51
|
Patani R, Hardingham GE, Liddelow SA. Functional roles of reactive astrocytes in neuroinflammation and neurodegeneration. Nat Rev Neurol 2023; 19:395-409. [PMID: 37308616 DOI: 10.1038/s41582-023-00822-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2023] [Indexed: 06/14/2023]
Abstract
Despite advances in uncovering the mechanisms that underlie neuroinflammation and neurodegenerative disease, therapies that prevent neuronal loss remain elusive. Targeting of disease-defining markers in conditions such as Alzheimer disease (amyloid-β and tau) or Parkinson disease (α-synuclein) has been met with limited success, suggesting that these proteins do not act in isolation but form part of a pathological network. This network could involve phenotypic alteration of multiple cell types in the CNS, including astrocytes, which have a major neurosupportive, homeostatic role in the healthy CNS but adopt reactive states under acute or chronic adverse conditions. Transcriptomic studies in human patients and disease models have revealed the co-existence of many putative reactive sub-states of astrocytes. Inter-disease and even intra-disease heterogeneity of reactive astrocytic sub-states are well established, but the extent to which specific sub-states are shared across different diseases is unclear. In this Review, we highlight how single-cell and single-nuclei RNA sequencing and other 'omics' technologies can enable the functional characterization of defined reactive astrocyte states in various pathological scenarios. We provide an integrated perspective, advocating cross-modal validation of key findings to define functionally important sub-states of astrocytes and their triggers as tractable therapeutic targets with cross-disease relevance.
Collapse
Affiliation(s)
- Rickie Patani
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, Human Stem Cells and Neurodegeneration Laboratory, London, UK
| | - Giles E Hardingham
- Euan MacDonald Centre for MND, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute at the University of Edinburgh, University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Neuroscience & Physiology, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA.
| |
Collapse
|
52
|
Kübler R, Ormel PR, Sommer IEC, Kahn RS, de Witte LD. Gene expression profiling of monocytes in recent-onset schizophrenia. Brain Behav Immun 2023; 111:334-342. [PMID: 37149105 DOI: 10.1016/j.bbi.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023] Open
Abstract
Immune-related mechanisms have been suggested to be involved in schizophrenia. Various studies have shown changes in monocytes isolated from the blood of schizophrenia patients, including changes in monocyte numbers, as well as altered protein and transcript levels of important markers. However, validation of these findings and understanding how these results are related to immune-related changes in the brain and schizophrenia genetic risk factors, is limited. The goal of this study was to better understand changes observed in monocytes of patients with early-onset schizophrenia. Using RNA sequencing, we analyzed gene expression profiles of monocytes isolated from twenty patients with early-onset schizophrenia and seventeen healthy controls. We validated expression changes of 7 out of 29 genes that were differentially expressed in previous studies including TNFAIP3, DUSP2, and IL6. At a transcriptome-wide level, we found 99 differentially expressed genes. Effect sizes of differentially expressed genes were moderately correlated with differential expression in brain tissue (Pearson's r = 0.49). Upregulated genes were enriched for genes in NF-κB and LPS signaling pathways. Downregulated genes were enriched for glucocorticoid response pathways. These pathways have been implicated in schizophrenia before and play a role in regulating the activation of myeloid cells. Interestingly, they are also involved in several non-inflammatory processes in the central nervous system, such as neurogenesis and neurotransmission. Future studies are needed to better understand how dysregulation of the NF-κB and glucocorticoid pathways affects inflammatory and non-inflammatory processes in schizophrenia. The fact that dysregulation of these pathways is also seen in brain tissue, provides potential possibilities for biomarker development.
Collapse
Affiliation(s)
- Raphael Kübler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul R Ormel
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Iris E C Sommer
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; Department of Neuroscience, University Medical Center Groningen, Groningen, the Netherlands
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands.
| |
Collapse
|
53
|
Kim JH, Afridi R, Lee WH, Suk K. Analyzing the glial proteome in Alzheimer's disease. Expert Rev Proteomics 2023; 20:197-209. [PMID: 37724426 DOI: 10.1080/14789450.2023.2260955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence indicates that dysfunction of glial cells, including astrocytes, microglia, and oligodendrocytes, may contribute to the development and progression of AD. Large-scale analysis of glial proteins sheds light on their roles in cellular processes and diseases. In AD, glial proteomics has been utilized to understand glia-based pathophysiology and identify potential biomarkers and therapeutic targets. AREA COVERED In this review, we provide an updated overview of proteomic analysis of glia in the context of AD. Additionally, we discuss current challenges in the field, involving glial complexity and heterogeneity, and describe some cutting-edge proteomic technologies to address them. EXPERT OPINION Unbiased comprehensive analysis of glial proteomes aids our understanding of the molecular and cellular mechanisms of AD pathogenesis. These investigations highlight the crucial role of glial cells and provide novel insights into the mechanisms of AD pathology. A deeper understanding of the AD-related glial proteome could offer a repertoire of potential biomarkers and therapeutics. Further technical advancement of glial proteomics will enable us to identify proteins within individual cells and specific cell types, thus significantly enhancing our comprehension of AD pathogenesis.
Collapse
Affiliation(s)
- Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
54
|
Lambert JC, Ramirez A, Grenier-Boley B, Bellenguez C. Step by step: towards a better understanding of the genetic architecture of Alzheimer's disease. Mol Psychiatry 2023; 28:2716-2727. [PMID: 37131074 PMCID: PMC10615767 DOI: 10.1038/s41380-023-02076-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023]
Abstract
Alzheimer's disease (AD) is considered to have a large genetic component. Our knowledge of this component has progressed over the last 10 years, thanks notably to the advent of genome-wide association studies and the establishment of large consortia that make it possible to analyze hundreds of thousands of cases and controls. The characterization of dozens of chromosomal regions associated with the risk of developing AD and (in some loci) the causal genes responsible for the observed disease signal has confirmed the involvement of major pathophysiological pathways (such as amyloid precursor protein metabolism) and opened up new perspectives (such as the central role of microglia and inflammation). Furthermore, large-scale sequencing projects are starting to reveal the major impact of rare variants - even in genes like APOE - on the AD risk. This increasingly comprehensive knowledge is now being disseminated through translational research; in particular, the development of genetic risk/polygenic risk scores is helping to identify the subpopulations more at risk or less at risk of developing AD. Although it is difficult to assess the efforts still needed to comprehensively characterize the genetic component of AD, several lines of research can be improved or initiated. Ultimately, genetics (in combination with other biomarkers) might help to redefine the boundaries and relationships between various neurodegenerative diseases.
Collapse
Affiliation(s)
- Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Neurodegenerative diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- Department of Psychiatry & Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Benjamin Grenier-Boley
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Céline Bellenguez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| |
Collapse
|
55
|
Cruchaga C, Western D, Timsina J, Wang L, Wang C, Yang C, Ali M, Beric A, Gorijala P, Kohlfeld P, Budde J, Levey A, Morris J, Perrin R, Ruiz A, Marquié M, Boada M, de Rojas I, Rutledge J, Oh H, Wilson E, Guen YL, Alvarez I, Aguilar M, Greicius M, Pastor P, Pulford D, Ibanez L, Wyss-Coray T, Sung YJ, Phillips B. Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and informs causal proteins for Alzheimer's disease. RESEARCH SQUARE 2023:rs.3.rs-2814616. [PMID: 37333337 PMCID: PMC10275048 DOI: 10.21203/rs.3.rs-2814616/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The integration of quantitative trait loci (QTL) with disease genome-wide association studies (GWAS) has proven successful at prioritizing candidate genes at disease-associated loci. QTL mapping has mainly been focused on multi-tissue expression QTL or plasma protein QTL (pQTL). Here we generated the largest-to-date cerebrospinal fluid (CSF) pQTL atlas by analyzing 7,028 proteins in 3,107 samples. We identified 3,373 independent study-wide associations for 1,961 proteins, including 2,448 novel pQTLs of which 1,585 are unique to CSF, demonstrating unique genetic regulation of the CSF proteome. In addition to the established chr6p22.2-21.32 HLA region, we identified pleiotropic regions on chr3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron-specificity and neurological development. We also integrated this pQTL atlas with the latest Alzheimer's disease (AD) GWAS through PWAS, colocalization and Mendelian Randomization and identified 42 putative causal proteins for AD, 15 of which have drugs available. Finally, we developed a proteomics-based risk score for AD that outperforms genetics-based polygenic risk scores. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.
Collapse
Affiliation(s)
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Washington University School of Medicine
| | | | | | | | | | | | - Patsy Kohlfeld
- Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | | | | | | | - Mercè Boada
- Memory Clinic of Fundaciò ACE, Catalan Institute of Applied Neurosciences
| | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca Mútua Terrassa, Terrassa, Barcelona, Spain
| | | | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
| | | | | | | | | | | |
Collapse
|
56
|
Nott A, Holtman IR. Genetic insights into immune mechanisms of Alzheimer's and Parkinson's disease. Front Immunol 2023; 14:1168539. [PMID: 37359515 PMCID: PMC10285485 DOI: 10.3389/fimmu.2023.1168539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 06/28/2023] Open
Abstract
Microglia, the macrophages of the brain, are vital for brain homeostasis and have been implicated in a broad range of brain disorders. Neuroinflammation has gained traction as a possible therapeutic target for neurodegeneration, however, the precise function of microglia in specific neurodegenerative disorders is an ongoing area of research. Genetic studies offer valuable insights into understanding causality, rather than merely observing a correlation. Genome-wide association studies (GWAS) have identified many genetic loci that are linked to susceptibility to neurodegenerative disorders. (Post)-GWAS studies have determined that microglia likely play an important role in the development of Alzheimer's disease (AD) and Parkinson's disease (PD). The process of understanding how individual GWAS risk loci affect microglia function and mediate susceptibility is complex. A rapidly growing number of publications with genomic datasets and computational tools have formulated new hypotheses that guide the biological interpretation of AD and PD genetic risk. In this review, we discuss the key concepts and challenges in the post-GWAS interpretation of AD and PD GWAS risk alleles. Post-GWAS challenges include the identification of target cell (sub)type(s), causal variants, and target genes. Crucially, the prediction of GWAS-identified disease-risk cell types, variants and genes require validation and functional testing to understand the biological consequences within the pathology of the disorders. Many AD and PD risk genes are highly pleiotropic and perform multiple important functions that might not be equally relevant for the mechanisms by which GWAS risk alleles exert their effect(s). Ultimately, many GWAS risk alleles exert their effect by changing microglia function, thereby altering the pathophysiology of these disorders, and hence, we believe that modelling this context is crucial for a deepened understanding of these disorders.
