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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips J, Iturbe A, Erquizi A, Moore BD, Ryu D, Natu A, Dillon K, Torrellas J, Moran C, Ladd T, Afroz F, Islam T, Jagirdar J, Funk CC, Robinson M, Rangaraju S, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson ECB, McFarland K, Levey AI, Prokop S, Seyfried NT, Golde TE. Integrative proteomics identifies a conserved Aβ amyloid responsome, novel plaque proteins, and pathology modifiers in Alzheimer's disease. Cell Rep Med 2024:101669. [PMID: 39127040 DOI: 10.1016/j.xcrm.2024.101669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/15/2024] [Accepted: 07/10/2024] [Indexed: 08/12/2024]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder that develops over decades. AD brain proteomics reveals vast alterations in protein levels and numerous altered biologic pathways. Here, we compare AD brain proteome and network changes with the brain proteomes of amyloid β (Aβ)-depositing mice to identify conserved and divergent protein networks with the conserved networks identifying an Aβ amyloid responsome. Proteins in the most conserved network (M42) accumulate in plaques, cerebrovascular amyloid (CAA), and/or dystrophic neuronal processes, and overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), increases the accumulation of Aβ in plaques and CAA. M42 proteins bind amyloid fibrils in vitro, and MDK and PTN co-accumulate with cardiac transthyretin amyloid. M42 proteins appear intimately linked to amyloid deposition and can regulate amyloid deposition, suggesting that they are pathology modifiers and thus putative therapeutic targets. We posit that amyloid-scaffolded accumulation of numerous M42+ proteins is a central mechanism mediating downstream pathophysiology in AD.
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Affiliation(s)
- Yona Levites
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Yong Ran
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Wangchen Tsering
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Duc Duong
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Measho Abreha
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshna Gadhavi
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kiara Lolo
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Jorge Trejo-Lopez
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Jennifer Phillips
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Andrea Iturbe
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Aya Erquizi
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Brenda D Moore
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Danny Ryu
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Aditya Natu
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristy Dillon
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jose Torrellas
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Corey Moran
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Thomas Ladd
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Farhana Afroz
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Tariful Islam
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Jaishree Jagirdar
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - David R Borchelt
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Nilüfer Ertekin-Taner
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA; Mayo Clinic, Department of Neurology, Jacksonville, FL, USA
| | - Jeffrey W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 110117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, 110117 Berlin, Germany; Cluster of Excellence, NeuroCure, Charitéplatz, 110117 Berlin, Germany
| | - Erik C B Johnson
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen McFarland
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan Prokop
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Nicholas T Seyfried
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
| | - Todd E Golde
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
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2
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Bartelt LC, Fakhri M, Adamek G, Trybus M, Samelak-Czajka A, Jackowiak P, Fiszer A, Lowe CB, La Spada AR, Switonski PM. Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue. CELL REPORTS METHODS 2024; 4:100816. [PMID: 38981474 PMCID: PMC11294835 DOI: 10.1016/j.crmeth.2024.100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
We developed a method that utilizes fluorescent labeling of nuclear envelopes alongside cytometry sorting for the selective isolation of Purkinje cell (PC) nuclei. Beginning with SUN1 reporter mice, we GFP-tagged envelopes to confirm that PC nuclei could be accurately separated from other cell types. We then developed an antibody-based protocol to make PC nuclear isolation more robust and adaptable to cerebellar tissues of any genotypic background. Immunofluorescent labeling of the nuclear membrane protein RanBP2 enabled the isolation of PC nuclei from C57BL/6 cerebellum. By analyzing the expression of PC markers, nuclear size, and nucleoli number, we confirmed that our method delivers a pure fraction of PC nuclei. To demonstrate its applicability, we isolated PC nuclei from spinocerebellar ataxia type 7 (SCA7) mice and identified transcriptional changes in known and new disease-associated genes. Access to pure PC nuclei offers insights into PC biology and pathology, including the nature of selective neuronal vulnerability.
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Affiliation(s)
- Luke C Bartelt
- University Program in Genetics & Genomics, Duke University Medical Center, Durham, NC 27710, USA; Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mouad Fakhri
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Grazyna Adamek
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Trybus
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Samelak-Czajka
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
| | - Pawel M Switonski
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
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3
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Wang N, Cai L, Pei X, Lin Z, Huang L, Liang C, Wei M, Shao L, Guo T, Huang F, Luo H, Zheng H, Chen XF, Leng L, Zhang YW, Wang X, Zhang J, Guo K, Wang Z, Zhang H, Zhao Y, Xu H. Microglial apolipoprotein E particles contribute to neuronal senescence and synaptotoxicity. iScience 2024; 27:110006. [PMID: 38868202 PMCID: PMC11167441 DOI: 10.1016/j.isci.2024.110006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/13/2023] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Apolipoprotein E (apoE) plays a crucial role in the pathogenesis of Alzheimer's disease (AD). Microglia exhibit a substantial upregulation of apoE in AD-associated circumstances, despite astrocytes being the primary source of apoE expression and secretion in the brain. Although the role of astrocytic apoE in the brain has been extensively investigated, it remains unclear that whether and how apoE particles generated from astrocytes and microglia differ in biological characteristic and function. Here, we demonstrate the differences in size between apoE particles generated from microglia and astrocytes. Microglial apoE particles impair neurite growth and synapses, and promote neuronal senescence, whereas depletion of GPNMB (glycoprotein non-metastatic melanoma protein B) in microglial apoE particles mitigated these deleterious effects. In addition, human APOE4-expressing microglia are more neurotoxic than APOE3-bearing microglia. For the first time, these results offer concrete evidence that apoE particles produced by microglia are involved in neuronal senescence and toxicity.
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Affiliation(s)
- Na Wang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Lujian Cai
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Xinyu Pei
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhihao Lin
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Lihong Huang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Chensi Liang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Min Wei
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Lin Shao
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Tiantian Guo
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Fang Huang
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing 400016, China
| | - Hong Luo
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Honghua Zheng
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiao-fen Chen
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Lige Leng
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Yun-wu Zhang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Xin Wang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Jie Zhang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Kai Guo
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing 400016, China
| | - Zhanxiang Wang
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Hongsheng Zhang
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China
- Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing 400016, China
| | - Yingjun Zhao
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Huaxi Xu
- Center for Brain Sciences, First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China
- Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China
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4
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Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O'Connell KMS, Singh S, Murdy TJ, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. Commun Biol 2024; 7:605. [PMID: 38769398 PMCID: PMC11106287 DOI: 10.1038/s42003-024-06242-1] [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: 08/16/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Alzheimer's disease (AD) is broadly characterized by neurodegeneration, pathology accumulation, and cognitive decline. There is considerable variation in the progression of clinical symptoms and pathology in humans, highlighting the importance of genetic diversity in the study of AD. To address this, we analyze cell composition and amyloid-beta deposition of 6- and 14-month-old AD-BXD mouse brains. We utilize the analytical QUINT workflow- a suite of software designed to support atlas-based quantification, which we expand to deliver a highly effective method for registering and quantifying cell and pathology changes in diverse disease models. In applying the expanded QUINT workflow, we quantify near-global age-related increases in microglia, astrocytes, and amyloid-beta, and we identify strain-specific regional variation in neuron load. To understand how individual differences in cell composition affect the interpretation of bulk gene expression in AD, we combine hippocampal immunohistochemistry analyses with bulk RNA-sequencing data. This approach allows us to categorize genes whose expression changes in response to AD in a cell and/or pathology load-dependent manner. Ultimately, our study demonstrates the use of the QUINT workflow to standardize the quantification of immunohistochemistry data in diverse mice, - providing valuable insights into regional variation in cellular load and amyloid deposition in the AD-BXD model.
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Affiliation(s)
- Brianna Gurdon
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gergely Csucs
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Niran Hadad
- The Jackson Laboratory, Bar Harbor, ME, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Andrew Ouellette
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
| | - Tionna Ouellette
- The Jackson Laboratory, Bar Harbor, ME, USA
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA
| | - Kristen M S O'Connell
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA
| | - Surjeet Singh
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ingvild Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
| | - Catherine C Kaczorowski
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA.
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA.
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
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5
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Reddy JS, Heath L, Vander Linden A, Allen M, de Paiva Lopes K, Seifar F, Wang E, Ma Y, Poehlman WL, Quicksall ZS, Runnels A, Wang Y, Duong DM, Yin L, Xu K, Modeste ES, Shantaraman A, Dammer EB, Ping L, Oatman SR, Scanlan J, Ho C, Carrasquillo MM, Atik M, Yepez G, Mitchell AO, Nguyen TT, Chen X, Marquez DX, Reddy H, Xiao H, Seshadri S, Mayeux R, Prokop S, Lee EB, Serrano GE, Beach TG, Teich AF, Haroutunian V, Fox EJ, Gearing M, Wingo A, Wingo T, Lah JJ, Levey AI, Dickson DW, Barnes LL, De Jager P, Zhang B, Bennett D, Seyfried NT, Greenwood AK, Ertekin-Taner N. Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589592. [PMID: 38659743 PMCID: PMC11042309 DOI: 10.1101/2024.04.16.589592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Multi-omics studies in Alzheimer's disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked African Americans (AA) and Latin Americans (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership in AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTS We generated multi-omics data and curated and harmonized phenotypic data from AA (n=306), LA (n=326), or AA and LA (n=4) brain donors plus Non-Hispanic White (n=252) and other (n=20) ethnic groups, to establish a foundational dataset enriched for AA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSION Inclusion of traditionally underrepresented groups in multi-omics studies is essential to discover the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD.
