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Juvenal G, Meinerz C, Ayupe AC, Campos HC, Reis EM, Longo BM, Pillat MM, Ulrich H. Bradykinin promotes immune responses in differentiated embryonic neurospheres carrying APP swe and PS1 dE9 mutations. Cell Biosci 2024; 14:82. [PMID: 38890712 PMCID: PMC11184896 DOI: 10.1186/s13578-024-01251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Neural progenitor cells (NPCs) can be cultivated from developing brains, reproducing many of the processes that occur during neural development. They can be isolated from a variety of animal models, such as transgenic mice carrying mutations in amyloid precursor protein (APP) and presenilin 1 and 2 (PSEN 1 and 2), characteristic of familial Alzheimer's disease (fAD). Modulating the development of these cells with inflammation-related peptides, such as bradykinin (BK) and its antagonist HOE-140, enables the understanding of the impact of such molecules in a relevant AD model. RESULTS We performed a global gene expression analysis on transgenic neurospheres treated with BK and HOE-140. To validate the microarray data, quantitative real-time reverse-transcription polymerase chain reaction (RT-PCR) was performed on 8 important genes related to the immune response in AD such as CCL12, CCL5, CCL3, C3, CX3CR1, TLR2 and TNF alpha and Iba-1. Furthermore, comparative analysis of the transcriptional profiles was performed between treatments, including gene ontology and reactome enrichment, construction and analysis of protein-protein interaction networks and, finally, comparison of our data with human dataset from AD patients. The treatments affected the expression levels of genes mainly related to microglia-mediated neuroinflammatory responses, with BK promoting an increase in the expression of genes that enrich processes, biological pathways, and cellular components related to immune dysfunction, neurodegeneration and cell cycle. B2 receptor inhibition by HOE-140 resulted in the reduction of AD-related anomalies caused in this system. CONCLUSIONS BK is an important immunomodulatory agent and enhances the immunological changes identified in transgenic neurospheres carrying the genetic load of AD. Bradykinin treatments modulate the expression rates of genes related to microglia-mediated neuroinflammation. Inhibiting bradykinin activity in Alzheimer's disease may slow disease progression.
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Affiliation(s)
- Guilherme Juvenal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil
| | - Carine Meinerz
- Department of Microbiology and Parasitology, Health Sciences Center, Federal University of Santa Maria, Santa Maria-RS, Brazil
| | - Ana Carolina Ayupe
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil
| | | | - Eduardo Moraes Reis
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil
| | | | - Micheli Mainardi Pillat
- Department of Microbiology and Parasitology, Health Sciences Center, Federal University of Santa Maria, Santa Maria-RS, Brazil.
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, 05508-900, Brazil.
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Zhou X, Song H, He J, Han W, Li Q. Deciphering microglial activation and neuronal apoptosis post‑traumatic brain injury: The role of TYROBP in inflammation regulation networks. Mol Med Rep 2024; 29:104. [PMID: 38639190 PMCID: PMC11063751 DOI: 10.3892/mmr.2024.13228] [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: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 04/20/2024] Open
Abstract
Traumatic Brain Injury (TBI) represents a significant public health challenge. Recovery from brain injury necessitates the collaborative efforts of various resident neural cells, predominantly microglia. The present study analyzed rat and mouse RNA expression micro‑arrays, high‑throughput RNA sequencing and single‑cell sequencing data sourced from public databases. To construct an inflammation regulation network around TYRO protein tyrosine kinase‑binding protein (TYROBP), to evaluate the role of TYROBP in cell death after TBI. These findings indicate that following TBI, neurons predominantly communicate with one another through the CXC chemokine ligand (CXCL) and CC chemokine ligand (CCL) signaling pathways, employing a paracrine mechanism to activate microglia. These activated microglia intensify the pathological progression of brain injury by releasing factors such as tumor necrosis factor α (TNF‑α), vascular endothelial growth factor and transforming growth factor β via the NF‑κB pathway. Cells co‑culture experiments demonstrated that neurons, impaired by mechanical injury, interact with microglia through non‑contact mechanisms. Activated microglia secrete cytokines, including TNF‑α, CXCL‑8 and CCL2, which trigger an inflammatory response and facilitate neuronal apoptosis. TYROBP gene knockout in microglia was demonstrated to reduce this interaction and reduce neuronal cell apoptosis rates.
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Affiliation(s)
- Xudong Zhou
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Emergency Department, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, P.R. China
| | - Huiping Song
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Jingjing He
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Wei Han
- Emergency Department, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, P.R. China
| | - Qin Li
- The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
- Emergency Department, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, P.R. China
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Kim B, Dabin LC, Tate MD, Karahan H, Sharify AD, Acri DJ, Al-Amin MM, Philtjens S, Smith DC, Wijeratne HRS, Park JH, Jucker M, Kim J. Effects of SPI1-mediated transcriptome remodeling on Alzheimer's disease-related phenotypes in mouse models of Aβ amyloidosis. Nat Commun 2024; 15:3996. [PMID: 38734693 PMCID: PMC11088624 DOI: 10.1038/s41467-024-48484-x] [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: 07/05/2023] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
SPI1 was recently reported as a genetic risk factor for Alzheimer's disease (AD) in large-scale genome-wide association studies. However, it is unknown whether SPI1 should be downregulated or increased to have therapeutic benefits. To investigate the effect of modulating SPI1 levels on AD pathogenesis, we performed extensive biochemical, histological, and transcriptomic analyses using both Spi1-knockdown and Spi1-overexpression mouse models. Here, we show that the knockdown of Spi1 expression significantly exacerbates insoluble amyloid-β (Aβ) levels, amyloid plaque deposition, and gliosis. Conversely, overexpression of Spi1 significantly ameliorates these phenotypes and dystrophic neurites. Further mechanistic studies using targeted and single-cell transcriptomics approaches demonstrate that altered Spi1 expression modulates several pathways, such as immune response pathways and complement system. Our data suggest that transcriptional reprogramming by targeting transcription factors, like Spi1, might hold promise as a therapeutic strategy. This approach could potentially expand the current landscape of druggable targets for AD.
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Affiliation(s)
- Byungwook Kim
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Luke Child Dabin
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mason Douglas Tate
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Hande Karahan
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ahmad Daniel Sharify
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dominic J Acri
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Md Mamun Al-Amin
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Stéphanie Philtjens
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Daniel Curtis Smith
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - H R Sagara Wijeratne
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jung Hyun Park
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 47405, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA
| | - Mathias Jucker
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Jungsu Kim
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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de Vries LE, Huitinga I, Kessels HW, Swaab DF, Verhaagen J. The concept of resilience to Alzheimer's Disease: current definitions and cellular and molecular mechanisms. Mol Neurodegener 2024; 19:33. [PMID: 38589893 PMCID: PMC11003087 DOI: 10.1186/s13024-024-00719-7] [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: 08/23/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Some individuals are able to maintain their cognitive abilities despite the presence of significant Alzheimer's Disease (AD) neuropathological changes. This discrepancy between cognition and pathology has been labeled as resilience and has evolved into a widely debated concept. External factors such as cognitive stimulation are associated with resilience to AD, but the exact cellular and molecular underpinnings are not completely understood. In this review, we discuss the current definitions used in the field, highlight the translational approaches used to investigate resilience to AD and summarize the underlying cellular and molecular substrates of resilience that have been derived from human and animal studies, which have received more and more attention in the last few years. From these studies the picture emerges that resilient individuals are different from AD patients in terms of specific pathological species and their cellular reaction to AD pathology, which possibly helps to maintain cognition up to a certain tipping point. Studying these rare resilient individuals can be of great importance as it could pave the way to novel therapeutic avenues for AD.
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Affiliation(s)
- Luuk E de Vries
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands.
| | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Helmut W Kessels
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, Netherlands
| | - Joost Verhaagen
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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Wißfeld J, Abou Assale T, Cuevas-Rios G, Liao H, Neumann H. Therapeutic potential to target sialylation and SIGLECs in neurodegenerative and psychiatric diseases. Front Neurol 2024; 15:1330874. [PMID: 38529039 PMCID: PMC10961342 DOI: 10.3389/fneur.2024.1330874] [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: 10/31/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Sialic acids, commonly found as the terminal carbohydrate on the glycocalyx of mammalian cells, are pivotal checkpoint inhibitors of the innate immune system, particularly within the central nervous system (CNS). Sialic acid-binding immunoglobulin-like lectins (SIGLECs) expressed on microglia are key players in maintaining microglial homeostasis by recognizing intact sialylation. The finely balanced sialic acid-SIGLEC system ensures the prevention of excessive and detrimental immune responses in the CNS. However, loss of sialylation and SIGLEC receptor dysfunctions contribute to several chronic CNS diseases. Genetic variants of SIGLEC3/CD33, SIGLEC11, and SIGLEC14 have been associated with neurodegenerative diseases such as Alzheimer's disease, while sialyltransferase ST8SIA2 and SIGLEC4/MAG have been linked to psychiatric diseases such as schizophrenia, bipolar disorders, and autism spectrum disorders. Consequently, immune-modulatory functions of polysialic acids and SIGLEC binding antibodies have been exploited experimentally in animal models of Alzheimer's disease and inflammation-induced CNS tissue damage, including retinal damage. While the potential of these therapeutic approaches is evident, only a few therapies to target either sialylation or SIGLEC receptors have been tested in patient clinical trials. Here, we provide an overview of the critical role played by the sialic acid-SIGLEC axis in shaping microglial activation and function within the context of neurodegeneration and synaptopathies and discuss the current landscape of therapies that target sialylation or SIGLECs.
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Affiliation(s)
- Jannis Wißfeld
- Institute of Reconstructive Neurobiology, Medical Faculty and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Tawfik Abou Assale
- Institute of Reconstructive Neurobiology, Medical Faculty and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - German Cuevas-Rios
- Institute of Reconstructive Neurobiology, Medical Faculty and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Huan Liao
- Florey Institute of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Harald Neumann
- Institute of Reconstructive Neurobiology, Medical Faculty and University Hospital Bonn, University of Bonn, Bonn, Germany
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Creus-Muncunill J, Haure-Mirande JV, Mattei D, Bons J, Ramirez AV, Hamilton BW, Corwin C, Chowdhury S, Schilling B, Ellerby LM, Ehrlich ME. TYROBP/DAP12 knockout in Huntington's disease Q175 mice cell-autonomously decreases microglial expression of disease-associated genes and non-cell-autonomously mitigates astrogliosis and motor deterioration. J Neuroinflammation 2024; 21:66. [PMID: 38459557 PMCID: PMC10924371 DOI: 10.1186/s12974-024-03052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG trinucleotide repeat in the Huntingtin gene (HTT). Immune activation is abundant in the striatum of HD patients. Detection of active microglia at presymptomatic stages suggests that microgliosis is a key early driver of neuronal dysfunction and degeneration. Recent studies showed that deletion of Tyrobp, a microglial protein, ameliorates neuronal dysfunction in Alzheimer's disease amyloidopathy and tauopathy mouse models while decreasing components of the complement subnetwork. OBJECTIVE While TYROBP/DAP12-mediated microglial activation is detrimental for some diseases such as peripheral nerve injury, it is beneficial for other diseases. We sought to determine whether the TYROBP network is implicated in HD and whether Tyrobp deletion impacts HD striatal function and transcriptomics. METHODS To test the hypothesis that Tyrobp deficiency would be beneficial in an HD model, we placed the Q175 HD mouse model on a Tyrobp-null background. We characterized these mice with a combination of behavioral testing, immunohistochemistry, transcriptomic and proteomic profiling. Further, we evaluated the gene signature in isolated Q175 striatal microglia, with and without Tyrobp. RESULTS Comprehensive analysis of publicly available human HD transcriptomic data revealed that the TYROBP network is overactivated in the HD putamen. The Q175 mice showed morphologic microglial activation, reduced levels of post-synaptic density-95 protein and motor deficits at 6 and 9 months of age, all of which were ameliorated on the Tyrobp-null background. Gene expression analysis revealed that lack of Tyrobp in the Q175 model does not prevent the decrease in the expression of striatal neuronal genes but reduces pro-inflammatory pathways that are specifically active in HD human brain, including genes identified as detrimental in neurodegenerative diseases, e.g. C1q and members of the Ccr5 signaling pathway. Integration of transcriptomic and proteomic data revealed that astrogliosis and complement system pathway were reduced after Tyrobp deletion, which was further validated by immunofluorescence analysis. CONCLUSIONS Our data provide molecular and functional support demonstrating that Tyrobp deletion prevents many of the abnormalities in the HD Q175 mouse model, suggesting that the Tyrobp pathway is a potential therapeutic candidate for Huntington's disease.