Collapse
Affiliation(s)
- Alexi Nott
- Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Inge R. Holtman
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| |
Collapse
|
57
|
Gazestani V, Kamath T, Nadaf NM, Burris SJ, Rooney B, Junkkari A, Vanderburg C, Rauramaa T, Therrien M, Tegtmeyer M, Herukka SK, Abdulraouf A, Marsh S, Malm T, Hiltunen M, Nehme R, Stevens B, Leinonen V, Macosko EZ. Early Alzheimer's disease pathology in human cortex is associated with a transient phase of distinct cell states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.03.543569. [PMID: 37333365 PMCID: PMC10274680 DOI: 10.1101/2023.06.03.543569] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Cellular perturbations underlying Alzheimer's disease are primarily studied in human postmortem samples and model organisms. Here we generated a single-nucleus atlas from a rare cohort of cortical biopsies from living individuals with varying degrees of Alzheimer's disease pathology. We next performed a systematic cross-disease and cross-species integrative analysis to identify a set of cell states that are specific to early AD pathology. These changes-which we refer to as the Early Cortical Amyloid Response-were prominent in neurons, wherein we identified a transient state of hyperactivity preceding loss of excitatory neurons, which correlated with the selective loss of layer 1 inhibitory neurons. Microglia overexpressing neuroinflammatory-related processes also expanded as AD pathological burden increased. Lastly, both oligodendrocytes and pyramidal neurons upregulated genes associated with amyloid beta production and processing during this early hyperactive phase. Our integrative analysis provides an organizing framework for targeting circuit dysfunction, neuroinflammation, and amyloid production early in AD pathogenesis.
Collapse
Affiliation(s)
| | - Tushar Kamath
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Harvard Graduate Program in Biophysics and Harvard/MIT MD-PhD Program, Harvard University, Cambridge, MA 02139 USA
| | - Naeem M. Nadaf
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - SJ Burris
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Brendan Rooney
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115 USA
| | - Antti Junkkari
- Institute of Clinical Medicine, Unit of Pathology, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
| | | | - Tuomas Rauramaa
- Institute of Clinical Medicine, Unit of Pathology, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Pathology, Kuopio University Hospital, Kuopio, Finland
| | | | | | - Sanna-Kaisa Herukka
- Institute of Clinical Medicine, Unit of Pathology, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | - Samuel Marsh
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115 USA
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ralda Nehme
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115 USA
- Howard Hughes Medical Institute (HHMI), Boston, MA 02115 USA
| | - Ville Leinonen
- Institute of Clinical Medicine, Unit of Pathology, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Neurosurgery, Kuopio University Hospital, Kuopio, Finland
| | - Evan Z. Macosko
- Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA 02114 USA
| |
Collapse
|
58
|
Arutyunov A, Klein RS. Microglia at the scene of the crime: what their transcriptomics reveal about brain health. Curr Opin Neurol 2023; 36:207-213. [PMID: 37078646 PMCID: PMC10867866 DOI: 10.1097/wco.0000000000001151] [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: 04/21/2023]
Abstract
PURPOSE OF REVIEW Microglia, which arise from primitive myeloid precursors that enter the central nervous system (CNS) during early development, are the first responders to any perturbance of homeostasis. Although their activation has become synonymous with neurologic disease, it remains unclear whether microglial responses are the cause of or response to neuropathology. Here, we review new insights in the roles of microglia during CNS health and disease, including preclinical studies that transcriptionally profile microglia to define their functional states. RECENT FINDINGS Converging evidence suggests that innate immune activation of microglia is associated with overlapping alterations in their gene expression profiles regardless of the trigger. Thus, recent studies examining neuroprotective microglial responses during infections and aging mirror those observed during chronic neurologic diseases, including neurodegeneration and stroke. Many of these insights derive from studies of microglial transcriptomes and function in preclinical models, some of which have been validated in human samples. During immune activation, microglia dismantle their homeostatic functions and transition into subsets capable of antigen presentation, phagocytosis of debris, and management of lipid homeostasis. These subsets can be identified during both normal and aberrant microglial responses, the latter of which may persist long-term. The loss of neuroprotective microglia, which maintain a variety of essential CNS functions, may therefore, in part, underlie the development of neurodegenerative diseases. SUMMARY Microglia exhibit a high level of plasticity, transforming into numerous subsets as they respond to innate immune triggers. Chronic loss of microglial homeostatic functions may underlie the development of diseases with pathological forgetting.
Collapse
Affiliation(s)
- Artem Arutyunov
- Center for Neuroimmunology & Neuroinfectious Diseases
- Departments of Medicine
| | - Robyn S. Klein
- Center for Neuroimmunology & Neuroinfectious Diseases
- Departments of Medicine
- Departments of Pathology & Immunology
- Departments of Neurosciences
| |
Collapse
|
59
|
Sun Y, Che J, Zhang J. Emerging non-proinflammatory roles of microglia in healthy and diseased brains. Brain Res Bull 2023; 199:110664. [PMID: 37192719 DOI: 10.1016/j.brainresbull.2023.110664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/04/2023] [Accepted: 05/13/2023] [Indexed: 05/18/2023]
Abstract
Microglia, the resident myeloid cells of the central nervous system, are the first line of defense against foreign pathogens, thereby confining the extent of brain injury. However, the role of microglia is not limited to macrophage-like functions. In addition to proinflammatory response mediation, microglia are involved in neurodevelopmental remodeling and homeostatic maintenance in the absence of disease. An increasing number of studies have also elucidated microglia-mediated regulation of tumor growth and neural repair in diseased brains. Here, we review the non-proinflammatory roles of microglia, with the aim of promoting a deeper understanding of the functions of microglia in healthy and diseased brains and contributing to the development of novel therapeutics that target microglia in neurological disorders.
Collapse
Affiliation(s)
- Yinying Sun
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, 200032, Shanghai China.
| | - Ji Che
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, 200032, Shanghai China.
| | - Jun Zhang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, 200032, Shanghai China; Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai China.
| |
Collapse
|
60
|
Cai W, Zhang Y, Chang T, Wang Z, Zhu B, Chen Y, Gao X, Xu L, Zhang L, Gao H, Song J, Li J. The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle. J Anim Sci Biotechnol 2023; 14:78. [PMID: 37165455 PMCID: PMC10173583 DOI: 10.1186/s40104-023-00876-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND A detailed understanding of genetic variants that affect beef merit helps maximize the efficiency of breeding for improved production merit in beef cattle. To prioritize the putative variants and genes, we ran a comprehensive genome-wide association studies (GWAS) analysis for 21 agronomic traits using imputed whole-genome variants in Simmental beef cattle. Then, we applied expression quantitative trait loci (eQTL) mapping between the genotype variants and transcriptome of three tissues (longissimus dorsi muscle, backfat, and liver) in 120 cattle. RESULTS We identified 1,580 association signals for 21 beef agronomic traits using GWAS. We then illuminated 854,498 cis-eQTLs for 6,017 genes and 46,970 trans-eQTLs for 1,903 genes in three tissues and built a synergistic network by integrating transcriptomics with agronomic traits. These cis-eQTLs were preferentially close to the transcription start site and enriched in functional regulatory regions. We observed an average of 43.5% improvement in cis-eQTL discovery using multi-tissue eQTL mapping. Fine-mapping analysis revealed that 111, 192, and 194 variants were most likely to be causative to regulate gene expression in backfat, liver, and muscle, respectively. The transcriptome-wide association studies identified 722 genes significantly associated with 11 agronomic traits. Via the colocalization and Mendelian randomization analyses, we found that eQTLs of several genes were associated with the GWAS signals of agronomic traits in three tissues, which included genes, such as NADSYN1, NDUFS3, LTF and KIFC2 in liver, GRAMD1C, TMTC2 and ZNF613 in backfat, as well as TIGAR, NDUFS3 and L3HYPDH in muscle that could serve as the candidate genes for economic traits. CONCLUSIONS The extensive atlas of GWAS, eQTL, fine-mapping, and transcriptome-wide association studies aid in the suggestion of potentially functional variants and genes in cattle agronomic traits and will be an invaluable source for genomics and breeding in beef cattle.
Collapse
Affiliation(s)
- Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yapeng Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zezhao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, 20742, USA.
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
61
|
Temple S. Advancing cell therapy for neurodegenerative diseases. Cell Stem Cell 2023; 30:512-529. [PMID: 37084729 PMCID: PMC10201979 DOI: 10.1016/j.stem.2023.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/20/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Cell-based therapies are being developed for various neurodegenerative diseases that affect the central nervous system (CNS). Concomitantly, the roles of individual cell types in neurodegenerative pathology are being uncovered by genetic and single-cell studies. With a greater understanding of cellular contributions to health and disease and with the arrival of promising approaches to modulate them, effective therapeutic cell products are now emerging. This review examines how the ability to generate diverse CNS cell types from stem cells, along with a deeper understanding of cell-type-specific functions and pathology, is advancing preclinical development of cell products for the treatment of neurodegenerative diseases.