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Affiliation(s)
- Joseph S Reddy
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Laura Heath
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | | | - Mariet Allen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Fatemeh Seifar
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - Yiyi Ma
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | | | - Alexi Runnels
- New York Genome Center, 101 6th Ave, New York, NY 10013
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Duc M Duong
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Luming Yin
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Kaiming Xu
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erica S Modeste
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Eric B Dammer
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Lingyan Ping
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Jo Scanlan
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | - Charlotte Ho
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Merve Atik
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Geovanna Yepez
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Thuy T Nguyen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Xianfeng Chen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - David X Marquez
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
- University of Illinois Chicago, 1200 West Harrison St., Chicago, Illinois 60607
| | - Hasini Reddy
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Harrison Xiao
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Sudha Seshadri
- The Glen Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas, 8300 Floyd Curl Drive, San Antonio TX 78229
| | - Richard Mayeux
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | - Edward B Lee
- Center for Neurodegenerative Disease Brain Bank at the University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104-2676
| | - Geidy E Serrano
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Thomas G Beach
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Andrew F Teich
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Varham Haroutunian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
| | - Edward J Fox
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Marla Gearing
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Aliza Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Thomas Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - James J Lah
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Allan I Levey
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Dennis W Dickson
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Philip De Jager
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
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6
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Bhattarai P, Gunasekaran TI, Belloy ME, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Turgutalp B, Sukumar G, Alba C, McGrath EM, Hupalo DN, Bacikova D, Le Guen Y, Lantigua R, Medrano M, Rivera D, Recio P, Nuriel T, Ertekin-Taner N, Teich AF, Dickson DW, Holley S, Greicius M, Dalgard CL, Zody M, Mayeux R, Kizil C, Vardarajan BN. Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer's disease. Acta Neuropathol 2024; 147:70. [PMID: 38598053 PMCID: PMC11006751 DOI: 10.1007/s00401-024-02721-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The risk of developing Alzheimer's disease (AD) significantly increases in individuals carrying the APOEε4 allele. Elderly cognitively healthy individuals with APOEε4 also exist, suggesting the presence of cellular mechanisms that counteract the pathological effects of APOEε4; however, these mechanisms are unknown. We hypothesized that APOEε4 carriers without dementia might carry genetic variations that could protect them from developing APOEε4-mediated AD pathology. To test this, we leveraged whole-genome sequencing (WGS) data in the National Institute on Aging Alzheimer's Disease Family Based Study (NIA-AD FBS), Washington Heights/Inwood Columbia Aging Project (WHICAP), and Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) cohorts and identified potentially protective variants segregating exclusively among unaffected APOEε4 carriers. In homozygous unaffected carriers above 70 years old, we identified 510 rare coding variants. Pathway analysis of the genes harboring these variants showed significant enrichment in extracellular matrix (ECM)-related processes, suggesting protective effects of functional modifications in ECM proteins. We prioritized two genes that were highly represented in the ECM-related gene ontology terms, (FN1) and collagen type VI alpha 2 chain (COL6A2) and are known to be expressed at the blood-brain barrier (BBB), for postmortem validation and in vivo functional studies. An independent analysis in a large cohort of 7185 APOEε4 homozygous carriers found that rs140926439 variant in FN1 was protective of AD (OR = 0.29; 95% CI [0.11, 0.78], P = 0.014) and delayed age at onset of disease by 3.37 years (95% CI [0.42, 6.32], P = 0.025). The FN1 and COL6A2 protein levels were increased at the BBB in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4-mediated AD-related pathology and cognitive decline. To validate our findings, we used zebrafish models with loss-of-function (LOF) mutations in fn1b-the ortholog for human FN1. We found that fibronectin LOF reduced gliosis, enhanced gliovascular remodeling, and potentiated the microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. Our study suggests that vascular deposition of FN1 is related to the pathogenicity of APOEε4, and LOF variants in FN1 may reduce APOEε4-related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk.
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Affiliation(s)
- Prabesh Bhattarai
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Tamil Iniyan Gunasekaran
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dolly Reyes-Dumeyer
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Dörthe Jülich
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Hüseyin Tayran
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Delaney Flaherty
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Bengisu Turgutalp
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Camille Alba
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Elisa Martinez McGrath
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Daniel N Hupalo
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Dagmar Bacikova
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rafael Lantigua
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University New York, New York, USA
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | - Diones Rivera
- Department of Neurology, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
- School of Medicine, Universidad Pedro Henriquez Urena (UNPHU), Santo Domingo, Dominican Republic
| | - Patricia Recio
- Department of Neurology, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
| | - Tal Nuriel
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Andrew F Teich
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Scott Holley
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Michael Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- The American Genome Center, Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Michael Zody
- New York Genome Center, New York, NY, 10013, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 W 168th St., New York, NY, 10032, USA
| | - Caghan Kizil
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Badri N Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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7
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Pak V, Adewale Q, Bzdok D, Dadar M, Zeighami Y, Iturria-Medina Y. Distinctive whole-brain cell types predict tissue damage patterns in thirteen neurodegenerative conditions. eLife 2024; 12:RP89368. [PMID: 38512130 PMCID: PMC10957173 DOI: 10.7554/elife.89368] [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] [Indexed: 03/22/2024] Open
Abstract
For over a century, brain research narrative has mainly centered on neuron cells. Accordingly, most neurodegenerative studies focus on neuronal dysfunction and their selective vulnerability, while we lack comprehensive analyses of other major cell types' contribution. By unifying spatial gene expression, structural MRI, and cell deconvolution, here we describe how the human brain distribution of canonical cell types extensively predicts tissue damage in 13 neurodegenerative conditions, including early- and late-onset Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies, amyotrophic lateral sclerosis, mutations in presenilin-1, and 3 clinical variants of frontotemporal lobar degeneration (behavioral variant, semantic and non-fluent primary progressive aphasia) along with associated three-repeat and four-repeat tauopathies and TDP43 proteinopathies types A and C. We reconstructed comprehensive whole-brain reference maps of cellular abundance for six major cell types and identified characteristic axes of spatial overlapping with atrophy. Our results support the strong mediating role of non-neuronal cells, primarily microglia and astrocytes, in spatial vulnerability to tissue loss in neurodegeneration, with distinct and shared across-disorder pathomechanisms. These observations provide critical insights into the multicellular pathophysiology underlying spatiotemporal advance in neurodegeneration. Notably, they also emphasize the need to exceed the current neuro-centric view of brain diseases, supporting the imperative for cell-specific therapeutic targets in neurodegeneration.
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Affiliation(s)
- Veronika Pak
- Department of Neurology and Neurosurgery, McGill UniversityMontrealCanada
- McConnell Brain Imaging Centre, Montreal Neurological InstituteMontrealCanada
- Ludmer Centre for Neuroinformatics & Mental HealthMontrealCanada
| | - Quadri Adewale
- Department of Neurology and Neurosurgery, McGill UniversityMontrealCanada
- McConnell Brain Imaging Centre, Montreal Neurological InstituteMontrealCanada
- Ludmer Centre for Neuroinformatics & Mental HealthMontrealCanada
| | - Danilo Bzdok
- McConnell Brain Imaging Centre, Montreal Neurological InstituteMontrealCanada
- Department of Biomedical Engineering, McGill UniversityMontrealCanada
- School of Computer Science, McGill UniversityMontrealCanada
- Mila – Quebec Artificial Intelligence InstituteMontrealCanada
| | | | | | - Yasser Iturria-Medina
- Department of Neurology and Neurosurgery, McGill UniversityMontrealCanada
- McConnell Brain Imaging Centre, Montreal Neurological InstituteMontrealCanada
- Ludmer Centre for Neuroinformatics & Mental HealthMontrealCanada
- Department of Biomedical Engineering, McGill UniversityMontrealCanada
- McGill Centre for Studies in AgingMontrealCanada
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8
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Bhattarai P, Gunasekaran TI, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Lantigua R, Medrano M, Rivera D, Recio P, Ertekin-Taner N, Teich AF, Dickson DW, Holley S, Mayeux R, Kizil C, Vardarajan BN. Rare genetic variation in Fibronectin 1 ( FN1 ) protects against APOEe4 in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573895. [PMID: 38260431 PMCID: PMC10802344 DOI: 10.1101/2024.01.02.573895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The risk of developing Alzheimer's disease (AD) significantly increases in individuals carrying the APOEε4 allele. Elderly cognitively healthy individuals with APOEε4 also exist, suggesting the presence of cellular mechanisms that counteract the pathological effects of APOEε4 ; however, these mechanisms are unknown. We hypothesized that APOEε4 carriers without dementia might carry genetic variations that could protect them from developing APOEε4- mediated AD pathology. To test this, we leveraged whole genome sequencing (WGS) data in National Institute on Aging Alzheimer's Disease Family Based Study (NIA-AD FBS), Washington Heights/Inwood Columbia Aging Project (WHICAP), and Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) cohorts and identified potentially protective variants segregating exclusively among unaffected APOEε4 carriers. In homozygous unaffected carriers above 70 years old, we identified 510 rare coding variants. Pathway analysis of the genes harboring these variants showed significant enrichment in extracellular matrix (ECM)-related processes, suggesting protective effects of functional modifications in ECM proteins. We prioritized two genes that were highly represented in the ECM-related gene ontology terms, (FN1) and collagen type VI alpha 2 chain ( COL6A2 ) and are known to be expressed at the blood-brain barrier (BBB), for postmortem validation and in vivo functional studies. The FN1 and COL6A2 protein levels were increased at the BBB in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4 -mediated AD-related pathology and cognitive decline. To validate our findings, we used zebrafish models with loss-of-function (LOF) mutations in fn1b - the ortholog for human FN1 . We found that fibronectin LOF reduced gliosis, enhanced gliovascular remodeling and potentiated the microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. Our study suggests vascular deposition of FN1 is related to the pathogenicity of APOEε4 , LOF variants in FN1 may reduce APOEε4 -related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk.
