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Scoyni F, Giudice L, Väänänen M, Downes N, Korhonen P, Choo XY, Välimäki N, Mäkinen P, Korvenlaita N, Rozemuller AJ, de Vries HE, Polo J, Turunen TA, Ylä‐Herttuala S, Hansen TB, Grubman A, Kaikkonen MU, Malm T. Alzheimer's disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs. Alzheimers Dement 2024; 20:954-974. [PMID: 37828821 PMCID: PMC10916983 DOI: 10.1002/alz.13502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/10/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disease and the main cause of dementia in the elderly. AD pathology is characterized by accumulation of microglia around the beta-amyloid (Aβ) plaques which assumes disease-specific transcriptional signatures, as for the disease-associated microglia (DAM). However, the regulators of microglial phagocytosis are still unknown. METHODS We isolated Aβ-laden microglia from the brain of 5xFAD mice for RNA sequencing to characterize the transcriptional signature in phagocytic microglia and to identify the key non-coding RNAs capable of regulating microglial phagocytosis. Through spatial sequencing, we show the transcriptional changes of microglia in the AD mouse brain in relation to Aβ proximity. RESULTS Finally, we show that phagocytic messenger RNAs are regulated by miR-7a-5p, miR-29a-3p and miR-146a-5p microRNAs and segregate the DAM population into phagocytic and non-phagocytic states. DISCUSSION Our study pinpoints key regulators of microglial Aβ clearing capacity suggesting new targets for future therapeutic approaches.
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Affiliation(s)
- Flavia Scoyni
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Luca Giudice
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Mari‐Anna Väänänen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Nicholas Downes
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Paula Korhonen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Xin Yi Choo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonAustralia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
| | - Nelli‐Noora Välimäki
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Petri Mäkinen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Nea Korvenlaita
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Annemieke J Rozemuller
- Department of Pathology, Amsterdam UMC, Vrije Universiteit AmsterdamVU University Medical CenterAmsterdamMBthe Netherlands
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit AmsterdamVU University Medical CenterAmsterdamMBthe Netherlands
| | - Jose Polo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonAustralia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
| | - Tiia A Turunen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Seppo Ylä‐Herttuala
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Thomas B Hansen
- Interdisciplinary Nanoscience CenterDepartment of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
- Present address:
Targovax ASALysaker1366Norway
| | - Alexandra Grubman
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonAustralia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
| | - Minna U Kaikkonen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Tarja Malm
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
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Toh HSY, Choo XY, Sun AX. Midbrain organoids-development and applications in Parkinson's disease. Oxf Open Neurosci 2023; 2:kvad009. [PMID: 38596240 PMCID: PMC10913847 DOI: 10.1093/oons/kvad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/31/2023] [Indexed: 04/11/2024]
Abstract
Human brain development is spatially and temporally complex. Insufficient access to human brain tissue and inadequacy of animal models has limited the study of brain development and neurodegenerative diseases. Recent advancements of brain organoid technology have created novel opportunities to model human-specific neurodevelopment and brain diseases. In this review, we discuss the use of brain organoids to model the midbrain and Parkinson's disease. We critically evaluate the extent of recapitulation of PD pathology by organoids and discuss areas of future development that may lead to the model to become a next-generation, personalized therapeutic strategy for PD and beyond.
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Affiliation(s)
- Hilary S Y Toh
- Neuroscience & Behavioural Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore
| | - Xin Yi Choo
- Neuroscience & Behavioural Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore
| | - Alfred Xuyang Sun
- Neuroscience & Behavioural Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore
- National Neuroscience Institute, 11 Jln Tan Tock Seng, Singapore
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Choo XY, Lim YM, Katwadi K, Yap L, Tryggvason K, Sun AX, Li S, Handoko L, Ouyang JF, Rackham OJL. Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments. ACS Synth Biol 2021; 10:640-645. [PMID: 33625849 DOI: 10.1021/acssynbio.0c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The combination of single-cell RNA sequencing with CRISPR inhibition/activation provides a high-throughput approach to simultaneously study the effects of hundreds if not thousands of gene perturbations in a single experiment. One recent development in CRISPR-based single-cell techniques introduces a feature barcoding technology that allows for the simultaneous capture of mRNA and guide RNA (gRNA) from the same cell. This is achieved by introducing a capture sequence, whose complement can be incorporated into each gRNA and that can be used to amplify these features prior to sequencing. However, because the technology is in its infancy, there is little information available on how such experimental parameters can be optimized. To overcome this, we varied the capture sequence, capture sequence position, and gRNA backbone to identify an optimal gRNA scaffold for CRISPR activation gene perturbation studies. We provide a report on our screening approach along with our observations and recommendations for future use.