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Affiliation(s)
| | | | - Daniele Mattei
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Angie V Ramirez
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - B Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Chuhyon Corwin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sarah Chowdhury
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | | | | | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA.
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7
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Batista AF, Khan KA, Papavergi MT, Lemere CA. The Importance of Complement-Mediated Immune Signaling in Alzheimer's Disease Pathogenesis. Int J Mol Sci 2024; 25:817. [PMID: 38255891 PMCID: PMC10815224 DOI: 10.3390/ijms25020817] [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: 12/16/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
As an essential component of our innate immune system, the complement system is responsible for our defense against pathogens. The complement cascade has complex roles in the central nervous system (CNS), most of what we know about it stems from its role in brain development. However, in recent years, numerous reports have implicated the classical complement cascade in both brain development and decline. More specifically, complement dysfunction has been implicated in neurodegenerative disorders, such as Alzheimer's disease (AD), which is the most common form of dementia. Synapse loss is one of the main pathological hallmarks of AD and correlates with memory impairment. Throughout the course of AD progression, synapses are tagged with complement proteins and are consequently removed by microglia that express complement receptors. Notably, astrocytes are also capable of secreting signals that induce the expression of complement proteins in the CNS. Both astrocytes and microglia are implicated in neuroinflammation, another hallmark of AD pathogenesis. In this review, we provide an overview of previously known and newly established roles for the complement cascade in the CNS and we explore how complement interactions with microglia, astrocytes, and other risk factors such as TREM2 and ApoE4 modulate the processes of neurodegeneration in both amyloid and tau models of AD.
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Affiliation(s)
- André F. Batista
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
| | - Khyrul A. Khan
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
| | - Maria-Tzousi Papavergi
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Cynthia A. Lemere
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (A.F.B.); (K.A.K.); (M.-T.P.)
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Nies YH, Yahaya MF, Lim WL, Teoh SL. Microarray-based Analysis of Differential Gene Expression Profile in Rotenone-induced Parkinson's Disease Zebrafish Model. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:761-772. [PMID: 37291778 DOI: 10.2174/1871527322666230608122552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND & OBJECTIVES Despite much clinical and laboratory research that has been performed to explore the mechanisms of Parkinson's disease (PD), its pathogenesis remains elusive to date. Therefore, this study aimed to identify possible regulators of neurodegeneration by performing microarray analysis of the zebrafish PD model's brain following rotenone exposure. METHODS A total of 36 adult zebrafish were divided into two groups: control (n = 17) and rotenonetreated (n = 19). Fish were treated with rotenone water (5 μg/L water) for 28 days and subjected to locomotor behavior analysis. Total RNA was extracted from the brain tissue after rotenone treatment. The cDNA synthesized was subjected to microarray analysis and subsequently validated by qPCR. RESULTS Administration of rotenone has significantly reduced locomotor activity in zebrafish (p < 0.05), dysregulated dopamine-related gene expression (dat, th1, and th2, p < 0.001), and reduced dopamine level in the brain (p < 0.001). In the rotenone-treated group, genes involved in cytotoxic T lymphocytes (gzm3, cd8a, p < 0.001) and T cell receptor signaling (themis, lck, p < 0.001) were upregulated significantly. Additionally, gene expression involved in microgliosis regulation (tyrobp, p < 0.001), cellular response to IL-1 (ccl34b4, il2rb, p < 0.05), and regulation of apoptotic process (dedd1, p < 0.001) were also upregulated significantly. CONCLUSION The mechanisms of T cell receptor signaling, microgliosis regulation, cellular response to IL-1, and apoptotic signaling pathways have potentially contributed to PD development in rotenonetreated zebrafish.
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Affiliation(s)
- Yong Hui Nies
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Mohamad Fairuz Yahaya
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Wei Ling Lim
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor, Malaysia
| | - Seong Lin Teoh
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Chen H, Fan L, Guo Q, Wong MY, Yu F, Foxe N, Wang W, Nessim A, Carling G, Liu B, Lopez-Lee C, Huang Y, Amin S, Patel T, Mok SA, Song WM, Zhang B, Ma Q, Fu H, Gan L, Luo W. DAP12 deficiency alters microglia-oligodendrocyte communication and enhances resilience against tau toxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563970. [PMID: 37961594 PMCID: PMC10634844 DOI: 10.1101/2023.10.26.563970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Pathogenic tau accumulation fuels neurodegeneration in Alzheimer's disease (AD). Enhancing aging brain's resilience to tau pathology would lead to novel therapeutic strategies. DAP12 (DNAX-activation protein 12) is critically involved in microglial immune responses. Previous studies have showed that mice lacking DAP12 in tauopathy mice exhibit higher tau pathology but are protected from tau-induced cognitive deficits. However, the exact mechanism remains elusive. Our current study uncovers a novel resilience mechanism via microglial interaction with oligodendrocytes. Despite higher tau inclusions, Dap12 deletion curbs tau-induced brain inflammation and ameliorates myelin and synapse loss. Specifically, removal of Dap12 abolished tau-induced disease-associated clusters in microglia (MG) and intermediate oligodendrocytes (iOli), which are spatially correlated with tau pathology in AD brains. Our study highlights the critical role of interactions between microglia and oligodendrocytes in tau toxicity and DAP12 signaling as a promising target for enhancing resilience in AD.
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Affiliation(s)
- Hao Chen
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Li Fan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Qi Guo
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Man Ying Wong
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Fangmin Yu
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nessa Foxe
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | | | - Aviram Nessim
- The State University of New York at Stony Brook, Long Island, New York, USA
| | - Gillian Carling
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Bangyan Liu
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Chloe Lopez-Lee
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Yige Huang
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Sadaf Amin
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Tark Patel
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB Canada
| | - Sue-Ann Mok
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB Canada
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Hongjun Fu
- Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Li Gan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Millburn High School, New Jersey, NJ, USA
| | - Wenjie Luo
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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10
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Chen H, Fan L, Guo Q, Wong MY, Yu F, Foxe N, Wang W, Nessim A, Carling G, Liu B, Lopez-Lee C, Huang Y, Amin S, Mok SA, Song WM, Zhang B, Ma Q, Fu H, Gan L, Luo W. DAP12 deficiency alters microglia-oligodendrocyte communication and enhances resilience against tau toxicity. RESEARCH SQUARE 2023:rs.3.rs-3454358. [PMID: 37961627 PMCID: PMC10635319 DOI: 10.21203/rs.3.rs-3454358/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Pathogenic tau accumulation fuels neurodegeneration in Alzheimer's disease (AD). Enhancing aging brain's resilience to tau pathology would lead to novel therapeutic strategies. DAP12 (DNAX-activation protein 12) is critically involved in microglial immune responses. Previous studies have showed that mice lacking DAP12 in tauopathy mice exhibit higher tau pathology but are protected from tau-induced cognitive deficits. However, the exact mechanism remains elusive. Our current study uncovers a novel resilience mechanism via microglial interaction with oligodendrocytes. Despite higher tau inclusions, Dap12 deletion curbs tau-induced brain inflammation and ameliorates myelin and synapse loss. Specifically, removal of Dap12 abolished tau-induced disease-associated clusters in microglia (MG) and intermediate oligodendrocytes (iOli), which are spatially correlated with tau pathology in AD brains. Our study highlights the critical role of interactions between microglia and oligodendrocytes in tau toxicity and DAP12 signaling as a promising target for enhancing resilience in AD.
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Affiliation(s)
- Hao Chen
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Li Fan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Qi Guo
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Man Ying Wong
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Fangmin Yu
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Nessa Foxe
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | | | - Aviram Nessim
- The State University of New York at Stony Brook, Long Island, New York, USA
| | - Gillian Carling
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Bangyan Liu
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Chloe Lopez-Lee
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Yige Huang
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Program of Neuroscience, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Sadaf Amin
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Sue-Ann Mok
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB Canada
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Hongjun Fu
- Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Li Gan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Millburn High School, New Jersey, NJ, USA
| | - Wenjie Luo
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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11
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Xie Z, Meng J, Wu Z, Nakanishi H, Hayashi Y, Kong W, Lan F, Narengaowa, Yang Q, Qing H, Ni J. The Dual Nature of Microglia in Alzheimer's Disease: A Microglia-Neuron Crosstalk Perspective. Neuroscientist 2023; 29:616-638. [PMID: 35348415 DOI: 10.1177/10738584211070273] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microglia are critical players in the neuroimmune system, and their involvement in Alzheimer's disease (AD) pathogenesis is increasingly being recognized. However, whether microglia play a positive or negative role in AD remains largely controversial and the precise molecular targets for intervention are not well defined. This partly results from the opposing roles of microglia in AD pathology, and is mainly reflected in the microglia-neuron interaction. Microglia can prune synapses resulting in excessive synapse loss and neuronal dysfunction, but they can also promote synapse formation, enhancing neural network plasticity. Neuroimmune crosstalk accelerates microglial activation, which induces neuron death and enhances the microglial phagocytosis of β-amyloid to protect neurons. Moreover, microglia have dual opposing roles in developing the major pathological features in AD, such as amyloid deposition and blood-brain barrier permeability. This review summarizes the dual opposing role of microglia in AD from the perspective of the interaction between neurons and microglia. Additionally, current AD treatments targeting microglia and the advantages and disadvantages of developing microglia-targeted therapeutic strategies are discussed.
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Affiliation(s)
- Zhen Xie
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Department of Biology, Beijing Institute of Technology, Beijing, China
- Research Center for Resource Peptide Drugs, Shanxi Engineering & Technological Research Center for Conversation & Utilization of Regional Biological Resources, Yanan University, Yanan, China
| | - Jie Meng
- Department of Neurology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Zhou Wu
- Department of Aging Science and Pharmacology, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
- OBT Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Hiroshi Nakanishi
- Department of Pharmacology, Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Yoshinori Hayashi
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Wei Kong
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Department of Biology, Beijing Institute of Technology, Beijing, China
| | - Fei Lan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Department of Biology, Beijing Institute of Technology, Beijing, China
| | - Narengaowa
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Department of Biology, Beijing Institute of Technology, Beijing, China
| | - Qinghu Yang
- Research Center for Resource Peptide Drugs, Shanxi Engineering & Technological Research Center for Conversation & Utilization of Regional Biological Resources, Yanan University, Yanan, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Department of Biology, Beijing Institute of Technology, Beijing, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Department of Biology, Beijing Institute of Technology, Beijing, China
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12
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Wu H, Wang J, Hu X, Zhuang C, Zhou J, Wu P, Li S, Zhao RC. Comprehensive transcript-level analysis reveals transcriptional reprogramming during the progression of Alzheimer's disease. Front Aging Neurosci 2023; 15:1191680. [PMID: 37396652 PMCID: PMC10308376 DOI: 10.3389/fnagi.2023.1191680] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Background Alzheimer's disease (AD) is a common neurodegenerative disorder that has a multi-step disease progression. Differences between moderate and advanced stages of AD have not yet been fully characterized. Materials and methods Herein, we performed a transcript-resolution analysis in 454 AD-related samples, including 145 non-demented control, 140 asymptomatic AD (AsymAD), and 169 AD samples. We comparatively characterized the transcriptome dysregulation in AsymAD and AD samples at transcript level. Results We identified 4,056 and 1,200 differentially spliced alternative splicing events (ASEs) that might play roles in the disease progression of AsymAD and AD, respectively. Our further analysis revealed 287 and 222 isoform switching events in AsymAD and AD, respectively. In particular, a total of 163 and 119 transcripts showed increased usage, while 124 and 103 transcripts exhibited decreased usage in AsymAD and AD, respectively. For example, gene APOA2 showed no expression changes between AD and non-demented control samples, but expressed higher proportion of transcript ENST00000367990.3 and lower proportion of transcript ENST00000463812.1 in AD compared to non-demented control samples. Furthermore, we constructed RNA binding protein (RBP)-ASE regulatory networks to reveal potential RBP-mediated isoform switch in AsymAD and AD. Conclusion In summary, our study provided transcript-resolution insights into the transcriptome disturbance of AsymAD and AD, which will promote the discovery of early diagnosis biomarkers and the development of new therapeutic strategies for patients with AD.