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9
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Tayran H, Yilmaz E, Bhattarai P, Min Y, Wang X, Ma Y, Nelson N, Kassara N, Cosacak MI, Dogru RM, Reyes-Dumeyer D, Reddy JS, Qiao M, Flaherty D, Teich AF, Gunasekaran TI, Yang Z, Tosto G, Vardarajan BN, İş Ö, Ertekin-Taner N, Mayeux R, Kizil C. ABCA7-dependent Neuropeptide-Y signalling is a resilience mechanism required for synaptic integrity in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573893. [PMID: 38260408 PMCID: PMC10802315 DOI: 10.1101/2024.01.02.573893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) remains a complex challenge characterized by cognitive decline and memory loss. Genetic variations have emerged as crucial players in the etiology of AD, enabling hope for a better understanding of the disease mechanisms; yet the specific mechanism of action for those genetic variants remain uncertain. Animal models with reminiscent disease pathology could uncover previously uncharacterized roles of these genes. Using CRISPR/Cas9 gene editing, we generated a knockout model for abca7, orthologous to human ABCA7 - an established AD-risk gene. The abca7 +/- zebrafish showed reduced astroglial proliferation, synaptic density, and microglial abundance in response to amyloid beta 42 (Aβ42). Single-cell transcriptomics revealed abca7 -dependent neuronal and glial cellular crosstalk through neuropeptide Y (NPY) signaling. The abca7 knockout reduced the expression of npy, bdnf and ngfra , which are required for synaptic integrity and astroglial proliferation. With clinical data in humans, we showed reduced NPY in AD correlates with elevated Braak stage, predicted regulatory interaction between NPY and BDNF , identified genetic variants in NPY associated with AD, found segregation of variants in ABCA7, BDNF and NGFR in AD families, and discovered epigenetic changes in the promoter regions of NPY, NGFR and BDNF in humans with specific single nucleotide polymorphisms in ABCA7 . These results suggest that ABCA7-dependent NPY signaling is required for synaptic integrity, the impairment of which generates a risk factor for AD through compromised brain resilience. Abstract Figure
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10
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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips JL, Iturbe A, Erqiuzi A, Moore BD, Ryu D, Natu A, Dillon KD, Torrellas J, Moran C, Ladd TB, Afroz KF, Islam T, Jagirdar J, Funk CC, Robinson M, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson EC, McFarland K, Levey AL, Prokop S, Seyfried NT, Golde TE. Aβ Amyloid Scaffolds the Accumulation of Matrisome and Additional Proteins in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.568318. [PMID: 38076912 PMCID: PMC10705437 DOI: 10.1101/2023.11.29.568318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
We report a highly significant correlation in brain proteome changes between Alzheimers disease (AD) and CRND8 APP695NL/F transgenic mice. However, integrating protein changes observed in the CRND8 mice with co-expression networks derived from human AD, reveals both conserved and divergent module changes. For the most highly conserved module (M42, matrisome) we find many proteins accumulate in plaques, cerebrovascular amyloid (CAA), dystrophic processes, or a combination thereof. Overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), in CRND8 mice brains leads to increased accumulation of A β ; in plaques and in CAA; further, recombinant MDK and PTN enhance A β ; aggregation into amyloid. Multiple M42 proteins, annotated as heparan sulfate binding proteins, bind to fibrillar A β 42 and a non-human amyloid fibril in vitro. Supporting this binding data, MDK and PTN co-accumulate with transthyretin (TTR) amyloid in the heart and islet amyloid polypeptide (IAPP) amyloid in the pancreas. Our findings establish several critical insights. Proteomic changes in modules observed in human AD brains define an A β ; amyloid responsome that is well conserved from mouse model to human. Further, distinct amyloid structures may serve as scaffolds, facilitating the co-accumulation of proteins with signaling functions. We hypothesize that this co-accumulation may contribute to downstream pathological sequalae. Overall, this contextualized understanding of proteomic changes and their interplay with amyloid deposition provides valuable insights into the complexity of AD pathogenesis and potential biomarkers and therapeutic targets.
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11
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Lynch MT, Taub MA, Farfel JM, Yang J, Abadir P, De Jager PL, Grodstein F, Bennett DA, Mathias RA. Evaluating genomic signatures of aging in brain tissue as it relates to Alzheimer's disease. Sci Rep 2023; 13:14747. [PMID: 37679407 PMCID: PMC10484923 DOI: 10.1038/s41598-023-41400-1] [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: 03/20/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Telomere length (TL) attrition, epigenetic age acceleration, and mitochondrial DNA copy number (mtDNAcn) decline are established hallmarks of aging. Each has been individually associated with Alzheimer's dementia, cognitive function, and pathologic Alzheimer's disease (AD). Epigenetic age and mtDNAcn have been studied in brain tissue directly but prior work on TL in brain is limited to small sample sizes and most studies have examined leukocyte TL. Importantly, TL, epigenetic age clocks, and mtDNAcn have not been studied jointly in brain tissue from an AD cohort. We examined dorsolateral prefrontal cortex (DLPFC) tissue from N = 367 participants of the Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP). TL and mtDNAcn were estimated from whole genome sequencing (WGS) data and cortical clock age was computed on 347 CpG sites. We examined dementia, MCI, and level of and change in cognition, pathologic AD, and three quantitative AD traits, as well as measures of other neurodegenerative diseases and cerebrovascular diseases (CVD). We previously showed that mtDNAcn from DLPFC brain tissue was associated with clinical and pathologic features of AD. Here, we show that those associations are independent of TL. We found TL to be associated with β-amyloid levels (beta = - 0.15, p = 0.023), hippocampal sclerosis (OR = 0.56, p = 0.0015) and cerebral atherosclerosis (OR = 1.44, p = 0.0007). We found strong associations between mtDNAcn and clinical measures of AD. The strongest associations with pathologic measures of AD were with cortical clock and there were associations of mtDNAcn with global AD pathology and tau tangles. Of the other pathologic traits, mtDNAcn was associated with hippocampal sclerosis, macroscopic infarctions and CAA and cortical clock was associated with Lewy bodies. Multi-modal age acceleration, accelerated aging on both mtDNAcn and cortical clock, had greater effect size than a single measure alone. These findings highlight for the first time that age acceleration determined on multiple genomic measures, mtDNAcn and cortical clock may have a larger effect on AD/AD related disorders (ADRD) pathogenesis than single measures.
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Affiliation(s)
- Megan T Lynch
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jose M Farfel
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Peter Abadir
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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12
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Batra R, Krumsiek J, Wang X, Allen M, Blach C, Kastenmüller G, Arnold M, Ertekin-Taner N, Kaddurah-Daouk RF. Comparative brain metabolomics reveals shared and distinct metabolic alterations in Alzheimer's disease and progressive supranuclear palsy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.25.23293055. [PMID: 37546878 PMCID: PMC10402214 DOI: 10.1101/2023.07.25.23293055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Metabolic dysregulation is a hallmark of neurodegenerative diseases, including Alzheimer's disease (AD) and progressive supranuclear palsy (PSP). While metabolic dysregulation is a common link between these two tauopathies, a comprehensive brain metabolic comparison of the diseases has not yet been performed. We analyzed 342 postmortem brain samples from the Mayo Clinic Brain Bank and examined 658 metabolites in the cerebellar cortex and the temporal cortex between the two tauopathies. Our findings indicate that both diseases display oxidative stress associated with lipid metabolism, mitochondrial dysfunction linked to lysine metabolism, and an indication of tau-induced polyamine stress response. However, specific to AD, we detected glutathione-related neuroinflammation, deregulations of enzymes tied to purines, and cognitive deficits associated with vitamin B. Taken together, our findings underscore vast alterations in the brain's metabolome, illuminating shared neurodegenerative pathways and disease-specific traits in AD and PSP.