Collapse
Affiliation(s)
- Sally Temple
- Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
| |
Collapse
|
62
|
Antignano I, Liu Y, Offermann N, Capasso M. Aging microglia. Cell Mol Life Sci 2023; 80:126. [PMID: 37081238 PMCID: PMC10119228 DOI: 10.1007/s00018-023-04775-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
Microglia are the tissue-resident macrophage population of the brain, specialized in supporting the CNS environment and protecting it from endogenous and exogenous insults. Nonetheless, their function declines with age, in ways that remain to be fully elucidated. Given the critical role played by microglia in neurodegenerative diseases, a better understanding of the aging microglia phenotype is an essential prerequisite in designing better preventive and therapeutic strategies. In this review, we discuss the most recent literature on microglia in aging, comparing findings in rodent models and human subjects.
Collapse
Affiliation(s)
- Ignazio Antignano
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Yingxiao Liu
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Nina Offermann
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Melania Capasso
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
| |
Collapse
|
63
|
Cortez Cardoso Penha R, Smith-Byrne K, Atkins JR, Haycock PC, Kar S, Codd V, Samani NJ, Nelson C, Milojevic M, Gabriel AAG, Amos C, Brennan P, Hung RJ, Kachuri L, Mckay JD. Common genetic variations in telomere length genes and lung cancer: a Mendelian randomisation study and its novel application in lung tumour transcriptome. eLife 2023; 12:e83118. [PMID: 37079368 PMCID: PMC10118386 DOI: 10.7554/elife.83118] [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: 08/31/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Background Genome-wide association studies (GWASs) have identified genetic susceptibility variants for both leukocyte telomere length (LTL) and lung cancer susceptibility. Our study aims to explore the shared genetic basis between these traits and investigate their impact on somatic environment of lung tumours. Methods We performed genetic correlation, Mendelian randomisation (MR), and colocalisation analyses using the largest available GWASs summary statistics of LTL (N=464,716) and lung cancer (N=29,239 cases and 56,450 controls). Principal components analysis based on RNA-sequencing data was used to summarise gene expression profile in lung adenocarcinoma cases from TCGA (N=343). Results Although there was no genome-wide genetic correlation between LTL and lung cancer risk, longer LTL conferred an increased risk of lung cancer regardless of smoking status in the MR analyses, particularly for lung adenocarcinoma. Of the 144 LTL genetic instruments, 12 colocalised with lung adenocarcinoma risk and revealed novel susceptibility loci, including MPHOSPH6, PRPF6, and POLI. The polygenic risk score for LTL was associated with a specific gene expression profile (PC2) in lung adenocarcinoma tumours. The aspect of PC2 associated with longer LTL was also associated with being female, never smokers, and earlier tumour stages. PC2 was strongly associated with cell proliferation score and genomic features related to genome stability, including copy number changes and telomerase activity. Conclusions This study identified an association between longer genetically predicted LTL and lung cancer and sheds light on the potential molecular mechanisms related to LTL in lung adenocarcinomas. Funding Institut National du Cancer (GeniLuc2017-1-TABAC-03-CIRC-1-TABAC17-022), INTEGRAL/NIH (5U19CA203654-03), CRUK (C18281/A29019), and Agence Nationale pour la Recherche (ANR-10-INBS-09).
Collapse
Affiliation(s)
- Ricardo Cortez Cardoso Penha
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, University of OxfordOxfordUnited Kingdom
| | - Joshua R Atkins
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit, Bristol Population Health Science Institute, Bristol Medical School (PHS)BristolUnited Kingdom
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, Bristol Population Health Science Institute, Bristol Medical School (PHS)BristolUnited Kingdom
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Christopher Nelson
- Department of Cardiovascular Sciences, University of LeicesterLeicesterUnited Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield HospitalLeicesterUnited Kingdom
| | - Maja Milojevic
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Aurélie AG Gabriel
- Ludwig Lausanne Branch, Faculty of Biology and MedicineLausanneSwitzerland
| | - Christopher Amos
- Institute for Clinical and Translational Research, Baylor College of MedicineHoustonUnited States
| | - Paul Brennan
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai HealthTorontoCanada
| | - Linda Kachuri
- Departament of Epidemiology and Population Health, Stanford UniversityStanfordUnited States
| | - James D Mckay
- Genomic Epidemiology branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO)LyonFrance
| |
Collapse
|
64
|
Castellani G, Croese T, Peralta Ramos JM, Schwartz M. Transforming the understanding of brain immunity. Science 2023; 380:eabo7649. [PMID: 37023203 DOI: 10.1126/science.abo7649] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Contemporary studies have completely changed the view of brain immunity from envisioning the brain as isolated and inaccessible to peripheral immune cells to an organ in close physical and functional communication with the immune system for its maintenance, function, and repair. Circulating immune cells reside in special niches in the brain's borders, the choroid plexus, meninges, and perivascular spaces, from which they patrol and sense the brain in a remote manner. These niches, together with the meningeal lymphatic system and skull microchannels, provide multiple routes of interaction between the brain and the immune system, in addition to the blood vasculature. In this Review, we describe current ideas about brain immunity and their implications for brain aging, diseases, and immune-based therapeutic approaches.
Collapse
Affiliation(s)
- Giulia Castellani
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tommaso Croese
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Michal Schwartz
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
65
|
Andrews SJ, Renton AE, Fulton-Howard B, Podlesny-Drabiniok A, Marcora E, Goate AM. The complex genetic architecture of Alzheimer's disease: novel insights and future directions. EBioMedicine 2023; 90:104511. [PMID: 36907103 PMCID: PMC10024184 DOI: 10.1016/j.ebiom.2023.104511] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a complex multifactorial neurodegenerative disorder and the most common form of dementia. AD is highly heritable, with heritability estimates of ∼70% from twin studies. Progressively larger genome-wide association studies (GWAS) have continued to expand our knowledge of AD/dementia genetic architecture. Until recently these efforts had identified 39 disease susceptibility loci in European ancestry populations. RECENT DEVELOPMENTS Two new AD/dementia GWAS have dramatically expanded the sample sizes and the number of disease susceptibility loci. The first increased total sample size to 1,126,563-with an effective sample size of 332,376-by predominantly including new biobank and population-based dementia datasets. The second, expands on an earlier GWAS from the International Genomics of Alzheimer's Project (IGAP) by increasing the number of clinically-defined AD cases/controls in addition to incorporating biobank dementia datasets, resulting in a total sample size to 788,989 and an effective sample size of 382,472. Collectively both GWAS identified 90 independent variants across 75 AD/dementia susceptibility loci, including 42 novel loci. Pathway analyses indicate the susceptibility loci are enriched for genes involved in amyloid plaque and neurofibrillary tangle formation, cholesterol metabolism, endocytosis/phagocytosis, and the innate immune system. Gene prioritization efforts for the novel loci identified 62 candidate causal genes. Many of the candidate genes from known and newly discovered loci play key roles in macrophages and highlight phagocytic clearance of cholesterol-rich brain tissue debris by microglia (efferocytosis) as a core pathogenetic hub and putative therapeutic target for AD. WHERE NEXT?: While GWAS in European ancestry populations have substantially enhanced our understanding of AD genetic architecture, heritability estimates from population based GWAS cohorts are markedly smaller than those from twin studies. While this missing heritability is likely due to a combination of factors, it highlights that our understanding of AD genetic architecture and genetic risk mechanisms remains incomplete. These knowledge gaps result from several underexplored areas in AD research. First, rare variants remain understudied due to methodological issues in identifying them and the cost of generating sufficiently powered whole exome/genome sequencing datasets. Second, sample sizes of non-European ancestry populations in AD GWAS remain small. Third, GWAS of AD neuroimaging and cerebrospinal fluid endophenotypes remains limited due to low compliance and high costs associated with measuring amyloid-β and tau levels and other disease-relevant biomarkers. Studies generating sequencing data, including diverse populations, and incorporating blood-based AD biomarkers are set to substantially improve our knowledge of AD genetic architecture.
Collapse
Affiliation(s)
- Shea J Andrews
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA.
| | - Alan E Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna Podlesny-Drabiniok
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
66
|
Mordelt A, de Witte LD. Microglia-mediated synaptic pruning as a key deficit in neurodevelopmental disorders: Hype or hope? Curr Opin Neurobiol 2023; 79:102674. [PMID: 36657237 DOI: 10.1016/j.conb.2022.102674] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/18/2022] [Accepted: 12/14/2022] [Indexed: 01/18/2023]
Abstract
There is a consensus in the field that microglia play a prominent role in neurodevelopmental processes like synaptic pruning and neuronal network maturation. Thus, a current momentum of associating microglia deficits with neurodevelopmental disorders (NDDs) emerged. This concept is challenged by rodent studies and clinical data. Intriguingly, reduced numbers of microglia or altered microglial functions do not necessarily lead to overt NDD phenotypes, and neuropsychiatric symptoms seem to develop primarily in adulthood. Hence, it remains open for discussion whether microglia are truly indispensable for healthy neurodevelopment. Here, we critically discuss the role of microglia in synaptic pruning and highlight area- and age dependency. We propose an updated model of microglia-mediated synaptic pruning in the context of NDDs and discuss the potential of targeting microglia for treatment of these disorders.