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Affiliation(s)
- Hao Wu
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Xiaoyuan Hu
- H. Milton Stewart School of Industrial and Systems Engineering, College of Engineering, Geogia Institute of Technology, Atlanta, GA, United States
| | - Cheng Zhuang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jianxin Zhou
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Peiru Wu
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Institute for Clinical Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Robert Chunhua Zhao
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
- School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China
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13
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Castranio EL, Hasel P, Haure-Mirande JV, Ramirez Jimenez AV, Hamilton BW, Kim RD, Glabe CG, Wang M, Zhang B, Gandy S, Liddelow SA, Ehrlich ME. Microglial INPP5D limits plaque formation and glial reactivity in the PSAPP mouse model of Alzheimer's disease. Alzheimers Dement 2023; 19:2239-2252. [PMID: 36448627 PMCID: PMC10481344 DOI: 10.1002/alz.12821] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 12/05/2022]
Abstract
INTRODUCTION The inositol polyphosphate-5-phosphatase D (INPP5D) gene encodes a dual-specificity phosphatase that can dephosphorylate both phospholipids and phosphoproteins. Single nucleotide polymorphisms in INPP5D impact risk for developing late onset sporadic Alzheimer's disease (LOAD). METHODS To assess the consequences of inducible Inpp5d knockdown in microglia of APPKM670/671NL /PSEN1Δexon9 (PSAPP) mice, we injected 3-month-old Inpp5dfl/fl /Cx3cr1CreER/+ and PSAPP/Inpp5dfl/fl /Cx3cr1CreER/+ mice with either tamoxifen (TAM) or corn oil (CO) to induce recombination. RESULTS At age 6 months, we found that the percent area of 6E10+ deposits and plaque-associated microglia in Inpp5d knockdown mice were increased compared to controls. Spatial transcriptomics identified a plaque-specific expression profile that was extensively altered by Inpp5d knockdown. DISCUSSION These results demonstrate that conditional Inpp5d downregulation in the PSAPP mouse increases plaque burden and recruitment of microglia to plaques. Spatial transcriptomics highlighted an extended gene expression signature associated with plaques and identified CST7 (cystatin F) as a novel marker of plaques. HIGHLIGHTS Inpp5d knockdown increases plaque burden and plaque-associated microglia number. Spatial transcriptomics identifies an expanded plaque-specific gene expression profile. Plaque-induced gene expression is altered by Inpp5d knockdown in microglia. Our plaque-associated gene signature overlaps with human Alzheimer's disease gene networks.
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Affiliation(s)
- Emilie L. Castranio
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
| | - Philip Hasel
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
| | | | | | - B. Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
| | - Rachel D. Kim
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
| | - Charles G. Glabe
- Department of Molecular Biology and Biochemistry,
University of California, Irvine, Irvine, California, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
- Department of Psychiatry and Alzheimer’s Disease
Research Center, Icahn School of Medicine at Mount Sinai, New York, New York,
USA
- James J. Peters VA Medical Center, Bronx, New York,
USA
| | - Shane A. Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine,
New York, New York, USA
- Department of Neuroscience & Physiology, NYU Grossman
School of Medicine, New York, New York, USA
- Department of Ophthalmology, NYU Grossman School of
Medicine, New York, New York, USA
- Parekh Center for Interdisciplinary Neurology, NYU Grossman
School of Medicine, New York, New York, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount
Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York, USA
- Department of Pediatrics, Icahn School of Medicine at
Mount Sinai, New York, New York, USA
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14
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Iguchi A, Takatori S, Kimura S, Muneto H, Wang K, Etani H, Ito G, Sato H, Hori Y, Sasaki J, Saito T, Saido TC, Ikezu T, Takai T, Sasaki T, Tomita T. INPP5D modulates TREM2 loss-of-function phenotypes in a β-amyloidosis mouse model. iScience 2023; 26:106375. [PMID: 37035000 PMCID: PMC10074152 DOI: 10.1016/j.isci.2023.106375] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
The genetic associations of TREM2 loss-of-function variants with Alzheimer disease (AD) indicate the protective roles of microglia in AD pathogenesis. Functional deficiencies of TREM2 disrupt microglial clustering around amyloid β (Aβ) plaques, impair their transcriptional response to Aβ, and worsen neuritic dystrophy. However, the molecular mechanism underlying these phenotypes remains unclear. In this study, we investigated the pathological role of another AD risk gene, INPP5D, encoding a phosphoinositide PI(3,4,5)P3 phosphatase expressed in microglia. In a Tyrobp-deficient TREM2 loss-of-function mouse model, Inpp5d haplodeficiency restored the association of microglia with Aβ plaques, partially restored plaque compaction, and astrogliosis, and reduced phosphorylated tau+ dystrophic neurites. Mechanistic analyses suggest that TREM2/TYROBP and INPP5D exert opposing effects on PI(3,4,5)P3 signaling pathways as well as on phosphoproteins involved in the actin assembly. Our results suggest that INPP5D acts downstream of TREM2/TYROBP to regulate the microglial barrier against Aβ toxicity, thereby modulates Aβ-dependent pathological conversion of tau.
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Affiliation(s)
- Akihiro Iguchi
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shingo Kimura
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki Muneto
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kai Wang
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hayato Etani
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
| | - Haruaki Sato
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yukiko Hori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junko Sasaki
- Department of Lipid Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8601, Japan
| | - Takaomi C. Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tsuneya Ikezu
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Toshiyuki Takai
- Department of Experimental Immunology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo, Sendai 980-8575, Japan
| | - Takehiko Sasaki
- Department of Lipid Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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Doust YV, Bindoff A, Holloway OG, Wilson R, King AE, Ziebell JM. Temporal changes in the microglial proteome of male and female mice after a diffuse brain injury using label-free quantitative proteomics. Glia 2023; 71:880-903. [PMID: 36468604 PMCID: PMC10952308 DOI: 10.1002/glia.24313] [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: 05/27/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Traumatic brain injury (TBI) triggers neuroinflammatory cascades mediated by microglia, which promotes tissue repair in the short-term. These cascades may exacerbate TBI-induced tissue damage and symptoms in the months to years post-injury. However, the progression of the microglial function across time post-injury and whether this differs between biological sexes is not well understood. In this study, we examined the microglial proteome at 3-, 7-, or 28-days after a midline fluid percussion injury (mFPI) in male and female mice using label-free quantitative proteomics. Data are available via ProteomeXchange with identifier PXD033628. We identified a reduction in microglial proteins involved with clearance of neuronal debris via phagocytosis at 3- and 7-days post-injury. At 28 days post-injury, pro-inflammatory proteins were decreased and anti-inflammatory proteins were increased in microglia. These results indicate a reduction in microglial clearance of neuronal debris in the days post-injury with a shift to anti-inflammatory function by 28 days following TBI. The changes in the microglial proteome that occurred across time post-injury did not differ between biological sexes. However, we did identify an increase in microglial proteins related to pro-inflammation and phagocytosis as well as insulin and estrogen signaling in males compared with female mice that occurred with or without a brain injury. Although the microglial response was similar between males and females up to 28 days following TBI, biological sex differences in the microglial proteome, regardless of TBI, has implications for the efficacy of treatment strategies targeting the microglial response post-injury.
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Affiliation(s)
- Yasmine V. Doust
- Wicking Dementia Research and Education Centre, College of Health and MedicineUniversity of TasmaniaHobartTasmaniaAustralia
| | - Aidan Bindoff
- Wicking Dementia Research and Education Centre, College of Health and MedicineUniversity of TasmaniaHobartTasmaniaAustralia
| | - Olivia G. Holloway
- Wicking Dementia Research and Education Centre, College of Health and MedicineUniversity of TasmaniaHobartTasmaniaAustralia
| | - Richard Wilson
- Central Science Laboratory (CSL)University of TasmaniaHobartTasmaniaAustralia
| | - Anna E. King
- Wicking Dementia Research and Education Centre, College of Health and MedicineUniversity of TasmaniaHobartTasmaniaAustralia
| | - Jenna M. Ziebell
- Wicking Dementia Research and Education Centre, College of Health and MedicineUniversity of TasmaniaHobartTasmaniaAustralia
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16
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Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
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Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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17
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Ming C, Wang M, Wang Q, Neff R, Wang E, Shen Q, Reddy JS, Wang X, Allen M, Ertekin‐Taner N, De Jager PL, Bennett DA, Haroutunian V, Schadt E, Zhang B. Whole genome sequencing-based copy number variations reveal novel pathways and targets in Alzheimer's disease. Alzheimers Dement 2022; 18:1846-1867. [PMID: 34918867 PMCID: PMC9264340 DOI: 10.1002/alz.12507] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 01/28/2023]
Abstract
INTRODUCTION A few copy number variations (CNVs) have been reported for Alzheimer's disease (AD). However, there is a lack of a systematic investigation of CNVs in AD based on whole genome sequencing (WGS) data. METHODS We used four methods to identify consensus CNVs from the WGS data of 1,411 individuals and further investigated their functional roles in AD using the matched transcriptomic and clinicopathological data. RESULTS We identified 3,012 rare AD-specific CNVs whose residing genes are enriched for cellular glucuronidation and neuron projection pathways. Genes whose mRNA expressions are significantly correlated with common CNVs are involved in major histocompatibility complex class II receptor activity. Integration of CNVs, gene expression, and clinical and pathological traits further pinpoints a key CNV that potentially regulates immune response in AD. DISCUSSION We identify CNVs as potential genetic regulators of immune response in AD. The identified CNVs and their downstream gene networks reveal novel pathways and targets for AD.
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Affiliation(s)
- Chen Ming
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Minghui Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Qian Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ryan Neff
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Erming Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Qi Shen
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Joseph S. Reddy
- Department of Quantitative Health SciencesMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Xue Wang
- Department of Quantitative Health SciencesMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
- Department of NeurologyMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Philip L. De Jager
- Center for Translational & Computational NeuroimmunologyDepartment of Neurology and the Taub InstituteColumbia University Medical CenterNew YorkNew YorkUSA
- The Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Vahram Haroutunian
- Nash Family Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Alzheimer's Disease Research CenterIcahn School of Medicine at Mount SinaiNew YorkNew York
- PsychiatryJJ Peters VA Medical CenterBronxNew YorkUSA
| | - Eric Schadt
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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18
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Haure-Mirande JV, Audrain M, Ehrlich ME, Gandy S. Microglial TYROBP/DAP12 in Alzheimer's disease: Transduction of physiological and pathological signals across TREM2. Mol Neurodegener 2022; 17:55. [PMID: 36002854 PMCID: PMC9404585 DOI: 10.1186/s13024-022-00552-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
TYROBP (also known as DAP12 or KARAP) is a transmembrane adaptor protein initially described as a receptor-activating subunit component of natural killer (NK) cells. TYROBP is expressed in numerous cell types, including peripheral blood monocytes, macrophages, dendritic cells, and osteoclasts, but a key point of recent interest is related to the critical role played by TYROBP in the function of many receptors expressed on the plasma membrane of microglia. TYROBP is the downstream adaptor and putative signaling partner for several receptors implicated in Alzheimer's disease (AD), including SIRP1β, CD33, CR3, and TREM2. TYROBP has received much of its current notoriety because of its importance in brain homeostasis by signal transduction across those receptors. In this review, we provide an overview of evidence indicating that the biology of TYROBP extends beyond its interaction with these four ligand-binding ectodomain-intramembranous domain molecules. In addition to reviewing the structure and localization of TYROBP, we discuss our recent progress using mouse models of either cerebral amyloidosis or tauopathy that were engineered to be TYROBP-deficient or TYROBP-overexpressing. Remarkably, constitutively TYROBP-deficient mice provided a model of genetic resilience to either of the defining proteinopathies of AD. Learning behavior and synaptic electrophysiological function were preserved at normal physiological levels even in the face of robust cerebral amyloidosis (in APP/PSEN1;Tyrobp-/- mice) or tauopathy (in MAPTP301S;Tyrobp-/- mice). A fundamental underpinning of the functional synaptic dysfunction associated with each proteotype was an accumulation of complement C1q. TYROBP deficiency prevented C1q accumulation associated with either proteinopathy. Based on these data, we speculate that TYROBP plays a key role in the microglial sensome and the emergence of the disease-associated microglia (DAM) phenotype. TYROBP may also play a key role in the loss of markers of synaptic integrity (e.g., synaptophysin-like immunoreactivity) that has long been held to be the feature of human AD molecular neuropathology that most closely correlates with concurrent clinical cognitive function.
