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Shui X, Chen J, Fu Z, Zhu H, Tao H, Li Z. Microglia in Ischemic Stroke: Pathogenesis Insights and Therapeutic Challenges. J Inflamm Res 2024; 17:3335-3352. [PMID: 38800598 PMCID: PMC11128258 DOI: 10.2147/jir.s461795] [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: 02/20/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Ischemic stroke is the most common type of stroke, which is the main cause of death and disability on a global scale. As the primary immune cells in the brain that are crucial for preserving homeostasis of the central nervous system microenvironment, microglia have been found to exhibit dual or even multiple effects at different stages of ischemic stroke. The anti-inflammatory polarization of microglia and release of neurotrophic factors may provide benefits by promoting neurological recovery at the lesion in the early phase after ischemic stroke. However, the pro-inflammatory polarization of microglia and secretion of inflammatory factors in the later phase of injury may exacerbate the ischemic lesion, suggesting the therapeutic potential of modulating the balance of microglial polarization to predispose them to anti-inflammatory transformation in ischemic stroke. Microglia-mediated signaling crosstalk with other cells may also be key to improving functional outcomes following ischemic stroke. Thus, this review provides an overview of microglial functions and responses under physiological and ischemic stroke conditions, including microglial activation, polarization, and interactions with other cells. We focus on approaches that promote anti-inflammatory polarization of microglia, inhibit microglial activation, and enhance beneficial cell-to-cell interactions. These targets may hold promise for the creation of innovative therapeutic strategies.
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Affiliation(s)
- Xinyao Shui
- Clinical Medical College, Southwest Medical University, Luzhou, People’s Republic of China
| | - Jingsong Chen
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, People’s Republic of China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, People’s Republic of China
| | - Ziyue Fu
- Clinical Medical College, Southwest Medical University, Luzhou, People’s Republic of China
| | - Haoyue Zhu
- Clinical Medical College, Southwest Medical University, Luzhou, People’s Republic of China
| | - Hualin Tao
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, People’s Republic of China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, People’s Republic of China
| | - Zhaoyinqian Li
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, People’s Republic of China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, People’s Republic of China
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2
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Pandya VA, Patani R. The role of glial cells in amyotrophic lateral sclerosis. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:381-450. [PMID: 38802179 DOI: 10.1016/bs.irn.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) has traditionally been considered a neuron-centric disease. This view is now outdated, with increasing recognition of cell autonomous and non-cell autonomous contributions of central and peripheral nervous system glia to ALS pathomechanisms. With glial research rapidly accelerating, we comprehensively interrogate the roles of astrocytes, microglia, oligodendrocytes, ependymal cells, Schwann cells and satellite glia in nervous system physiology and ALS-associated pathology. Moreover, we highlight the inter-glial, glial-neuronal and inter-system polylogue which constitutes the healthy nervous system and destabilises in disease. We also propose classification based on function for complex glial reactive phenotypes and discuss the pre-requisite for integrative modelling to advance translation. Given the paucity of life-enhancing therapies currently available for ALS patients, we discuss the promising potential of harnessing glia in driving ALS therapeutic discovery.
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Affiliation(s)
- Virenkumar A Pandya
- University College London Medical School, London, United Kingdom; The Francis Crick Institute, London, United Kingdom.
| | - Rickie Patani
- The Francis Crick Institute, London, United Kingdom; Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology, Queen Square, London, United Kingdom.
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3
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Odierna GL, Vucic S, Dyer M, Dickson T, Woodhouse A, Blizzard C. How do we get from hyperexcitability to excitotoxicity in amyotrophic lateral sclerosis? Brain 2024; 147:1610-1621. [PMID: 38408864 PMCID: PMC11068114 DOI: 10.1093/brain/awae039] [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: 07/17/2023] [Revised: 11/15/2023] [Accepted: 12/10/2023] [Indexed: 02/28/2024] Open
Abstract
Amyotrophic lateral sclerosis is a devastating neurodegenerative disease that, at present, has no effective cure. Evidence of increased circulating glutamate and hyperexcitability of the motor cortex in patients with amyotrophic lateral sclerosis have provided an empirical support base for the 'dying forward' excitotoxicity hypothesis. The hypothesis postulates that increased activation of upper motor neurons spreads pathology to lower motor neurons in the spinal cord in the form of excessive glutamate release, which triggers excitotoxic processes. Many clinical trials have focused on therapies that target excitotoxicity via dampening neuronal activation, but not all are effective. As such, there is a growing tension between the rising tide of evidence for the 'dying forward' excitotoxicity hypothesis and the failure of therapies that target neuronal activation. One possible solution to these contradictory outcomes is that our interpretation of the current evidence requires revision in the context of appreciating the complexity of the nervous system and the limitations of the neurobiological assays we use to study it. In this review we provide an evaluation of evidence relevant to the 'dying forward' excitotoxicity hypothesis and by doing so, identify key gaps in our knowledge that need to be addressed. We hope to provide a road map from hyperexcitability to excitotoxicity so that we can better develop therapies for patients suffering from amyotrophic lateral sclerosis. We conclude that studies of upper motor neuron activity and their synaptic output will play a decisive role in the future of amyotrophic lateral sclerosis therapy.
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Affiliation(s)
- G Lorenzo Odierna
- Tasmanian School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Steve Vucic
- Brain and Nerve Research Center, The University of Sydney, Sydney 2050, Australia
| | - Marcus Dyer
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
- Department of Pharmaceutical and Pharmacological Sciences, Center for Neurosciences, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Tracey Dickson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Adele Woodhouse
- The Wicking Dementia Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - Catherine Blizzard
- Tasmanian School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
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4
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Ding F, Sun Q, Long C, Rasmussen RN, Peng S, Xu Q, Kang N, Song W, Weikop P, Goldman SA, Nedergaard M. Dysregulation of extracellular potassium distinguishes healthy ageing from neurodegeneration. Brain 2024; 147:1726-1739. [PMID: 38462589 PMCID: PMC11068329 DOI: 10.1093/brain/awae075] [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: 11/01/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/12/2024] Open
Abstract
Progressive neuronal loss is a hallmark feature distinguishing neurodegenerative diseases from normal ageing. However, the underlying mechanisms remain unknown. Extracellular K+ homeostasis is a potential mediator of neuronal injury as K+ elevations increase excitatory activity. The dysregulation of extracellular K+ and potassium channel expressions during neurodegeneration could contribute to this distinction. Here we measured the cortical extracellular K+ concentration ([K+]e) in awake wild-type mice as well as murine models of neurodegeneration using K+-sensitive microelectrodes. Unexpectedly, aged wild-type mice exhibited significantly lower cortical [K+]e than young mice. In contrast, cortical [K+]e was consistently elevated in Alzheimer's disease (APP/PS1), amyotrophic lateral sclerosis (ALS) (SOD1G93A) and Huntington's disease (R6/2) models. Cortical resting [K+]e correlated inversely with neuronal density and the [K+]e buffering rate but correlated positively with the predicted neuronal firing rate. Screening of astrocyte-selective genomic datasets revealed a number of potassium channel genes that were downregulated in these disease models but not in normal ageing. In particular, the inwardly rectifying potassium channel Kcnj10 was downregulated in ALS and Huntington's disease models but not in normal ageing, while Fxyd1 and Slc1a3, each of which acts as a negative regulator of potassium uptake, were each upregulated by astrocytes in both Alzheimer's disease and ALS models. Chronic elevation of [K+]e in response to changes in gene expression and the attendant neuronal hyperexcitability may drive the neuronal loss characteristic of these neurodegenerative diseases. These observations suggest that the dysregulation of extracellular K+ homeostasis in a number of neurodegenerative diseases could be due to aberrant astrocytic K+ buffering and as such, highlight a fundamental role for glial dysfunction in neurodegeneration.
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Affiliation(s)
- Fengfei Ding
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Pharmacology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qian Sun
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Pharmacology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Carter Long
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Rune Nguyen Rasmussen
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sisi Peng
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Qiwu Xu
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ning Kang
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Wei Song
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Pia Weikop
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
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5
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You Y, Chen Z, Hu WW. The role of microglia heterogeneity in synaptic plasticity and brain disorders: Will sequencing shed light on the discovery of new therapeutic targets? Pharmacol Ther 2024; 255:108606. [PMID: 38346477 DOI: 10.1016/j.pharmthera.2024.108606] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Microglia play a crucial role in interacting with neuronal synapses and modulating synaptic plasticity. This function is particularly significant during postnatal development, as microglia are responsible for removing excessive synapses to prevent neurodevelopmental deficits. Dysregulation of microglial synaptic function has been well-documented in various pathological conditions, notably Alzheimer's disease and multiple sclerosis. The recent application of RNA sequencing has provided a powerful and unbiased means to decipher spatial and temporal microglial heterogeneity. By identifying microglia with varying gene expression profiles, researchers have defined multiple subgroups of microglia associated with specific pathological states, including disease-associated microglia, interferon-responsive microglia, proliferating microglia, and inflamed microglia in multiple sclerosis, among others. However, the functional roles of these distinct subgroups remain inadequately characterized. This review aims to refine our current understanding of the potential roles of heterogeneous microglia in regulating synaptic plasticity and their implications for various brain disorders, drawing from recent sequencing research and functional studies. This knowledge may aid in the identification of pathogenetic biomarkers and potential factors contributing to pathogenesis, shedding new light on the discovery of novel drug targets. The field of sequencing-based data mining is evolving toward a multi-omics approach. With advances in viral tools for precise microglial regulation and the development of brain organoid models, we are poised to elucidate the functional roles of microglial subgroups detected through sequencing analysis, ultimately identifying valuable therapeutic targets.