Collapse
Affiliation(s)
- Annika Mordelt
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, the Netherlands.
| | - Lot D de Witte
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, the Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
67
|
Naggan L, Robinson E, Dinur E, Goldenberg H, Kozela E, Yirmiya R. Suicide in bipolar disorder patients is associated with hippocampal microglia activation and reduction of lymphocytes-activation gene 3 (LAG3) microglial checkpoint expression. Brain Behav Immun 2023; 110:185-194. [PMID: 36863492 DOI: 10.1016/j.bbi.2023.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/20/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Bipolar disorder (BD) is associated with marked functional impairments along with increased rate of suicide. Although there is ample evidence for the involvement of inflammatory processes and microglia activation in the pathophysiology of BD, the mechanisms that regulate these cells in BD patients, and particularly the role of microglia checkpoints, is still unclear. METHODS Immunohistochemical analyses of hippocampal sections from post-mortem brains of 15 BD patients and 12 control subjects were used to assess microglia density, by staining the microglia-specific receptor P2RY12, and microglia activation, by staining the activation marker MHC II. Given recent findings on the involvement of LAG3, which interacts with MHC II and serves as a negative microglia checkpoint, in depression and electroconvulsive therapy, we assessed the levels of LAG3 expression and their correlations with microglia density and activation. RESULTS There were no overall differences between BD patients and controls, but BD patients who committed suicide (N = 9) displayed a significant elevation in the overall microglia density and the density of MHC II-labeled microglia (but not other MHC II-labeled cells), compared with no suicide BD patients (N = 6) and controls. Furthermore, the percent of microglia expressing LAG3 was significantly reduced only in suicidal BD patients, with significant negative correlations between microglial LAG3 expression levels and the density of microglia, in general, and activated microglia, in particular. CONCLUSION Suicidal BD patients exhibit microglia activation, which is possibly mediated by reduced LAG3 checkpoint expression, suggesting that anti-microglial therapeutics, including LAG3 modulators, may be beneficial for this subgroup of patients.
Collapse
Affiliation(s)
- Lior Naggan
- Department of Psychology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elad Robinson
- Department of Psychology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Dinur
- Department of Psychology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hagar Goldenberg
- Department of Psychology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ewa Kozela
- Department of Psychology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Raz Yirmiya
- Department of Psychology, The Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
68
|
Abstract
Parkinson's disease (PD) is clinically, pathologically, and genetically heterogeneous, resisting distillation to a single, cohesive disorder. Instead, each affected individual develops a virtually unique form of Parkinson's syndrome. Clinical manifestations consist of variable motor and nonmotor features, and myriad overlaps are recognized with other neurodegenerative conditions. Although most commonly characterized by alpha-synuclein protein pathology throughout the central and peripheral nervous systems, the distribution varies and other pathologies commonly modify PD or trigger similar manifestations. Nearly all PD is genetically influenced. More than 100 genes or genetic loci have been identified, and most cases likely arise from interactions among many common and rare genetic variants. Despite its complex architecture, insights from experimental genetic dissection coalesce to reveal unifying biological themes, including synaptic, lysosomal, mitochondrial, andimmune-mediated mechanisms of pathogenesis. This emerging understanding of Parkinson's syndrome, coupled with advances in biomarkers and targeted therapies, presages successful precision medicine strategies.
Collapse
Affiliation(s)
- Hui Ye
- Department of Neurology, Baylor College of Medicine, Houston, Texas, USA; ,
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Laurie A Robak
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
| | - Meigen Yu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA;
| | - Matthew Cykowski
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA;
- Department of Neurology, Houston Methodist Hospital, Houston, Texas, USA
| | - Joshua M Shulman
- Department of Neurology, Baylor College of Medicine, Houston, Texas, USA; ,
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA;
- Center for Alzheimer's and Neurodegenerative Diseases, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
69
|
Gotoh M, Miyamoto Y, Ikeshima-Kataoka H. Astrocytic Neuroimmunological Roles Interacting with Microglial Cells in Neurodegenerative Diseases. Int J Mol Sci 2023; 24:ijms24021599. [PMID: 36675113 PMCID: PMC9865248 DOI: 10.3390/ijms24021599] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Both astrocytic and microglial functions have been extensively investigated in healthy subjects and neurodegenerative diseases. For astrocytes, not only various sub-types were identified but phagocytic activity was also clarified recently and is making dramatic progress. In this review paper, we mostly focus on the functional role of astrocytes in the extracellular matrix and on interactions between reactive astrocytes and reactive microglia in normal states and in neurodegenerative diseases, because the authors feel it is necessary to elucidate the mechanisms among activated glial cells in the pathology of neurological diseases in order to pave the way for drug discovery. Finally, we will review cyclic phosphatidic acid (cPA), a naturally occurring phospholipid mediator that induces a variety of biological activities in the brain both in vivo and in vitro. We propose that cPA may serve as a novel therapeutic molecule for the treatment of brain injury and neuroinflammation.
Collapse
Affiliation(s)
- Mari Gotoh
- Department of Clinical Laboratory Medicine, Faculty of Medical Technology, Teikyo University, 2-11-1, Itabashi-ku, Tokyo 173-8605, Japan
- Institute for Human Life Science, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yasunori Miyamoto
- Institute for Human Life Science, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hiroko Ikeshima-Kataoka
- Department of Biology, Keio University, 4-1-1, Hiyoshi, Kohoku-ku, Yokohama 223-8521, Japan
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Correspondence:
| |
Collapse
|
70
|
Hu J, Chen Q, Zhu H, Hou L, Liu W, Yang Q, Shen H, Chai G, Zhang B, Chen S, Cai Z, Wu C, Hong F, Li H, Chen S, Xiao N, Wang ZX, Zhang X, Wang B, Zhang L, Mo W. Microglial Piezo1 senses Aβ fibril stiffness to restrict Alzheimer's disease. Neuron 2023; 111:15-29.e8. [PMID: 36368316 DOI: 10.1016/j.neuron.2022.10.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/15/2022] [Accepted: 10/12/2022] [Indexed: 11/12/2022]
Abstract
The pathology of Alzheimer's disease (AD) is featured with extracellular amyloid-β (Aβ) plaques, whose impact on the mechanical properties of the surrounding brain tissues is unclear. Microglia sense and integrate biochemical cues of the microenvironment. However, whether the microglial mechanosensing pathways influence AD pathogenesis is unknown. Here, we surveyed the elevated stiffness of Aβ-plaque-associated tissues and observed the selective upregulation of the mechanosensitive ion channel Piezo1 in Aβ-plaque-associated microglia. Piezo1 sensed the stiffness stimuli of Aβ fibrils and subsequently induced Ca2+ influx for microglial clustering, phagocytosis, and compacting of Aβ plaques. Microglia lacking Piezo1 led to the exacerbation of Aβ pathology and cognitive decline, whereas pharmacological activation of microglial Piezo1 ameliorated brain Aβ burden and cognitive impairment in 5 × FAD mice. Together, our results reveal that Piezo1, a mechanosensor of Aβ fibril stiffness in microglia, represents a potential therapeutic target for AD.
Collapse
Affiliation(s)
- Jin Hu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Qiang Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hongrui Zhu
- Department of Anesthesiology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Lichao Hou
- Department of Anesthesiology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Wei Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Qihua Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Huidan Shen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China; Department of Anesthesiology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Guolin Chai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Boxin Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Shaoxuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Zhiyu Cai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Chongxin Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Fan Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hongda Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Sifang Chen
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Naian Xiao
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhan-Xiang Wang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Xueqin Zhang
- Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Liang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Wei Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Department of Neuroscience, the First Affiliated Hospital, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| |
Collapse
|
71
|
Humphrey J, Venkatesh S, Hasan R, Herb JT, de Paiva Lopes K, Küçükali F, Byrska-Bishop M, Evani US, Narzisi G, Fagegaltier D, Sleegers K, Phatnani H, Knowles DA, Fratta P, Raj T. Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes. Nat Neurosci 2023; 26:150-162. [PMID: 36482247 DOI: 10.1038/s41593-022-01205-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2022] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease affecting motor neurons in the brain and spinal cord. In this study, we investigated gene expression changes in ALS via RNA sequencing in 380 postmortem samples from cervical, thoracic and lumbar spinal cord segments from 154 individuals with ALS and 49 control individuals. We observed an increase in microglia and astrocyte gene expression, accompanied by a decrease in oligodendrocyte gene expression. By creating a gene co-expression network in the ALS samples, we identified several activated microglia modules that negatively correlate with retrospective disease duration. We mapped molecular quantitative trait loci and found several potential ALS risk loci that may act through gene expression or splicing in the spinal cord and assign putative cell types for FNBP1, ACSL5, SH3RF1 and NFASC. Finally, we outline how common genetic variants associated with splicing of C9orf72 act as proxies for the well-known repeat expansion, and we use the same mechanism to suggest ATXN3 as a putative risk gene.
Collapse
Affiliation(s)
- Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Sanan Venkatesh
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rahat Hasan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jake T Herb
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fahri Küçükali
- Complex Genetics of Alzheimer's Disease Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Delphine Fagegaltier
- New York Genome Center, New York, NY, USA
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - David A Knowles
- New York Genome Center, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
72
|
Crary JF. Neurodegeneration: 2023 update. FREE NEUROPATHOLOGY 2023; 4:4-13. [PMID: 37694160 PMCID: PMC10484115 DOI: 10.17879/freeneuropathology-2023-4899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
This paper reviews ten highly impactful studies published in the previous year selected by the author from the neurodegenerative neuropathology literature. As in previous years, the focus is to highlight human tissue-based experimentation most relevant to neuropathologists. A concerted effort was made to balance the selected studies across disease categories, approaches, and methodologies to capture the breadth of the research landscape. Studies include an integrated proteomic and transcriptomic study of Alzheimer disease (AD) and new consensus diagnostic neuropathological criteria for progressive supranuclear palsy. A number of studies looking at TAR DNA-binding protein 43 (TDP-43) are highlighted. One examined interaction between AD and limbic age-related TDP-43 encephalopathy (LATE) and yet another demonstrated how TDP-43 represses cryptic exon inclusion in UNC13A, suggesting a novel pathogenic mechanism. Most surprisingly, three cryogenic electron microscopy (cryo-EM) studies showed that TMEM106B filaments form the core of TDP-43-positive inclusions. Cryo-EM revealed a prion protein amyloid structure from aggregates in Gerstmann-Sträussler-Scheinker disease. There was an elegant functional genomic study cataloging microglial gene expression in the human brain. A study shed light on how APOE influences chronic traumatic encephalopathy. A pathoanatomical study tested the dual hit hypothesis of Lewy body progression throughout the nervous system. And finally, deep learning continues to show its promise with application of a weakly supervised multiple instance learning paradigm to assess aging post-mortem brains.
