1
|
Guo W, Hu Y, Qian J, Zhu L, Cheng J, Liao J, Fan X. Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution. J Genet Genomics 2023; 50:641-651. [PMID: 37544594 DOI: 10.1016/j.jgg.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023]
Abstract
Spatial omics technologies have become powerful methods to provide valuable insights into cells and tissues within a complex context, significantly enhancing our understanding of the intricate and multifaceted biological system. With an increasing focus on spatial heterogeneity, there is a growing need for unbiased, spatially resolved omics technologies. Laser capture microdissection (LCM) is a cutting-edge method for acquiring spatial information that can quickly collect regions of interest (ROIs) from heterogeneous tissues, with resolutions ranging from single cells to cell populations. Thus, LCM has been widely used for studying the cellular and molecular mechanisms of diseases. This review focuses on the differences among four types of commonly used LCM technologies and their applications in omics and disease research. Key attributes of application cases are also highlighted, such as throughput and spatial resolution. In addition, we comprehensively discuss the existing challenges and the great potential of LCM in biomedical research, disease diagnosis, and targeted therapy from the perspective of high-throughput, multi-omics, and single-cell resolution.
Collapse
Affiliation(s)
- Wenbo Guo
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Yining Hu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Jingyang Qian
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Lidan Zhu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Junyun Cheng
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Speidell A, Bin Abid N, Yano H. Brain-Derived Neurotrophic Factor Dysregulation as an Essential Pathological Feature in Huntington's Disease: Mechanisms and Potential Therapeutics. Biomedicines 2023; 11:2275. [PMID: 37626771 PMCID: PMC10452871 DOI: 10.3390/biomedicines11082275] [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: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a major neurotrophin whose loss or interruption is well established to have numerous intersections with the pathogenesis of progressive neurological disorders. There is perhaps no greater example of disease pathogenesis resulting from the dysregulation of BDNF signaling than Huntington's disease (HD)-an inherited neurodegenerative disorder characterized by motor, psychiatric, and cognitive impairments associated with basal ganglia dysfunction and the ultimate death of striatal projection neurons. Investigation of the collection of mechanisms leading to BDNF loss in HD highlights this neurotrophin's importance to neuronal viability and calls attention to opportunities for therapeutic interventions. Using electronic database searches of existing and forthcoming research, we constructed a literature review with the overarching goal of exploring the diverse set of molecular events that trigger BDNF dysregulation within HD. We highlighted research that investigated these major mechanisms in preclinical models of HD and connected these studies to those evaluating similar endpoints in human HD subjects. We also included a special focus on the growing body of literature detailing key transcriptomic and epigenetic alterations that affect BDNF abundance in HD. Finally, we offer critical evaluation of proposed neurotrophin-directed therapies and assessed clinical trials seeking to correct BDNF expression in HD individuals.
Collapse
Affiliation(s)
- Andrew Speidell
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Noman Bin Abid
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| |
Collapse
|
4
|
Guebel DV. Human hippocampal astrocytes: Computational dissection of their transcriptome, sexual differences and exosomes across ageing and mild-cognitive impairment. Eur J Neurosci 2023; 58:2677-2707. [PMID: 37427765 DOI: 10.1111/ejn.16081] [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: 09/04/2022] [Revised: 02/20/2023] [Accepted: 06/16/2023] [Indexed: 07/11/2023]
Abstract
The role of astrocytes in Alzheimer's disease is often disregarded. Hence, characterization of astrocytes along their early evolution toward Alzheimer would be greatly beneficial. However, due to their exquisite responsiveness, in vivo studies are difficult. So public microarray data of hippocampal homogenates from (healthy) young, (healthy) elder and elder with mild cognitive impairment (MCI) were subjected to re-analysis by a multi-step computational pipeline. Ontologies and pathway analyses were compared after determining the differential genes that, belonging to astrocytes, have splice forms. Likewise, the subset of molecules exportable to exosomes was also determined. The results showed that astrocyte's phenotypes changed significantly. While already 'activated' astrocytes were found in the younger group, major changes occurred during ageing (increased vascular remodelling and response to mechanical stimulus, diminished long-term potentiation and increased long-term depression). MCI's astrocytes showed some 'rejuvenated' features, but their sensitivity to shear stress was markedly lost. Importantly, most of the changes showed to be sex biassed. Men's astrocytes are enriched in a type 'endfeet-astrocytome', whereas women's astrocytes appear close to the 'scar-forming' type (prone to endothelial dysfunction, hypercholesterolemia, loss of glutamatergic synapses, Ca+2 dysregulation, hypoxia, oxidative stress and 'pro-coagulant' phenotype). In conclusion, the computational dissection of the networks based on the hippocampal gene isoforms provides a relevant proxy to in vivo astrocytes, also revealing the occurrence of sexual differences. Analyses of the astrocytic exosomes did not provide an acceptable approximation to the overall functioning of astrocytes in the hippocampus, probably due to the selective cellular mechanisms which charge the cargo molecules.