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Affiliation(s)
- Yi You
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhong Chen
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China; Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Wei-Wei Hu
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China.
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6
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He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [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: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
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Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
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7
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Naratadam GT, Mecklenburg J, Shein SA, Zou Y, Lai Z, Tumanov AV, Price TJ, Akopian AN. Degenerative and regenerative peripheral processes are associated with persistent painful chemotherapy-induced neuropathies in males and females. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577218. [PMID: 38328207 PMCID: PMC10849728 DOI: 10.1101/2024.01.25.577218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
This study aimed to investigate the time course of gene expression changes during the progression of persistent painful neuropathy caused by paclitaxel (PTX) in male and female mouse hind paws and dorsal root ganglia (DRG). Bulk RNA-seq was used to investigate the gene expression changes in the paw and DRG collected at 1, 16, and 31 days post-PTX. At these time points, differentially expressed DEGs were predominantly related to reduction or increase in epithelial, skin, bone, and muscle development and to angiogenesis, myelination, axonogenesis, and neurogenesis. These processes were accompanied by regulation of DEGs related to cytoskeleton, extracellular matrix organization and cellular energy production. This gene plasticity during persistent painful neuropathy progression likely represents biological processes linked to tissue regeneration and degeneration. Unlike regeneration/degeneration, gene plasticity related to immune processes was minimal at 1-31 days post-PTX. It was also noted that despite similarities in biological processes and pain chronicity in males and females, specific DEGs showed dramatic sex-dependency. The main conclusions of this study are that gene expression plasticity in paws and DRG during PTX neuropathy progression relates to tissue regeneration and degeneration, minimally affects the immune system processes, and is heavily sex-dependent at the individual gene level.
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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Awuah WA, Ahluwalia A, Ghosh S, Roy S, Tan JK, Adebusoye FT, Ferreira T, Bharadwaj HR, Shet V, Kundu M, Yee ALW, Abdul-Rahman T, Atallah O. The molecular landscape of neurological disorders: insights from single-cell RNA sequencing in neurology and neurosurgery. Eur J Med Res 2023; 28:529. [PMID: 37974227 PMCID: PMC10652629 DOI: 10.1186/s40001-023-01504-w] [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: 08/10/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Single-cell ribonucleic acid sequencing (scRNA-seq) has emerged as a transformative technology in neurological and neurosurgical research, revolutionising our comprehension of complex neurological disorders. In brain tumours, scRNA-seq has provided valuable insights into cancer heterogeneity, the tumour microenvironment, treatment resistance, and invasion patterns. It has also elucidated the brain tri-lineage cancer hierarchy and addressed limitations of current models. Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis have been molecularly subtyped, dysregulated pathways have been identified, and potential therapeutic targets have been revealed using scRNA-seq. In epilepsy, scRNA-seq has explored the cellular and molecular heterogeneity underlying the condition, uncovering unique glial subpopulations and dysregulation of the immune system. ScRNA-seq has characterised distinct cellular constituents and responses to spinal cord injury in spinal cord diseases, as well as provided molecular signatures of various cell types and identified interactions involved in vascular remodelling. Furthermore, scRNA-seq has shed light on the molecular complexities of cerebrovascular diseases, such as stroke, providing insights into specific genes, cell-specific expression patterns, and potential therapeutic interventions. This review highlights the potential of scRNA-seq in guiding precision medicine approaches, identifying clinical biomarkers, and facilitating therapeutic discovery. However, challenges related to data analysis, standardisation, sample acquisition, scalability, and cost-effectiveness need to be addressed. Despite these challenges, scRNA-seq has the potential to transform clinical practice in neurological and neurosurgical research by providing personalised insights and improving patient outcomes.
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Affiliation(s)
- Wireko Andrew Awuah
- Faculty of Medicine, Sumy State University, Zamonstanksya 7, Sumy, 40007, Ukraine
| | | | - Shankaneel Ghosh
- Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
| | - Sakshi Roy
- School of Medicine, Queen's University Belfast, Belfast, UK
| | | | | | - Tomas Ferreira
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Vallabh Shet
- Faculty of Medicine, Bangalore Medical College and Research Institute, Bangalore, Karnataka, India
| | - Mrinmoy Kundu
- Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
| | | | - Toufik Abdul-Rahman
- Faculty of Medicine, Sumy State University, Zamonstanksya 7, Sumy, 40007, Ukraine
| | - Oday Atallah
- Department of Neurosurgery, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
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10
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Seki S, Kitaoka Y, Kawata S, Nishiura A, Uchihashi T, Hiraoka SI, Yokota Y, Isomura ET, Kogo M, Tanaka S. Characteristics of Sensory Neuron Dysfunction in Amyotrophic Lateral Sclerosis (ALS): Potential for ALS Therapy. Biomedicines 2023; 11:2967. [PMID: 38001967 PMCID: PMC10669304 DOI: 10.3390/biomedicines11112967] [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: 09/07/2023] [Revised: 10/24/2023] [Accepted: 10/29/2023] [Indexed: 11/26/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterised by the progressive degeneration of motor neurons, resulting in muscle weakness, paralysis, and, ultimately, death. Presently, no effective treatment for ALS has been established. Although motor neuron dysfunction is a hallmark of ALS, emerging evidence suggests that sensory neurons are also involved in the disease. In clinical research, 30% of patients with ALS had sensory symptoms and abnormal sensory nerve conduction studies in the lower extremities. Peroneal nerve biopsies show histological abnormalities in 90% of the patients. Preclinical research has reported several genetic abnormalities in the sensory neurons of animal models of ALS, as well as in motor neurons. Furthermore, the aggregation of misfolded proteins like TAR DNA-binding protein 43 has been reported in sensory neurons. This review aims to provide a comprehensive description of ALS-related sensory neuron dysfunction, focusing on its clinical changes and underlying mechanisms. Sensory neuron abnormalities in ALS are not limited to somatosensory issues; proprioceptive sensory neurons, such as MesV and DRG neurons, have been reported to form networks with motor neurons and may be involved in motor control. Despite receiving limited attention, sensory neuron abnormalities in ALS hold potential for new therapies targeting proprioceptive sensory neurons.
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Affiliation(s)
- Soju Seki
- Department of Oral and Maxillofacial Surgery, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita 565-0871, Osaka, Japan
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11
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You J, Youssef MMM, Santos JR, Lee J, Park J. Microglia and Astrocytes in Amyotrophic Lateral Sclerosis: Disease-Associated States, Pathological Roles, and Therapeutic Potential. BIOLOGY 2023; 12:1307. [PMID: 37887017 PMCID: PMC10603852 DOI: 10.3390/biology12101307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Microglial and astrocytic reactivity is a prominent feature of amyotrophic lateral sclerosis (ALS). Microglia and astrocytes have been increasingly appreciated to play pivotal roles in disease pathogenesis. These cells can adopt distinct states characterized by a specific molecular profile or function depending on the different contexts of development, health, aging, and disease. Accumulating evidence from ALS rodent and cell models has demonstrated neuroprotective and neurotoxic functions from microglia and astrocytes. In this review, we focused on the recent advancements of knowledge in microglial and astrocytic states and nomenclature, the landmark discoveries demonstrating a clear contribution of microglia and astrocytes to ALS pathogenesis, and novel therapeutic candidates leveraging these cells that are currently undergoing clinical trials.
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Affiliation(s)
- Justin You
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.); (M.M.M.Y.); (J.R.S.); (J.L.)
| | - Mohieldin M. M. Youssef
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.); (M.M.M.Y.); (J.R.S.); (J.L.)
| | - Jhune Rizsan Santos
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.); (M.M.M.Y.); (J.R.S.); (J.L.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Jooyun Lee
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.); (M.M.M.Y.); (J.R.S.); (J.L.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Jeehye Park
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (J.Y.); (M.M.M.Y.); (J.R.S.); (J.L.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
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12
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Gao MY, Wang JQ, He J, Gao R, Zhang Y, Li X. Single-Cell RNA-Sequencing in Astrocyte Development, Heterogeneity, and Disease. Cell Mol Neurobiol 2023; 43:3449-3464. [PMID: 37552355 DOI: 10.1007/s10571-023-01397-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Astrocytes are the most plentiful cell type in the central nervous system (CNS) and perform complicated functions in health and disease. It is obvious that different astrocyte subpopulations, or activation states, are relevant with specific genomic programs and functions. In recent years, the emergence of new technologies such as single-cell RNA sequencing (scRNA-seq) has made substantial advance in the characterization of astrocyte heterogeneity, astrocyte developmental trajectory, and its role in CNS diseases which has had a significant impact on neuroscience. In this review, we present an overview of astrocyte development, heterogeneity, and its essential role in the physiological and pathological environments of the CNS. We focused on the critical role of single-cell sequencing in revealing astrocyte development, heterogeneity, and its role in different CNS diseases.