Collapse
Affiliation(s)
- John F Crary
- Department of Pathology, Nash Family Department of Neuroscience, Department of Artificial Intelligence & Human Health, Neuropathology Brain Bank & Research CoRE, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
73
|
Zhou Y, Wang X, Liu Y, Gu Y, Gu R, Zhang G, Lin Q. Mechanisms of abnormal adult hippocampal neurogenesis in Alzheimer's disease. Front Neurosci 2023; 17:1125376. [PMID: 36875663 PMCID: PMC9975352 DOI: 10.3389/fnins.2023.1125376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Alzheimer's disease (AD) is a degenerative disease of the central nervous system, the most common type of dementia in old age, which causes progressive loss of cognitive functions such as thoughts, memory, reasoning, behavioral abilities and social skills, affecting the daily life of patients. The dentate gyrus of the hippocampus is a key area for learning and memory functions, and an important site of adult hippocampal neurogenesis (AHN) in normal mammals. AHN mainly consists of the proliferation, differentiation, survival and maturation of newborn neurons and occurs throughout adulthood, but the level of AHN decreases with age. In AD, the AHN will be affected to different degrees at different times, and its exact molecular mechanisms are increasingly elucidated. In this review, we summarize the changes of AHN in AD and its alteration mechanism, which will help lay the foundation for further research on the pathogenesis and diagnostic and therapeutic approaches of AD.
Collapse
Affiliation(s)
- Yujuan Zhou
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
| | - Xu Wang
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
| | - Yingying Liu
- Department of Physiology and Pathophysiology, Health Science Center, Peking University, Beijing, China
| | - Yulu Gu
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
| | - Renjun Gu
- School of Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Geng Zhang
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China.,Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qing Lin
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China.,Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| |
Collapse
|
74
|
Hou J, Chen Y, Grajales-Reyes G, Colonna M. TREM2 dependent and independent functions of microglia in Alzheimer's disease. Mol Neurodegener 2022; 17:84. [PMID: 36564824 PMCID: PMC9783481 DOI: 10.1186/s13024-022-00588-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/02/2022] [Indexed: 12/25/2022] Open
Abstract
Microglia are central players in brain innate immunity and have been the subject of extensive research in Alzheimer's disease (AD). In this review, we aim to summarize the genetic and functional discoveries that have advanced our understanding of microglia reactivity to AD pathology. Given the heightened AD risk posed by rare variants of the microglial triggering receptor expressed on myeloid cells 2 (TREM2), we will focus on the studies addressing the impact of this receptor on microglia responses to amyloid plaques, tauopathy and demyelination pathologies in mouse and human. Finally, we will discuss the implications of recent discoveries on microglia and TREM2 biology on potential therapeutic strategies for AD.
Collapse
Affiliation(s)
- Jinchao Hou
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Yun Chen
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Gary Grajales-Reyes
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Marco Colonna
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| |
Collapse
|
75
|
Ando K, Nagaraj S, Küçükali F, de Fisenne MA, Kosa AC, Doeraene E, Lopez Gutierrez L, Brion JP, Leroy K. PICALM and Alzheimer's Disease: An Update and Perspectives. Cells 2022; 11:3994. [PMID: 36552756 PMCID: PMC9776874 DOI: 10.3390/cells11243994] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified the PICALM (Phosphatidylinositol binding clathrin-assembly protein) gene as the most significant genetic susceptibility locus after APOE and BIN1. PICALM is a clathrin-adaptor protein that plays a critical role in clathrin-mediated endocytosis and autophagy. Since the effects of genetic variants of PICALM as AD-susceptibility loci have been confirmed by independent genetic studies in several distinct cohorts, there has been a number of in vitro and in vivo studies attempting to elucidate the underlying mechanism by which PICALM modulates AD risk. While differential modulation of APP processing and Aβ transcytosis by PICALM has been reported, significant effects of PICALM modulation of tau pathology progression have also been evidenced in Alzheimer's disease models. In this review, we summarize the current knowledge about PICALM, its physiological functions, genetic variants, post-translational modifications and relevance to AD pathogenesis.
Collapse
Affiliation(s)
- Kunie Ando
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Siranjeevi Nagaraj
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Fahri Küçükali
- Complex Genetics of Alzheimer’s Disease Group, VIB Center for Molecular Neurology, VIB Antwerp, Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium
| | - Marie-Ange de Fisenne
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Andreea-Claudia Kosa
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Emilie Doeraene
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Lidia Lopez Gutierrez
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Jean-Pierre Brion
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Karelle Leroy
- Laboratory of Histology, Neuropathology and Neuroanatomy, Faculty of Medicine, Université Libre de Bruxelles, ULB Neuroscience Institute, 808 Route de Lennik, 1070 Brussels, Belgium
| |
Collapse
|
76
|
Dang X, Zhang Z, Luo XJ. Mendelian Randomization Study Using Dopaminergic Neuron-Specific eQTL Nominates Potential Causal Genes for Parkinson's Disease. Mov Disord 2022; 37:2451-2456. [PMID: 36177513 DOI: 10.1002/mds.29239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Large-scale genome-wide association studies (GWASs) have reported multiple risk variants for Parkinson's disease (PD). However, little is known about how these reported risk variants confer risk of PD. OBJECTIVE To nominate genes whose genetically regulated expression in dopaminergic neurons may have a causal role in PD. METHODS We conducted a two-sample Mendelian randomization (MR) study by integrating large-scale genome-wide associations and expression quantitative trait loci (eQTL) data from dopaminergic neurons. RESULTS MR analysis nominated 10 risk genes whose genetically regulated expression in dopaminergic neurons may have a causal role in PD. These MR significant genes include FAM200B, NDUFAF2, NUP42, SH3GL2, STX1B, CCDC189, KAT8, PRSS36, VAMP4, and ZSWIM7. CONCLUSIONS We report the first MR study of PD by using dopaminergic neuron-specific eQTL and nominate novel risk genes for PD. Further functional characterization of the nominated risk genes will provide mechanistic insights into PD pathogenesis and potential therapeutic targets. © 2022 International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Xinglun Dang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhijun Zhang
- Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, China.,Department of Neurology, Affiliated Zhongda Hospital, Institution of Neuropsychiatry, Southeast University, Nanjing, China.,Department of Mental Health and Public Health, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiong-Jian Luo
- Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, China.,Department of Neurology, Affiliated Zhongda Hospital, Institution of Neuropsychiatry, Southeast University, Nanjing, China
| |
Collapse
|
77
|
Lang AL, Eulalio T, Fox E, Yakabi K, Bukhari SA, Kawas CH, Corrada MM, Montgomery SB, Heppner FL, Capper D, Nachun D, Montine TJ. Methylation differences in Alzheimer's disease neuropathologic change in the aged human brain. Acta Neuropathol Commun 2022; 10:174. [PMID: 36447297 PMCID: PMC9710143 DOI: 10.1186/s40478-022-01470-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia with advancing age as its strongest risk factor. AD neuropathologic change (ADNC) is known to be associated with numerous DNA methylation changes in the human brain, but the oldest old (> 90 years) have so far been underrepresented in epigenetic studies of ADNC. Our study participants were individuals aged over 90 years (n = 47) from The 90+ Study. We analyzed DNA methylation from bulk samples in eight precisely dissected regions of the human brain: middle frontal gyrus, cingulate gyrus, entorhinal cortex, dentate gyrus, CA1, substantia nigra, locus coeruleus and cerebellar cortex. We deconvolved our bulk data into cell-type-specific (CTS) signals using computational methods. CTS methylation differences were analyzed across different levels of ADNC. The highest amount of ADNC related methylation differences was found in the dentate gyrus, a region that has so far been underrepresented in large scale multi-omic studies. In neurons of the dentate gyrus, DNA methylation significantly differed with increased burden of amyloid beta (Aβ) plaques at 5897 promoter regions of protein-coding genes. Amongst these, higher Aβ plaque burden was associated with promoter hypomethylation of the Presenilin enhancer 2 (PEN-2) gene, one of the rate limiting genes in the formation of gamma-secretase, a multicomponent complex that is responsible in part for the endoproteolytic cleavage of amyloid precursor protein into Aβ peptides. In addition to novel ADNC related DNA methylation changes, we present the most detailed array-based methylation survey of the old aged human brain to date. Our open-sourced dataset can serve as a brain region reference panel for future studies and help advance research in aging and neurodegenerative diseases.
Collapse
Affiliation(s)
- Anna-Lena Lang
- Department of Neuropathology, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA
| | - Eddie Fox
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| | - Koya Yakabi
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| | - Syed A. Bukhari
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| | - Claudia H. Kawas
- Department of Neurology, University of California Irvine, Orange, CA 92868-4280 USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697 USA
| | - Maria M. Corrada
- Department of Neurology, University of California Irvine, Orange, CA 92868-4280 USA
- Department of Epidemiology, University of California, Irvine, CA 92617 USA
| | - Stephen B. Montgomery
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA
| | - Frank L. Heppner
- Department of Neuropathology, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Cluster of Excellence, NeuroCure, 10117 Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Daniel Nachun
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
| | - Thomas J. Montine
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| |
Collapse
|
78
|
Guo L, Ni Z, Wei G, Cheng W, Huang X, Yue W. Epigenome-wide DNA methylation analysis of whole blood cells derived from patients with GAD and OCD in the Chinese Han population. Transl Psychiatry 2022; 12:465. [PMID: 36344488 PMCID: PMC9640561 DOI: 10.1038/s41398-022-02236-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/14/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Generalized anxiety disorder (GAD) and obsessive-compulsive disorder (OCD) had high comorbidity and affected more than 44 million people around the world leading to a huge burden on health and economy. Here, we conducted an epigenome-wide DNA methylation study employing 93 patients with GAD, 65 patients with OCD, and 302 health controls, to explore epigenetic alterations associated with the onset and differences of GAD and OCD. We identified multiple differentially methylated positions (DMPs) and regions (DMRs): three DMP genes included RIOK3 (cg21515243, p = 8.00 × 10-10), DNASE2 (cg09379601, p = 1.10 × 10-9), and PSMB4 (cg01334186, p = 3.70 × 10-7) and two DMR genes USP6NL (p = 4.50 × 10-4) and CPLX1 (p = 6.95 × 10-4) were associated with the onset of GAD and OCD; three DMPs genes included LDLRAP1 (cg21400344, p = 4.40 × 10-12), ACIN1 (cg23712970, p = 2.98×10-11), and SCRT1 (cg25472897, p = 5.60 × 10-11) and three DMR genes WDR19 (p = 3.39 × 10-3), SYCP1 (p = 6.41 × 10-3), and FAM172A (p = 5.74 × 10-3) were associated with the differences between GAD and OCD. Investigation of epigenetic age and chronological age revealed a different epigenetic development trajectory of GAD and OCD. Conclusively, our findings which yielded robust models may aid in distinguishing patients from healthy controls (AUC = 0.90-0.99) or classifying patients with GAD and OCD (AUC = 0.89-0.99), and may power the precision medicine for them.