Collapse
|
5
|
Burtscher J, Pepe G, Maharjan N, Riguet N, Di Pardo A, Maglione V, Millet GP. Sphingolipids and impaired hypoxic stress responses in Huntington disease. Prog Lipid Res 2023; 90:101224. [PMID: 36898481 DOI: 10.1016/j.plipres.2023.101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/20/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
Huntington disease (HD) is a debilitating, currently incurable disease. Protein aggregation and metabolic deficits are pathological hallmarks but their link to neurodegeneration and symptoms remains debated. Here, we summarize alterations in the levels of different sphingolipids in an attempt to characterize sphingolipid patterns specific to HD, an additional molecular hallmark of the disease. Based on the crucial role of sphingolipids in maintaining cellular homeostasis, the dynamic regulation of sphingolipids upon insults and their involvement in cellular stress responses, we hypothesize that maladaptations or blunted adaptations, especially following cellular stress due to reduced oxygen supply (hypoxia) contribute to the development of pathology in HD. We review how sphingolipids shape cellular energy metabolism and control proteostasis and suggest how these functions may fail in HD and in combination with additional insults. Finally, we evaluate the potential of improving cellular resilience in HD by conditioning approaches (improving the efficiency of cellular stress responses) and the role of sphingolipids therein. Sphingolipid metabolism is crucial for cellular homeostasis and for adaptations following cellular stress, including hypoxia. Inadequate cellular management of hypoxic stress likely contributes to HD progression, and sphingolipids are potential mediators. Targeting sphingolipids and the hypoxic stress response are novel treatment strategies for HD.
Collapse
Affiliation(s)
- Johannes Burtscher
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland.
| | - Giuseppe Pepe
- IRCCS Neuromed, Via Dell'Elettronica, 86077 Pozzilli, Italy
| | - Niran Maharjan
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland
| | | | - Alba Di Pardo
- IRCCS Neuromed, Via Dell'Elettronica, 86077 Pozzilli, Italy
| | | | - Grégoire P Millet
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland
| |
Collapse
|
6
|
Riggins TE, Whitsitt QA, Saxena A, Hunter E, Hunt B, Thompson CH, Moore MG, Purcell EK. Gene Expression Changes in Cultured Reactive Rat Astrocyte Models and Comparison to Device-Associated Effects in the Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.522870. [PMID: 36712012 PMCID: PMC9881929 DOI: 10.1101/2023.01.06.522870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Implanted microelectrode arrays hold immense therapeutic potential for many neurodegenerative diseases. However, a foreign body response limits long-term device performance. Recent literature supports the role of astrocytes in the response to damage to the central nervous system (CNS) and suggests that reactive astrocytes exist on a spectrum of phenotypes, from beneficial to neurotoxic. The goal of our study was to gain insight into the subtypes of reactive astrocytes responding to electrodes implanted in the brain. In this study, we tested the transcriptomic profile of two reactive astrocyte culture models (cytokine cocktail or lipopolysaccharide, LPS) utilizing RNA sequencing, which we then compared to differential gene expression surrounding devices inserted into rat motor cortex via spatial transcriptomics. We interpreted changes in the genetic expression of the culture models to that of 24 hour, 1 week and 6 week rat tissue samples at multiple distances radiating from the injury site. We found overlapping expression of up to ∼250 genes between in vitro models and in vivo effects, depending on duration of implantation. Cytokine-induced cells shared more genes in common with chronically implanted tissue (≥1 week) in comparison to LPS-exposed cells. We revealed localized expression of a subset of these intersecting genes (e.g., Serping1, Chi3l1, and Cyp7b1) in regions of device-encapsulating, glial fibrillary acidic protein (GFAP)-expressing astrocytes identified with immunohistochemistry. We applied a factorization approach to assess the strength of the relationship between reactivity markers and the spatial distribution of GFAP-expressing astrocytes in vivo . We also provide lists of hundreds of differentially expressed genes between reactive culture models and untreated controls, and we observed 311 shared genes between the cytokine induced model and the LPS-reaction induced control model. Our results show that comparisons of reactive astrocyte culture models with spatial transcriptomics data can reveal new biomarkers of the foreign body response to implantable neurotechnology. These comparisons also provide a strategy to assess the development of in vitro models of the tissue response to implanted electrodes.
Collapse
|
7
|
Mengaziol J, Dunn AD, Salimando G, Wooldridge L, Crues-Muncunill J, Eacret D, Chen C, Bland K, Liu- Chen LY, Ehrlich ME, Corder G, Blendy JA. A novel Oprm1-Cre mouse maintains endogenous expression, function and enables detailed molecular characterization of μ-opioid receptor cells. PLoS One 2022; 17:e0270317. [PMID: 36534642 PMCID: PMC9762562 DOI: 10.1371/journal.pone.0270317] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
Key targets of both the therapeutic and abused properties of opioids are μ-opioid receptors (MORs). Despite years of research investigating the biochemistry and signal transduction pathways associated with MOR activation, we do not fully understand the cellular mechanisms underlying opioid addiction. Given that addictive opioids such as morphine, oxycodone, heroin, and fentanyl all activate MORs, and current therapies such as naloxone and buprenorphine block this activation, the availability of tools to mechanistically investigate opioid-mediated cellular and behavioral phenotypes are necessary. Therefore, we derived, validated, and applied a novel MOR-specific Cre mouse line, inserting a T2A cleavable peptide sequence and the Cre coding sequence into the MOR 3'UTR. Importantly, this line shows specificity and fidelity of MOR expression throughout the brain and with respect to function, there were no differences in behavioral responses to morphine when compared to wild type mice, nor are there any alterations in Oprm1 gene expression or receptor density. To assess Cre recombinase activity, MOR-Cre mice were crossed with the floxed GFP-reporters, RosaLSLSun1-sfGFP or RosaLSL-GFP-L10a. The latter allowed for cell type specific RNA sequencing via TRAP (Translating Ribosome Affinity Purification) of striatal MOR+ neurons following opioid withdrawal. The breadth of utility of this new tool will greatly facilitate the study of opioid biology under varying conditions.