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Affiliation(s)
- Richa Batra
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Colette Blach
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Rima F Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke Institute for Brain Sciences and Department of Medicine, Duke University, Durham, NC, USA
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13
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Siddiqui T, Cosacak MI, Popova S, Bhattarai P, Yilmaz E, Lee AJ, Min Y, Wang X, Allen M, İş Ö, Atasavum ZT, Rodriguez-Muela N, Vardarajan BN, Flaherty D, Teich AF, Santa-Maria I, Freudenberg U, Werner C, Tosto G, Mayeux R, Ertekin-Taner N, Kizil C. Nerve growth factor receptor (Ngfr) induces neurogenic plasticity by suppressing reactive astroglial Lcn2/Slc22a17 signaling in Alzheimer's disease. NPJ Regen Med 2023; 8:33. [PMID: 37429840 DOI: 10.1038/s41536-023-00311-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Neurogenesis, crucial for brain resilience, is reduced in Alzheimer's disease (AD) that induces astroglial reactivity at the expense of the pro-neurogenic potential, and restoring neurogenesis could counteract neurodegenerative pathology. However, the molecular mechanisms promoting pro-neurogenic astroglial fate despite AD pathology are unknown. In this study, we used APP/PS1dE9 mouse model and induced Nerve growth factor receptor (Ngfr) expression in the hippocampus. Ngfr, which promotes neurogenic fate of astroglia during the amyloid pathology-induced neuroregeneration in zebrafish brain, stimulated proliferative and neurogenic outcomes. Histological analyses of the changes in proliferation and neurogenesis, single-cell transcriptomics, spatial proteomics, and functional knockdown studies showed that the induced expression of Ngfr reduced the reactive astrocyte marker Lipocalin-2 (Lcn2), which we found was sufficient to reduce neurogenesis in astroglia. Anti-neurogenic effects of Lcn2 was mediated by Slc22a17, blockage of which recapitulated the pro-neurogenicity by Ngfr. Long-term Ngfr expression reduced amyloid plaques and Tau phosphorylation. Postmortem human AD hippocampi and 3D human astroglial cultures showed elevated LCN2 levels correlate with reactive gliosis and reduced neurogenesis. Comparing transcriptional changes in mouse, zebrafish, and human AD brains for cell intrinsic differential gene expression and weighted gene co-expression networks revealed common altered downstream effectors of NGFR signaling, such as PFKP, which can enhance proliferation and neurogenesis in vitro when blocked. Our study suggests that the reactive non-neurogenic astroglia in AD can be coaxed to a pro-neurogenic fate and AD pathology can be alleviated with Ngfr. We suggest that enhancing pro-neurogenic astroglial fate may have therapeutic ramifications in AD.
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Affiliation(s)
- Tohid Siddiqui
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Stanislava Popova
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
- Neuron D GmbH, Tatzberg 47, 01307, Dresden, Germany
| | - Prabesh Bhattarai
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Annie J Lee
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Özkan İş
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Zeynep Tansu Atasavum
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Natalia Rodriguez-Muela
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany
| | - Badri N Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Delaney Flaherty
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Andrew F Teich
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Edificio E, 28223, Pozuelo de Alarcon, Madrid, Spain
| | - Uwe Freudenberg
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Str. 6, D-01069, Dresden, Germany
| | - Carsten Werner
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Str. 6, D-01069, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, D-01307, Dresden, Germany
| | - Giuseppe Tosto
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, 01307, Dresden, Germany.
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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14
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Gomes Moreira D, Jan A. A beginner's guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration. Sci Data 2023; 10:432. [PMID: 37414779 PMCID: PMC10325954 DOI: 10.1038/s41597-023-02338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this "beginner's guide" will benefit the research community in NDDs, and would serve as a useful educational tool.
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Affiliation(s)
- Diana Gomes Moreira
- Department of Clinical Medicine, Palle Juul-Jensens Boulevard 165, DK-8200, Aarhus N, Denmark
| | - Asad Jan
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK-8000, Aarhus C, Denmark.
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15
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Tosoni G, Ayyildiz D, Bryois J, Macnair W, Fitzsimons CP, Lucassen PJ, Salta E. Mapping human adult hippocampal neurogenesis with single-cell transcriptomics: Reconciling controversy or fueling the debate? Neuron 2023; 111:1714-1731.e3. [PMID: 37015226 DOI: 10.1016/j.neuron.2023.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
The notion of exploiting the regenerative potential of the human brain in physiological aging or neurological diseases represents a particularly attractive alternative to conventional strategies for enhancing or restoring brain function. However, a major first question to address is whether the human brain does possess the ability to regenerate. The existence of human adult hippocampal neurogenesis (AHN) has been at the center of a fierce scientific debate for many years. The advent of single-cell transcriptomic technologies was initially viewed as a panacea to resolving this controversy. However, recent single-cell RNA sequencing studies in the human hippocampus yielded conflicting results. Here, we critically discuss and re-analyze previously published AHN-related single-cell transcriptomic datasets. We argue that, although promising, the single-cell transcriptomic profiling of AHN in the human brain can be confounded by methodological, conceptual, and biological factors that need to be consistently addressed across studies and openly discussed within the scientific community.
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Affiliation(s)
- Giorgia Tosoni
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Will Macnair
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Carlos P Fitzsimons
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Paul J Lucassen
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands; Center for Urban Mental Health, University of Amsterdam, 1098 SM, Amsterdam, the Netherlands
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands.
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16
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Dai R, Chu T, Zhang M, Wang X, Jourdon A, Wu F, Mariani J, Vaccarino FM, Lee D, Fullard JF, Hoffman GE, Roussos P, Wang Y, Wang X, Pinto D, Wang SH, Zhang C, Chen C, Liu C. Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532468. [PMID: 36993743 PMCID: PMC10054947 DOI: 10.1101/2023.03.13.532468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Sample-wise deconvolution methods have been developed to estimate cell-type proportions and gene expressions in bulk-tissue samples. However, the performance of these methods and their biological applications has not been evaluated, particularly on human brain transcriptomic data. Here, nine deconvolution methods were evaluated with sample-matched data from bulk-tissue RNAseq, single-cell/nuclei (sc/sn) RNAseq, and immunohistochemistry. A total of 1,130,767 nuclei/cells from 149 adult postmortem brains and 72 organoid samples were used. The results showed the best performance of dtangle for estimating cell proportions and bMIND for estimating sample-wise cell-type gene expression. For eight brain cell types, 25,273 cell-type eQTLs were identified with deconvoluted expressions (decon-eQTLs). The results showed that decon-eQTLs explained more schizophrenia GWAS heritability than bulk-tissue or single-cell eQTLs alone. Differential gene expression associated with multiple phenotypes were also examined using the deconvoluted data. Our findings, which were replicated in bulk-tissue RNAseq and sc/snRNAseq data, provided new insights into the biological applications of deconvoluted data.
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Affiliation(s)
- Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Tianyao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Xuan Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | | | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT, USA
| | | | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Departments of Psychiatry and Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Departments of Psychiatry and Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Departments of Psychiatry and Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Departments of Psychiatry and Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, VA, USA
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Dalila Pinto
- Department of Psychiatry, Department of Genetics and Genomic Sciences, Mindich Child Health and Development Institute, and Icahn Genomics Institute for Data Science and Genomic Technology, Seaver Autism Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sidney H Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Chunling Zhang
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
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17
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Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O'Connell K, Singh S, Murdy T, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530226. [PMID: 36909528 PMCID: PMC10002670 DOI: 10.1101/2023.02.27.530226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Alzheimer's disease (AD) is characterized by neurodegeneration, pathology accumulation, and progressive cognitive decline. There is significant variation in age at onset and severity of symptoms highlighting the importance of genetic diversity in the study of AD. To address this, we analyzed cell and pathology composition of 6- and 14-month-old AD-BXD mouse brains using the semi-automated workflow (QUINT); which we expanded to allow for nonlinear refinement of brain atlas-registration, and quality control assessment of atlas-registration and brain section integrity. Near global age-related increases in microglia, astrocyte, and amyloid-beta accumulation were measured, while regional variation in neuron load existed among strains. Furthermore, hippocampal immunohistochemistry analyses were combined with bulk RNA-sequencing results to demonstrate the relationship between cell composition and gene expression. Overall, the additional functionality of the QUINT workflow delivers a highly effective method for registering and quantifying cell and pathology changes in diverse disease models.
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Affiliation(s)
- Brianna Gurdon
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gergely Csucs
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | - Andrew Ouellette
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
| | - Tionna Ouellette
- The Jackson Laboratory, Bar Harbor, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
| | - Kristen O'Connell
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
| | | | - Tom Murdy
- The Jackson Laboratory, Bar Harbor, ME
| | | | - Ingvild Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Catherine C Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
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18
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Salta E, Lazarov O, Fitzsimons CP, Tanzi R, Lucassen PJ, Choi SH. Adult hippocampal neurogenesis in Alzheimer's disease: A roadmap to clinical relevance. Cell Stem Cell 2023; 30:120-136. [PMID: 36736288 PMCID: PMC10082636 DOI: 10.1016/j.stem.2023.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Adult hippocampal neurogenesis (AHN) drops sharply during early stages of Alzheimer's disease (AD), via unknown mechanisms, and correlates with cognitive status in AD patients. Understanding AHN regulation in AD could provide a framework for innovative pharmacological interventions. We here combine molecular, behavioral, and clinical data and critically discuss the multicellular complexity of the AHN niche in relation to AD pathophysiology. We further present a roadmap toward a better understanding of the role of AHN in AD by probing the promises and caveats of the latest technological advancements in the field and addressing the conceptual and methodological challenges ahead.