Collapse
Affiliation(s)
- Liangkun Guo
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191 China ,grid.459847.30000 0004 1798 0615National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191 China ,grid.506261.60000 0001 0706 7839NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Zhaojun Ni
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191 China ,grid.459847.30000 0004 1798 0615National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191 China ,grid.506261.60000 0001 0706 7839NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191 China
| | - Guiming Wei
- Department of Neurology, Shandong Daizhuang Hospital, 272051 Jining, Shandong China
| | - Weiqiu Cheng
- grid.5510.10000 0004 1936 8921NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xuebing Huang
- Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191, China. .,National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China. .,NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China.
| | - Weihua Yue
- Institute of Mental Health, Peking University Sixth Hospital, Beijing, 100191, China. .,National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China. .,NHC Key Laboratory of Mental Health, & Research Unit of Diagnosis and Treatment of Mood Cognitive Disorder, Chinese Academy of Medical Sciences, Beijing, 100191, China. .,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China. .,Chinese Institute for Brain Research, Beijing, 102206, China.
| |
Collapse
|
79
|
Romero-Molina C, Garretti F, Andrews SJ, Marcora E, Goate AM. Microglial efferocytosis: Diving into the Alzheimer's disease gene pool. Neuron 2022; 110:3513-3533. [PMID: 36327897 DOI: 10.1016/j.neuron.2022.10.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Genome-wide association studies and functional genomics studies have linked specific cell types, genes, and pathways to Alzheimer's disease (AD) risk. In particular, AD risk alleles primarily affect the abundance or structure, and thus the activity, of genes expressed in macrophages, strongly implicating microglia (the brain-resident macrophages) in the etiology of AD. These genes converge on pathways (endocytosis/phagocytosis, cholesterol metabolism, and immune response) with critical roles in core macrophage functions such as efferocytosis. Here, we review these pathways, highlighting relevant genes identified in the latest AD genetics and genomics studies, and describe how they may contribute to AD pathogenesis. Investigating the functional impact of AD-associated variants and genes in microglia is essential for elucidating disease risk mechanisms and developing effective therapeutic approaches.
Collapse
Affiliation(s)
- Carmen Romero-Molina
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Garretti
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shea J Andrews
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Edoardo Marcora
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA; Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
80
|
Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022; 31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [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: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023] Open
Abstract
Aberrant splicing underlies many human diseases, including cancer, cardiovascular diseases and neurological disorders. Genome-wide mapping of splicing quantitative trait loci (sQTLs) has shown that genetic regulation of alternative splicing is widespread. However, identification of the corresponding isoform or protein products associated with disease-associated sQTLs is challenging with short-read RNA-seq, which cannot precisely characterize full-length transcript isoforms. Furthermore, contemporary sQTL interpretation often relies on reference transcript annotations, which are incomplete. Solutions to these issues may be found through integration of newly emerging long-read sequencing technologies. Long-read sequencing offers the capability to sequence full-length mRNA transcripts and, in some cases, to link sQTLs to transcript isoforms containing disease-relevant protein alterations. Here, we provide an overview of sQTL mapping approaches, the use of long-read sequencing to characterize sQTL effects on isoforms, the linkage of RNA isoforms to protein-level functions and comment on future directions in the field. Based on recent progress, long-read RNA sequencing promises to be part of the human disease genetics toolkit to discover and treat protein isoforms causing rare and complex diseases.
Collapse
Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of General Medicine and Primary Care, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Abdullah Abood
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gloria M Sheynkman
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
81
|
Chen J, Wang L, De Jager PL, Bennett DA, Buchman AS, Yang J. A scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications for studying Alzheimer disease. HGG ADVANCES 2022; 3:100143. [PMID: 36204489 PMCID: PMC9530673 DOI: 10.1016/j.xhgg.2022.100143] [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: 01/28/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022] Open
Abstract
Existing methods for integrating functional annotations in genome-wide association studies (GWASs) to fine-map and prioritize potential causal variants are limited to using non-overlapped categorical annotations or limited by the computation burden of modeling genome-wide variants. To overcome these limitations, we propose a scalable Bayesian functional GWAS method to account for multivariate quantitative functional annotations (BFGWAS_QUANT), accompanied by a scalable computation algorithm enabling joint modeling of genome-wide variants. Simulation studies validated the performance of BFGWAS_QUANT for accurately quantifying annotation enrichment and improving GWAS power. Applying BFGWAS_QUANT to study five Alzheimer disease (AD)-related phenotypes using individual-level GWAS data (n = ∼1,000), we found that histone modification annotations have higher enrichment than expression quantitative trait locus (eQTL) annotations for all considered phenotypes, with the highest enrichment in H3K27me3 (polycomb regression). We also found that cis-eQTLs in microglia had higher enrichment than eQTLs of bulk brain frontal cortex tissue for all considered phenotypes. A similar enrichment pattern was also identified using the International Genomics of Alzheimer's Project (IGAP) summary-level GWAS data of AD (n = ∼54,000). The strongest known APOE E4 risk allele was identified for all five phenotypes, and the APOE locus was validated using the IGAP data. BFGWAS_QUANT fine-mapped 32 significant variants from 1,073 genome-wide significant variants in the IGAP data. We also demonstrated that the polygenic risk scores (PRSs) using effect size estimates by BFGWAS_QUANT had a similar prediction accuracy as other methods assuming a sparse causal model. Overall, BFGWAS_QUANT is a useful GWAS tool for quantifying annotation enrichment and prioritizing potential causal variants.
Collapse
Affiliation(s)
- Junyu Chen
- Department of Epidemiology, Emory University School of Public Health, Atlanta, GA 30322, USA
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lei Wang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, 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
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
82
|
Kung PJ, Elsayed I, Reyes-Pérez P, Bandres-Ciga S. Immunogenetic Determinants of Parkinson’s Disease Etiology. JOURNAL OF PARKINSON'S DISEASE 2022; 12:S13-S27. [PMID: 35367971 PMCID: PMC9535568 DOI: 10.3233/jpd-223176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Parkinson’s disease (PD) is increasingly recognised as a systemic disorder in which inflammation might play a causative role rather than being a consequence or an epiphenomenon of the neurodegenerative process. Although growing genetic evidence links the central and peripheral immune system with both monogenic and sporadic PD, our understanding on how the immune system contributes to PD pathogenesis remains a daunting challenge. In this review, we discuss recent literature aimed at exploring the role of known genes and susceptibility loci to PD pathogenesis through immune system related mechanisms. Furthermore, we outline shared genetic etiologies and interrelations between PD and autoimmune diseases and underlining challenges and limitations faced in the translation of relevant allelic and regulatory risk loci to immune-pathological mechanisms. Lastly, with the field of immunogenetics expanding rapidly, we place these insights into a future context highlighting the prospect of immune modulation as a promising disease-modifying strategy.
Collapse
Affiliation(s)
- Pin-Jui Kung
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Inas Elsayed
- Faculty of Pharmacy, University of Gezira, Wad Medani, Sudan
- International Parkinson Disease Genomics Consortium (IPDGC)-Africa, University of Gezira, Wad Medani, Sudan
| | - Paula Reyes-Pérez
- Laboratorio Internacional de Investigacion sobre el Genoma Humano, Universidad Autonoma de México, Queretaro, Mexico
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
83
|
Li C, Ren J, Zhang M, Wang H, Yi F, Wu J, Tang Y. The heterogeneity of microglial activation and its epigenetic and non-coding RNA regulations in the immunopathogenesis of neurodegenerative diseases. Cell Mol Life Sci 2022; 79:511. [PMID: 36066650 DOI: 10.1007/s00018-022-04536-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 12/15/2022]
Abstract
Microglia are resident immune cells in the brain and play a central role in the development and surveillance of the nervous system. Extensive gliosis is a common pathological feature of several neurodegenerative diseases, such as Alzheimer's disease (AD), the most common cause of dementia. Microglia can respond to multiple inflammatory insults and later transform into different phenotypes, such as pro- and anti-inflammatory phenotypes, thereby exerting different functions. In recent years, an increasing number of studies based on both traditional bulk sequencing and novel single-cell/nuclear sequencing and multi-omics analysis, have shown that microglial phenotypes are highly heterogeneous and dynamic, depending on the severity and stage of the disease as well as the particular inflammatory milieu. Thus, redirecting microglial activation to beneficial and neuroprotective phenotypes promises to halt the progression of neurodegenerative diseases. To this end, an increasing number of studies have focused on unraveling heterogeneous microglial phenotypes and their underlying molecular mechanisms, including those due to epigenetic and non-coding RNA modulations. In this review, we summarize the epigenetic mechanisms in the form of DNA and histone modifications, as well as the general non-coding RNA regulations that modulate microglial activation during immunopathogenesis of neurodegenerative diseases and discuss promising research approaches in the microglial era.