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Affiliation(s)
- Meng-Yuan Gao
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Jia-Qi Wang
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Jin He
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Rui Gao
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yuan Zhang
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Xing Li
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
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13
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Abdullatef S, Farina C. Publicly available ex vivo transcriptomics datasets to explore CNS physiology and neurodegeneration: state of the art and perspectives. Front Neurosci 2023; 17:1211079. [PMID: 37680966 PMCID: PMC10481165 DOI: 10.3389/fnins.2023.1211079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/08/2023] [Indexed: 09/09/2023] Open
Abstract
The central nervous system (CNS) is characterized by an intricate composition of diverse cell types, including neurons and glia cells (astrocytes, oligodendrocytes, and microglia), whose functions may differ along time, between sexes and upon pathology. The advancements in high-throughput transcriptomics are providing fundamental insights on cell phenotypes, so that molecular codes and instructions are ever more described for CNS physiology and neurodegeneration. To facilitate the search of relevant information, this review provides an overview of key CNS transcriptomics studies ranging from CNS development to ageing and from physiology to pathology as defined for five neurodegenerative disorders and their relative animal models, with a focus on molecular descriptions whose raw data were publicly available. Accurate phenotypic descriptions of cellular states correlate with functional changes and this knowledge may support research devoted to the development of therapeutic strategies supporting CNS repair and function.
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Affiliation(s)
- Sandra Abdullatef
- Division of Neuroscience, Institute of Experimental Neurology (INSpe), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
| | - Cinthia Farina
- Division of Neuroscience, Institute of Experimental Neurology (INSpe), IRCCS San Raffaele Scientific Institute, Milan, Italy
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14
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Morello G, La Cognata V, Guarnaccia M, La Bella V, Conforti FL, Cavallaro S. A Diagnostic Gene-Expression Signature in Fibroblasts of Amyotrophic Lateral Sclerosis. Cells 2023; 12:1884. [PMID: 37508548 PMCID: PMC10378077 DOI: 10.3390/cells12141884] [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: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease with limited treatment options. Diagnosis can be difficult due to the heterogeneity and non-specific nature of the initial symptoms, resulting in delays that compromise prompt access to effective therapeutic strategies. Transcriptome profiling of patient-derived peripheral cells represents a valuable benchmark in overcoming such challenges, providing the opportunity to identify molecular diagnostic signatures. In this study, we characterized transcriptome changes in skin fibroblasts of sporadic ALS patients (sALS) and controls and evaluated their utility as a molecular classifier for ALS diagnosis. Our analysis identified 277 differentially expressed transcripts predominantly involved in transcriptional regulation, synaptic transmission, and the inflammatory response. A support vector machine classifier based on this 277-gene signature was developed to discriminate patients with sALS from controls, showing significant predictive power in both the discovery dataset and in six independent publicly available gene expression datasets obtained from different sALS tissue/cell samples. Taken together, our findings support the utility of transcriptional signatures in peripheral cells as valuable biomarkers for the diagnosis of ALS.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Center and Neurochemistry Laboratory, BiND, University of Palermo, 90133 Palermo, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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15
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Qian K, Jiang X, Liu ZQ, Zhang J, Fu P, Su Y, Brazhe NA, Liu D, Zhu LQ. Revisiting the critical roles of reactive astrocytes in neurodegeneration. Mol Psychiatry 2023; 28:2697-2706. [PMID: 37037874 DOI: 10.1038/s41380-023-02061-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
Astrocytes, an integral component of the central nervous system (CNS), contribute to the maintenance of physiological homeostasis through their roles in synaptic function, K+ buffering, blood-brain barrier (BBB) maintenance, and neuronal metabolism. Reactive astrocytes refer to astrocytes undergoing morphological, molecular and functional remodelling in response to pathological stimuli. The activation and differentiation of astrocytes are implicated in the pathogenesis of multiple neurodegenerative diseases. However, there are still controversies regarding their subset identification, function and nomenclature in neurodegeneration. In this review, we revisit the multidimensional roles of reactive astrocytes in Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Furthermore, we propose a precise linkage between astrocyte subsets and their functions based on single-cell sequencing analyses.
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Affiliation(s)
- Kang Qian
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Neurosurgery, Union Hospital, Huazhong University of Science and Technology, Jiefang Avenue No. 1277, 430022, Wuhan, China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Huazhong University of Science and Technology, Jiefang Avenue No. 1277, 430022, Wuhan, China
| | - Zhi-Qiang Liu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Zhang
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Fu
- Department of Neurosurgery, Union Hospital, Huazhong University of Science and Technology, Jiefang Avenue No. 1277, 430022, Wuhan, China
| | - Ying Su
- Department of Neurology, Union Hospital, Huazhong University of Science and Technology, Jiefang Avenue No. 1277, 430022, Wuhan, China
| | - Nadezda A Brazhe
- Biophysics Department, Biological Faculty, Moscow State University, Moscow, Russia
| | - Dan Liu
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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16
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Truong L, Chen YW, Barrere-Cain R, Levenson MT, Shuck K, Xiao W, da Veiga Beltrame E, Panter B, Reich E, Sternberg PW, Yang X, Allard P. Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol. Cell Rep 2023; 42:112535. [PMID: 37227821 PMCID: PMC10592506 DOI: 10.1016/j.celrep.2023.112535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Single-cell transcriptomic platforms provide an opportunity to map an organism's response to environmental cues with high resolution. Here, we applied single-nucleus RNA sequencing (snRNA-seq) to establish the tissue and cell type-resolved transcriptome of the adult C. elegans and characterize the inter- and trans-generational transcriptional impact of ethanol. We profiled the transcriptome of 41,749 nuclei resolving into 31 clusters, representing a diverse array of adult cell types including syncytial tissues. Following exposure to human-relevant doses of alcohol, several germline, striated muscle, and neuronal clusters were identified as being the most transcriptionally impacted at the F1 and F3 generations. The effect on germline clusters was confirmed by phenotypic enrichment analysis as well as by functional validation, which revealed a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq represents a valuable approach for the detailed examination of an adult organism's response to environmental exposures.
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Affiliation(s)
- Lisa Truong
- Human Genetics Graduate Program, UCLA, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Rio Barrere-Cain
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Max T Levenson
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Karissa Shuck
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | | | - Blake Panter
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ella Reich
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Paul W Sternberg
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xia Yang
- Integrative Biology and Physiology Department, UCLA, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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17
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Lui KNC, Li Z, Lai FPL, Lau ST, Ngan ESW. Organoid models of breathing disorders reveal patterning defect of hindbrain neurons caused by PHOX2B-PARMs. Stem Cell Reports 2023:S2213-6711(23)00199-6. [PMID: 37352849 PMCID: PMC10362500 DOI: 10.1016/j.stemcr.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/25/2023] Open
Abstract
Retrotrapezoid nucleus (RTN) neurons in the brainstem regulate the ventilatory response to hypercarbia. It is unclear how PHOX2B-polyalanine repeat mutations (PHOX2B-PARMs) alter the function of PHOX2B and perturb the formation of RTN neurons. Here, we generated human brainstem organoids (HBSOs) with RTN-like neurons from human pluripotent stem cells. Single-cell transcriptomics revealed that expression of PHOX2B+7Ala PARM alters the differentiation trajectories of the hindbrain neurons and hampers the formation of the RTN-like neurons in HBSOs. With the unguided cerebral organoids (HCOs), PHOX2B+7Ala PARM interrupted the patterning of PHOX2B+ neurons with dysregulation of Hedgehog pathway and HOX genes. With complementary use of HBSOs and HCOs with a patient and two mutant induced pluripotent stem cell lines carrying different polyalanine repetition in PHOX2B, we further defined the association between the length of polyalanine repetition and malformation of RTN-respiratory center and demonstrated the potential toxic gain of function of PHOX2B-PARMs, highlighting the uniqueness of these organoid models for disease modeling.
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Affiliation(s)
- Kathy Nga-Chu Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Zhixin Li
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Frank Pui-Ling Lai
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Sin-Ting Lau
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Elly Sau-Wai Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR.