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Affiliation(s)
| | - Mickael Audrain
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Psychiatry and the NIA-Designated Mount Sinai Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- James J Peters VA Medical Center, New York, Bronx NY 10468 USA
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19
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Ibanez KR, McFarland KN, Phillips J, Allen M, Lessard CB, Zobel L, De La Cruz EG, Shah S, Vo Q, Wang X, Quicksall Z, Ryu D, Funk C, Ertekin-Taner N, Prokop S, Golde TE, Chakrabarty P. Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways. Alzheimers Res Ther 2022; 14:104. [PMID: 35897046 PMCID: PMC9327202 DOI: 10.1186/s13195-022-01044-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND The S209F variant of Abelson Interactor Protein 3 (ABI3) increases risk for Alzheimer's disease (AD), but little is known about its function in relation to AD pathogenesis. METHODS Here, we use a mouse model that is deficient in Abi3 locus to study how the loss of function of Abi3 impacts two cardinal neuropathological hallmarks of AD-amyloid β plaques and tau pathology. Our study employs extensive neuropathological and transcriptomic characterization using transgenic mouse models and adeno-associated virus-mediated gene targeting strategies. RESULTS Analysis of bulk RNAseq data confirmed age-progressive increase in Abi3 levels in rodent models of AD-type amyloidosis and upregulation in AD patients relative to healthy controls. Using RNAscope in situ hybridization, we localized the cellular distribution of Abi3 in mouse and human brains, finding that Abi3 is expressed in both microglial and non-microglial cells. Next, we evaluated Abi3-/- mice and document that both Abi3 and its overlapping gene, Gngt2, are disrupted in these mice. Using multiple transcriptomic datasets, we show that expression of Abi3 and Gngt2 are tightly correlated in rodent models of AD and human brains, suggesting a tight co-expression relationship. RNAseq of the Abi3-Gngt2-/- mice revealed upregulation of Trem2, Plcg2, and Tyrobp, concomitant with induction of an AD-associated neurodegenerative signature, even in the absence of AD-typical neuropathology. In APP mice, loss of Abi3-Gngt2 resulted in a gene dose- and age-dependent reduction in Aβ deposition. Additionally, in Abi3-Gngt2-/- mice, expression of a pro-aggregant form of human tau exacerbated tauopathy and astrocytosis. Further, using in vitro culture assays, we show that the AD-associated S209F mutation alters the extent of ABI3 phosphorylation. CONCLUSIONS These data provide an important experimental framework for understanding the role of Abi3-Gngt2 function and early inflammatory gliosis in AD. Our studies also demonstrate that inflammatory gliosis could have opposing effects on amyloid and tau pathology, highlighting the unpredictability of targeting immune pathways in AD.
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Affiliation(s)
- Kristen R Ibanez
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Karen N McFarland
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Department of Neurology, University of Florida, Gainesville, FL, 32610, USA
| | - Jennifer Phillips
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Christian B Lessard
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Lillian Zobel
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Elsa Gonzalez De La Cruz
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Shivani Shah
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Quan Vo
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Daniel Ryu
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Stefan Prokop
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Department of Pathology, University of Florida, Gainesville, FL, 32610, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
- Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Center for Translational Research in Neurodegenerative Disease, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA.
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
- Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA.
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20
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Horgusluoglu E, Neff R, Song W, Wang M, Wang Q, Arnold M, Krumsiek J, Galindo‐Prieto B, Ming C, Nho K, Kastenmüller G, Han X, Baillie R, Zeng Q, Andrews S, Cheng H, Hao K, Goate A, Bennett DA, Saykin AJ, Kaddurah‐Daouk R, Zhang B. Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease. Alzheimers Dement 2022; 18:1260-1278. [PMID: 34757660 PMCID: PMC9085975 DOI: 10.1002/alz.12468] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/29/2022]
Abstract
Metabolites, the biochemical products of the cellular process, can be used to measure alterations in biochemical pathways related to the pathogenesis of Alzheimer's disease (AD). However, the relationships between systemic abnormalities in metabolism and the pathogenesis of AD are poorly understood. In this study, we aim to identify AD-specific metabolomic changes and their potential upstream genetic and transcriptional regulators through an integrative systems biology framework for analyzing genetic, transcriptomic, metabolomic, and proteomic data in AD. Metabolite co-expression network analysis of the blood metabolomic data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) shows short-chain acylcarnitines/amino acids and medium/long-chain acylcarnitines are most associated with AD clinical outcomes, including episodic memory scores and disease severity. Integration of the gene expression data in both the blood from the ADNI and the brain from the Accelerating Medicines Partnership Alzheimer's Disease (AMP-AD) program reveals ABCA1 and CPT1A are involved in the regulation of acylcarnitines and amino acids in AD. Gene co-expression network analysis of the AMP-AD brain RNA-seq data suggests the CPT1A- and ABCA1-centered subnetworks are associated with neuronal system and immune response, respectively. Increased ABCA1 gene expression and adiponectin protein, a regulator of ABCA1, correspond to decreased short-chain acylcarnitines and amines in AD in the ADNI. In summary, our integrated analysis of large-scale multiomics data in AD systematically identifies novel metabolites and their potential regulators in AD and the findings pave a way for not only developing sensitive and specific diagnostic biomarkers for AD but also identifying novel molecular mechanisms of AD pathogenesis.
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Affiliation(s)
- Emrin Horgusluoglu
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Ryan Neff
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Won‐Min Song
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Minghui Wang
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Qian Wang
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Matthias Arnold
- Institute of Computational BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNorth CarolinaUSA
| | - Jan Krumsiek
- Department of Physiology and BiophysicsWeill Cornell MedicineInstitute for Computational BiomedicineEnglander Institute for Precision MedicineNew YorkNew YorkUSA
| | - Beatriz Galindo‐Prieto
- Department of Physiology and BiophysicsWeill Cornell MedicineInstitute for Computational BiomedicineEnglander Institute for Precision MedicineNew YorkNew YorkUSA
- Helen and Robert Appel Alzheimer's Disease Research InstituteBrain and Mind Research InstituteWeill Cornell MedicineNew YorkNew YorkUSA
| | - Chen Ming
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences; Indiana Alzheimer Disease CenterIndiana University School of MedicineIndianapolisIndianaUSA
| | - Gabi Kastenmüller
- Institute of Computational BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
| | - Xianlin Han
- Barshop Institute for Longevity and Aging StudiesUniversity of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | | | - Qi Zeng
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Shea Andrews
- Department of NeuroscienceRonald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Haoxiang Cheng
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Ke Hao
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
| | - Alison Goate
- Department of NeuroscienceRonald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences; Indiana Alzheimer Disease CenterIndiana University School of MedicineIndianapolisIndianaUSA
| | - Rima Kaddurah‐Daouk
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNorth CarolinaUSA
- Duke Institute of Brain SciencesDuke UniversityDurhamNorth CarolinaUSA
- Department of MedicineDuke UniversityDurhamNorth CarolinaUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesMount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiIcahn Institute of Genomics and Multiscale BiologyNew YorkNew YorkUSA
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21
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Connor SM, Rashid M, Ryan KJ, Patel K, Boyd JD, Smith J, Elyaman W, Bennett DA, Bradshaw EM. GW5074 Increases Microglial Phagocytic Activities: Potential Therapeutic Direction for Alzheimer's Disease. Front Cell Neurosci 2022; 16:894601. [PMID: 35677758 PMCID: PMC9169965 DOI: 10.3389/fncel.2022.894601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/21/2022] [Indexed: 11/17/2022] Open
Abstract
Microglia, the resident immune cells of the central nervous system (CNS), are responsible for maintaining homeostasis in the brain by clearing debris and are suggested to be inefficient in Alzheimer's Disease (AD), a progressive neurodegenerative disorder for which there is no disease-modifying drug. Besides pathological approaches, unbiased evidence from genome-wide association studies (GWAS) and gene network analysis implicate genes expressed in microglia that reduce phagocytic ability as susceptibility genes for AD. Thus, a central feature toward AD therapy is to increase the microglial phagocytic activities while maintaining synaptic integrity. Here, we developed a robust unbiased high content screening assay to identify potential therapeutics which can reduce the amyloid-beta (Aβ1-42) load by increasing microglial uptake ability. Our screen identified the small-molecule GW5074, an inhibitor of c-RAF, a serine/threonine kinase, which significantly increased the Aβ1-42 clearance activities in human monocyte-derived microglia-like (MDMi) cells, a microglia culture model that recapitulates many genetic and phenotypic aspects of human microglia. Notably, GW5074 was previously reported to be neuroprotective for cerebellar granule cells and cortical neurons. We found that GW5074 significantly increased the expression of key AD-associated microglial molecules known to modulate phagocytosis: TYROBP, SIRPβ1, and TREM2. Our results demonstrated that GW5074 is a potential therapeutic for AD, by targeting microglia.
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Affiliation(s)
- Sarah M. Connor
- Columbia University Irving Medical Center, New York, NY, United States
| | - Mamunur Rashid
- Columbia University Irving Medical Center, New York, NY, United States
| | - Katie J. Ryan
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - Kruti Patel
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - Justin D. Boyd
- Laboratory for Drug Discovery in Neurodegeneration at the Harvard NeuroDiscovery Center, Harvard Medical School, Boston, MA, United States
| | - Jennifer Smith
- The Institute of Chemistry and Cell Biology (ICCB)-Longwood Screening Facility, Harvard Medical School, Boston, MA, United States
| | - Wassim Elyaman
- Columbia University Irving Medical Center, New York, NY, United States
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, United States
| | - David A. Bennett
- Alzheimer Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - Elizabeth M. Bradshaw
- Columbia University Irving Medical Center, New York, NY, United States
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, United States
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22
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Dong Q, Song N, Qin N, Chen C, Li Z, Sun X, Easton J, Mulder H, Plyler E, Neale G, Walker E, Li Q, Ma X, Chen X, Huang IC, Yasui Y, Ness KK, Zhang J, Hudson MM, Robison LL, Wang Z. Genome-wide association studies identify novel genetic loci for epigenetic age acceleration among survivors of childhood cancer. Genome Med 2022; 14:32. [PMID: 35313970 PMCID: PMC8939156 DOI: 10.1186/s13073-022-01038-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Background Increased epigenetic age acceleration (EAA) in survivors of childhood cancer is associated with specific treatment exposures, unfavorable health behaviors, and presence of certain chronic health conditions. To better understand inter-individual variability, we investigated the genetic basis underlying EAA. Methods Genome-wide association studies of EAA based on multiple epigenetic clocks (Hannum, Horvath, PhenoAge, and GrimAge) were performed. MethylationEPIC BeadChip array and whole-genome sequencing data were generated with blood-derived DNA from participants in the St. Jude Lifetime Cohort Study (discovery: 2138 pre-existing and 502 newly generated data, all survivors; exploratory: 282 community controls). Linear regression models were fit for each epigenetic age against the allelic dose of each genetic variant, adjusting for age at sampling, sex, and cancer treatment exposures. Fixed-effects meta-analysis was used to combine summary statistics from two discovery data sets. LD (Linkage disequilibrium) score regression was used to estimate single-nucleotide polymorphism (SNP)-based heritability. Results For EAA-Horvath, a genome-wide significant association was mapped to the SELP gene with the strongest SNP rs732314 (meta-GWAS: β=0.57, P=3.30×10-11). Moreover, the stratified analysis of the association between rs732314 and EAA-Horvath showed a substantial heterogeneity between children and adults (meta-GWAS: β=0.97 vs. 0.51, I2=73.1%) as well as between survivors with and without chest/abdominal/pelvic-RT exposure (β=0.64 vs. 0.31, I2=66.3%). For EAA-Hannum, an association was mapped to the HLA locus with the strongest SNP rs28366133 (meta-GWAS: β=0.78, P=3.78×10-11). There was no genome-wide significant hit for EAA-PhenoAge or EAA-GrimAge. Interestingly, among community controls, rs732314 was associated with EAA-Horvath (β=1.09, P=5.43×10-5), whereas rs28366133 was not associated with EAA-Hannum (β=0.21, P=0.49). The estimated heritability was 0.33 (SE=0.20) for EAA-Horvath and 0.17 (SE=0.23) for EAA-Hannum, but close to zero for EAA-PhenoAge and EAA-GrimAge. Conclusions We identified novel genetic variants in the SELP gene and HLA region associated with EAA-Horvath and EAA-Hannum, respectively, among survivors of childhood cancer. The new genetic variants in combination with other replicated known variants can facilitate the identification of survivors at higher risk in developing accelerated aging and potentially inform drug targets for future intervention strategies among vulnerable survivors. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01038-6.