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Affiliation(s)
- Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Orly Lazarov
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, 808 S Wood St., Chicago, IL 60612, USA
| | - Carlos P Fitzsimons
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Rudolph Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, McCance Center for Brain Health, 114 16th Street, Boston, MA 02129, USA.
| | - Paul J Lucassen
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands; Center for Urban Mental Health, University of Amsterdam, Kruislaan 404, 1098 SM, Amsterdam, The Netherlands.
| | - Se Hoon Choi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, McCance Center for Brain Health, 114 16th Street, Boston, MA 02129, USA.
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19
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Luquez T, Gaur P, Kosater IM, Lam M, Lee DI, Mares J, Paryani F, Yadav A, Menon V. Cell type-specific changes identified by single-cell transcriptomics in Alzheimer's disease. Genome Med 2022; 14:136. [PMID: 36447241 PMCID: PMC9710120 DOI: 10.1186/s13073-022-01136-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022] Open
Abstract
The rapid advancement of single-cell transcriptomics in neurology has allowed for profiling of post-mortem human brain tissue across multiple diseases. Over the past 3 years, several studies have examined tissue from donors with and without diagnoses of Alzheimer's disease, highlighting key changes in cell type composition and molecular signatures associated with pathology and, in some cases, cognitive decline. Although all of these studies have generated single-cell/nucleus RNA-seq or ATAC-seq data from the full array of major cell classes in the brain, they have each focused on changes in specific cell types. Here, we synthesize the main findings from these studies and contextualize them in the overall space of large-scale omics studies of Alzheimer's disease. Finally, we touch upon new horizons in the field, in particular advancements in high-resolution spatial interrogation of tissue and multi-modal efforts-and how they are likely to further advance mechanistic and target-selection studies on Alzheimer's disease.
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Affiliation(s)
- Tain Luquez
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Pallavi Gaur
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Ivy M Kosater
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Matti Lam
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Dylan I Lee
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Jason Mares
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Fahad Paryani
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Archana Yadav
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Immunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA.
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20
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Kandimalla R, Manczak M, Pradeepkiran JA, Morton H, Reddy PH. A partial reduction of Drp1 improves cognitive behavior and enhances mitophagy, autophagy and dendritic spines in a transgenic Tau mouse model of Alzheimer disease. Hum Mol Genet 2022; 31:1788-1805. [PMID: 34919689 PMCID: PMC9169458 DOI: 10.1093/hmg/ddab360] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/18/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
The purpose of our study is to understand the impact of a partial dynamin-related protein 1 (Drp1) on cognitive behavior, mitophagy, autophagy and mitochondrial and synaptic activities in transgenic Tau mice in Alzheimer's disease (AD). Our laboratory reported increased levels of amyloid-beta (Aβ) and phosphorylated Tau (P-Tau) and reported that abnormal interactions between Aβ and Drp1, P-Tau and Drp1 induced increased mitochondrial fragmentation and reduced fusion and synaptic activities in AD. These abnormal interactions result in the proliferation of dysfunctional mitochondria in AD neurons. Recent research on mitochondria revealed that fission protein Drp1 is largely implicated in mitochondrial dynamics in AD. To determine the impact of reduced Drp1 in AD, we recently crossed transgenic Tau mice with Drp1 heterozygote knockout (Drp1+/-) mice and generated double mutant (P301LDrp1+/-) mice. In the current study, we assessed the cognitive behavior, mRNA and protein levels of mitophagy, autophagy, mitochondrial biogenesis, dynamics and synaptic genes, mitochondrial morphology and mitochondrial function and dendritic spines in Tau mice relative to double mutant mice. When compared with Tau mice, double mutant mice did better on the Morris Maze (reduced latency to find hidden platform, increased swimming speed and time spent on quadrant) and rotarod (stayed a longer period of time) tests. Both mRNA- and protein-level autophagy, mitophagy, mitochondrial biogenesis and synaptic proteins were increased in double mutant mice compared with Tau (P301L) mice. Dendritic spines were significantly increased; mitochondrial number was reduced and length was increased in double mutant mice. Based on these observations, we conclude that reduced Drp1 is beneficial in a symptomatic-transgenic Tau (P301L) mice.
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Affiliation(s)
- Ramesh Kandimalla
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad, Telangana 50000, India
| | - Maria Manczak
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Hallie Morton
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- To whom correspondence should be addressed at: Department of Internal Medicine, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA. Tel: +1 8067433194;
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21
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Trumpff C, Owusu-Ansah E, Klein HU, Lee AJ, Petyuk V, Wingo TS, Wingo AP, Thambisetty M, Ferrucci L, Seyfried NT, Bennett DA, De Jager PL, Picard M. Mitochondrial respiratory chain protein co-regulation in the human brain. Heliyon 2022; 8:e09353. [PMID: 35600441 PMCID: PMC9118667 DOI: 10.1016/j.heliyon.2022.e09353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/12/2022] [Accepted: 04/27/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial respiratory chain (RC) function requires the stoichiometric interaction among dozens of proteins but their co-regulation has not been defined in the human brain. Here, using quantitative proteomics across three independent cohorts we systematically characterized the co-regulation patterns of mitochondrial RC proteins in the human dorsolateral prefrontal cortex (DLPFC). Whereas the abundance of RC protein subunits that physically assemble into stable complexes were correlated, indicating their co-regulation, RC assembly factors exhibited modest co-regulation. Within complex I, nuclear DNA-encoded subunits exhibited >2.5-times higher co-regulation than mitochondrial (mt)DNA-encoded subunits. Moreover, mtDNA copy number was unrelated to mtDNA-encoded subunits abundance, suggesting that mtDNA content is not limiting. Alzheimer's disease (AD) brains exhibited reduced abundance of complex I RC subunits, an effect largely driven by a 2-4% overall lower mitochondrial protein content. These findings provide foundational knowledge to identify molecular mechanisms contributing to age- and disease-related erosion of mitochondrial function in the human brain.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, USA
| | - Annie J. Lee
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, USA
| | - Vladislav Petyuk
- Pacific Northwest National Laboratory, Richland, Washington State, USA
| | - Thomas S. Wingo
- Departments of Neurology and Human Genetics, Emory University, Atlanta, GA, USA
| | - Aliza P. Wingo
- Atlanta VA Medical Center, Decatur, GA, USA
- Department of Psychiatry, Emory University, Atlanta, GA, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging Intramural Research Program, Baltimore, USA
| | - Luigi Ferrucci
- Longitudinal Study Section, National Institute on Aging, Baltimore, USA
| | | | - David A. Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
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22
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Patel T, Carnwath TP, Wang X, Allen M, Lincoln SJ, Lewis‐Tuffin L, Quicksall ZS, Lin S, Tutor‐New FQ, Ho CC, Min Y, Malphrus KG, Nguyen TT, Martin E, Garcia CA, Alkharboosh RM, Grewal S, Chaichana K, Wharen R, Guerrero‐Cazares H, Quinones‐Hinojosa A, Ertekin‐Taner N. Transcriptional landscape of human microglia implicates age, sex, and APOE-related immunometabolic pathway perturbations. Aging Cell 2022; 21:e13606. [PMID: 35388616 PMCID: PMC9124307 DOI: 10.1111/acel.13606] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
Microglia have fundamental roles in health and disease; however, effects of age, sex, and genetic factors on human microglia have not been fully explored. We applied bulk and single-cell approaches to comprehensively characterize human microglia transcriptomes and their associations with age, sex, and APOE. We identified a novel microglial signature, characterized its expression in bulk tissue and single-cell microglia transcriptomes. We discovered microglial co-expression network modules associated with age, sex, and APOE-ε4 that are enriched for lipid and carbohydrate metabolism genes. Integrated analyses of modules with single-cell transcriptomes revealed significant overlap between age-associated module genes and both pro-inflammatory and disease-associated microglial clusters. These modules and clusters harbor known neurodegenerative disease genes including APOE, PLCG2, and BIN1. Meta-analyses with published bulk and single-cell microglial datasets further supported our findings. Thus, these data represent a well-characterized human microglial transcriptome resource and highlight age, sex, and APOE-related microglial immunometabolism perturbations with potential relevance in neurodegeneration.