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18
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Valori CF, Sulmona C, Brambilla L, Rossi D. Astrocytes: Dissecting Their Diverse Roles in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Cells 2023; 12:1450. [PMID: 37296571 PMCID: PMC10252425 DOI: 10.3390/cells12111450] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders often co-occurring in the same patient, a feature that suggests a common origin of the two diseases. Consistently, pathological inclusions of the same proteins as well as mutations in the same genes can be identified in both ALS/FTD. Although many studies have described several disrupted pathways within neurons, glial cells are also regarded as crucial pathogenetic contributors in ALS/FTD. Here, we focus our attention on astrocytes, a heterogenous population of glial cells that perform several functions for optimal central nervous system homeostasis. Firstly, we discuss how post-mortem material from ALS/FTD patients supports astrocyte dysfunction around three pillars: neuroinflammation, abnormal protein aggregation, and atrophy/degeneration. Furthermore, we summarize current attempts at monitoring astrocyte functions in living patients using either novel imaging strategies or soluble biomarkers. We then address how astrocyte pathology is recapitulated in animal and cellular models of ALS/FTD and how we used these models both to understand the molecular mechanisms driving glial dysfunction and as platforms for pre-clinical testing of therapeutics. Finally, we present the current clinical trials for ALS/FTD, restricting our discussion to treatments that modulate astrocyte functions, directly or indirectly.
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Affiliation(s)
- Chiara F. Valori
- Molecular Neuropathology of Neurodegenerative Diseases, German Centre for Neurodegenerative Diseases (DZNE), 72072 Tübingen, Germany
- Department of Neuropathology, University of Tübingen, 72076 Tübingen, Germany
| | - Claudia Sulmona
- Laboratory for Research on Neurodegenerative Disorders, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy
| | - Liliana Brambilla
- Laboratory for Research on Neurodegenerative Disorders, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy
| | - Daniela Rossi
- Laboratory for Research on Neurodegenerative Disorders, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy
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19
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Ho NJ, Chen X, Lei Y, Gu S. Decoding hereditary spastic paraplegia pathogenicity through transcriptomic profiling. Zool Res 2023; 44:650-662. [PMID: 37161652 PMCID: PMC10236304 DOI: 10.24272/j.issn.2095-8137.2022.281] [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: 12/30/2022] [Accepted: 05/10/2023] [Indexed: 05/11/2023] Open
Abstract
Hereditary spastic paraplegia (HSP) is a group of genetic motor neuron diseases resulting from length-dependent axonal degeneration of the corticospinal upper motor neurons. Due to the advancement of next-generation sequencing, more than 70 novel HSP disease-causing genes have been identified in the past decade. Despite this, our understanding of HSP physiopathology and the development of efficient management and treatment strategies remain poor. One major challenge in studying HSP pathogenicity is selective neuronal vulnerability, characterized by the manifestation of clinical symptoms that are restricted to specific neuronal populations, despite the presence of germline disease-causing variants in every cell of the patient. Furthermore, disease genes may exhibit ubiquitous expression patterns and involve a myriad of different pathways to cause motor neuron degeneration. In the current review, we explore the correlation between transcriptomic data and clinical manifestations, as well as the importance of interspecies models by comparing tissue-specific transcriptomic profiles of humans and mice, expression patterns of different genes in the brain during development, and single-cell transcriptomic data from related tissues. Furthermore, we discuss the potential of emerging single-cell RNA sequencing technologies to resolve unanswered questions related to HSP pathogenicity.
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Affiliation(s)
- Nicolas James Ho
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao Chen
- Dr. Li Dak Sum-Yip Yio Chin Center for Stem Cells and Regenerative Medicine and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang University-University of Edinburgh Institute & School of Basic Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang, 310058 China
| | - Yong Lei
- School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, China
- The Chinese University of Hong Kong (Shenzhen), Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518172, China. E-mail:
| | - Shen Gu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China. E-mail:
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20
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Swanson MEV, Mrkela M, Murray HC, Cao MC, Turner C, Curtis MA, Faull RLM, Walker AK, Scotter EL. Microglial CD68 and L-ferritin upregulation in response to phosphorylated-TDP-43 pathology in the amyotrophic lateral sclerosis brain. Acta Neuropathol Commun 2023; 11:69. [PMID: 37118836 PMCID: PMC10142752 DOI: 10.1186/s40478-023-01561-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/29/2023] [Indexed: 04/30/2023] Open
Abstract
Microglia, the innate immune cells of the brain, are activated by damage or disease. In mouse models of amyotrophic lateral sclerosis (ALS), microglia shift from neurotrophic to neurotoxic states with disease progression. It remains unclear how human microglia change relative to the TAR DNA-binding protein 43 (TDP-43) aggregation that occurs in 97% of ALS cases. Here we examine spatial relationships between microglial activation and TDP-43 pathology in brain tissue from people with ALS and from a TDP-43-driven ALS mouse model. Post-mortem human brain tissue from the Neurological Foundation Human Brain Bank was obtained from 10 control and 10 ALS cases in parallel with brain tissue from a bigenic NEFH-tTA/tetO-hTDP-43∆NLS (rNLS) mouse model of ALS at disease onset, early disease, and late disease stages. The spatiotemporal relationship between microglial activation and ALS pathology was determined by investigating microglial functional marker expression in brain regions with low and high TDP-43 burden at end-stage human disease: hippocampus and motor cortex, respectively. Sections were immunohistochemically labelled with a two-round multiplexed antibody panel against; microglial functional markers (L-ferritin, HLA-DR, CD74, CD68, and Iba1), a neuronal marker, an astrocyte marker, and pathological phosphorylated TDP-43 (pTDP-43). Single-cell levels of microglial functional markers were quantified using custom analysis pipelines and mapped to anatomical regions and ALS pathology. We identified a significant increase in microglial Iba1 and CD68 expression in the human ALS motor cortex, with microglial CD68 being significantly correlated with pTDP-43 pathology load. We also identified two subpopulations of microglia enriched in the ALS motor cortex that were defined by high L-ferritin expression. A similar pattern of microglial changes was observed in the rNLS mouse, with an increase first in CD68 and then in L-ferritin expression, with both occurring only after pTDP-43 inclusions were detectable. Our data strongly suggest that microglia are phagocytic at early-stage ALS but transition to a dysfunctional state at end-stage disease, and that these functional states are driven by pTDP-43 aggregation. Overall, these findings enhance our understanding of microglial phenotypes and function in ALS.
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Affiliation(s)
- Molly E V Swanson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Miran Mrkela
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Helen C Murray
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Maize C Cao
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Department of Anatomical Pathology, Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Maurice A Curtis
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Adam K Walker
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Emma L Scotter
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
- Centre for Brain Research, University of Auckland, Auckland, New Zealand.
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21
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Filipi T, Matusova Z, Abaffy P, Vanatko O, Tureckova J, Benesova S, Kubiskova M, Kirdajova D, Zahumensky J, Valihrach L, Anderova M. Cortical glia in SOD1(G93A) mice are subtly affected by ALS-like pathology. Sci Rep 2023; 13:6538. [PMID: 37085528 PMCID: PMC10121704 DOI: 10.1038/s41598-023-33608-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/15/2023] [Indexed: 04/23/2023] Open
Abstract
The role of glia in amyotrophic lateral sclerosis (ALS) is undeniable. Their disease-related activity has been extensively studied in the spinal cord, but only partly in the brain. We present herein a comprehensive study of glia in the cortex of SOD1(G93A) mice-a widely used model of ALS. Using single-cell RNA sequencing (scRNA-seq) and immunohistochemistry, we inspected astrocytes, microglia, and oligodendrocytes, in four stages of the disease, respecting the factor of sex. We report minimal changes of glia throughout the disease progression and regardless of sex. Pseudobulk and single-cell analyses revealed subtle disease-related transcriptional alterations at the end-stage in microglia and oligodendrocytes, which were supported by immunohistochemistry. Therefore, our data support the hypothesis that the SOD1(G93A) mouse cortex does not recapitulate the disease in patients, and we recommend the use of a different model for future studies of the cortical ALS pathology.
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Affiliation(s)
- Tereza Filipi
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, V Uvalu 84, 15006, Prague, Czech Republic
| | - Zuzana Matusova
- Laboratory of Gene Expression, Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic
- Faculty of Science, Charles University, Albertov 6, 12800, Prague, Czech Republic
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic
| | - Ondrej Vanatko
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, V Uvalu 84, 15006, Prague, Czech Republic
| | - Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technicka 5, 16628, Prague, Czech Republic
| | - Monika Kubiskova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Denisa Kirdajova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Jakub Zahumensky
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic.
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic.