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Affiliation(s)
- Qian Dong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Nan Song
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA.,College of Pharmacy, Chungbuk National University, Cheongju, Korea
| | - Na Qin
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Chen
- School of Public Health, Shanghai Jiaotong University, Shanghai, China
| | - Zhenghong Li
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Xiaojun Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily Plyler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily Walker
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qian Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - I-Chan Huang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA. .,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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23
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Lv Z, Xu T, Li R, Zheng D, Li Y, Li W, Yang Y, Hao Y. Downregulation of m6A Methyltransferase in the Hippocampus of Tyrobp–/– Mice and Implications for Learning and Memory Deficits. Front Neurosci 2022; 16:739201. [PMID: 35386591 PMCID: PMC8978996 DOI: 10.3389/fnins.2022.739201] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
Loss-of-function mutations in the gene that encodes TYRO protein kinase-binding protein (TYROBP) cause Nasu-Hakola disease, a heritable disease resembling Alzheimer’s disease (AD). Methylation of N6 methyl-adenosine (m6A) in mRNA plays essential roles in learning and memory. Aberrant m6A methylation has been detected in AD patients and animal models. In the present study, Tyrobp–/– mice showed learning and memory deficits in the Morris water maze, which worsened with age. Tyrobp–/– mice also showed elevated levels of total tau, Ser202/Thr205-phosphorylated tau and amyloid β in the hippocampus and cerebrocortex, which worsened with aging. The m6A methyltransferase components METTL3, METTL14, and WTAP were downregulated in Tyrobp–/– mice, while expression of demethylases that remove the m6A modification (e.g., FTO and ALKBH5) were unaltered. Methylated RNA immunoprecipitation sequencing identified 498 m6A peaks that were upregulated in Tyrobp–/– mice, and 312 m6A peaks that were downregulated. Bioinformatic analysis suggested that most of these m6A peaks occur in sequences near stop codons and 3′-untranslated regions. These findings suggest an association between m6A RNA methylation and pathological TYROBP deficiency.
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Affiliation(s)
- Zhanyun Lv
- Zhejiang University Medical Center, Hangzhou, China
- School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
| | - Tongxiao Xu
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Ran Li
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dejie Zheng
- Health Management Center, Weifang People’s Hospital, Weifang, China
| | - Yanxin Li
- Department of Neurology, Pingdu People’s Hospital, Qingdao, China
| | - Wei Li
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Yan Yang
- College of Clinical Medicine, Jining Medical University, Jining, China
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Yanlei Hao
- College of Clinical Medicine, Jining Medical University, Jining, China
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
- *Correspondence: Yanlei Hao,
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Mauduit O, Delcroix V, Umazume T, de Paiva CS, Dartt DA, Makarenkova HP. Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation. Front Immunol 2022; 13:1011125. [PMID: 36341342 PMCID: PMC9628215 DOI: 10.3389/fimmu.2022.1011125] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open
Abstract
The lacrimal gland (LG) is an exocrine gland that produces the watery part of the tear film that lubricates the ocular surface. Chronic inflammation, such as Sjögren's syndrome (SS), is one of the leading causes of aqueous-deficiency dry eye (ADDE) disease worldwide. In this study we analyzed the chronic inflammation in the LGs of the NOD.B10Sn-H2b/J (NOD.H-2b) mice, a mouse model of SS, utilizing bulk RNAseq and Visium spatial gene expression. With Seurat we performed unsupervised clustering and analyzed the spatial cell distribution and gene expression changes in all cell clusters within the LG sections. Moreover, for the first time, we analyzed and validated specific pathways defined by bulk RNAseq using Visium technology to determine activation of these pathways within the LG sections. This analysis suggests that altered metabolism and the hallmarks of inflammatory responses from both epithelial and immune cells drive inflammation. The most significant pathway enriched in upregulated DEGs was the "TYROBP Causal Network", that has not been described previously in SS. We also noted a significant decrease in lipid metabolism in the LG of the NOD.H-2b mice. Our data suggests that modulation of these pathways can provide a therapeutic strategy to treat ADDE.
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Affiliation(s)
- Olivier Mauduit
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Vanessa Delcroix
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Takeshi Umazume
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Cintia S de Paiva
- The Ocular Surface Center, Department of Ophthalmology, Baylor College of Medicine, Cullen Eye Institute, Houston, TX, United States
| | - Darlene A Dartt
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Helen P Makarenkova
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
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25
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Ai R, Jin X, Tang B, Yang G, Niu Z, Fang EF. Aging and Alzheimer’s Disease. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Hernandez M, Vaughan J, Gordon T, Lippmann M, Gandy S, Chen LC. World Trade Center dust induces nasal and neurological tissue injury while propagating reduced olfaction capabilities and increased anxiety behaviors. Inhal Toxicol 2022; 34:175-188. [PMID: 35533138 PMCID: PMC9728549 DOI: 10.1080/08958378.2022.2072027] [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: 11/05/2022]
Abstract
Objective: Previous in vitro and in vivo World Trade Center particulate matter (WTCPM) exposure studies have provided evidence of exposure-driven oxidative/nitrative stress and inflammation on respiratory tract and aortic tissues. What remains to be fully understood are secondary organ impacts due to WTCPM exposure. This study was designed to test if WTC particle-induced nasal and neurologic tissue injury may result in unforeseen functional and behavioral outcomes.Material and Methods: WTCPM was intranasally administered in mice, evaluating genotypic, histopathologic, and olfaction latency endpoints.Results: WTCPM exposure was found to incite neurologic injury and olfaction latency in intranasally (IN) exposed mice. Single high-dose and repeat low-dose nasal cavity insults from WTCPM dust resulted in significant olfaction delays and enduring olfaction deficits. Anxiety-dependent behaviors also occurred in mice experiencing olfaction loss including significant body weight loss, increased incidence and time spent in hind stretch postures, as well as increased stationary time and decreased exploratory time. Additionally, WTCPM exposure resulted in increased whole brain wet/dry ratios and wet whole brain to body mass ratios that were correlated with exposure and increased exposure dose (p<0.05).Discussion: The potential molecular drivers of WTCPM-driven tissue injury and olfaction latency may be linked to oxidative/nitrative stress and inflammatory cascades in both upper respiratory nasal and brain tissues.Conclusion: Cumulatively, these data provide evidence of WTCPM exposure in relation to tissue damage related to oxidative stress-driven inflammation identified in the nasal cavity, propagated to olfactory bulb tissues and, potentially, over extended periods, to other CNS tissues.
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Affiliation(s)
- Michelle Hernandez
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Joshua Vaughan
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Terry Gordon
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Morton Lippmann
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Sam Gandy
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J Peter VA Medical Center, Bronx, NY, USA
| | - Lung-Chi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
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McFarland KN, Chakrabarty P. Microglia in Alzheimer's Disease: a Key Player in the Transition Between Homeostasis and Pathogenesis. Neurotherapeutics 2022; 19:186-208. [PMID: 35286658 PMCID: PMC9130399 DOI: 10.1007/s13311-021-01179-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Immune activation accompanies the development of proteinopathy in the brains of Alzheimer's dementia patients. Evolving from the long-held viewpoint that immune activation triggers the pathological trajectory in Alzheimer's disease, there is accumulating evidence now that microglial activation is neither pro-amyloidogenic nor just a simple reactive process to the proteinopathy. Preclinical studies highlight an interesting aspect of immunity, i.e., spurring immune system activity may be beneficial under certain circumstances. Indeed, a dynamic evolving relationship between different activation states of the immune system and its neuronal neighbors is thought to regulate overall brain organ health in both healthy aging and progression of Alzheimer's dementia. A new premise evolving from genome, transcriptome, and proteome data is that there might be at least two major phases of immune activation that accompany the pathological trajectory in Alzheimer's disease. Though activation on a chronic scale will certainly lead to neurodegeneration, this emerging knowledge of a potential beneficial aspect of immune activation allows us to form holistic insights into when, where, and how much immune system activity would need to be tuned to impact the Alzheimer's neurodegenerative cascade. Even with the trove of recently emerging -omics data from patients and preclinical models, how microglial phenotypes are functionally related to the transition of a healthy aging brain towards progressive degenerative state remains unknown. A deeper understanding of the synergism between microglial functional states and brain organ health could help us discover newer interventions and therapies that enable us to address the current paucity of disease-modifying therapies in Alzheimer's disease.
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Affiliation(s)
- Karen N McFarland
- Department of Neurology, University of Florida, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA.
- McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
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28
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Brain Immunoinformatics: A Symmetrical Link between Informatics, Wet Lab and the Clinic. Symmetry (Basel) 2021. [DOI: 10.3390/sym13112168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Breakthrough advances in informatics over the last decade have thoroughly influenced the field of immunology. The intermingling of machine learning with wet lab applications and clinical results has hatched the newly defined immunoinformatics society. Immunoinformatics of the central neural system, referred to as neuroimmunoinformatics (NII), investigates symmetrical and asymmetrical interactions of the brain-immune interface. This interdisciplinary overview on NII is addressed to bioscientists and computer scientists. We delineate the dominating trajectories and field-shaping achievements and elaborate on future directions using bridging language and terminology. Computation, varying from linear modeling to complex deep learning approaches, fuels neuroimmunology through three core directions. Firstly, by providing big-data analysis software for high-throughput methods such as next-generation sequencing and genome-wide association studies. Secondly, by designing models for the prediction of protein morphology, functions, and symmetrical and asymmetrical protein–protein interactions. Finally, NII boosts the output of quantitative pathology by enabling the automatization of tedious processes such as cell counting, tracing, and arbor analysis. The new classification of microglia, the brain’s innate immune cells, was an NII achievement. Deep sequencing classifies microglia in “sensotypes” to accurately describe the versatility of immune responses to physiological and pathological challenges, as well as to experimental conditions such as xenografting and organoids. NII approaches complex tasks in the brain-immune interface, recognizes patterns and allows for hypothesis-free predictions with ultimate targeted individualized treatment strategies, and personalizes disease prognosis and treatment response.