Collapse
Affiliation(s)
- Juliet Mengaziol
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amelia D. Dunn
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gregory Salimando
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lisa Wooldridge
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jordi Crues-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Darrell Eacret
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Chongguang Chen
- Center for Substance Abuse Research and Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Kathryn Bland
- Center for Substance Abuse Research and Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Lee-Yuan Liu- Chen
- Center for Substance Abuse Research and Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gregory Corder
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Julie A. Blendy
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
8
|
Zhang L, Liu Y, Lu Y, Wang G. Targeting epigenetics as a promising therapeutic strategy for treatment of neurodegenerative diseases. Biochem Pharmacol 2022; 206:115295. [DOI: 10.1016/j.bcp.2022.115295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
|
9
|
Altered activity-regulated H3K9 acetylation at TGF-beta signaling genes during egocentric memory in Huntington's disease. Prog Neurobiol 2022; 219:102363. [PMID: 36179935 DOI: 10.1016/j.pneurobio.2022.102363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/25/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022]
Abstract
Molecular mechanisms underlying cognitive deficits in Huntington's disease (HD), a striatal neurodegenerative disorder, are unknown. Here, we generated ChIPseq, 4Cseq and RNAseq data on striatal tissue of HD and control mice during striatum-dependent egocentric memory process. Multi-omics analyses showed altered activity-dependent epigenetic gene reprogramming of neuronal and glial genes regulating striatal plasticity in HD mice, which correlated with memory deficit. First, our data reveal that spatial chromatin re-organization and transcriptional induction of BDNF-related markers, regulating neuronal plasticity, were reduced since memory acquisition in the striatum of HD mice. Second, our data show that epigenetic memory implicating H3K9 acetylation, which established during late phase of memory process (e.g. during consolidation/recall) and contributed to glia-mediated, TGFβ-dependent plasticity, was compromised in HD mouse striatum. Specifically, memory-dependent regulation of H3K9 acetylation was impaired at genes controlling extracellular matrix and myelination. Our study investigating the interplay between epigenetics and memory identifies H3K9 acetylation and TGFβ signaling as new targets of striatal plasticity, which might offer innovative leads to improve HD.
Collapse
|
10
|
Hemonnot-Girard AL, Meersseman C, Pastore M, Garcia V, Linck N, Rey C, Chebbi A, Jeanneteau F, Ginsberg SD, Lachuer J, Reynes C, Rassendren F, Hirbec H. Comparative analysis of transcriptome remodeling in plaque-associated and plaque-distant microglia during amyloid-β pathology progression in mice. J Neuroinflammation 2022; 19:234. [PMID: 36153535 PMCID: PMC9508749 DOI: 10.1186/s12974-022-02581-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Research in recent years firmly established that microglial cells play an important role in the pathogenesis of Alzheimer's disease (AD). In parallel, a series of studies showed that, under both homeostatic and pathological conditions, microglia are a heterogeneous cell population. In AD, amyloid-β (Aβ) plaque-associated microglia (PAM) display a clearly distinct phenotype compared to plaque-distant microglia (PCM), suggesting that these two microglia subtypes likely differently contribute to disease progression. So far, molecular characterization of PAM was performed indirectly using single cell RNA sequencing (scRNA-seq) approaches or based on markers that are supposedly up-regulated in this microglia subpopulation. Methods In this study based on a well-characterized AD mouse model, we combined cell-specific laser capture microdissection and RNA-seq analysis to i) identify, without preconceived notions of the molecular and/or functional changes that would affect these cells, the genes and gene networks that are dysregulated in PAM or PCM at three critical stages of the disease, and ii) to investigate the potential contribution of both plaque-associated and plaque-distant microglia. Results First, we established that our approach allows selective isolation of microglia, while preserving spatial information and preventing transcriptome changes induced by classical purification approaches. Then, we identified, in PAM and PCM subpopulations, networks of co-deregulated genes and analyzed their potential functional roles in AD. Finally, we investigated the dynamics of microglia transcriptomic remodeling at early, intermediate and late stages of the disease and validated select findings in postmortem human AD brain. Conclusions Our comprehensive study provides useful transcriptomic information regarding the respective contribution of PAM and PCM across the Aβ pathology progression. It highlights specific pathways that would require further study to decipher their roles across disease progression. It demonstrates that the proximity of microglia to Aβ-plaques dramatically alters the microglial transcriptome and reveals that these changes can have both positive and negative impacts on the surrounding cells. These opposing effects may be driven by local microglia heterogeneity also demonstrated by this study. Our approach leads to molecularly define the less well studied plaque-distant microglia. We show that plaque-distant microglia are not bystanders of the disease, although the transcriptomic changes are far less striking compared to what is observed in plaque-associated microglia. In particular, our results suggest they may be involved in Aβ oligomer detection and in Aβ-plaque initiation, with increased contribution as the disease progresses.
Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02581-0.