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22
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Venugopal S, Ghulam-Jhelani Z, Ahn IS, Yang X, Wiedau M, Simmons D, Chandler SH. Early deficits in GABA inhibition parallels an increase in L-type Ca 2+ currents in the jaw motor neurons of SOD1 G93A mouse model for ALS. Neurobiol Dis 2023; 177:105992. [PMID: 36623607 DOI: 10.1016/j.nbd.2023.105992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) involves protracted pre-symptomatic periods of abnormal motor neuron (MN) excitability occurring in parallel with central and peripheral synaptic perturbations. Focusing on inhibitory control of MNs, we first compared longitudinal changes in pre-synaptic terminal proteins for GABA and glycine neurotransmitters around the soma of retrogradely identified trigeminal jaw closer (JC) MNs and ChAT-labeled midbrain extraocular (EO) MNs in the SOD1G93A mouse model for ALS. Fluorescence immunocytochemistry and confocal imaging were used to quantify GAD67 and GlyT2 synaptic bouton density (SBD) around MN soma at pre-symptomatic ages ∼P12 (postnatal), ∼P50 (adult) and near disease end-stage (∼P135) in SOD1G93A mice and age-matched wild-type (WT) controls. We noted reduced GAD67 innervation in the SOD1G93A trigeminal jaw closer MNs around P12, relative to age-matched WT and no significant difference around P50 and P135. In contrast, both GAD67 and GlyT2 innervation were elevated in the SOD1G93A EO MNs at the pre-symptomatic time points. Considering trigeminal MNs are vulnerable in ALS while EO MNs are spared, we suggest that upregulation of inhibition in the latter might be compensatory. Notable contrast also existed in the innate co-expression patterns of GAD67 and GlyT2 with higher mutual information (co-dependency) in EO MNs compared to JC in both SOD1G93A and WT mice, especially at adult stages (P50 and P135). Around P12 when GAD67 terminals expression was low in the mutant, we further tested for persistent GABA inhibition in those MNs using in vitro patch-clamp electrophysiology. Our results show that SOD1G93A JC MNs have reduced persistent GABA inhibition, relative to WT. Pharmacological blocking of an underlying tonically active GABA conductance using the GABA-α5 subunit inverse agonist, L-655-708, disinhibited WT JC MNs and lowered their recruitment threshold, suggesting its role in the control of intrinsic MN excitability. Quantitative RT-PCR in laser dissected JC MNs further supported a reduction in GABA-α5 subunit mRNA expression in the mutant. In light of our previous report that JC MNs forming putative fast motor units have lower input threshold in the SOD1G93A mice, we suggest that our present result on reduced GABA-α5 tonic inhibition provides for a mechanism contributing to such imbalance. In parallel with reduced GABA inhibition, we noted an increase in voltage-gated L-type Ca2+ currents in the mutant JC MNs around P12. Together these results support that, early modifications in intrinsic properties of vulnerable MNs could be an adaptive response to counter synaptic deficits.
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Affiliation(s)
- Sharmila Venugopal
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Zohal Ghulam-Jhelani
- Undergraduate Interdepartmental Program for Neuroscience, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Martina Wiedau
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dwayne Simmons
- Department of Biology, Baylor University, Waco, TX 76798, USA
| | - Scott H Chandler
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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23
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Founta K, Dafou D, Kanata E, Sklaviadis T, Zanos TP, Gounaris A, Xanthopoulos K. Gene targeting in amyotrophic lateral sclerosis using causality-based feature selection and machine learning. Mol Med 2023; 29:12. [PMID: 36694130 PMCID: PMC9872307 DOI: 10.1186/s10020-023-00603-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease that affects upper and lower motor neurons. As the molecular basis of the disease is still elusive, the development of high-throughput sequencing technologies, combined with data mining techniques and machine learning methods, could provide remarkable results in identifying pathogenetic mechanisms. High dimensionality is a major problem when applying machine learning techniques in biomedical data analysis, since a huge number of features is available for a limited number of samples. The aim of this study was to develop a methodology for training interpretable machine learning models in the classification of ALS and ALS-subtypes samples, using gene expression datasets. METHODS We performed dimensionality reduction in gene expression data using a semi-automated preprocessing systematic gene selection procedure using Statistically Equivalent Signature (SES), a causality-based feature selection algorithm, followed by Boosted Regression Trees (XGBoost) and Random Forest to train the machine learning classifiers. The SHapley Additive exPlanations (SHAP values) were used for interpretation of the machine learning classifiers. The methodology was developed and tested using two distinct publicly available ALS RNA-seq datasets. We evaluated the performance of SES as a dimensionality reduction method against: (a) Least Absolute Shrinkage and Selection Operator (LASSO), and (b) Local Outlier Factor (LOF). RESULTS The proposed methodology achieved 85.18% accuracy for the classification of cerebellum or frontal cortex samples as C9orf72-related familial ALS, sporadic ALS or healthy samples. Importantly, the genes identified as the most determinative have also been reported as disease-associated in ALS literature. When tested in the evaluation dataset, the methodology achieved 88.89% accuracy for the classification of sporadic ALS motor neuron samples. When LASSO was used as feature selection method instead of SES, the accuracy of the machine learning classifiers ranged from 74.07 to 96.30%, depending on tissue assessed, while LOF underperformed significantly (77.78% accuracy for the classification of pooled cerebellum and frontal cortex samples). CONCLUSIONS Using SES, we addressed the challenge of high dimensionality in gene expression data analysis, and we trained accurate machine learning ALS classifiers, specific for the gene expression patterns of different disease subtypes and tissue samples, while identifying disease-associated genes.
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Affiliation(s)
- Kyriaki Founta
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eirini Kanata
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros P Zanos
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Feinstein Institutes for Medical Research, Institute of Health Systems Science, Northwell Health, Manhasset, NY, 11030, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
| | - Anastasios Gounaris
- School of Informatics, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantinos Xanthopoulos
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001, Thermi, Greece.
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24
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Lyu M, Xin L, Jin H, Chitkushev LT, Zhang G, Keskin DB, Brusic V. Protocol for Classification Single-Cell PBMC Types from Pathological Samples Using Supervised Machine Learning. Methods Mol Biol 2023; 2673:53-67. [PMID: 37258906 DOI: 10.1007/978-1-0716-3239-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Peripheral blood mononuclear cells (PBMC) are mixed subpopulations of blood cells composed of five cell types. PBMC are widely used in the study of the immune system, infectious diseases, cancer, and vaccine development. Single-cell transcriptomics (SCT) allows the labeling of cell types by gene expression patterns from biological samples. Classifying cells into cell types and states is essential for single-cell analyses, especially in the classification of diseases and the assessment of therapeutic interventions, and for many secondary analyses. Most of the classification of cell types from SCT data use unsupervised clustering or a combination of unsupervised and supervised methods including manual correction. In this chapter, we describe a protocol that uses supervised machine learning (ML) methods with SCT data for the classification of PBMC cell types in samples representing pathological states. This protocol has three parts: (1) data preprocessing, (2) labeling of reference PBMC SCT datasets and training supervised ML models, and (3) labeling new PBMC datasets from disease samples. This protocol enables building classification models that are of high accuracy and efficiency. Our example focuses on 10× Genomics technology but applies to datasets from other SCT platforms.
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Affiliation(s)
- Minjie Lyu
- School of Computer Science, University of Nottingham, Ningbo, Zhejiang, China
| | - Lin Xin
- School of Computer Science, University of Nottingham, Ningbo, Zhejiang, China
| | - Huan Jin
- School of Computer Science, University of Nottingham, Ningbo, Zhejiang, China
| | - Lou T Chitkushev
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
| | - Guanglan Zhang
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
| | - Derin B Keskin
- Translational Immuno-Genomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vladimir Brusic
- School of Computer Science, University of Nottingham, Ningbo, Zhejiang, China.
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25
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Abdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice. eLife 2022; 11:e81453. [PMID: 36346385 PMCID: PMC9668333 DOI: 10.7554/elife.81453] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, α-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, although mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces α-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.
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Affiliation(s)
- Reem Abdel-Haq
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Johannes CM Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University West LafayetteWest LafayetteUnited States
| | - Taren Thron
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Mengying Zhang
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - John W Bostick
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Tahmineh Khazaei
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Sujatha Chilakala
- Lawrence J Ellison Institute for Transformative Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Livia H Morais
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Greg Humphrey
- Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical CenterChicagoUnited States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical CenterChicagoUnited States
| | - Jonathan E Katz
- Lawrence J Ellison Institute for Transformative Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Matthew Thomson
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Rob Knight
- Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Department of Computer Science and Engineering, University of California, San DiegoSan DiegoUnited States
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
- Center for Microbiome Innovation, University of California San DiegoSan DiegoUnited States
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University West LafayetteWest LafayetteUnited States
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
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26
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Nelles DG, Hazrati LN. Ependymal cells and neurodegenerative disease: outcomes of compromised ependymal barrier function. Brain Commun 2022; 4:fcac288. [PMID: 36415662 PMCID: PMC9677497 DOI: 10.1093/braincomms/fcac288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 11/01/2022] [Indexed: 08/08/2023] Open
Abstract
Within the central nervous system, ependymal cells form critical components of the blood-cerebrospinal fluid barrier and the cerebrospinal fluid-brain barrier. These barriers provide biochemical, immunological and physical protection against the entry of molecules and foreign substances into the cerebrospinal fluid while also regulating cerebrospinal fluid dynamics, such as the composition, flow and removal of waste from the cerebrospinal fluid. Previous research has demonstrated that several neurodegenerative diseases, such as Alzheimer's disease and multiple sclerosis, display irregularities in ependymal cell function, morphology, gene expression and metabolism. Despite playing key roles in maintaining overall brain health, ependymal barriers are largely overlooked and understudied in the context of disease, thus limiting the development of novel diagnostic and treatment options. Therefore, this review explores the anatomical properties, functions and structures that define ependymal cells in the healthy brain, as well as the ways in which ependymal cell dysregulation manifests across several neurodegenerative diseases. Specifically, we will address potential mechanisms, causes and consequences of ependymal cell dysfunction and describe how compromising the integrity of ependymal barriers may initiate, contribute to, or drive widespread neurodegeneration in the brain.