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Affiliation(s)
- Xin Yi Choo
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Yu Ming Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Khairunnisa Katwadi
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Lynn Yap
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Alfred Xuyang Sun
- National Neuroscience Institute, Singapore 308433
- Genome Institute of Singapore, Singapore 138672
| | - Shang Li
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857
| | - Lusy Handoko
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
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Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci 2019; 22:2087-2097. [PMID: 31768052 DOI: 10.1038/s41593-019-0539-4] [Citation(s) in RCA: 434] [Impact Index Per Article: 86.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is currently little information available about how individual cell types contribute to Alzheimer's disease. Here we applied single-nucleus RNA sequencing to entorhinal cortex samples from control and Alzheimer's disease brains (n = 6 per group), yielding a total of 13,214 high-quality nuclei. We detail cell-type-specific gene expression patterns, unveiling how transcriptional changes in specific cell subpopulations are associated with Alzheimer's disease. We report that the Alzheimer's disease risk gene APOE is specifically repressed in Alzheimer's disease oligodendrocyte progenitor cells and astrocyte subpopulations and upregulated in an Alzheimer's disease-specific microglial subopulation. Integrating transcription factor regulatory modules with Alzheimer's disease risk loci revealed drivers of cell-type-specific state transitions towards Alzheimer's disease. For example, transcription factor EB, a master regulator of lysosomal function, regulates multiple disease genes in a specific Alzheimer's disease astrocyte subpopulation. These results provide insights into the coordinated control of Alzheimer's disease risk genes and their cell-type-specific contribution to disease susceptibility. These results are available at http://adsn.ddnetbio.com.
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Affiliation(s)
- Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Gabriel Chew
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xin Yi Choo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona McLean
- Victorian Brain Bank, Florey Institute of Neurosciences, Parkville, Victoria, Australia
| | - Rebecca K Simmons
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Sam Buckberry
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landin
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Daniel Poppe
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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5
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Choo XY, Liddell JR, Huuskonen MT, Grubman A, Moujalled D, Roberts J, Kysenius K, Patten L, Quek H, Oikari LE, Duncan C, James SA, McInnes LE, Hayne DJ, Donnelly PS, Pollari E, Vähätalo S, Lejavová K, Kettunen MI, Malm T, Koistinaho J, White AR, Kanninen KM. Cu II(atsm) Attenuates Neuroinflammation. Front Neurosci 2018; 12:668. [PMID: 30319344 PMCID: PMC6165894 DOI: 10.3389/fnins.2018.00668] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/05/2018] [Indexed: 12/31/2022] Open
Abstract
Background: Neuroinflammation and biometal dyshomeostasis are key pathological features of several neurodegenerative diseases, including Alzheimer’s disease (AD). Inflammation and biometals are linked at the molecular level through regulation of metal buffering proteins such as the metallothioneins. Even though the molecular connections between metals and inflammation have been demonstrated, little information exists on the effect of copper modulation on brain inflammation. Methods: We demonstrate the immunomodulatory potential of the copper bis(thiosemicarbazone) complex CuII(atsm) in an neuroinflammatory model in vivo and describe its anti-inflammatory effects on microglia and astrocytes in vitro. Results: By using a sophisticated in vivo magnetic resonance imaging (MRI) approach, we report the efficacy of CuII(atsm) in reducing acute cerebrovascular inflammation caused by peripheral administration of bacterial lipopolysaccharide (LPS). CuII(atsm) also induced anti-inflammatory outcomes in primary microglia [significant reductions in nitric oxide (NO), monocyte chemoattractant protein 1 (MCP-1), and tumor necrosis factor (TNF)] and astrocytes [significantly reduced NO, MCP-1, and interleukin 6 (IL-6)] in vitro. These anti-inflammatory actions were associated with increased cellular copper levels and increased the neuroprotective protein metallothionein-1 (MT1) in microglia and astrocytes. Conclusion: The beneficial effects of CuII(atsm) on the neuroimmune system suggest copper complexes are potential therapeutics for the treatment of neuroinflammatory conditions.
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Affiliation(s)
- Xin Yi Choo
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - Jeffrey R Liddell
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - Mikko T Huuskonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Alexandra Grubman
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Diane Moujalled
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jessica Roberts
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kai Kysenius
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Lauren Patten
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Hazel Quek
- Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lotta E Oikari
- Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Clare Duncan
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Simon A James
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia.,Australian Synchrotron, Clayton, VIC, Australia
| | - Lachlan E McInnes
- School of Chemistry, Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Melbourne, VIC, Australia
| | - David J Hayne
- School of Chemistry, Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Melbourne, VIC, Australia
| | - Paul S Donnelly
- School of Chemistry, Bio21 Institute for Molecular Science and Biotechnology, The University of Melbourne, Melbourne, VIC, Australia
| | - Eveliina Pollari
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Suvi Vähätalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Katarína Lejavová
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mikko I Kettunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.,Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Anthony R White
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Katja M Kanninen
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia.,A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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