Collapse
|
11
|
Song S, Creus Muncunill J, Galicia Aguirre C, Tshilenge KT, Hamilton BW, Gerencser AA, Benlhabib H, Cirnaru MD, Leid M, Mooney SD, Ellerby LM, Ehrlich ME. Postnatal Conditional Deletion of Bcl11b in Striatal Projection Neurons Mimics the Transcriptional Signature of Huntington's Disease. Biomedicines 2022; 10:2377. [PMID: 36289639 PMCID: PMC9598565 DOI: 10.3390/biomedicines10102377] [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: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The dysregulation of striatal gene expression and function is linked to multiple diseases, including Huntington's disease (HD), Parkinson's disease, X-linked dystonia-parkinsonism (XDP), addiction, autism, and schizophrenia. Striatal medium spiny neurons (MSNs) make up 90% of the neurons in the striatum and are critical to motor control. The transcription factor, Bcl11b (also known as Ctip2), is required for striatal development, but the function of Bcl11b in adult MSNs in vivo has not been investigated. We conditionally deleted Bcl11b specifically in postnatal MSNs and performed a transcriptomic and behavioral analysis on these mice. Multiple enrichment analyses showed that the D9-Cre-Bcl11btm1.1Leid transcriptional profile was similar to the HD gene expression in mouse and human data sets. A Gene Ontology enrichment analysis linked D9-Cre-Bcl11btm1.1Leid to calcium, synapse organization, specifically including the dopaminergic synapse, protein dephosphorylation, and HDAC-signaling, commonly dysregulated pathways in HD. D9-Cre-Bcl11btm1.1Leid mice had decreased DARPP-32/Ppp1r1b in MSNs and behavioral deficits, demonstrating the dysregulation of a subtype of the dopamine D2 receptor expressing MSNs. Finally, in human HD isogenic MSNs, the mislocalization of BCL11B into nuclear aggregates points to a mechanism for BCL11B loss of function in HD. Our results suggest that BCL11B is important for the function and maintenance of mature MSNs and Bcl11b loss of function drives, in part, the transcriptomic and functional changes in HD.
Collapse
Affiliation(s)
- Sicheng Song
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jordi Creus Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Galicia Aguirre
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | | | - B. Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Houda Benlhabib
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Maria-Daniela Cirnaru
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark Leid
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Lisa M. Ellerby
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
12
|
Neuropathology of the Basal Ganglia in SNCA Transgenic Rat Model of Parkinson's Disease: Involvement of Parvalbuminergic Interneurons and Glial-Derived Neurotropic Factor. Int J Mol Sci 2022; 23:ijms231710126. [PMID: 36077524 PMCID: PMC9456397 DOI: 10.3390/ijms231710126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disease characterized by the accumulation of alpha-synuclein, encoded by the SNCA gene. The main neuropathological hallmark of PD is the degeneration of dopaminergic neurons leading to striatal dopamine depletion. Trophic support by a neurotrophin called glial-derived neurotrophic factor (GDNF) is also lacking in PD. We performed immunohistochemical studies to investigate neuropathological changes in the basal ganglia of a rat transgenic model of PD overexpressing alfa-synuclein. We observed that neuronal loss also occurs in the dorsolateral part of the striatum in the advanced stages of the disease. Moreover, along with the degeneration of the medium spiny projection neurons, we found a dramatic loss of parvalbumin interneurons. A marked decrease in GDNF, which is produced by parvalbumin interneurons, was observed in the striatum and in the substantia nigra of these animals. This confirmed the involvement of the striatum in the pathophysiology of PD and the importance of GDNF in maintaining the health of the substantia nigra.
Collapse
|
13
|
Molecular Pathophysiological Mechanisms in Huntington's Disease. Biomedicines 2022; 10:biomedicines10061432. [PMID: 35740453 PMCID: PMC9219859 DOI: 10.3390/biomedicines10061432] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
Huntington’s disease is an inherited neurodegenerative disease described 150 years ago by George Huntington. The genetic defect was identified in 1993 to be an expanded CAG repeat on exon 1 of the huntingtin gene located on chromosome 4. In the following almost 30 years, a considerable amount of research, using mainly animal models or in vitro experiments, has tried to unravel the complex molecular cascades through which the transcription of the mutant protein leads to neuronal loss, especially in the medium spiny neurons of the striatum, and identified excitotoxicity, transcriptional dysregulation, mitochondrial dysfunction, oxidative stress, impaired proteostasis, altered axonal trafficking and reduced availability of trophic factors to be crucial contributors. This review discusses the pathogenic cascades described in the literature through which mutant huntingtin leads to neuronal demise. However, due to the ubiquitous presence of huntingtin, astrocytes are also dysfunctional, and neuroinflammation may additionally contribute to Huntington’s disease pathology. The quest for therapies to delay the onset and reduce the rate of Huntington’s disease progression is ongoing, but is based on findings from basic research.