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Affiliation(s)
- Diana G Nelles
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Ave, Canada
| | - Lili-Naz Hazrati
- Correspondence to: Dr. Lili-Naz Hazrati 555 University Ave, Toronto ON M5G 1X8, Canada E-mail:
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27
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Sun J, Qiu J, Yang Q, Ju Q, Qu R, Wang X, Wu L, Xing L. Single-cell RNA sequencing reveals dysregulation of spinal cord cell types in a severe spinal muscular atrophy mouse model. PLoS Genet 2022; 18:e1010392. [PMID: 36074806 PMCID: PMC9488758 DOI: 10.1371/journal.pgen.1010392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/20/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Although spinal muscular atrophy (SMA) is a motor neuron disease caused by the loss of survival of motor neuron (SMN) proteins, there is growing evidence that non-neuronal cells play important roles in SMA pathogenesis. However, transcriptome alterations occurring at the single-cell level in SMA spinal cord remain unknown, preventing us from fully comprehending the role of specific cells. Here, we performed single-cell RNA sequencing of the spinal cord of a severe SMA mouse model, and identified ten cell types as well as their differentially expressed genes. Using CellChat, we found that cellular communication between different cell types in the spinal cord of SMA mice was significantly reduced. A dimensionality reduction analysis revealed 29 cell subtypes and their differentially expressed gene. A subpopulation of vascular fibroblasts showed the most significant change in the SMA spinal cord at the single-cell level. This subpopulation was drastically reduced, possibly causing vascular defects and resulting in widespread protein synthesis and energy metabolism reductions in SMA mice. This study reveals for the first time a single-cell atlas of the spinal cord of mice with severe SMA, and sheds new light on the pathogenesis of SMA.
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Affiliation(s)
- Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
- * E-mail: (JS); (LW); (LX)
| | - Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, China
| | - Qiongxia Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Qianqian Ju
- Laboratory Animal Center, Nantong University, Nantong, China
| | - Ruobing Qu
- Biomedical Polymers Laboratory, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China
| | - Xu Wang
- Laboratory Animal Center, Nantong University, Nantong, China
| | - Liucheng Wu
- Laboratory Animal Center, Nantong University, Nantong, China
- * E-mail: (JS); (LW); (LX)
| | - Lingyan Xing
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
- * E-mail: (JS); (LW); (LX)
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28
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Kilzheimer A, Hentrich T, Rotermund C, Kahle PJ, Schulze-Hentrich JM. Failure of diet-induced transcriptional adaptations in alpha-synuclein transgenic mice. Hum Mol Genet 2022; 32:450-461. [PMID: 36001352 PMCID: PMC9851747 DOI: 10.1093/hmg/ddac205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 08/03/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Nutritional influences have been discussed as potential modulators of Parkinson's disease (PD) pathology through various epidemiological and physiological studies. In animal models, a high-fat diet (HFD) with greater intake of lipid-derived calories leads to accelerated disease onset and progression. The underlying molecular mechanisms of HFD-induced aggravated pathology, however, remain largely unclear. In this study, we aimed to further illuminate the effects of a fat-enriched diet in PD by examining the brainstem and hippocampal transcriptome of alpha-synuclein transgenic mice exposed to a life-long HFD. Investigating individual transcript isoforms, differential gene expression and co-expression clusters, we observed that transcriptional differences between wild-type (WT) and transgenic animals intensified in both regions under HFD. Both brainstem and hippocampus displayed strikingly similar transcriptomic perturbation patterns. Interestingly, expression differences resulted mainly from responses in WT animals to HFD, while these genes remained largely unchanged or were even slightly oppositely regulated by diet in transgenic animals. Genes and co-expressed gene groups exhibiting this dysregulation were linked to metabolic and mitochondrial pathways. Our findings propose the failure of metabolic adaptions as the potential explanation for accelerated disease unfolding under exposure to HFD. From the identified clusters of co-expressed genes, several candidates lend themselves to further functional investigations.
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Affiliation(s)
| | | | - Carola Rotermund
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, 72074 Tübingen, Germany,German Center for Neurodegenerative Diseases (DZNE), 72074 Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, 72074 Tübingen, Germany
| | - Julia M Schulze-Hentrich
- To whom correspondence should be addressed at: Calwerstr. 7, 72076 Tübingen, Germany. Tel: +49-7071-2972276; Fax: +49-7071-29-5171;
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29
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Torres P, Anerillas C, Ramírez-Núñez O, Fernàndez A, Encinas M, Povedano M, Andrés-Benito P, Ferrer I, Ayala V, Pamplona R, Portero-Otín M. The motor neuron disease mouse model hSOD1-G93A shows a non-canonical profile of senescence biomarkers. Dis Model Mech 2022; 15:276182. [PMID: 35916061 PMCID: PMC9459393 DOI: 10.1242/dmm.049059] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Abstract
To evaluate senescence mechanisms, including senescence-associated secretory phenotype (SASP), in the motor-neuron disease model hSOD1-G93A, we quantified the expression of p16 and p21 and the senescence-associated β galactosidase (SA-β-gal) in nervous tissue. As SASP markers, we measured the mRNA levels of Il1a, Il6, Ifna, and Ifnb. Furthermore, we explored if an alteration of alternative splicing is associated with senescence by measuring the Adipor2 cryptic exon inclusion levels, a specific splicing variant repressed by TAR-DNA binding of 43 kDa (Tdp-43). Transgenic mice show an atypical senescence profile with high p16 and p21 mRNA and protein in glia, without the canonical increase in SA-β-gal activity. Consistent with SASP, there is an increase in Il1a and Il6 expression, associated with increased TNFR and M-CSF protein levels, with females being partially protected. TDP-43 splicing activity is compromised in this model. Senolytic drug Navitoclax does not alter the present 'model's disease progression. This lack of effect is reproduced in vitro, in contrast with Dasatinib and quercetin, which diminish p16 and p21. Our findings show a non-canonical profile of senescence biomarkers in the model hSOD1-G93A.
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Affiliation(s)
- Pascual Torres
- Metabolic Pathophysiology Research Group, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Carlos Anerillas
- Oncogenic Signalling and Development, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Omar Ramírez-Núñez
- Metabolic Pathophysiology Research Group, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Anna Fernàndez
- Metabolic Pathophysiology Research Group, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Mario Encinas
- Oncogenic Signalling and Development, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Mònica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, Hospitalet de Llobregat, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain
| | - Isidre Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute Carlos III, Hospitalet de Llobregat, Spain
| | - Victòria Ayala
- Metabolic Pathophysiology Research Group, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Reinald Pamplona
- Metabolic Pathophysiology Research Group, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
| | - Manuel Portero-Otín
- Metabolic Pathophysiology Research Group, Department of Experimental Medicine, University of Lleida-IRBLleida, Lleida, Spain
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30
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Single-Cell RNA-Sequencing: Astrocyte and Microglial Heterogeneity in Health and Disease. Cells 2022; 11:cells11132021. [PMID: 35805105 PMCID: PMC9265979 DOI: 10.3390/cells11132021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
Astrocytes and microglia are non-neuronal cells that maintain homeostasis within the central nervous system via their capacity to regulate neuronal transmission and prune synapses. Both astrocytes and microglia can undergo morphological and transcriptomic changes in response to infection with human immunodeficiency virus (HIV). While both astrocytes and microglia can be infected with HIV, HIV viral proteins in the local environment can interact with and activate these cells. Given that both astrocytes and microglia play critical roles in maintaining neuronal function, it will be critical to have an understanding of their heterogeneity and to identify genes and mechanisms that modulate their responses to HIV. Heterogeneity may include a depletion or increase in one or more astrocyte or microglial subtypes in different regions of the brain or spine as well as the gain or loss of a specific function. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool that can be used to characterise these changes within a given population. The use of this method facilitates the identification of subtypes and changes in cellular transcriptomes that develop in response to activation and various disease processes. In this review, we will examine recent studies that have used scRNA-seq to explore astrocyte and microglial heterogeneity in neurodegenerative diseases including Alzheimer’s disease and amyotrophic lateral sclerosis as well as in response to HIV infection. A careful review of these studies will expand our current understanding of cellular heterogeneity at homeostasis and in response to specific disease states.