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Affiliation(s)
- Tulsi Patel
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | - Xue Wang
- Department of Quantitative Health SciencesMayo ClinicJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | - Shu Lin
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Yuhao Min
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | - Thuy T. Nguyen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Rawan M. Alkharboosh
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
- Neuroscience Graduate ProgramMayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMinnesotaUSA
- Regenerative Sciences Training ProgramCenter for Regenerative MedicineMayo ClinicRochesterMinnesotaUSA
| | - Sanjeet Grewal
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
| | | | - Robert Wharen
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Department of NeurologyMayo ClinicJacksonvilleFloridaUSA
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23
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Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
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24
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Wang Q, Chen K, Su Y, Reiman EM, Dudley JT, Readhead B. Deep learning-based brain transcriptomic signatures associated with the neuropathological and clinical severity of Alzheimer's disease. Brain Commun 2022; 4:fcab293. [PMID: 34993477 PMCID: PMC8728025 DOI: 10.1093/braincomms/fcab293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/20/2023] Open
Abstract
Brain tissue gene expression from donors with and without Alzheimer's disease has been used to help inform the molecular changes associated with the development and potential treatment of this disorder. Here, we use a deep learning method to analyse RNA-seq data from 1114 brain donors from the Accelerating Medicines Project for Alzheimer's Disease consortium to characterize post-mortem brain transcriptome signatures associated with amyloid-β plaque, tau neurofibrillary tangles and clinical severity in multiple Alzheimer's disease dementia populations. Starting from the cross-sectional data in the Religious Orders Study and Memory and Aging Project cohort (n = 634), a deep learning framework was built to obtain a trajectory that mirrors Alzheimer's disease progression. A severity index was defined to quantitatively measure the progression based on the trajectory. Network analysis was then carried out to identify key gene (index gene) modules present in the model underlying the progression. Within this data set, severity indexes were found to be very closely correlated with all Alzheimer's disease neuropathology biomarkers (R ∼ 0.5, P < 1e-11) and global cognitive function (R = -0.68, P < 2.2e-16). We then applied the model to additional transcriptomic data sets from different brain regions (MAYO, n = 266; Mount Sinai Brain Bank, n = 214), and observed that the model remained significantly predictive (P < 1e-3) of neuropathology and clinical severity. The index genes that significantly contributed to the model were integrated with Alzheimer's disease co-expression regulatory networks, resolving four discrete gene modules that are implicated in vascular and metabolic dysfunction in different cell types, respectively. Our work demonstrates the generalizability of this signature to frontal and temporal cortex measurements and additional brain donors with Alzheimer's disease, other age-related neurological disorders and controls, and revealed that the transcriptomic network modules contribute to neuropathological and clinical disease severity. This study illustrates the promise of using deep learning methods to analyse heterogeneous omics data and discover potentially targetable molecular networks that can inform the development, treatment and prevention of neurodegenerative diseases like Alzheimer's disease.
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Affiliation(s)
- Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
| | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ 85006, USA
| | - Yi Su
- Banner Alzheimer's Institute, Phoenix, AZ 85006, USA
| | - Eric M Reiman
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA.,Banner Alzheimer's Institute, Phoenix, AZ 85006, USA
| | - Joel T Dudley
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA.,Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
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25
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Teng IT, Nazzari AF, Choe M, Liu T, Oliveira de Souza M, Petrova Y, Tsybovsky Y, Wang S, Zhang B, Artamonov M, Madan B, Huang A, Lopez Acevedo SN, Pan X, Ruckwardt TJ, DeKosky BJ, Mascola JR, Misasi J, Sullivan NJ, Zhou T, Kwong PD. Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.29.474491. [PMID: 35018379 DOI: 10.1101/2021.01.18.426999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Since the outbreak of the COVID-19 pandemic, widespread infections have allowed SARS-CoV-2 to evolve in human, leading to the emergence of multiple circulating variants. Some of these variants show increased resistance to vaccines, convalescent plasma, or monoclonal antibodies. In particular, mutations in the SARS-CoV-2 spike have drawn attention. To facilitate the isolation of neutralizing antibodies and the monitoring the vaccine effectiveness against these variants, we designed and produced biotin-labeled molecular probes of variant SARS-CoV-2 spikes and their subdomains, using a structure-based construct design that incorporated an N-terminal purification tag, a specific amino acid sequence for protease cleavage, the variant spike-based region of interest, and a C-terminal sequence targeted by biotin ligase. These probes could be produced by a single step using in-process biotinylation and purification. We characterized the physical properties and antigenicity of these probes, comprising the N-terminal domain (NTD), the receptor-binding domain (RBD), the RBD and subdomain 1 (RBD-SD1), and the prefusion-stabilized spike ectodomain (S2P) with sequences from SARS-CoV-2 variants of concern or of interest, including variants Alpha, Beta, Gamma, Epsilon, Iota, Kappa, Delta, Lambda, Mu, and Omicron. We functionally validated probes by using yeast expressing a panel of nine SARS-CoV-2 spike-binding antibodies and confirmed sorting capabilities of variant probes using yeast displaying libraries of plasma antibodies from COVID-19 convalescent donors. We deposited these constructs to Addgene to enable their dissemination. Overall, this study describes a matrix of SARS-CoV-2 variant molecular probes that allow for assessment of immune responses, identification of serum antibody specificity, and isolation and characterization of neutralizing antibodies.
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Affiliation(s)
- I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Alexandra F Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, United States of America
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Yuliya Petrova
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Mykhaylo Artamonov
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, United States of America
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Aric Huang
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, United States of America
| | - Sheila N Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, United States of America
| | - Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, United States of America
| | - Tracy J Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, United States of America
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Department of Chemical Engineering, The University of Kansas, Lawrence, Kansas, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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26
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Pottier C, Mateiu L, Baker MC, DeJesus-Hernandez M, Teixeira Vicente C, Finch NA, Tian S, van Blitterswijk M, Murray ME, Ren Y, Petrucelli L, Oskarsson B, Biernacka JM, Graff-Radford NR, Boeve BF, Petersen RC, Josephs KA, Asmann YW, Dickson DW, Rademakers R. Shared brain transcriptomic signature in TDP-43 type A FTLD patients with or without GRN mutations. Brain 2021; 145:2472-2485. [PMID: 34918030 PMCID: PMC9337811 DOI: 10.1093/brain/awab437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/24/2021] [Accepted: 10/24/2021] [Indexed: 11/28/2022] Open
Abstract
Frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) is a complex heterogeneous neurodegenerative disorder for which mechanisms are poorly understood. To explore transcriptional changes underlying FTLD-TDP, we performed RNA-sequencing on 66 genetically unexplained FTLD-TDP patients, 24 FTLD-TDP patients with GRN mutations and 24 control participants. Using principal component analysis, hierarchical clustering, differential expression and coexpression network analyses, we showed that GRN mutation carriers and FTLD-TDP-A patients without a known mutation shared a common transcriptional signature that is independent of GRN loss-of-function. After combining both groups, differential expression as compared to the control group and coexpression analyses revealed alteration of processes related to immune response, synaptic transmission, RNA metabolism, angiogenesis and vesicle-mediated transport. Deconvolution of the data highlighted strong cellular alterations that were similar in FTLD-TDP-A and GRN mutation carriers with NSF as a potentially important player in both groups. We propose several potentially druggable pathways such as the GABAergic, GDNF and sphingolipid pathways. Our findings underline new disease mechanisms and strongly suggest that affected pathways in GRN mutation carriers extend beyond GRN and contribute to genetically unexplained forms of FTLD-TDP-A.
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Affiliation(s)
- Cyril Pottier
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ligia Mateiu
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Cristina Teixeira Vicente
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | - Yingxue Ren
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Joanna M Biernacka
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Yan W Asmann
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Rosa Rademakers
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
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27
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Wang X, Allen M, İş Ö, Reddy JS, Tutor-New FQ, Castanedes Casey M, Carrasquillo MM, Oatman SR, Min Y, Asmann YW, Funk C, Nguyen T, Ho CC, Malphrus KG, Seyfried NT, Levey AI, Younkin SG, Murray ME, Dickson DW, Price ND, Golde TE, Ertekin-Taner N. Alzheimer's disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions. J Clin Invest 2021; 132:149904. [PMID: 34813500 PMCID: PMC8759790 DOI: 10.1172/jci149904] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Vast numbers of differentially expressed genes and perturbed networks have been identified in Alzheimer’s disease (AD), however, neither disease nor brain region specificity of these transcriptome alterations has been explored. Using RNA-Seq data from 231 temporal cortex and 224 cerebellum samples from patients with AD and progressive supranuclear palsy (PSP), a tauopathy, we identified a striking correlation in the directionality and magnitude of gene expression changes between these 2 neurodegenerative proteinopathies. Further, the transcriptomic changes in AD and PSP brains ware highly conserved between the temporal and cerebellar cortices, indicating that highly similar transcriptional changes occur in pathologically affected and grossly less affected, albeit functionally connected, areas of the brain. Shared up- or downregulated genes in AD and PSP are enriched in biological pathways. Many of these genes also have concordant protein changes and evidence of epigenetic control. These conserved transcriptomic alterations of 2 distinct proteinopathies in brain regions with and without significant gross neuropathology have broad implications. AD and other neurodegenerative diseases are likely characterized by common disease or compensatory pathways with widespread perturbations in the whole brain. These findings can be leveraged to develop multifaceted therapies and biomarkers that address these common, complex, and ubiquitous molecular alterations in neurodegenerative diseases.