Collapse
|
14
|
Kim HB, Lu Y, Oh SC, Morris J, Miyashiro K, Kim J, Eberwine J, Sul JY. Astrocyte ethanol exposure reveals persistent and defined calcium response subtypes and associated gene signatures. J Biol Chem 2022; 298:102147. [PMID: 35716779 PMCID: PMC9293641 DOI: 10.1016/j.jbc.2022.102147] [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: 03/18/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/26/2022] Open
Abstract
Astrocytes play a critical role in brain function, but their contribution during ethanol (EtOH) consumption remains largely understudied. In light of recent findings on the heterogeneity of astrocyte physiology and gene expression, an approach with the ability to identify subtypes and capture this heterogeneity is necessary. Here, we combined measurements of calcium signaling and gene expression to define EtOH-induced astrocyte subtypes. In the absence of a demonstrated EtOH receptor, EtOH is believed to have effects on the function of many receptors and downstream biological cascades that underlie calcium responsiveness. This mechanism of EtOH-induced calcium signaling is unknown and this study provides the first step in understanding the characteristics of cells displaying these observed responses. To characterize underlying astrocyte subtypes, we assessed the correlation between calcium signaling and astrocyte gene expression signature in response to EtOH. We found that various EtOH doses increased intracellular calcium levels in a subset of astrocytes, distinguishing three cellular response types and one nonresponsive subtype as categorized by response waveform properties. Furthermore, single-cell RNA-seq analysis of astrocytes from the different response types identified type-enriched discriminatory gene expression signatures. Combining single-cell calcium responses and gene expression analysis identified specific astrocyte subgroups among astrocyte populations defined by their response to EtOH. This result provides a basis for identifying the relationship between astrocyte susceptibility to EtOH and corresponding measurable markers of calcium signaling and gene expression, which will be useful to investigate potential subgroup-specific influences of astrocytes on the physiology and pathology of EtOH exposure in the brain.
Collapse
Affiliation(s)
- Hyun-Bum Kim
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Seonkyung C Oh
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacqueline Morris
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Miyashiro
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA; PENN Program in Single Cell Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; PENN Program in Single Cell Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jai-Yoon Sul
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; PENN Program in Single Cell Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
15
|
Nussinov R, Tsai CJ, Jang H. Allostery, and how to define and measure signal transduction. Biophys Chem 2022; 283:106766. [PMID: 35121384 PMCID: PMC8898294 DOI: 10.1016/j.bpc.2022.106766] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/15/2022]
Abstract
Here we ask: What is productive signaling? How to define it, how to measure it, and most of all, what are the parameters that determine it? Further, what determines the strength of signaling from an upstream to a downstream node in a specific cell? These questions have either not been considered or not entirely resolved. The requirements for the signal to propagate downstream to activate (repress) transcription have not been considered either. Yet, the questions are pivotal to clarify, especially in diseases such as cancer where determination of signal propagation can point to cell proliferation and to emerging drug resistance, and to neurodevelopmental disorders, such as RASopathy, autism, attention-deficit/hyperactivity disorder (ADHD), and cerebral palsy. Here we propose a framework for signal transduction from an upstream to a downstream node addressing these questions. Defining cellular processes, experimentally measuring them, and devising powerful computational AI-powered algorithms that exploit the measurements, are essential for quantitative science.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
16
|
Sproviero D, Gagliardi S, Zucca S, Arigoni M, Giannini M, Garofalo M, Fantini V, Pansarasa O, Avenali M, Ramusino MC, Diamanti L, Minafra B, Perini G, Zangaglia R, Costa A, Ceroni M, Calogero RA, Cereda C. Extracellular Vesicles Derived From Plasma of Patients With Neurodegenerative Disease Have Common Transcriptomic Profiling. Front Aging Neurosci 2022; 14:785741. [PMID: 35250537 PMCID: PMC8889100 DOI: 10.3389/fnagi.2022.785741] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/13/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives There is a lack of effective biomarkers for neurodegenerative diseases (NDs) such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia. Extracellular vesicle (EV) RNA cargo can have an interesting potential as a non-invasive biomarker for NDs. However, the knowledge about the abundance of EV-mRNAs and their contribution to neurodegeneration is not clear. Methods Large and small EVs (LEVs and SEVs) were isolated from plasma of patients and healthy volunteers (control, CTR) by differential centrifugation and filtration, and RNA was extracted. Whole transcriptome was carried out using next generation sequencing (NGS). Results Coding RNA (i.e., mRNA) but not long non-coding RNAs (lncRNAs) in SEVs and LEVs of patients with ALS could be distinguished from healthy CTRs and from other NDs using the principal component analysis (PCA). Some mRNAs were found in commonly deregulated between SEVs of patients with ALS and frontotemporal dementia (FTD), and they were classified in mRNA processing and splicing pathways. In LEVs, instead, one mRNA and one antisense RNA (i.e., MAP3K7CL and AP003068.3) were found to be in common among ALS, FTD, and PD. No deregulated mRNAs were found in EVs of patients with AD. Conclusion Different RNA regulation occurs in LEVs and SEVs of NDs. mRNAs and lncRNAs are present in plasma-derived EVs of NDs, and there are common and specific transcripts that characterize LEVs and SEVs from the NDs considered in this study.