Collapse
Affiliation(s)
- Chaoyi Li
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Ren
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Mengfei Zhang
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Huakun Wang
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Fang Yi
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junjiao Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yu Tang
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, Hunan, China.
- The Biobank of Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
84
|
Jianing W, Jingyi X, Pingting Y. Neuropsychiatric lupus erythematosus: Focusing on autoantibodies. J Autoimmun 2022; 132:102892. [PMID: 36030137 DOI: 10.1016/j.jaut.2022.102892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
Abstract
Patients with systemic lupus erythematosus (SLE) frequently suffer from nervous system complications, termed neuropsychiatric lupus erythematosus (NPLE). NPLE accounts for the poor prognosis of SLE. Correct attribution of NP events to SLE is the primary principle in managing NPLE. The vascular injuries and neuroinflammation are the fundamental neuropathologic changes in NPLE. Specific autoantibody-mediated central nerve system (CNS) damages distinguish NPLE from other CNS disorders. Though the central antibodies in NPLE are generally thought to be raised from the periphery immune system, they may be produced in the meninges and choroid plexus. On this basis, abnormal activation of microglia and disease-associated microglia (DAM) should be the common mechanisms of NPLE and other CNS disturbances. Improved understanding of both characteristic and sharing features of NPLE might yield further options for managing this disease.
Collapse
Affiliation(s)
- Wang Jianing
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Xu Jingyi
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Yang Pingting
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, Shenyang, 110001, People's Republic of China.
| |
Collapse
|
85
|
Cooper YA, Teyssier N, Dräger NM, Guo Q, Davis JE, Sattler SM, Yang Z, Patel A, Wu S, Kosuri S, Coppola G, Kampmann M, Geschwind DH. Functional regulatory variants implicate distinct transcriptional networks in dementia. Science 2022; 377:eabi8654. [PMID: 35981026 DOI: 10.1126/science.abi8654] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Predicting the function of noncoding variation is a major challenge in modern genetics. In this study, we used massively parallel reporter assays to screen 5706 variants identified from genome-wide association studies for both Alzheimer's disease (AD) and progressive supranuclear palsy (PSP), identifying 320 functional regulatory variants (frVars) across 27 loci, including the complex 17q21.31 region. We identified and validated multiple risk loci using CRISPR interference or excision, including complement 4 (C4A) and APOC1 in AD and PLEKHM1 and KANSL1 in PSP. Functional variants disrupt transcription factor binding sites converging on enhancers with cell type-specific activity in PSP and AD, implicating a neuronal SP1-driven regulatory network in PSP pathogenesis. These analyses suggest that noncoding genetic risk is driven by common genetic variants through their aggregate activity on specific transcriptional programs.
Collapse
Affiliation(s)
- Yonatan A Cooper
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Noam Teyssier
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Nina M Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Qiuyu Guo
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Sydney M Sattler
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Zhongan Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Abdulsamie Patel
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Sarah Wu
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
- Institute of Precision Health, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
86
|
Mitochondrial Damage-Associated Molecular Patterns Content in Extracellular Vesicles Promotes Early Inflammation in Neurodegenerative Disorders. Cells 2022; 11:cells11152364. [PMID: 35954208 PMCID: PMC9367540 DOI: 10.3390/cells11152364] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/06/2023] Open
Abstract
Neuroinflammation is a common hallmark in different neurodegenerative conditions that share neuronal dysfunction and a progressive loss of a selectively vulnerable brain cell population. Alongside ageing and genetics, inflammation, oxidative stress and mitochondrial dysfunction are considered key risk factors. Microglia are considered immune sentinels of the central nervous system capable of initiating an innate and adaptive immune response. Nevertheless, the pathological mechanisms underlying the initiation and spread of inflammation in the brain are still poorly described. Recently, a new mechanism of intercellular signalling mediated by small extracellular vesicles (EVs) has been identified. EVs are nanosized particles (30–150 nm) with a bilipid membrane that carries cell-specific bioactive cargos that participate in physiological or pathological processes. Damage-associated molecular patterns (DAMPs) are cellular components recognised by the immune receptors of microglia, inducing or aggravating neuroinflammation in neurodegenerative disorders. Diverse evidence links mitochondrial dysfunction and inflammation mediated by mitochondrial-DAMPs (mtDAMPs) such as mitochondrial DNA, mitochondrial transcription factor A (TFAM) and cardiolipin, among others. Mitochondrial-derived vesicles (MDVs) are a subtype of EVs produced after mild damage to mitochondria and, upon fusion with multivesicular bodies are released as EVs to the extracellular space. MDVs are particularly enriched in mtDAMPs which can induce an immune response and the release of pro-inflammatory cytokines. Importantly, growing evidence supports the association between mitochondrial dysfunction, EV release and inflammation. Here, we describe the role of extracellular vesicles-associated mtDAMPS in physiological conditions and as neuroinflammation activators contributing to neurodegenerative disorders.
Collapse
|
87
|
Kosoy R, Fullard JF, Zeng B, Bendl J, Dong P, Rahman S, Kleopoulos SP, Shao Z, Girdhar K, Humphrey J, de Paiva Lopes K, Charney AW, Kopell BH, Raj T, Bennett D, Kellner CP, Haroutunian V, Hoffman GE, Roussos P. Genetics of the human microglia regulome refines Alzheimer's disease risk loci. Nat Genet 2022; 54:1145-1154. [PMID: 35931864 PMCID: PMC9388367 DOI: 10.1038/s41588-022-01149-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/08/2022] [Indexed: 02/07/2023]
Abstract
Microglia are brain myeloid cells that play a critical role in neuroimmunity and the etiology of Alzheimer's disease (AD), yet our understanding of how the genetic regulatory landscape controls microglial function and contributes to AD is limited. Here, we performed transcriptome and chromatin accessibility profiling in primary human microglia from 150 donors to identify genetically driven variation and cell-specific enhancer-promoter (E-P) interactions. Integrative fine-mapping analysis identified putative regulatory mechanisms for 21 AD risk loci, of which 18 were refined to a single gene, including 3 new candidate risk genes (KCNN4, FIBP and LRRC25). Transcription factor regulatory networks captured AD risk variation and identified SPI1 as a key putative regulator of microglia expression and AD risk. This comprehensive resource capturing variation in the human microglia regulome provides insights into the etiology of neurodegenerative disease.
Collapse
Affiliation(s)
- Roman Kosoy
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Biao Zeng
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Steven P Kleopoulos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Zhiping Shao
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jack Humphrey
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katia de Paiva Lopes
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Alexander W Charney
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Brian H Kopell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Towfique Raj
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | | | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA.
- Mental Illness Research Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA.
| |
Collapse
|
88
|
Microglia Phenotypes in Aging and Neurodegenerative Diseases. Cells 2022; 11:cells11132091. [PMID: 35805174 PMCID: PMC9266143 DOI: 10.3390/cells11132091] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 02/08/2023] Open
Abstract
Neuroinflammation is a hallmark of many neurodegenerative diseases (NDs) and plays a fundamental role in mediating the onset and progression of disease. Microglia, which function as first-line immune guardians of the central nervous system (CNS), are the central drivers of neuroinflammation. Numerous human postmortem studies and in vivo imaging analyses have shown chronically activated microglia in patients with various acute and chronic neuropathological diseases. While microglial activation is a common feature of many NDs, the exact role of microglia in various pathological states is complex and often contradictory. However, there is a consensus that microglia play a biphasic role in pathological conditions, with detrimental and protective phenotypes, and the overall response of microglia and the activation of different phenotypes depends on the nature and duration of the inflammatory insult, as well as the stage of disease development. This review provides a comprehensive overview of current research on the various microglia phenotypes and inflammatory responses in health, aging, and NDs, with a special emphasis on the heterogeneous phenotypic response of microglia in acute and chronic diseases such as hemorrhagic stroke (HS), Alzheimer’s disease (AD), and Parkinson’s disease (PD). The primary focus is translational research in preclinical animal models and bulk/single-cell transcriptome studies in human postmortem samples. Additionally, this review covers key microglial receptors and signaling pathways that are potential therapeutic targets to regulate microglial inflammatory responses during aging and in NDs. Additionally, age-, sex-, and species-specific microglial differences will be briefly reviewed.
Collapse
|
89
|
Lozupone M, Berardino G, Mollica A, Sardone R, Dibello V, Zupo R, Lampignano L, Castellana F, Bortone I, Stallone R, Daniele A, Altamura M, Bellomo A, Solfrizzi V, Panza F. ALZT-OP1: An experimental combination regimen for the treatment of Alzheimer's Disease. Expert Opin Investig Drugs 2022; 31:759-771. [PMID: 35758153 DOI: 10.1080/13543784.2022.2095261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION For Alzheimer's disease (AD) treatment, US FDA granted accelerated approval for aducanumab due to its amyloid-β (Aβ)-lowering effects, notwithstanding the reported poor correlation between amyloid plaque reduction and clinical change for this drug. The diversification of drug targets appears to be the future of the AD field and from this perspective, drugs modulating microglia dysfunction and combination treatment regimens offer some promise. AREAS COVERED The aim of the present article was to provide a comprehensive review of ALZT-OP1 (cromolyn sodium plus ibuprofen), an experimental combination treatment regimen for AD, discussing their mechanisms of action targeting Aβ and neuroinflammation, examining the role of microglia in AD and offering our own insights on the role of present and alternative approaches directed toward neuroinflammation. EXPERT OPINION Enrolling high-risk participants with elevated brain amyloid could help to slow cognitive decline in secondary prevention trials during AD preclinical stages. Long-term follow-up indicated that non-steroidal anti-inflammatory drugs use begun when the brain was still normal may benefit these patients, suggesting that the timing of therapy could be crucial. However, previous clinical failures and the present incomplete understanding of the Aβ pathophysiological role in AD put this novel experimental combination regimen at substantial risk of failure.