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29
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Alzheimer's Disease Interventions: Implications of therapeutic promises amidst questions and doubts about clinically meaningful outcomes. Alzheimers Dement 2021; 17:1591-1594. [PMID: 34717294 DOI: 10.1002/alz.12490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 12/23/2022]
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30
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Serrano-Pozo A, Li Z, Noori A, Nguyen HN, Mezlini A, Li L, Hudry E, Jackson RJ, Hyman BT, Das S. Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer's disease. NATURE AGING 2021; 1:919-931. [PMID: 36199750 PMCID: PMC9531903 DOI: 10.1038/s43587-021-00123-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 09/03/2021] [Indexed: 05/02/2023]
Abstract
The roles of APOEε4 and APOEε2-the strongest genetic risk and protective factors for Alzheimer's disease-in glial responses remain elusive. We tested the hypothesis that APOE alleles differentially impact glial responses by investigating their effects on the glial transcriptome from elderly control brains with no neuritic amyloid plaques. We identified a cluster of microglial genes that are upregulated in APOEε4 and downregulated in APOEε2 carriers relative to APOEε3 homozygotes. This microglia-APOE cluster is enriched in phagocytosis-including TREM2 and TYROBP-and proinflammatory genes, and is also detectable in brains with frequent neuritic plaques. Next, we tested these findings in APOE knock-in mice exposed to acute (lipopolysaccharide challenge) and chronic (cerebral β-amyloidosis) insults and found that these mice partially recapitulate human APOE-linked expression patterns. Thus, the APOEε4 allele might prime microglia towards a phagocytic and proinflammatory state through an APOE-TREM2-TYROBP axis in normal aging as well as in Alzheimer's disease.
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Affiliation(s)
- Alberto Serrano-Pozo
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Zhaozhi Li
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
| | - Ayush Noori
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
| | - Huong N. Nguyen
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Aziz Mezlini
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Liang Li
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Eloise Hudry
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Rosemary J. Jackson
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bradley T. Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
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31
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Deerhake ME, Shinohara ML. Emerging roles of Dectin-1 in noninfectious settings and in the CNS. Trends Immunol 2021; 42:891-903. [PMID: 34489167 DOI: 10.1016/j.it.2021.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/15/2022]
Abstract
Dectin-1 is a C-type lectin receptor (CLR) expressed on the surface of various mammalian myeloid cells. Dectin-1 recognizes β-glucans and elicits antifungal proinflammatory immune responses. Recent studies have begun to examine the biology of Dectin-1 in previously less explored settings, such as homeostasis, sterile inflammation, and in the central nervous system. Indeed, in certain contexts, Dectin-1 is now known to promote tolerance, and anti-inflammatory and neuroprotective responses. In this review, we provide an overview of the current understanding of the roles of Dectin-1 in immunology beyond the context of fungal infections, mainly focusing on in vivo neuroimmunology studies, which could reveal new therapeutic approaches to modify innate immune responses in neurologic disorders.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27705, USA.
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32
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Senjor E, Perišić Nanut M, Breznik B, Mitrović A, Mlakar J, Rotter A, Porčnik A, Lah Turnšek T, Kos J. Cystatin F acts as a mediator of immune suppression in glioblastoma. Cell Oncol (Dordr) 2021; 44:1051-1063. [PMID: 34189679 DOI: 10.1007/s13402-021-00618-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2021] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Glioblastoma, the most aggressive type of brain cancer, is composed of heterogeneous populations of differentiated cells, cancer stem cells and immune cells. Cystatin F, an endogenous inhibitor of lysosomal cysteine peptidases, regulates the function of cytotoxic immune cells. The aim of this study was to determine which type of cells expresses cystatin F in glioblastoma and to determine the role of cystatin F during disease progression. METHODS RT-qPCR and immunohistochemistry were used to determine cystatin F mRNA and protein levels in glioblastoma tissue samples. The internalization of cystatin F was analyzed by Western blotting. Enzyme kinetics, real time invasion and calcein release cytotoxicity assays were used to assess the role of internalized cystatin F. RESULTS We found that cystatin F was not expressed in non-cancer brain tissues, but that its expression increased with glioma progression. In tumor tissues, extensive staining was observed in cancer stem-like cells and microglia/monocytes, which secrete cystatin F into their microenvironment. In trans activity of cystatin F was confirmed using an in vitro glioblastoma cell model. Internalized cystatin F affected cathepsin L activity in glioblastoma cells and decreased their invasiveness. In addition, we found that cystatin F decreased the susceptibility of glioblastoma cells to the cytotoxic activity of natural killer (NK) cells. CONCLUSIONS Our data implicate cystatin F as a mediator of immune suppression in glioblastoma. Increased cystatin F mRNA and protein levels in immune, glioblastoma and glioblastoma stem-like cells or trans internalized cystatin F may have an impact on decreased susceptibility of glioblastoma cells to NK cytotoxicity.
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Affiliation(s)
- Emanuela Senjor
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia
| | - Milica Perišić Nanut
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia
| | - Barbara Breznik
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia
| | - Jernej Mlakar
- Institute of Pathology, Medical Faculty, University of Ljubljana, Korytkova 2, SI-1000, Ljubljana, Slovenia
| | - Ana Rotter
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Andrej Porčnik
- Department of Neurosurgery, University Clinical Centre Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Tamara Lah Turnšek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova cesta 39, SI-1000, Ljubljana, Slovenia. .,Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia.
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33
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Zhang J, Zheng Y, Zhao Y, Zhang Y, Liu Y, Ma F, Wang X, Fu J. Andrographolide ameliorates neuroinflammation in APP/PS1 transgenic mice. Int Immunopharmacol 2021; 96:107808. [PMID: 34162168 DOI: 10.1016/j.intimp.2021.107808] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/29/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease is a devastating neurodegenerative disorder, with no disease-modifying treatment available yet. There is increasing evidence that neuroinflammation plays a critical role in the pathogenesis of AD. Andrographolide (Andro), a labdane diterpene extracted from the herb Andrographis paniculata, has been reported to exhibit neuroprotective property in central nervous system diseases. However, its effects on Aβ and Aβ-induced neuroinflammation have not yet been studied. In the present study, we found that Andro administration significantly alleviated cognitive impairments, reduced amyloid-β deposition, inhibited microglial activation, and decreased the secretion of proinflammatory factors in APP/PS1 mice. Furthermore, transcriptome sequencing analysis revealed that Andro could significantly decrease the expression of Itgax, TLR2, CD14, CCL3, CCL4, TLR1, and C3ar1 in APP/PS1 mice, which was further validated by qRT-PCR. Our results suggest that Andro might be a potential therapeutic drug for AD by regulating neuroinflammation.
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Affiliation(s)
- Jiawei Zhang
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Yaling Zheng
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Yao Zhao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Yaxuan Zhang
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Yu Liu
- Department of Medicine, Shanghai Eighth People's Hospital, Shanghai 200235, China
| | - Fang Ma
- Department of Neurosurgery, Lushi People's Hospital, Henan 472200, China
| | - Xiuzhe Wang
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China.
| | - Jianliang Fu
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China.
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Schwab N, Ju Y, Hazrati LN. Early onset senescence and cognitive impairment in a murine model of repeated mTBI. Acta Neuropathol Commun 2021; 9:82. [PMID: 33964983 PMCID: PMC8106230 DOI: 10.1186/s40478-021-01190-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022] Open
Abstract
Mild traumatic brain injury (mTBI) results in broad neurological symptoms and an increased risk of being diagnosed with a neurodegenerative disease later in life. While the immediate oxidative stress response and post-mortem pathology of the injured brain has been well studied, it remains unclear how early pathogenic changes may drive persistent symptoms and confer susceptibility to neurodegeneration. In this study we have used a mouse model of repeated mTBI (rmTBI) to identify early gene expression changes at 24 h or 7 days post-injury (7 dpi). At 24 h post-injury, gene expression of rmTBI mice shows activation of the DNA damage response (DDR) towards double strand DNA breaks, altered calcium and cell–cell signalling, and inhibition of cell death pathways. By 7 dpi, rmTBI mice had a gene expression signature consistent with induction of cellular senescence, activation of neurodegenerative processes, and inhibition of the DDR. At both timepoints gliosis, microgliosis, and axonal damage were evident in the absence of any gross lesion, and by 7 dpi rmTBI also mice had elevated levels of IL1β, p21, 53BP1, DNA2, and p53, supportive of DNA damage-induced cellular senescence. These gene expression changes reflect establishment of processes usually linked to brain aging and suggests that cellular senescence occurs early and most likely prior to the accumulation of toxic proteins. These molecular changes were accompanied by spatial learning and memory deficits in the Morris water maze. To conclude, we have identified DNA damage-induced cellular senescence as a repercussion of repeated mild traumatic brain injury which correlates with cognitive impairment. Pathways involved in senescence may represent viable treatment targets of post-concussive syndrome. Senescence has been proposed to promote neurodegeneration and appears as an effective target to prevent long-term complications of mTBI, such as chronic traumatic encephalopathy and other related neurodegenerative pathologies.
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Sepers B, Erven JAM, Gawehns F, Laine VN, van Oers K. Epigenetics and Early Life Stress: Experimental Brood Size Affects DNA Methylation in Great Tits (Parus major). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.609061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Early developmental conditions are known to have life-long effects on an individual’s behavior, physiology and fitness. In altricial birds, a majority of these conditions, such as the number of siblings and the amount of food provisioned, are controlled by the parents. This opens up the potential for parents to adjust the behavior and physiology of their offspring according to local post-natal circumstances. However, the mechanisms underlying such intergenerational regulation remain largely unknown. A mechanism often proposed to possibly explain how parental effects mediate consistent phenotypic change is DNA methylation. To investigate whether early life effects on offspring phenotypes are mediated by DNA methylation, we cross-fostered great tit (Parus major) nestlings and manipulated their brood size in a natural study population. We assessed genome-wide DNA methylation levels of CpG sites in erythrocyte DNA, using Reduced Representation Bisulfite Sequencing (RRBS). By comparing DNA methylation levels between biological siblings raised in enlarged and reduced broods and between biological siblings of control broods, we assessed which CpG sites were differentially methylated due to brood size. We found 32 differentially methylated sites (DMS) between siblings from enlarged and reduced broods, a larger number than in the comparison between siblings from control broods. A considerable number of these DMS were located in or near genes involved in development, growth, metabolism, behavior and cognition. Since the biological functions of these genes line up with previously found effects of brood size and food availability, it is likely that the nestlings in the enlarged broods suffered from nutritional stress. We therefore conclude that early life stress might directly affect epigenetic regulation of genes related to early life conditions. Future studies should link such experimentally induced DNA methylation changes to expression of phenotypic traits and assess whether these effects affect parental fitness to determine if such changes are also adaptive.
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Wang Q, Zhang B, Yue Z. Disentangling the Molecular Pathways of Parkinson's Disease using Multiscale Network Modeling. Trends Neurosci 2021; 44:182-188. [PMID: 33358606 PMCID: PMC10942661 DOI: 10.1016/j.tins.2020.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/28/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disorder. The identification of genetic variants has shed light on the molecular pathways for inherited PD, while the disease mechanism for idiopathic PD remains elusive, partly due to a lack of robust tools. The complexity of PD arises from the heterogeneity of clinical symptoms, pathologies, environmental insults contributing to the disease, and disease comorbidities. Molecular networks have been increasingly used to identify molecular pathways and drug targets in complex human diseases. Here, we review recent advances in molecular network approaches and their application to PD. We discuss how network modeling can predict functions of PD genetic risk factors through network context and assist in the discovery of network-based therapeutics for neurodegenerative diseases.
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Affiliation(s)
- Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029-6501, USA; Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029-6501, USA.
| | - Zhenyu Yue
- Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA.