Collapse
Affiliation(s)
- Daisy Sproviero
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Stella Gagliardi
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- *Correspondence: Stella Gagliardi
| | - Susanna Zucca
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- EnGenome SRL, Pavia, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, Bioinformatics and Genomics Unit, University of Turin, Turin, Italy
| | - Marta Giannini
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Maria Garofalo
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
- Department of Biology and Biotechnology (“L. Spallanzani”), University of Pavia, Pavia, Italy
| | - Valentina Fantini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Laboratory of Neurobiology and Neurogenetic, Golgi-Cenci Foundation, Milan, Italy
| | - Orietta Pansarasa
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Micol Avenali
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Neurorehabilitation Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Matteo Cotta Ramusino
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Luca Diamanti
- Neuro-Oncology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (SRCCS) Mondino Foundation, Pavia, Italy
| | - Brigida Minafra
- Parkinson Disease and Movement Disorders Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Giulia Perini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Roberta Zangaglia
- Parkinson Disease and Movement Disorders Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Alfredo Costa
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Mauro Ceroni
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Unit of Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Raffaele A. Calogero
- Department of Molecular Biotechnology and Health Sciences, Bioinformatics and Genomics Unit, University of Turin, Turin, Italy
| | - Cristina Cereda
- Genomic and Post-genomic Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| |
Collapse
|
17
|
Tyagi S, Chan EC, Barker D, McElduff P, Taylor KA, Riveros C, Singh E, Smith R. Transcriptomic analysis reveals myometrial topologically associated domains linked to onset of human term labor. Mol Hum Reprod 2022; 28:6527642. [PMID: 35150271 PMCID: PMC8903000 DOI: 10.1093/molehr/gaac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in cell phenotype are thought to occur through the expression of groups of co-regulated genes within topologically associated domains (TADs). In this paper we allocate genes expressed within the myometrium of the human uterus during the onset of term labor into TADs. Transformation of the myometrial cells of the uterus into a contractile phenotype during term human labor is the result of a complex interaction of different epigenomic and genomic layers. Recent work suggests that the transcription factor RELA lies at the top of this regulatory network. Using deep RNA sequencing (RNAseq) analysis of myometrial samples (n = 16) obtained at term from women undergoing Caesarean section prior to or after the onset of labor we have identified evidence for how other gene expression regulatory elements interact with transcription factors in the labor phenotype transition. Gene set enrichment analysis of our RNAseq data identified three modules of enriched genes (M1, M2 and M3), which in gene ontology studies are linked to matrix degradation, smooth muscle and immune gene signatures, respectively. These genes were predominantly located within chromosomal TADs suggesting co-regulation of expression. Our transcriptomic analysis also identified significant differences in the expression of long non-coding RNAs (lncRNA), microRNAs (miRNA) and transcription factors that were predicted to target genes within the TADs. Additionally, network analysis revealed 15 new lncRNA (MCM3AP-AS1, TUG1, MIR29B2CHG, HCG18, LINC00963, KCNQ1OT1, NEAT1, HELLPAR, SNHG16, NUTM2B-AS1, MALAT1, PSMA3-AS1, GABPB1-AS1, NORAD, NKILA) and four miRNA (mir-145, mir-223, mir-let-7a, mir-132) as top gene hubs with three transcription factors (NFKB1, RELA, ESR1) as master regulators. Together, these factors are likely to be involved in co-regulatory networks driving a myometrial transformation to generate an estrogen sensitive phenotype. We conclude that lncRNA and miRNA targeting the estrogen receptor 1 and nuclear factor kappa B pathways play a key role in the initiation of human labor. For the first time we perform an integrative analysis to present a multi-level genomic signature made of mRNA, ncRNA and transcription factors in the myometrium for spontaneous term labor.
Collapse
Affiliation(s)
- Sonika Tyagi
- Central Clinical School, Monash University and the Alfred Hospital, Melbourne, VIC, Australia
| | - Eng-Cheng Chan
- Mothers and Babies Research Centre, HMRI University of Newcastle, NSW, Australia
| | | | | | - Kelly A Taylor
- Mothers and Babies Research Centre, HMRI University of Newcastle, NSW, Australia
| | | | - Esha Singh
- Department of Biotechnology and Biochemical Engineering, Indian Institute of Technology, New Delhi, India
| | - Roger Smith
- Mothers and Babies Research Centre, HMRI University of Newcastle, NSW, Australia.,University of Newcastle, Newcastle, NSW, Australia
| |
Collapse
|
18
|
Nussinov R, Tsai CJ, Jang H. How can same-gene mutations promote both cancer and developmental disorders? SCIENCE ADVANCES 2022; 8:eabm2059. [PMID: 35030014 PMCID: PMC8759737 DOI: 10.1126/sciadv.abm2059] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/22/2021] [Indexed: 05/05/2023]
Abstract
The question of how same-gene mutations can drive both cancer and neurodevelopmental disorders has been puzzling. It has also been puzzling why those with neurodevelopmental disorders have a high risk of cancer. Ras, MEK, PI3K, PTEN, and SHP2 are among the oncogenic proteins that can harbor mutations that encode diseases other than cancer. Understanding why some of their mutations can promote cancer, whereas others promote neurodevelopmental diseases, and why even the same mutations may promote both phenotypes, has important clinical ramifications. Here, we review the literature and address these tantalizing questions. We propose that cell type–specific expression of the mutant protein, and of other proteins in the respective pathway, timing of activation (during embryonic development or sporadic emergence), and the absolute number of molecules that the mutations activate, alone or in combination, are pivotal in determining the pathological phenotypes—cancer and (or) developmental disorders.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
19
|
Qu W, Zhuang Y, Li X. The roles of epigenetic modifications in neurodegenerative diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 50:642-650. [PMID: 34986527 PMCID: PMC8732261 DOI: 10.3724/zdxbyxb-2021-0160] [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: 06/04/2021] [Accepted: 08/30/2021] [Indexed: 06/14/2023]
Abstract
In neuronal system, epigenetic modifications are essential for neuronal development, the fate determination of neural stem cells and neuronal function. The dysfunction of epigenetic regulation is closely related to occurrence and development of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease. Abnormally elevated DNA methylation inhibits the expression of some DNA repair-related genes and affects the progression of Huntington's disease. In the brain of Alzheimer's disease patients, the levels of H3K27ac and H3K9ac histone modifications increased. In addition, the alteration of RNA methylation in animal models of Alzheimer's disease and Parkinson's disease showed discrepancy trends. Therefore, epigenetic modifications may serve as potential therapeutic targets for neurodegenerative diseases. Here, we summarize the recent progress of the roles of epigenetic modifications in neurodegenerative diseases.