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Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
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Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
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Yoshikawa M, Aizawa S, Oppenheim RW, Milligan C. Neurovascular unit pathology is observed very early in disease progression in the mutant SOD1G93A mouse model of amyotrophic lateral sclerosis. Exp Neurol 2022; 353:114084. [DOI: 10.1016/j.expneurol.2022.114084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 11/26/2022]
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33
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Ruffo P, Strafella C, Cascella R, Caputo V, Conforti FL, Andò S, Giardina E. Deregulation of ncRNA in Neurodegenerative Disease: Focus on circRNA, lncRNA and miRNA in Amyotrophic Lateral Sclerosis. Front Genet 2021; 12:784996. [PMID: 34925464 PMCID: PMC8674781 DOI: 10.3389/fgene.2021.784996] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 01/17/2023] Open
Abstract
Parallel and massive sequencing of total RNA samples derived from different samples are possible thanks to the use of NGS (Next Generation Sequencing) technologies. This allowed characterizing the transcriptomic profile of both cell and tissue populations, increasing the knowledge of the molecular pathological processes of complex diseases, such as neurodegenerative diseases (NDs). Among the NDs, Amyotrophic Lateral Sclerosis (ALS) is caused by the progressive loss of motor neurons (MNs), and, to date, the diagnosis is often made by exclusion because there is no specific symptomatologic picture. For this reason, it is important to search for biomarkers that are clinically useful for carrying out a fast and accurate diagnosis of ALS. Thanks to various studies, it has been possible to propose several molecular mechanisms associated with the disease, some of which include the action of non-coding RNA, including circRNAs, miRNAs, and lncRNAs which will be discussed in the present review. The evidence analyzed in this review highlights the importance of conducting studies to better characterize the different ncRNAs in the disease to use them as possible diagnostic, prognostic, and/or predictive biomarkers of ALS and other NDs.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
- Centro Sanitario, University of Calabria, Arcavacata di Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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34
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Ahmadi A, Gispert JD, Navarro A, Vilor-Tejedor N, Sadeghi I. Single-cell Transcriptional Changes in Neurodegenerative Diseases. Neuroscience 2021; 479:192-205. [PMID: 34748859 DOI: 10.1016/j.neuroscience.2021.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/25/2023]
Abstract
In recent decades, our understanding of the molecular changes involved in neurodegenerative diseases has been transformed. Single-cell RNA sequencing and single-nucleus RNA sequencing technologies have been applied to provide cellular and molecular details of the brain at the single-cell level. This has expanded our knowledge of the central nervous system and provided insights into the molecular vulnerability of brain cell types and underlying mechanisms in neurodegenerative diseases. In this review, we highlight the recent advances and findings related to neurodegenerative diseases using these cutting-edge technologies.
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Affiliation(s)
- Amirhossein Ahmadi
- Department of Biology, Faculty of Nano and BioScience and Technology, Persian Gulf University, Bushehr 75169, Iran
| | - Juan D Gispert
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Arcadi Navarro
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Natalia Vilor-Tejedor
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Erasmus MC University Medical Center. Department of Clinical Genetics, Rotterdam, the Netherlands.
| | - Iman Sadeghi
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
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35
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Namboori SC, Thomas P, Ames R, Hawkins S, Garrett LO, Willis CRG, Rosa A, Stanton LW, Bhinge A. Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons. Stem Cell Reports 2021; 16:3020-3035. [PMID: 34767750 PMCID: PMC8693652 DOI: 10.1016/j.stemcr.2021.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 01/09/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative condition characterized by the loss of motor neurons. We utilized single-cell transcriptomics to uncover dysfunctional pathways in degenerating motor neurons differentiated from SOD1 E100G ALS patient-derived induced pluripotent stem cells (iPSCs) and respective isogenic controls. Differential gene expression and network analysis identified activation of developmental pathways and core transcriptional factors driving the ALS motor neuron gene dysregulation. Specifically, we identified activation of SMAD2, a downstream mediator of the transforming growth factor β (TGF-β) signaling pathway as a key driver of SOD1 iPSC-derived motor neuron degeneration. Importantly, our analysis indicates that activation of TGFβ signaling may be a common mechanism shared between SOD1, FUS, C9ORF72, VCP, and sporadic ALS motor neurons. Our results demonstrate the utility of single-cell transcriptomics in mapping disease-relevant gene regulatory networks driving neurodegeneration in ALS motor neurons. We find that ALS-associated mutant SOD1 targets transcriptional networks that perturb motor neuron homeostasis. Single-cell transcriptomic analysis of SOD1 E100G ALS iPSC-derived motor neurons Mapping an ALS-relevant transcriptional network Upregulation of developmental programs in familial and sporadic ALS motor neurons Inhibition of TGFβ pathway improves SOD1 ALS iPSC-derived motor neuron survival
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Affiliation(s)
- Seema C Namboori
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK; College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Patricia Thomas
- Institute of Metabolism and Systems Research, Birmingham Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Ryan Ames
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sophie Hawkins
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK; College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | | | - Craig R G Willis
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK
| | - Alessandro Rosa
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Viale Regina Elena 291, 00161 Rome, Italy
| | - Lawrence W Stanton
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Akshay Bhinge
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK; College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK.
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36
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Molecular Classification and Interpretation of Amyotrophic Lateral Sclerosis Using Deep Convolution Neural Networks and Shapley Values. Genes (Basel) 2021; 12:genes12111754. [PMID: 34828360 PMCID: PMC8626003 DOI: 10.3390/genes12111754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a prototypical neurodegenerative disease characterized by progressive degeneration of motor neurons to severely effect the functionality to control voluntary muscle movement. Most of the non-additive genetic aberrations responsible for ALS make its molecular classification very challenging along with limited sample size, curse of dimensionality, class imbalance and noise in the data. Deep learning methods have been successful in many other related areas but have low minority class accuracy and suffer from the lack of explainability when used directly with RNA expression features for ALS molecular classification. In this paper, we propose a deep-learning-based molecular ALS classification and interpretation framework. Our framework is based on training a convolution neural network (CNN) on images obtained from converting RNA expression values into pixels based on DeepInsight similarity technique. Then, we employed Shapley additive explanations (SHAP) to extract pixels with higher relevance to ALS classifications. These pixels were mapped back to the genes which made them up. This enabled us to classify ALS samples with high accuracy for a minority class along with identifying genes that might be playing an important role in ALS molecular classifications. Taken together with RNA expression images classified with CNN, our preliminary analysis of the genes identified by SHAP interpretation demonstrate the value of utilizing Machine Learning to perform molecular classification of ALS and uncover disease-associated genes.
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37
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Van Harten ACM, Phatnani H, Przedborski S. Non-cell-autonomous pathogenic mechanisms in amyotrophic lateral sclerosis. Trends Neurosci 2021; 44:658-668. [PMID: 34006386 DOI: 10.1016/j.tins.2021.04.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/05/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common adult-onset paralytic disorder, characterized mainly by a loss of motor neurons (MNs) in the CNS. Over the past decades, thanks to intense investigations performed in both in vivo and in vitro models of ALS, major progress has been made toward gaining insights into the pathobiology of this incurable, fatal disorder. Among these advances is the growing recognition that non-neuronal cells participate in the degeneration of MNs in ALS, which could transform our understanding of the neurobiology of disease and the ability to devise effective disease-modifying therapies. In this review, we examine the contribution of non-cell-autonomous processes to the pathogenesis of ALS, with a focus on glial cells and in particular on astrocytes.
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Affiliation(s)
- Alexandra C M Van Harten
- Graduate School of Life and Earth Sciences, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, The Netherlands
| | - Hemali Phatnani
- Department of Neurology, Columbia University Medical Center, New York, NY, USA; Center for Motor Neuron Biology and Diseases, Columbia University Medical Center, New York, NY, USA; Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Serge Przedborski
- Department of Neurology, Columbia University Medical Center, New York, NY, USA; Center for Motor Neuron Biology and Diseases, Columbia University Medical Center, New York, NY, USA; Departments of Pathology and Cell Biology and Neuroscience, Columbia University Irving Medical Center, New York, NY, USA.
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38
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Pietrowski MJ, Gabr AA, Kozlov S, Blum D, Halle A, Carvalho K. Glial Purinergic Signaling in Neurodegeneration. Front Neurol 2021; 12:654850. [PMID: 34054698 PMCID: PMC8160300 DOI: 10.3389/fneur.2021.654850] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/16/2021] [Indexed: 12/15/2022] Open
Abstract
Purinergic signaling regulates neuronal and glial cell functions in the healthy CNS. In neurodegenerative diseases, purinergic signaling becomes dysregulated and can affect disease-associated phenotypes of glial cells. In this review, we discuss how cell-specific expression patterns of purinergic signaling components change in neurodegeneration and how dysregulated glial purinergic signaling and crosstalk may contribute to disease pathophysiology, thus bearing promising potential for the development of new therapeutical options for neurodegenerative diseases.