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37
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Giovagnoni C, Ali M, Eijssen LMT, Maes R, Choe K, Mulder M, Kleinjans J, Del Sol A, Glaab E, Mastroeni D, Delvaux E, Coleman P, Losen M, Pishva E, Martinez-Martinez P, van den Hove DLA. Altered sphingolipid function in Alzheimer's disease; a gene regulatory network approach. Neurobiol Aging 2021; 102:178-187. [PMID: 33773368 DOI: 10.1016/j.neurobiolaging.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/04/2020] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
Sphingolipids (SLs) are bioactive lipids involved in various important physiological functions. The SL pathway has been shown to be affected in several brain-related disorders, including Alzheimer's disease (AD). Recent evidence suggests that epigenetic dysregulation plays an important role in the pathogenesis of AD as well. Here, we use an integrative approach to better understand the relationship between epigenetic and transcriptomic processes in regulating SL function in the middle temporal gyrus of AD patients. Transcriptomic analysis of 252 SL-related genes, selected based on GO term annotations, from 46 AD patients and 32 healthy age-matched controls, revealed 103 differentially expressed SL-related genes in AD patients. Additionally, methylomic analysis of the same subjects revealed parallel hydroxymethylation changes in PTGIS, GBA, and ITGB2 in AD. Subsequent gene regulatory network-based analysis identified 3 candidate genes, that is, SELPLG, SPHK1 and CAV1 whose alteration holds the potential to revert the gene expression program from a diseased towards a healthy state. Together, this epigenomic and transcriptomic approach highlights the importance of SL-related genes in AD, and may provide novel biomarkers and therapeutic alternatives to traditionally investigated biological pathways in AD.
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Affiliation(s)
- Caterina Giovagnoni
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands.
| | - Muhammad Ali
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Computational Biology Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; Biomedical Data Science Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Lars M T Eijssen
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Richard Maes
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Kyonghwan Choe
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Monique Mulder
- Department of Internal Medicine, Division of Pharmacology, Vascular and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Diego Mastroeni
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Paul Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Mario Losen
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Ehsan Pishva
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Pilar Martinez-Martinez
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
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Wang M, Li A, Sekiya M, Beckmann ND, Quan X, Schrode N, Fernando MB, Yu A, Zhu L, Cao J, Lyu L, Horgusluoglu E, Wang Q, Guo L, Wang YS, Neff R, Song WM, Wang E, Shen Q, Zhou X, Ming C, Ho SM, Vatansever S, Kaniskan HÜ, Jin J, Zhou MM, Ando K, Ho L, Slesinger PA, Yue Z, Zhu J, Katsel P, Gandy S, Ehrlich ME, Fossati V, Noggle S, Cai D, Haroutunian V, Iijima KM, Schadt E, Brennand KJ, Zhang B. Transformative Network Modeling of Multi-omics Data Reveals Detailed Circuits, Key Regulators, and Potential Therapeutics for Alzheimer's Disease. Neuron 2021; 109:257-272.e14. [PMID: 33238137 PMCID: PMC7855384 DOI: 10.1016/j.neuron.2020.11.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/16/2020] [Accepted: 10/30/2020] [Indexed: 01/11/2023]
Abstract
To identify the molecular mechanisms and novel therapeutic targets of late-onset Alzheimer's Disease (LOAD), we performed an integrative network analysis of multi-omics profiling of four cortical areas across 364 donors with varying cognitive and neuropathological phenotypes. Our analyses revealed thousands of molecular changes and uncovered neuronal gene subnetworks as the most dysregulated in LOAD. ATP6V1A was identified as a key regulator of a top-ranked neuronal subnetwork, and its role in disease-related processes was evaluated through CRISPR-based manipulation in human induced pluripotent stem cell-derived neurons and RNAi-based knockdown in Drosophila models. Neuronal impairment and neurodegeneration caused by ATP6V1A deficit were improved by a repositioned compound, NCH-51. This study provides not only a global landscape but also detailed signaling circuits of complex molecular interactions in key brain regions affected by LOAD, and the resulting network models will serve as a blueprint for developing next-generation therapeutic agents against LOAD.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,These authors contributed equally
| | - Aiqun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,These authors contributed equally
| | - Michiko Sekiya
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan 467-8603,These authors contributed equally
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,These authors contributed equally
| | - Xiuming Quan
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,These authors contributed equally
| | - Nadine Schrode
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Michael B. Fernando
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Alex Yu
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Li Zhu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Jiqing Cao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Liwei Lyu
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Emrin Horgusluoglu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Yuan-shuo Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ryan Neff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qi Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Seok-Man Ho
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - H. Ümit Kaniskan
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States
| | - Jian Jin
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Kanae Ando
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan 192-0397
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Paul A. Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Zhenyu Yue
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Sam Gandy
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Scott Noggle
- The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,Neurology, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Koichi M. Iijima
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan 467-8603,Senior author
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Senior author
| | - Kristen J. Brennand
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Senior author
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Senior author,Lead Contact,Correspondence: (B.Z.)
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39
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Ai R, Jin X, Tang B, Yang G, Niu Z, Fang EF. Ageing and Alzheimer’s Disease. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_74-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Audrain M, Haure-Mirande JV, Mleczko J, Wang M, Griffin JK, St George-Hyslop PH, Fraser P, Zhang B, Gandy S, Ehrlich ME. Reactive or transgenic increase in microglial TYROBP reveals a TREM2-independent TYROBP-APOE link in wild-type and Alzheimer's-related mice. Alzheimers Dement 2020; 17:149-163. [PMID: 33314529 PMCID: PMC7938663 DOI: 10.1002/alz.12256] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/19/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
Introduction Microglial TYROBP (DAP12) is a network hub and driver in sporadic late‐onset Alzheimer's disease (AD). TYROBP is a cytoplasmic adaptor for TREM2 and other receptors, but little is known about its roles and actions in AD. Herein, we demonstrate that endogenous Tyrobp transcription is specifically increased in recruited microglia. Methods Using a novel transgenic mouse overexpressing TYROBP in microglia, we observed a decrease of the amyloid burden and an increase of TAU phosphorylation stoichiometry when crossed with APP/PSEN1 or MAPTP301S mice, respectively. Characterization of these mice revealed Tyrobp‐related modulation of apolipoprotein E (Apoe) transcription. We also showed that Tyrobp and Apoe mRNAs were increased in Trem2‐null microglia recruited around either amyloid beta deposits or a cortical stab injury. Conversely, microglial Apoe transcription was dramatically diminished when Tyrobp was absent. Conclusions Our results provide evidence that TYROBP‐APOE signaling does not require TREM2 and could be an initiating step in establishment of the disease‐associated microglia (DAM) phenotype.
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Affiliation(s)
- Mickael Audrain
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Justyna Mleczko
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences and Icahn Institute of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jennifer K Griffin
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Peter H St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Paul Fraser
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Bin Zhang
- Department of Genetics and Genomic Sciences and Icahn Institute of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,National Institute on Aging-Designated Alzheimer's Disease Research Center and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Research and Development, James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences and Icahn Institute of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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41
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Propson NE, Gedam M, Zheng H. Complement in Neurologic Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 16:277-298. [PMID: 33234021 DOI: 10.1146/annurev-pathol-031620-113409] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Classic innate immune signaling pathways provide most of the immune response in the brain. This response activates many of the canonical signaling mechanisms identified in peripheral immune cells, despite their relative absence in this immune-privileged tissue. Studies over the past decade have strongly linked complement protein production and activation to age-related functional changes and neurodegeneration. The reactivation of the complement signaling pathway in aging and disease has opened new avenues for understanding brain aging and neurological disease pathogenesis and has implicated cell types such as astrocytes, microglia, endothelial cells, oligodendrocytes, neurons, and even peripheral immune cells in these processes. In this review, we aim to unravel the past decade of research related to complement activation and its numerous consequences in aging and neurological disease.
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Affiliation(s)
- Nicholas E Propson
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manasee Gedam
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hui Zheng
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA;
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Seol Y, Ki S, Ryu HL, Chung S, Lee J, Ryu H. How Microglia Manages Non-cell Autonomous Vicious Cycling of Aβ Toxicity in the Pathogenesis of AD. Front Mol Neurosci 2020; 13:593724. [PMID: 33328884 PMCID: PMC7718019 DOI: 10.3389/fnmol.2020.593724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/20/2020] [Indexed: 01/17/2023] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease and a common form of dementia that affects cognition and memory mostly in aged people. AD pathology is characterized by the accumulation of β-amyloid (Aβ) senile plaques and the neurofibrillary tangles of phosphorylated tau, resulting in cell damage and neurodegeneration. The extracellular deposition of Aβ is regarded as an important pathological marker and a principal-agent of neurodegeneration. However, the exact mechanism of Aβ-mediated pathogenesis is not fully understood yet. Recently, a growing body of evidence provides novel insights on the major role of microglia and its non-cell-autonomous cycling of Aβ toxicity. Hence, this article provides a comprehensive overview of microglia as a significant player in uncovering the underlying disease mechanisms of AD.
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Affiliation(s)
- YunHee Seol
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Soomin Ki
- Department of Brain and Cognitive Science, Ewha Womens University, Seoul, South Korea
| | - Hannah L Ryu
- Department of Neurology, Boston University Alzheimer's Disease Center, Boston University School of Medicine, Boston, MA, United States
| | - Sooyoung Chung
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Junghee Lee
- Department of Neurology, Boston University Alzheimer's Disease Center, Boston University School of Medicine, Boston, MA, United States.,VA Boston Healthcare System, Boston, MA, United States
| | - Hoon Ryu
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea.,Department of Neurology, Boston University Alzheimer's Disease Center, Boston University School of Medicine, Boston, MA, United States
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Jiang J, Ding Y, Wu M, Lyu X, Wang H, Chen Y, Wang H, Teng L. Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis. Front Oncol 2020; 10:1765. [PMID: 33014868 PMCID: PMC7516284 DOI: 10.3389/fonc.2020.01765] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Gastric cancer (GC) is the fifth most frequently diagnosed malignancy, and the third leading cause of tumor-related mortalities worldwide. Due to a high heterogeneity in GC, its treatment and prognosis are challenging, necessitating urgent identification of novel prognostic predictors for GC patients. Methods: We downloaded RNA sequence data, from the Cancer Genome Atlas and microarray data from Gene Expression Omnibus database, then identified common differentially-expressed genes (DEGs) between GC and normal gastric tissues across four datasets. We then used a combination of protein-protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) to identify key genes with prognostic value in GC. Thereafter, we used quantitative real time polymerase chain reaction (qRT-PCR) to validate expression of the identified key genes in the Zhejiang University (ZJU) cohort. Finally, we evaluated the relationships between gene expression and immune factors, including immune cells and biomarkers of immunotherapy. Results: Among 426 common DEGs screened, 333 and 93 were upregulated and downregulated, respectively. PPI network and WGCNA successfully identified the top 30 hub genes, among which PTPRC, TYROBP, CCR1, CYBB, LCP2, and C1QB were common. Furthermore, TYROBP and C1QB were negatively associated with prognosis of GC patients, implying that they were key GC predictors. Interestingly, TYROBP and C1QB were positively correlated with predictive biomarkers for GC immunotherapy, including PD-L1 expression, CD8+ T cells infiltration, and EBV status. Conclusions: TYROBP and C1QB were identified as two novel key genes with prognostic value in GC by network analysis.