Collapse
Affiliation(s)
- Wenzheng Qu
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Yingliang Zhuang
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Xuekun Li
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| |
Collapse
|
20
|
Dell’Orco M, Elyaderani A, Vannan A, Sekar S, Powell G, Liang WS, Neisewander JL, Perrone-Bizzozero NI. HuD Regulates mRNA-circRNA-miRNA Networks in the Mouse Striatum Linked to Neuronal Development and Drug Addiction. BIOLOGY 2021; 10:biology10090939. [PMID: 34571817 PMCID: PMC8468275 DOI: 10.3390/biology10090939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary Gene expression controls all aspects of life, including that of humans. Genes are expressed by copying the information stored in the DNA into RNA molecules, and this process is regulated in part by multiple RNA-binding proteins (RBPs). One such protein, HuD, plays a critical role in the development of neurons and has been implicated in childhood brain tumors, neurodegenerative disorders (Parkinson’s, Alzheimer’s, and ALS), and drug abuse. In addition, HuD participates in neuronal remodeling mechanisms in the mature brain and promotes regeneration of peripheral nerves. HuD primarily binds to transcribed messenger RNAs, which are then stabilized for translation into proteins. However, recent studies demonstrate that HuD also regulates the expression of non-coding RNAs, such as circular RNAs (circRNAs) and microRNAs (miRNAs). In this study, we examined the role of HuD in the control of non-coding RNA expression in the mouse striatum, a brain region associated both with normal behaviors and pathological conditions such as drug abuse. Our results show that HuD regulates mRNA-circRNA-miRNA networks involved in the expression of genes associated with brain development and remodeling of neuronal connections. These findings suggest the possibility of new mechanisms controlling brain development, neurodegenerative diseases, and substance use disorders. Abstract The RNA-binding protein HuD (a.k.a., ELAVL4) is involved in neuronal development and synaptic plasticity mechanisms, including addiction-related processes such as cocaine conditioned-place preference (CPP) and food reward. The most studied function of this protein is mRNA stabilization; however, we have recently shown that HuD also regulates the levels of circular RNAs (circRNAs) in neurons. To examine the role of HuD in the control of coding and non-coding RNA networks associated with substance use, we identified sets of differentially expressed mRNAs, circRNAs and miRNAs in the striatum of HuD knockout (KO) mice. Our findings indicate that significantly downregulated mRNAs are enriched in biological pathways related to cell morphology and behavior. Furthermore, deletion of HuD altered the levels of 15 miRNAs associated with drug seeking. Using these sets of data, we predicted that a large number of upregulated miRNAs form competing endogenous RNA (ceRNA) networks with circRNAs and mRNAs associated with the neuronal development and synaptic plasticity proteins LSAMP and MARK3. Additionally, several downregulated miRNAs form ceRNA networks with mRNAs and circRNAs from MEF2D, PIK3R3, PTRPM and other neuronal proteins. Together, our results indicate that HuD regulates ceRNA networks controlling the levels of mRNAs associated with neuronal differentiation and synaptic physiology.
Collapse
Affiliation(s)
- Michela Dell’Orco
- Department of Neurosciences, University of New Mexico Health Science Center, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Amir Elyaderani
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ 85004, USA; (A.E.); (S.S.); (W.S.L.)
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.V.); (G.P.); (J.L.N.)
| | - Shobana Sekar
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ 85004, USA; (A.E.); (S.S.); (W.S.L.)
| | - Gregory Powell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.V.); (G.P.); (J.L.N.)
| | - Winnie S. Liang
- Neurogenomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ 85004, USA; (A.E.); (S.S.); (W.S.L.)
| | - Janet L. Neisewander
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.V.); (G.P.); (J.L.N.)
| | - Nora I. Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico Health Science Center, University of New Mexico, Albuquerque, NM 87131, USA;
- Correspondence:
| |
Collapse
|
21
|
Ma W, Su K, Wu H. Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction. Genome Biol 2021; 22:264. [PMID: 34503564 PMCID: PMC8427961 DOI: 10.1186/s13059-021-02480-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cell type identification is one of the most important questions in single-cell RNA sequencing (scRNA-seq) data analysis. With the accumulation of public scRNA-seq data, supervised cell type identification methods have gained increasing popularity due to better accuracy, robustness, and computational performance. Despite all the advantages, the performance of the supervised methods relies heavily on several key factors: feature selection, prediction method, and, most importantly, choice of the reference dataset. RESULTS In this work, we perform extensive real data analyses to systematically evaluate these strategies in supervised cell identification. We first benchmark nine classifiers along with six feature selection strategies and investigate the impact of reference data size and number of cell types in cell type prediction. Next, we focus on how discrepancies between reference and target datasets and how data preprocessing such as imputation and batch effect correction affect prediction performance. We also investigate the strategies of pooling and purifying reference data. CONCLUSIONS Based on our analysis results, we provide guidelines for using supervised cell typing methods. We suggest combining all individuals from available datasets to construct the reference dataset and use multi-layer perceptron (MLP) as the classifier, along with F-test as the feature selection method. All the code used for our analysis is available on GitHub ( https://github.com/marvinquiet/RefConstruction_supervisedCelltyping ).