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Affiliation(s)
- Marie J Pietrowski
- Microglia and Neuroinflammation Laboratory, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Amr Ahmed Gabr
- Microglia and Neuroinflammation Laboratory, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Physiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Stanislav Kozlov
- Microglia and Neuroinflammation Laboratory, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Blum
- University of Lille, Inserm, CHU Lille, U1172 LilNCog - Lille Neuroscience and Cognition, Lille, France.,Alzheimer and Tauopathies, Labex DISTALZ, Lille, France
| | - Annett Halle
- Microglia and Neuroinflammation Laboratory, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute of Neuropathology, University of Bonn, Bonn, Germany
| | - Kevin Carvalho
- University of Lille, Inserm, CHU Lille, U1172 LilNCog - Lille Neuroscience and Cognition, Lille, France.,Alzheimer and Tauopathies, Labex DISTALZ, Lille, France
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39
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Zhang Z, Park JW, Ahn IS, Diamante G, Sivakumar N, Arneson D, Yang X, van Veen JE, Correa SM. Estrogen receptor alpha in the brain mediates tamoxifen-induced changes in physiology in mice. eLife 2021; 10:63333. [PMID: 33647234 PMCID: PMC7924955 DOI: 10.7554/elife.63333] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
Adjuvant tamoxifen therapy improves survival in breast cancer patients. Unfortunately, long-term treatment comes with side effects that impact health and quality of life, including hot flashes, changes in bone density, and fatigue. Partly due to a lack of proven animal models, the tissues and cells that mediate these negative side effects are unclear. Here, we show that mice undergoing tamoxifen treatment experience changes in temperature, bone, and movement. Single-cell RNA sequencing reveals that tamoxifen treatment induces widespread gene expression changes in the hypothalamus and preoptic area (hypothalamus-POA). These expression changes are dependent on estrogen receptor alpha (ERα), as conditional knockout of ERα in the hypothalamus-POA ablates or reverses tamoxifen-induced gene expression. Accordingly, ERα-deficient mice do not exhibit tamoxifen-induced changes in temperature, bone, or movement. These findings provide mechanistic insight into the effects of tamoxifen on the hypothalamus-POA and indicate that ERα mediates several physiological effects of tamoxifen treatment in mice.
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Affiliation(s)
- Zhi Zhang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States.,Laboratory of Neuroendocrinology of the Brain Research Institute, University of California Los Angeles, Los Angeles, United States
| | - Jae Whan Park
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States.,Laboratory of Neuroendocrinology of the Brain Research Institute, University of California Los Angeles, Los Angeles, United States
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States
| | - Nilla Sivakumar
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States.,Laboratory of Neuroendocrinology of the Brain Research Institute, University of California Los Angeles, Los Angeles, United States
| | - Douglas Arneson
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States
| | - J Edward van Veen
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States.,Laboratory of Neuroendocrinology of the Brain Research Institute, University of California Los Angeles, Los Angeles, United States
| | - Stephanie M Correa
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, United States.,Laboratory of Neuroendocrinology of the Brain Research Institute, University of California Los Angeles, Los Angeles, United States
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40
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Astrocyte-immune cell interactions in physiology and pathology. Immunity 2021; 54:211-224. [DOI: 10.1016/j.immuni.2021.01.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/29/2020] [Accepted: 01/15/2021] [Indexed: 12/23/2022]
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41
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Cihankaya H, Theiss C, Matschke V. Little Helpers or Mean Rogue-Role of Microglia in Animal Models of Amyotrophic Lateral Sclerosis. Int J Mol Sci 2021; 22:ijms22030993. [PMID: 33498186 PMCID: PMC7863915 DOI: 10.3390/ijms22030993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is one of the most common neurodegenerative diseases, causing degeneration of both upper and lower motor neurons in the central nervous system (CNS). ALS patients suffer from hyperreflexia, spasticity, paralysis and muscle atrophy and typically die due to respiratory failure 1–5 years after disease onset. In addition to the degeneration of motor neurons on the cellular level, ALS has been associated with neuroinflammation, such as microgliosis. Microglial activation in ALS can either be protective or degenerative to the neurons. Among others, mutations in superoxide dismutase 1 (SOD1), chromosome 9 open reading frame 72 (C9Orf72), transactive response DNA binding protein (TDP) 43 and vacuolar protein sorting-associated protein 54 (VPS54) genes have been associated with ALS. Here, we describe the dual role and functionality of microglia in four different in vivo ALS models and search for the lowest common denominator with respect to the role of microglia in the highly heterogeneous disease of ALS.
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Affiliation(s)
- Hilal Cihankaya
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, D-44801 Bochum, Germany; (H.C.); (C.T.)
- International Graduate School of Neuroscience (IGSN), Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Carsten Theiss
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, D-44801 Bochum, Germany; (H.C.); (C.T.)
- International Graduate School of Neuroscience (IGSN), Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Veronika Matschke
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, D-44801 Bochum, Germany; (H.C.); (C.T.)
- Correspondence: ; Tel.: +49-234-32-25018
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42
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Liao H, Chen Q, Xiao J. Reflections on the Role of Malat1 in Gynecological Cancer. Cancer Manag Res 2020; 12:13489-13500. [PMID: 33408521 PMCID: PMC7779295 DOI: 10.2147/cmar.s286804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have received significant attention over the last few years. Malat1, as one of the most extensively studied ncRNAs, is believed to be not only a potential biomarker for disease diagnosis and prognosis, but also a candidate drug target for gynecological cancers. This potential is supported by a growing body of experimental evidence demonstrating that Malat1 participates in the occurrence, progression, and metastasis of tumors. Research has also shown that Malat1 can influence patient survival by regulating a range of target genes and signaling pathways. However, previous review articles have generally failed to consider the role of Malat1 in gynecological cancer in detail. In the present review, we summarize recent progress in research relating to the clinical relevance of Malat1 and the molecular mechanisms underlying the action of this ncRNA. Besides, we put forward some action points for further research after taking into consideration the sub-location and other essential properties of Malat1, which might enable us to have a better understanding of the potential of this molecule regarding clinical diagnosis and treatment.
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Affiliation(s)
- Huiyan Liao
- The 2nd Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, People's Republic of China
| | - Qi Chen
- The 6th Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, People's Republic of China
| | - Jing Xiao
- Department of Gynecology, the University Town Branch, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510120, People's Republic of China
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43
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Morello G, Salomone S, D’Agata V, Conforti FL, Cavallaro S. From Multi-Omics Approaches to Precision Medicine in Amyotrophic Lateral Sclerosis. Front Neurosci 2020; 14:577755. [PMID: 33192262 PMCID: PMC7661549 DOI: 10.3389/fnins.2020.577755] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disorder, caused by the degeneration of upper and lower motor neurons for which there is no truly effective cure. The lack of successful treatments can be well explained by the complex and heterogeneous nature of ALS, with patients displaying widely distinct clinical features and progression patterns, and distinct molecular mechanisms underlying the phenotypic heterogeneity. Thus, stratifying ALS patients into consistent and clinically relevant subgroups can be of great value for the development of new precision diagnostics and targeted therapeutics for ALS patients. In the last years, the use and integration of high-throughput "omics" approaches have dramatically changed our thinking about ALS, improving our understanding of the complex molecular architecture of ALS, distinguishing distinct patient subtypes and providing a rational foundation for the discovery of biomarkers and new individualized treatments. In this review, we discuss the most significant contributions of omics technologies in unraveling the biological heterogeneity of ALS, highlighting how these approaches are revealing diagnostic, prognostic and therapeutic targets for future personalized interventions.
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Affiliation(s)
- Giovanna Morello
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Salomone
- Section of Pharmacology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Velia D’Agata
- Human Anatomy and Histology, University of Catania, Catania, Italy
| | | | - Sebastiano Cavallaro
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy
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44
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Provenzano F, Pérez MJ, Deleidi M. Redefining Microglial Identity in Health and Disease at Single-Cell Resolution. Trends Mol Med 2020; 27:47-59. [PMID: 33008729 DOI: 10.1016/j.molmed.2020.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022]
Abstract
Microglia have long been considered a homogenous cell population that uniformly responds to extrinsic factors. Here, we describe how the recent development of single-cell technologies has revealed the heterogeneity of both human and mouse microglia and identified distinct microglial states linked to specific developmental, aging, and disease stages. We discuss progress and future developments in data analysis, essential tools for the comprehension of big data derived from single-cell omics, and the necessity of integrating such data with functional studies to correlate genetic cues with the relevant biological functions of microglia. Defining the functional correlates of distinct microglia states is fundamental to dissecting the 'microglial etiology' of aging and complex neurological diseases and identifying novel therapeutic and diagnostic targets.
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Affiliation(s)
- Francesca Provenzano
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - María José Pérez
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Michela Deleidi
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
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