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Affiliation(s)
- Junjie Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengjie Wu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiadong Lyu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haifeng Wang
- Department of Hematology & Oncology, The People's Hospital of Beilun District, Beilun Branch Hospital of the First Affiliated Hospital of Medical School of Zhejiang University, Ningbo, China
| | - Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Readhead B, Haure-Mirande JV, Mastroeni D, Audrain M, Fanutza T, Kim SH, Blitzer RD, Gandy S, Dudley JT, Ehrlich ME. miR155 regulation of behavior, neuropathology, and cortical transcriptomics in Alzheimer's disease. Acta Neuropathol 2020; 140:295-315. [PMID: 32666270 PMCID: PMC8414561 DOI: 10.1007/s00401-020-02185-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]
Abstract
MicroRNAs are recognized as important regulators of many facets of physiological brain function while also being implicated in the pathogenesis of several neurological disorders. Dysregulation of miR155 is widely reported across a variety of neurodegenerative conditions, including Alzheimer's disease (AD), Parkinson's disease, amyotrophic lateral sclerosis, and traumatic brain injury. In previous work, we observed that experimentally validated miR155 gene targets were consistently enriched among genes identified as differentially expressed across multiple brain tissue and disease contexts. In particular, we found that human herpesvirus-6A (HHV-6A) suppressed miR155, recapitulating reports of miR155 inhibition by HHV-6A in infected T-cells, thyrocytes, and natural killer cells. In earlier studies, we also reported the effects of constitutive deletion of miR155 on accelerating the accumulation of Aβ deposits in 4-month-old APP/PSEN1 mice. Herein, we complete the cumulative characterization of transcriptomic, electrophysiological, neuropathological, and learning behavior profiles from 4-, 8- and 10-month-old WT and APP/PSEN1 mice in the absence or presence of miR155. We also integrated human post-mortem brain RNA-sequences from four independent AD consortium studies, together comprising 928 samples collected from six brain regions. We report that gene expression perturbations associated with miR155 deletion in mouse cortex are in aggregate observed to be concordant with AD-associated changes across these independent human late-onset AD (LOAD) data sets, supporting the relevance of our findings to human disease. LOAD has recently been formulated as the clinicopathological manifestation of a multiplex of genetic underpinnings and pathophysiological mechanisms. Our accumulated data are consistent with such a formulation, indicating that miR155 may be uniquely positioned at the intersection of at least four components of this LOAD "multiplex": (1) innate immune response pathways; (2) viral response gene networks; (3) synaptic pathology; and (4) proamyloidogenic pathways involving the amyloid β peptide (Aβ).
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Affiliation(s)
- Ben Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
- Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Diego Mastroeni
- Arizona State University-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Mickael Audrain
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tomas Fanutza
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Soong H Kim
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert D Blitzer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Cognitive Health and NFL Neurological Care, Department of Neurology, New York, NY, 10029, USA
- James J. Peters VA Medical Center, 130 West Kingsbridge Road, New York, NY, 10468, USA
| | - Joel T Dudley
- Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Michelle E Ehrlich
- Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Fitz NF, Wolfe CM, Playso BE, Biedrzycki RJ, Lu Y, Nam KN, Lefterov I, Koldamova R. Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice. Mol Neurodegener 2020; 15:41. [PMID: 32703241 PMCID: PMC7379780 DOI: 10.1186/s13024-020-00394-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Alzheimer's Disease (AD) is a neurodegenerative disorder influenced by aging and genetic risk factors. The inheritance of APOEε4 and variants of Triggering Receptor Expressed on Myeloid cells 2 (TREM2) are major genetic risk factors for AD. Recent studies showed that APOE binds to TREM2, thus raising the possibility of an APOE-TREM2 interaction that can modulate AD pathology. METHODS The aim of this study was to investigate this interaction using complex AD model mice - a crossbreed of Trem2ko and APP/PSEN1dE9 mice expressing human APOE3 or APOE4 isoforms (APP/E3 and APP/E4 respectively), and their WT littermates (E3 and E4), and evaluate cognition, steady-state amyloid load, plaque compaction, plaque growth rate, glial response, and brain transcriptome. RESULTS In both, APP/E3 and APP/E4 mice, Trem2 deletion reduced plaque compaction but did not significantly affect steady-state plaque load. Importantly, the lack of TREM2 increased plaque growth that negatively correlated to the diminished microglia barrier, an effect most pronounced at earlier stages of amyloid deposition. We also found that Trem2 deficiency significantly decreased plaque-associated APOE protein in APP/E4 but not in APP/E3 mice in agreement with RNA-seq data. Interestingly, we observed a significant decrease of Apoe mRNA expression in plaque-associated microglia of APP/E4/Trem2ko vs APP/E4 mice. The absence of TREM2, worsened cognitive performance in APP transgenic mice but not their WT littermates. Gene expression analysis identified Trem2 signature - a cluster of highly connected immune response genes, commonly downregulated as a result of Trem2 deletion in all genotypes including APP and WT littermates. Furthermore, we identified sets of genes that were affected in TREM2- and APOE isoform-dependent manner. Among them were Clec7a and Csf1r upregulated in APP/E4 vs APP/E3 mice, a result further validated by in situ hybridization analysis. In contrast, Tyrobp and several genes involved in the C1Q complement cascade had a higher expression level in APP/E3 versus their APP/E4 counterparts. CONCLUSIONS Our data demonstrate that lack of Trem2 differentially impacts the phenotype and brain transcriptome of APP mice expressing human APOE isoforms. The changes probably reflect the different effect of APOE isoforms on amyloid deposition.
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Affiliation(s)
- Nicholas F. Fitz
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Cody M. Wolfe
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Brittany E. Playso
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Richard J. Biedrzycki
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Yi Lu
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Kyong Nyon Nam
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Iliya Lefterov
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Radosveta Koldamova
- Department of Environmental & Occupational Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
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Myszczynska MA, Ojamies PN, Lacoste AMB, Neil D, Saffari A, Mead R, Hautbergue GM, Holbrook JD, Ferraiuolo L. Applications of machine learning to diagnosis and treatment of neurodegenerative diseases. Nat Rev Neurol 2020; 16:440-456. [DOI: 10.1038/s41582-020-0377-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 12/11/2022]
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Abstract
Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the accumulation of amyloid plaques and neurofibrillary tangles in the brain. The AD pathophysiology entails chronic inflammation involving innate immune cells including microglia, astrocytes, and other peripheral blood cells. Inflammatory mediators such as cytokines and complements are also linked to AD pathogenesis. Despite increasing evidence supporting the association between abnormal inflammation and AD, no well-established inflammatory biomarkers are currently available for AD. Since many reports have shown that abnormal inflammation precedes the outbreak of the disease, non-invasive and readily available peripheral inflammatory biomarkers should be considered as possible biomarkers for early diagnosis of AD. In this mini-review, we introduce the peripheral biomarker candidates related to abnormal inflammation in AD and discuss their possible molecular mechanisms. Furthermore, we also summarize the current state of inflammatory biomarker research in clinical practice and molecular diagnostics. We believe this review will provide new insights into biomarker candidates for the early diagnosis of AD with systemic relevance to inflammation during AD pathogenesis.
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Affiliation(s)
- Jong-Chan Park
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Sun-Ho Han
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Inhee Mook-Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
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Wang Y, Zhang X, Song Q, Hou Y, Liu J, Sun Y, Wang P. Characterization of the chromatin accessibility in an Alzheimer's disease (AD) mouse model. ALZHEIMERS RESEARCH & THERAPY 2020; 12:29. [PMID: 32293531 PMCID: PMC7092509 DOI: 10.1186/s13195-020-00598-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Background The pathological hallmarks of Alzheimer’s disease (AD) involve alterations in the expression of numerous genes associated with transcriptional levels, which are determined by chromatin accessibility. Here, the landscape of chromatin accessibility was studied to understand the outline of the transcription and expression of AD-associated metabolism genes in an AD mouse model. Methods The assay for transposase-accessible chromatin by sequencing (ATAC-seq) was used to investigate the AD-associated chromatin reshaping in the APPswe/PS1dE9 (APP/PS1) mouse model. ATAC-seq data in the hippocampus of 8-month-old APP/PS1 mice were generated, and the relationship between chromatin accessibility and gene expression was analyzed in combination with RNA sequencing. Gene ontology (GO) analysis was applied to elucidate biological processes and signaling pathways altered in APP/PS1 mice. Critical transcription factors were identified; alterations in chromatin accessibility were further confirmed using chromatin immunoprecipitation assays. Results We identified 1690 increased AD-associated chromatin-accessible regions in the hippocampal tissues of APP/PS1 mice. These regions were enriched in genes related to diverse signaling pathways, including the PI3K-Akt, Hippo, TGF-β, and Jak-Stat signaling pathways, which play essential roles in regulating cell proliferation, apoptosis, and inflammatory responses. A total of 1003 decreased chromatin-accessible regions were considered to be related with declined AD-associated biological processes including cellular response to hyperoxia and insulin stimulus, synaptic transmission, and positive regulation of autophagy. In the APP/PS1 hippocampus, 1090 genes were found to be upregulated and 1081 downregulated. Interestingly, enhanced ATAC-seq signal was found in approximately 740 genes, with 43 exhibiting upregulated mRNA levels. Several genes involved in AD development were found to have a significantly increased expression in APP/PS1 mice compared to controls, including Sele, Clec7a, Cst7, and Ccr6. The signatures of numerous transcription factors, including Olig2, NeuroD1, TCF4, and NeuroG2, were found enriched in the AD-associated accessible chromatin regions. The transcription-activating marks of H3K4me3 and H3K27ac were also found increased in the promoters of these genes. These results indicate that the mechanism for the upregulation of genes could be attributed to the enrichment of open chromatin regions with transcription factors motifs and the histone marks H3K4me3 and H3K27ac. Conclusion Our study reveals that alterations in chromatin accessibility may be an initial mechanism in AD pathogenesis. Supplementary information Supplementary information accompanies this paper at 10.1186/s13195-020-00598-2.
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Affiliation(s)
- Yaqi Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Xiaomin Zhang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Qiao Song
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Yuli Hou
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Jing Liu
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China
| | - Yu Sun
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China.
| | - Peichang Wang
- Clinical Laboratory of Xuanwu Hospital, Capital Medical University, Beijing, 100053, People's Republic of China.
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Tenner AJ. Complement-Mediated Events in Alzheimer's Disease: Mechanisms and Potential Therapeutic Targets. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:306-315. [PMID: 31907273 PMCID: PMC6951444 DOI: 10.4049/jimmunol.1901068] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022]
Abstract
An estimated 5.7 million Americans suffer from Alzheimer's disease in the United States, with no disease-modifying treatments to prevent or treat cognitive deficits associated with the disease. Genome-wide association studies suggest that an enhancement of clearance mechanisms and/or promotion of an anti-inflammatory response may slow or prevent disease progression. Increasing awareness of distinct roles of complement components in normal brain development and function and in neurodegenerative disorders align with complement-mediated responses, and thus, thorough understanding of these molecular pathways is needed to facilitate successful therapeutic design. Both beneficial and detrimental effects of C1q as well as contributions to local inflammation by C5a-C5aR1 signaling in brain highlight the need for precision of therapeutic design. The potential benefit of β-amyloid clearance from the circulation via CR1-mediated mechanisms is also reviewed. Therapies that suppress inflammation while preserving protective effects of complement could be tested now to slow the progression of this debilitating disease.
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Affiliation(s)
- Andrea J Tenner
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697;
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697;
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA 92697; and
- Institute for Memory Impairment and Neurological Disorders, University of California Irvine, Irvine, CA 92697
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The landscape of multiscale transcriptomic networks and key regulators in Parkinson's disease. Nat Commun 2019; 10:5234. [PMID: 31748532 PMCID: PMC6868244 DOI: 10.1038/s41467-019-13144-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 10/21/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic and genomic studies have advanced our knowledge of inherited Parkinson’s disease (PD), however, the etiology and pathophysiology of idiopathic PD remain unclear. Herein, we perform a meta-analysis of 8 PD postmortem brain transcriptome studies by employing a multiscale network biology approach to delineate the gene-gene regulatory structures in the substantia nigra and determine key regulators of the PD transcriptomic networks. We identify STMN2, which encodes a stathmin family protein and is down-regulated in PD brains, as a key regulator functionally connected to known PD risk genes. Our network analysis predicts a function of human STMN2 in synaptic trafficking, which is validated in Stmn2-knockdown mouse dopaminergic neurons. Stmn2 reduction in the mouse midbrain causes dopaminergic neuron degeneration, phosphorylated α-synuclein elevation, and locomotor deficits. Our integrative analysis not only begins to elucidate the global landscape of PD transcriptomic networks but also pinpoints potential key regulators of PD pathogenic pathways. Parkinson’s disease (PD) is characterized by neurodegeneration associated with loss of dopaminergic (DA) neurons and deposition of Lewy bodies. Here, Wang et al. use co-expression network analysis to pinpoint disease pathways and propose reduced expression of STMN2 as a cause of presynaptic function loss in PD.
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