Collapse
Affiliation(s)
- Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Giuseppe Berardino
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, Foggia
| | - Anita Mollica
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, Foggia
| | - Rodolfo Sardone
- Unit of Research Methodology and Data Sciences for Population Health, National Institute of Gastroenterology and Research Hospital IRCCS "S. De Bellis" Castellana Grotte, Bari, Italy
| | - Vittorio Dibello
- Department of Orofacial Pain and Dysfunction, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Roberta Zupo
- Unit of Research Methodology and Data Sciences for Population Health, National Institute of Gastroenterology and Research Hospital IRCCS "S. De Bellis" Castellana Grotte, Bari, Italy
| | - Luisa Lampignano
- Unit of Research Methodology and Data Sciences for Population Health, National Institute of Gastroenterology and Research Hospital IRCCS "S. De Bellis" Castellana Grotte, Bari, Italy
| | - Fabio Castellana
- Unit of Research Methodology and Data Sciences for Population Health, National Institute of Gastroenterology and Research Hospital IRCCS "S. De Bellis" Castellana Grotte, Bari, Italy
| | - Ilaria Bortone
- Unit of Research Methodology and Data Sciences for Population Health, National Institute of Gastroenterology and Research Hospital IRCCS "S. De Bellis" Castellana Grotte, Bari, Italy
| | - Roberta Stallone
- Neuroscience and Education, Human Resources Excellence in Research, University of Foggia, Foggia, Italy
| | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, Rome, Italy.,Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
| | - Mario Altamura
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, Foggia
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, Foggia
| | - Vincenzo Solfrizzi
- "Cesare Frugoni" Internal and Geriatric Medicine and Memory Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Panza
- Unit of Research Methodology and Data Sciences for Population Health, National Institute of Gastroenterology and Research Hospital IRCCS "S. De Bellis" Castellana Grotte, Bari, Italy
| |
Collapse
|
90
|
Cholesterol and matrisome pathways dysregulated in astrocytes and microglia. Cell 2022; 185:2213-2233.e25. [PMID: 35750033 DOI: 10.1016/j.cell.2022.05.017] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/07/2020] [Accepted: 05/16/2022] [Indexed: 12/12/2022]
Abstract
The impact of apolipoprotein E ε4 (APOE4), the strongest genetic risk factor for Alzheimer's disease (AD), on human brain cellular function remains unclear. Here, we investigated the effects of APOE4 on brain cell types derived from population and isogenic human induced pluripotent stem cells, post-mortem brain, and APOE targeted replacement mice. Population and isogenic models demonstrate that APOE4 local haplotype, rather than a single risk allele, contributes to risk. Global transcriptomic analyses reveal human-specific, APOE4-driven lipid metabolic dysregulation in astrocytes and microglia. APOE4 enhances de novo cholesterol synthesis despite elevated intracellular cholesterol due to lysosomal cholesterol sequestration in astrocytes. Further, matrisome dysregulation is associated with upregulated chemotaxis, glial activation, and lipid biosynthesis in astrocytes co-cultured with neurons, which recapitulates altered astrocyte matrisome signaling in human brain. Thus, APOE4 initiates glia-specific cell and non-cell autonomous dysregulation that may contribute to increased AD risk.
Collapse
|
91
|
Region-Specific Characteristics of Astrocytes and Microglia: A Possible Involvement in Aging and Diseases. Cells 2022; 11:cells11121902. [PMID: 35741031 PMCID: PMC9220858 DOI: 10.3390/cells11121902] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Although different regions of the brain are dedicated to specific functions, the intra- and inter-regional heterogeneity of astrocytes and microglia in these regions has not yet been fully understood. Recently, an advancement in various technologies, such as single-cell RNA sequencing, has allowed for the discovery of astrocytes and microglia with distinct molecular fingerprints and varying functions in the brain. In addition, the regional heterogeneity of astrocytes and microglia exhibits different functions in several situations, such as aging and neurodegenerative diseases. Therefore, investigating the region-specific astrocytes and microglia is important in understanding the overall function of the brain. In this review, we summarize up-to-date research on various intra- and inter-regional heterogeneities of astrocytes and microglia, and provide information on how they can be applied to aging and neurodegenerative diseases.
Collapse
|
92
|
Mildenberger W, Stifter SA, Greter M. Diversity and function of brain-associated macrophages. Curr Opin Immunol 2022; 76:102181. [DOI: 10.1016/j.coi.2022.102181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 02/07/2023]
|
93
|
Zhang X, Zhang R, Nisa Awan MU, Bai J. The Mechanism and Function of Glia in Parkinson's Disease. Front Cell Neurosci 2022; 16:903469. [PMID: 35722618 PMCID: PMC9205200 DOI: 10.3389/fncel.2022.903469] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease that primarily affects elderly people. The mechanism on onset and progression of PD is unknown. Currently, there are no effective treatment strategies for PD. PD is thought to be the loss of midbrain dopaminergic neurons, but it has recently been discovered that glia also affects brain tissue homeostasis, defense, and repair in PD. The neurodegenerative process is linked to both losses of glial supportive-defensive functions and toxic gain of glial functions. In this article, we reviewed the roles of microglia, astrocytes, and oligodendrocytes in the development of PD, as well as the potential use of glia-related medications in PD treatment.
Collapse
|
94
|
Olajide OA, Iwuanyanwu VU, Banjo OW, Kato A, Penkova YB, Fleet GWJ, Nash RJ. Iminosugar Amino Acid idoBR1 Reduces Inflammatory Responses in Microglia. Molecules 2022; 27:3342. [PMID: 35630818 PMCID: PMC9143674 DOI: 10.3390/molecules27103342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background. Inflammation is reported to be a key factor in neurodegeneration. The microglia are immune cells present in the central nervous system; their activation results in the release of inflammatory cytokines and is thought to be related to aging and neurodegenerative disorders, such as Alzheimer's disease. (2) Methods. A mouse BV-2 microglia cell line was activated using LPS and the anti-inflammatory cucumber-derived iminosugar amino acid idoBR1, (2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid, was used alongside dexamethasone as the control to determine whether it could reduce the inflammatory responses. (3) Results. A dose-dependent reduction in the LPS-induced production of the proinflammatory factors TNFα, IL-6, and nitric oxide and the transcription factor NF-κB was found. (4) Conclusions. Further investigations of the anti-inflammatory effects of idoBR1 in other models of neurodegenerative diseases are warranted.
Collapse
Affiliation(s)
- Olumayokun A. Olajide
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK; (O.A.O.); (V.U.I.); (O.W.B.)
| | - Victoria U. Iwuanyanwu
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK; (O.A.O.); (V.U.I.); (O.W.B.)
| | - Owolabi W. Banjo
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK; (O.A.O.); (V.U.I.); (O.W.B.)
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan;
| | - Yana B. Penkova
- Phytoquest Limited, Plas Gogerddan, Aberystwyth SY23 3EB, UK;
| | - George W. J. Fleet
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK;
| | - Robert J. Nash
- Phytoquest Limited, Plas Gogerddan, Aberystwyth SY23 3EB, UK;
| |
Collapse
|
95
|
Rosmus DD, Lange C, Ludwig F, Ajami B, Wieghofer P. The Role of Osteopontin in Microglia Biology: Current Concepts and Future Perspectives. Biomedicines 2022; 10:biomedicines10040840. [PMID: 35453590 PMCID: PMC9027630 DOI: 10.3390/biomedicines10040840] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022] Open
Abstract
The innate immune landscape of the central nervous system (CNS), including the brain and the retina, consists of different myeloid cell populations with distinct tasks to fulfill. Whereas the CNS borders harbor extraparenchymal CNS-associated macrophages whose main duty is to build up a defense against invading pathogens and other damaging factors from the periphery, the resident immune cells of the CNS parenchyma and the retina, microglia, are highly dynamic cells with a plethora of functions during homeostasis and disease. Therefore, microglia are constantly sensing their environment and closely interacting with surrounding cells, which is in part mediated by soluble factors. One of these factors is Osteopontin (OPN), a multifunctional protein that is produced by different cell types in the CNS, including microglia, and is upregulated in neurodegenerative and neuroinflammatory conditions. In this review, we discuss the current literature about the interaction between microglia and OPN in homeostasis and several disease entities, including multiple sclerosis (MS), Alzheimer’s and cerebrovascular diseases (AD, CVD), amyotrophic lateral sclerosis (ALS), age-related macular degeneration (AMD) and diabetic retinopathy (DR), in the context of the molecular pathways involved in OPN signaling shaping the function of microglia. As nearly all CNS diseases are characterized by pathological alterations in microglial cells, accompanied by the disturbance of the homeostatic microglia phenotype, the emergence of disease-associated microglia (DAM) states and their interplay with factors shaping the DAM-signature, such as OPN, is of great interest for therapeutical interventions in the future.
Collapse
Affiliation(s)
| | - Clemens Lange
- Eye Center, Freiburg Medical Center, University of Freiburg, 79106 Freiburg, Germany; (C.L.); (F.L.)
- Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital, 48145 Muenster, Germany
| | - Franziska Ludwig
- Eye Center, Freiburg Medical Center, University of Freiburg, 79106 Freiburg, Germany; (C.L.); (F.L.)
| | - Bahareh Ajami
- Department of Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Peter Wieghofer
- Institute of Anatomy, Leipzig University, 04103 Leipzig, Germany;
- Cellular Neuroanatomy, Institute of Theoretical Medicine, Medical Faculty, Augsburg University, 86159 Augsburg, Germany
- Correspondence:
| |
Collapse
|
96
|
Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nat Neurosci 2022; 25:306-316. [PMID: 35260865 DOI: 10.1038/s41593-022-01022-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples.
Collapse
|
97
|
Microglial transcriptomics meets genetics: new disease leads. Nat Rev Neurol 2022; 18:191-192. [DOI: 10.1038/s41582-022-00633-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
98
|
Uranova N, Vikhreva O, Rakhmanova V. Specific interactions between microglia and oligodendrocytes in white matter in continuous schizophrenia. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:128-137. [DOI: 10.17116/jnevro2022122121128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|