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Affiliation(s)
- Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, United States of America
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Özkan İş
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, United States of America
| | - Frederick Q Tutor-New
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | | | | | - Stephanie R Oatman
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Yan W Asmann
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, United States of America
| | - Cory Funk
- Systems Biology, Institute of Systems Biology, Seattle, United States of America
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Charlotte Cg Ho
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Kimberly G Malphrus
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory Univeristy, Atlanta, United States of America
| | | | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Nathan D Price
- Systems Biology, Institute for Systems Biology, Seattle, United States of America
| | - Todd E Golde
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, United States of America
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28
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Klein HU, Trumpff C, Yang HS, Lee AJ, Picard M, Bennett DA, De Jager PL. Characterization of mitochondrial DNA quantity and quality in the human aged and Alzheimer's disease brain. Mol Neurodegener 2021; 16:75. [PMID: 34742335 PMCID: PMC8572491 DOI: 10.1186/s13024-021-00495-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mitochondrial dysfunction is a feature of neurodegenerative diseases, including Alzheimer's disease (AD). Changes in the mitochondrial DNA copy number (mtDNAcn) and increased mitochondrial DNA mutation burden have both been associated with neurodegenerative diseases and cognitive decline. This study aims to systematically identify which common brain pathologies in the aged human brain are associated with mitochondrial recalibrations and to disentangle the relationship between these pathologies, mtDNAcn, mtDNA heteroplasmy, aging, neuronal loss, and cognitive function. METHODS Whole-genome sequencing data from n = 1361 human brain samples from 5 different regions were used to quantify mtDNAcn as well as heteroplasmic mtDNA point mutations and small indels. Brain samples were assessed for 10 common pathologies. Annual cognitive test results were used to assess cognitive function proximal to death. For a subset of samples, neuronal proportions were estimated from RNA-seq profiles, and mass spectrometry was used to quantify the mitochondrial protein content of the tissue. RESULTS mtDNAcn was 7-14% lower in AD relative to control participants. When accounting for all 10 common neuropathologies, only tau was significantly associated with lower mtDNAcn in the dorsolateral prefrontal cortex. In the posterior cingulate cortex, TDP-43 pathology demonstrated a distinct association with mtDNAcn. No changes were observed in the cerebellum, which is affected late by pathologies. Neither age nor gender was associated with mtDNAcn in the studied brain regions when adjusting for pathologies. Mitochondrial content and mtDNAcn independently explained variance in cognitive function unaccounted by pathologies, implicating complex mitochondrial recalibrations in cognitive decline. In contrast, mtDNA heteroplasmy levels increased by 1.5% per year of life in the cortical regions, but displayed no association with any of the pathologies or cognitive function. CONCLUSIONS We studied mtDNA quantity and quality in relation to mixed pathologies of aging and showed that tau and not amyloid-β is primarily associated with reduced mtDNAcn. In the posterior cingulate cortex, the association of TDP-43 with low mtDNAcn points to a vulnerability of this region in limbic-predominant age-related TDP-43 encephalopathy. While we found low mtDNAcn in brain regions affected by pathologies, the absence of associations with mtDNA heteroplasmy burden indicates that mtDNA point mutations and small indels are unlikely to be involved in the pathogenesis of late-onset neurodegenerative diseases.
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Affiliation(s)
- Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Caroline Trumpff
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Hyun-Sik Yang
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Annie J. Lee
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Martin Picard
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032 USA
- Merritt Center and Columbia Translational Neuroscience Initiative, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612 USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
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29
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Quinn JP, Kandigian SE, Trombetta BA, Arnold SE, Carlyle BC. VGF as a biomarker and therapeutic target in neurodegenerative and psychiatric diseases. Brain Commun 2021; 3:fcab261. [PMID: 34778762 PMCID: PMC8578498 DOI: 10.1093/braincomms/fcab261] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Neurosecretory protein VGF (non-acronymic) belongs to the granin family of neuropeptides. VGF and VGF-derived peptides have been repeatedly identified in well-powered and well-designed multi-omic studies as dysregulated in neurodegenerative and psychiatric diseases. New therapeutics is urgently needed for these devastating and costly diseases, as are new biomarkers to improve disease diagnosis and mechanistic understanding. From a list of 537 genes involved in Alzheimer's disease pathogenesis, VGF was highlighted by the Accelerating Medicines Partnership in Alzheimer's disease as the potential therapeutic target of greatest interest. VGF levels are consistently decreased in brain tissue and CSF samples from patients with Alzheimer's disease compared to controls, and its levels correlate with disease severity and Alzheimer's disease pathology. In the brain, VGF exists as multiple functional VGF-derived peptides. Full-length human VGF1-615 undergoes proteolytic processing by prohormone convertases and other proteases in the regulated secretory pathway to produce at least 12 active VGF-derived peptides. In cell and animal models, these VGF-derived peptides have been linked to energy balance regulation, neurogenesis, synaptogenesis, learning and memory, and depression-related behaviours throughout development and adulthood. The C-terminal VGF-derived peptides, TLQP-62 (VGF554-615) and TLQP-21 (VGF554-574) have differential effects on Alzheimer's disease pathogenesis, neuronal and microglial activity, and learning and memory. TLQP-62 activates neuronal cell-surface receptors and regulates long-term hippocampal memory formation. TLQP-62 also prevents immune-mediated memory impairment, depression-like and anxiety-like behaviours in mice. TLQP-21 binds to microglial cell-surface receptors, triggering microglial chemotaxis and phagocytosis. These actions were reported to reduce amyloid-β plaques and decrease neuritic dystrophy in a transgenic mouse model of familial Alzheimer's disease. Expression differences of VGF-derived peptides have also been associated with frontotemporal lobar dementias, amyotrophic lateral sclerosis, Lewy body diseases, Huntington's disease, pain, schizophrenia, bipolar disorder, depression and antidepressant response. This review summarizes current knowledge and highlights questions for future investigation regarding the roles of VGF and its dysregulation in neurodegenerative and psychiatric disease. Finally, the potential of VGF and VGF-derived peptides as biomarkers and novel therapeutic targets for neurodegenerative and psychiatric diseases is highlighted.
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Affiliation(s)
- James P Quinn
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Savannah E Kandigian
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Bianca A Trombetta
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven E Arnold
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Becky C Carlyle
- Department of Neurology, Alzheimer's Clinical & Translational Research Unit, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
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30
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Serrano-Pozo A, Li Z, Noori A, Nguyen HN, Mezlini A, Li L, Hudry E, Jackson RJ, Hyman BT, Das S. Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer's disease. NATURE AGING 2021; 1:919-931. [PMID: 36199750 PMCID: PMC9531903 DOI: 10.1038/s43587-021-00123-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 09/03/2021] [Indexed: 05/02/2023]
Abstract
The roles of APOEε4 and APOEε2-the strongest genetic risk and protective factors for Alzheimer's disease-in glial responses remain elusive. We tested the hypothesis that APOE alleles differentially impact glial responses by investigating their effects on the glial transcriptome from elderly control brains with no neuritic amyloid plaques. We identified a cluster of microglial genes that are upregulated in APOEε4 and downregulated in APOEε2 carriers relative to APOEε3 homozygotes. This microglia-APOE cluster is enriched in phagocytosis-including TREM2 and TYROBP-and proinflammatory genes, and is also detectable in brains with frequent neuritic plaques. Next, we tested these findings in APOE knock-in mice exposed to acute (lipopolysaccharide challenge) and chronic (cerebral β-amyloidosis) insults and found that these mice partially recapitulate human APOE-linked expression patterns. Thus, the APOEε4 allele might prime microglia towards a phagocytic and proinflammatory state through an APOE-TREM2-TYROBP axis in normal aging as well as in Alzheimer's disease.
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Affiliation(s)
- Alberto Serrano-Pozo
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Zhaozhi Li
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
| | - Ayush Noori
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
| | - Huong N. Nguyen
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Aziz Mezlini
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Liang Li
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Eloise Hudry
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Rosemary J. Jackson
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bradley T. Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
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31
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Li H, Funk CC, McFarland K, Dammer EB, Allen M, Carrasquillo MM, Levites Y, Chakrabarty P, Burgess JD, Wang X, Dickson D, Seyfried NT, Duong DM, Lah JJ, Younkin SG, Levey AI, Omenn GS, Ertekin‐Taner N, Golde TE, Price ND. Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease. Alzheimers Dement 2021; 17:984-1004. [PMID: 33480174 PMCID: PMC8248162 DOI: 10.1002/alz.12254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 10/08/2020] [Accepted: 10/17/2020] [Indexed: 12/21/2022]
Abstract
Intron retention (IR) has been implicated in the pathogenesis of complex diseases such as cancers; its association with Alzheimer's disease (AD) remains unexplored. We performed genome-wide analysis of IR through integrating genetic, transcriptomic, and proteomic data of AD subjects and mouse models from the Accelerating Medicines Partnership-Alzheimer's Disease project. We identified 4535 and 4086 IR events in 2173 human and 1736 mouse genes, respectively. Quantitation of IR enabled the identification of differentially expressed genes that conventional exon-level approaches did not reveal. There were significant correlations of intron expression within innate immune genes, like HMBOX1, with AD in humans. Peptides with a high probability of translation from intron-retained mRNAs were identified using mass spectrometry. Further, we established AD-specific intron expression Quantitative Trait Loci, and identified splicing-related genes that may regulate IR. Our analysis provides a novel resource for the search for new AD biomarkers and pathological mechanisms.
