curtis JA, Borders JC, Dakin AE, Troche MS. The Role of Aspiration Amount on Airway Protective Responses in People with Neurogenic Dysphagia. Dysphagia 2022:10.1007/s00455-022-10546-x. [DOI: 10.1007/s00455-022-10546-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
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Beach TG, Sue LI, Intorcia AJ, Glass MJ, Walker JE, Arce R, Nelson CM, Serrano GE. Acute Brain Ischemia, Infarction and Hemorrhage in Subjects Dying with or Without Autopsy-Proven Acute Pneumonia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.22.21254139. [PMID: 33791728 PMCID: PMC8010760 DOI: 10.1101/2021.03.22.21254139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Stroke is one of the most serious complications of Covid-19 disease but it is still unclear whether stroke is more common with Covid-19 pneumonia as compared to non-Covid-19 pneumonia. We investigated the concurrence rate of autopsy-confirmed acute brain ischemia, acute brain infarction and acute brain hemorrhage with autopsy-proven acute non-Covid pneumonia in consecutive autopsies in the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND), a longitudinal clinicopathological study of normal aging and neurodegenerative diseases. Of 691 subjects with a mean age of 83.4 years, acute pneumonia was histopathologically diagnosed in 343 (49.6%); the concurrence rates for histopathologically-confirmed acute ischemia, acute infarction or subacute infarction was 14% and did not differ between pneumonia and non-pneumonia groups while the rates of acute brain hemorrhage were 1.4% and 2.0% of those with or without acute pneumonia, respectively. In comparison, in reviews of Covid-19 publications, reported clinically-determined rates of acute brain infarction range from 0.5% to 20% while rates of acute brain hemorrhage range from 0.13% to 2%. In reviews of Covid-19 autopsy studies, concurrence rates for both acute brain infarction and acute brain hemorrhage average about 10%. Covid-19 pneumonia and non-Covid-19 pneumonia may have similar risks tor concurrent acute brain infarction and acute brain hemorrhage when pneumonia is severe enough to cause death. Additionally, acute brain ischemia, infarction or hemorrhage may not be more common in subjects dying of acute pneumonia than in subjects dying without acute pneumonia.
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Affiliation(s)
| | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, AZ
| | | | | | | | - Richard Arce
- Banner Sun Health Research Institute, Sun City, AZ
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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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.15.21251511. [PMID: 33619496 PMCID: PMC7899461 DOI: 10.1101/2021.02.15.21251511] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [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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