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Affiliation(s)
- Hong‐Dong Li
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangshaHunanP.R. China
- Institute for Systems BiologySeattleWashingtonUSA
| | - Cory C. Funk
- Institute for Systems BiologySeattleWashingtonUSA
| | - Karen McFarland
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Eric B. Dammer
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
| | - Mariet Allen
- Mayo ClinicDepartment ofNeuroscienceJacksonvilleFloridaUSA
| | | | - Yona Levites
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Paramita Chakrabarty
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | | | - Xue Wang
- Mayo ClinicDepartment of Health Sciences ResearchJacksonvilleFloridaUSA
| | - Dennis Dickson
- Mayo ClinicDepartment ofNeuroscienceJacksonvilleFloridaUSA
| | - Nicholas T. Seyfried
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
- Department of NeurologyEmory UniversityAtlantaGeorgiaUSA
| | - Duc M. Duong
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
| | - James J. Lah
- Department of NeurologyEmory UniversityAtlantaGeorgiaUSA
| | | | - Allan I. Levey
- Department of NeurologyEmory UniversityAtlantaGeorgiaUSA
| | - Gilbert S. Omenn
- Institute for Systems BiologySeattleWashingtonUSA
- Department of Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Nilüfer Ertekin‐Taner
- Mayo ClinicDepartment ofNeuroscienceJacksonvilleFloridaUSA
- Mayo ClinicDepartment of NeurologyJacksonvilleFloridaUSA
| | - Todd E. Golde
- Department of Neuroscience and NeurologyCenter for Translational Research in Neurodegenerative diseaseand McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
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32
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Ginsberg SD, Neubert TA, Sharma S, Digwal CS, Yan P, Timbus C, Wang T, Chiosis G. Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease. FEBS J 2021; 289:2047-2066. [PMID: 34028172 DOI: 10.1111/febs.16031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022]
Abstract
The increasingly appreciated prevalence of complicated stressor-to-phenotype associations in human disease requires a greater understanding of how specific stressors affect systems or interactome properties. Many currently untreatable diseases arise due to variations in, and through a combination of, multiple stressors of genetic, epigenetic, and environmental nature. Unfortunately, how such stressors lead to a specific disease phenotype or inflict a vulnerability to some cells and tissues but not others remains largely unknown and unsatisfactorily addressed. Analysis of cell- and tissue-specific interactome networks may shed light on organization of biological systems and subsequently to disease vulnerabilities. However, deriving human interactomes across different cell and disease contexts remains a challenge. To this end, this opinion article links stressor-induced protein interactome network perturbations to the formation of pathologic scaffolds termed epichaperomes, revealing a viable and reproducible experimental solution to obtaining rigorous context-dependent interactomes. This article presents our views on how a specialized 'omics platform called epichaperomics may complement and enhance the currently available conventional approaches and aid the scientific community in defining, understanding, and ultimately controlling interactome networks of complex diseases such as Alzheimer's disease. Ultimately, this approach may aid the transition from a limited single-alteration perspective in disease to a comprehensive network-based mindset, which we posit will result in precision medicine paradigms for disease diagnosis and treatment.
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Affiliation(s)
- Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, USA.,Departments of Psychiatry, Neuroscience & Physiology, The NYU Neuroscience Institute, New York University Grossman School of Medicine, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, USA
| | - Sahil Sharma
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Chander S Digwal
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Pengrong Yan
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Calin Timbus
- Department of Mathematics, Technical University of Cluj-Napoca, CJ, Romania
| | - Tai Wang
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA.,Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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33
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Zhao X, Yao H, Li X. Unearthing of Key Genes Driving the Pathogenesis of Alzheimer's Disease via Bioinformatics. Front Genet 2021; 12:641100. [PMID: 33936168 PMCID: PMC8085575 DOI: 10.3389/fgene.2021.641100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/15/2021] [Indexed: 01/23/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease with unelucidated molecular pathogenesis. Herein, we aimed to identify potential hub genes governing the pathogenesis of AD. The AD datasets of GSE118553 and GSE131617 were collected from the NCBI GEO database. The weighted gene coexpression network analysis (WGCNA), differential gene expression analysis, and functional enrichment analysis were performed to reveal the hub genes and verify their role in AD. Hub genes were validated by machine learning algorithms. We identified modules and their corresponding hub genes from the temporal cortex (TC), frontal cortex (FC), entorhinal cortex (EC), and cerebellum (CE). We obtained 33, 42, 42, and 41 hub genes in modules associated with AD in TC, FC, EC, and CE tissues, respectively. Significant differences were recorded in the expression levels of hub genes between AD and the control group in the TC and EC tissues (P < 0.05). The differences in the expressions of FCGRT, SLC1A3, PTN, PTPRZ1, and PON2 in the FC and CE tissues among the AD and control groups were significant (P < 0.05). The expression levels of PLXNB1, GRAMD3, and GJA1 were statistically significant between the Braak NFT stages of AD. Overall, our study uncovered genes that may be involved in AD pathogenesis and revealed their potential for the development of AD biomarkers and appropriate AD therapeutics targets.
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Affiliation(s)
- Xingxing Zhao
- Department of Neurology, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China.,Department of Cardiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongmei Yao
- Department of Cardiology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinyi Li
- Department of Neurology, Bethune Hospital Affiliated to Shanxi Medical University, Taiyuan, China
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34
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De Jager PL. Deconstructing the epigenomic architecture of human neurodegeneration. Neurobiol Dis 2021; 153:105331. [PMID: 33711493 DOI: 10.1016/j.nbd.2021.105331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022] Open
Abstract
The past 10 years have seen a rapid advance in our ability to profile the epigenome from human pathologic material, opening up new study designs to investigate the role of epigenomic features in human disease. Moderate to large scale studies have now been conducted in the target tissue of neurodegenerative diseases, the brain, and, through the use of rigorous statistical methodologies, have laid a foundation of validated observations and successful study designs that inform our perspective on the role of the epigenome in these diseases, generate new hypotheses, and guide our path forward for a second generation of studies. It is clear that sampling the epigenome is not redundant with other "omic" profiling of the same tissue and that it can serve as an important vehicle for the integration of the effect of multiple environmental exposures on risk of disease. In some cases, change in the epigenome may thus have a causal impact on disease, but we now have evidence that such changes may also mediate some of the effect of tau proteinopathy and that other changes may moderate the impact of genetic risk factors. Thus, the epigenome may be involved at multiple different stages of the sequence of events that leads to human neurodegeneration, and we review the study designs that may begin to guide the development of a more comprehensive perspective on the aging brain's epigenome.
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Affiliation(s)
- Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, United States of America; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States of America; Department of Neurology, Columbia University Medical Center, New York, NY, United States of America.
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35
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Lau SF, Cao H, Fu AKY, Ip NY. Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer's disease. Proc Natl Acad Sci U S A 2020; 117:25800-25809. [PMID: 32989152 PMCID: PMC7568283 DOI: 10.1073/pnas.2008762117] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia but has no effective treatment. A comprehensive investigation of cell type-specific responses and cellular heterogeneity in AD is required to provide precise molecular and cellular targets for therapeutic development. Accordingly, we perform single-nucleus transcriptome analysis of 169,496 nuclei from the prefrontal cortical samples of AD patients and normal control (NC) subjects. Differential analysis shows that the cell type-specific transcriptomic changes in AD are associated with the disruption of biological processes including angiogenesis, immune activation, synaptic signaling, and myelination. Subcluster analysis reveals that compared to NC brains, AD brains contain fewer neuroprotective astrocytes and oligodendrocytes. Importantly, our findings show that a subpopulation of angiogenic endothelial cells is induced in the brain in patients with AD. These angiogenic endothelial cells exhibit increased expression of angiogenic growth factors and their receptors (i.e., EGFL7, FLT1, and VWF) and antigen-presentation machinery (i.e., B2M and HLA-E). This suggests that these endothelial cells contribute to angiogenesis and immune response in AD pathogenesis. Thus, our comprehensive molecular profiling of brain samples from patients with AD reveals previously unknown molecular changes as well as cellular targets that potentially underlie the functional dysregulation of endothelial cells, astrocytes, and oligodendrocytes in AD, providing important insights for therapeutic development.
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Affiliation(s)
- Shun-Fat Lau
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Han Cao
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Amy K Y Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, Hong Kong University of Science and Technology Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, 518057 Shenzhen, Guangdong, China
| | - Nancy Y Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China;
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, Hong Kong University of Science and Technology Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, 518057 Shenzhen, Guangdong, China
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36
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Wang X, Allen M, Li S, Quicksall ZS, Patel TA, Carnwath TP, Reddy JS, Carrasquillo MM, Lincoln SJ, Nguyen TT, Malphrus KG, Dickson DW, Crook JE, Asmann YW, Ertekin-Taner N. Correction to: Deciphering cellular transcriptional alterations in Alzheimer's disease brains. Mol Neurodegener 2020; 15:54. [PMID: 32928256 PMCID: PMC7490892 DOI: 10.1186/s13024-020-00403-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA.
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Shaoyu Li
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary S Quicksall
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Troy P Carnwath
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Sarah J Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Thuy T Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA. .,Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA.
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