Collapse
Affiliation(s)
- Wenjing Ma
- Department of Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA
| | - Kenong Su
- Department of Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA
| | - Hao Wu
- Department of Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA.
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
| |
Collapse
|
22
|
Manatakis DV, VanDevender A, Manolakos ES. An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures. Bioinformatics 2021; 36:5194-5204. [PMID: 32683449 PMCID: PMC7850114 DOI: 10.1093/bioinformatics/btaa654] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/26/2020] [Accepted: 07/14/2020] [Indexed: 12/02/2022] Open
Abstract
Motivation Recapitulating aspects of human organ functions using in vitro (e.g.
plates, transwells, etc.), in vivo (e.g. mouse, rat, etc.), or
ex vivo (e.g. organ chips, 3D systems, etc.) organ models is of
paramount importance for drug discovery and precision medicine. It will allow us to
identify potential side effects and test the effectiveness of new therapeutic approaches
early in their design phase, and will inform the development of better disease models.
Developing mathematical methods to reliably compare the ‘distance/similarity’ of organ
models from/to the real human organ they represent is an understudied problem with
important applications in biomedicine and tissue engineering. Results We introduce the Transcriptomic Signature Distance (TSD), an
information-theoretic distance for assessing the transcriptomic similarity of two tissue
samples, or two groups of tissue samples. In developing TSD, we are
leveraging next-generation sequencing data as well as information retrieved from
well-curated databases providing signature gene sets characteristic for human organs. We
present the justification and mathematical development of the new distance and
demonstrate its effectiveness and advantages in different scenarios of practical
importance using several publicly available RNA-seq datasets. Availability and Implementation The computation of both TSD versions (simple and weighted) has been
implemented in R and can be downloaded from
https://github.com/Cod3B3nd3R/Transcriptomic-Signature-Distance. Contact dimitris.manatakis@emulatebio.com Supplementary information Supplementary data are
available at Bioinformatics online.
Collapse
Affiliation(s)
| | | | - Elias S Manolakos
- Department of Informatics and Telecommunications, University of Athens, Athens 15784, Greece.,Bouve College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
23
|
Zhu J, Chen F, Luo L, Wu W, Dai J, Zhong J, Lin X, Chai C, Ding P, Liang L, Wang S, Ding X, Chen Y, Wang H, Qiu J, Wang F, Sun C, Zeng Y, Fang J, Jiang X, Liu P, Tang G, Qiu X, Zhang X, Ruan Y, Jiang S, Li J, Zhu S, Xu X, Li F, Liu Z, Cao G, Chen D. Single-cell atlas of domestic pig cerebral cortex and hypothalamus. Sci Bull (Beijing) 2021; 66:1448-1461. [PMID: 36654371 DOI: 10.1016/j.scib.2021.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/07/2020] [Accepted: 03/12/2021] [Indexed: 01/20/2023]
Abstract
The brain of the domestic pig (Sus scrofa domesticus) has drawn considerable attention due to its high similarities to that of humans. However, the cellular compositions of the pig brain (PB) remain elusive. Here we investigated the single-nucleus transcriptomic profiles of five regions of the PB (frontal lobe, parietal lobe, temporal lobe, occipital lobe, and hypothalamus) and identified 21 cell subpopulations. The cross-species comparison of mouse and pig hypothalamus revealed the shared and specific gene expression patterns at the single-cell resolution. Furthermore, we identified cell types and molecular pathways closely associated with neurological disorders, bridging the gap between gene mutations and pathogenesis. We reported, to our knowledge, the first single-cell atlas of domestic pig cerebral cortex and hypothalamus combined with a comprehensive analysis across species, providing extensive resources for future research regarding neural science, evolutionary developmental biology, and regenerative medicine.
Collapse
Affiliation(s)
- Jiacheng Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen 518083, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Lihua Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Weiying Wu
- BGI-Shenzhen, Shenzhen 518083, China; Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, and the MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310031, China
| | - Jinxia Dai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jixing Zhong
- School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Chaochao Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Peiwen Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Langchao Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyou Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiangning Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Yin Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiaying Qiu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | | | - Chengcheng Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China; School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Yuying Zeng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China; College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Jian Fang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Ping Liu
- BGI-Shenzhen, Shenzhen 518083, China; MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Gen Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China
| | - Xin Qiu
- Shenzhen Children's Hospital, Shenzhen 518083, China
| | | | - Yetian Ruan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | | | | | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zhongmin Liu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China.
| | | |
Collapse
|
24
|
Ferreira M, Francisco S, Soares AR, Nobre A, Pinheiro M, Reis A, Neto S, Rodrigues AJ, Sousa N, Moura G, Santos MAS. Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. Aging (Albany NY) 2021; 13:18150-18190. [PMID: 34330884 PMCID: PMC8351669 DOI: 10.18632/aging.203379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023]
Abstract
Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.
Collapse
Affiliation(s)
- Margarida Ferreira
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Stephany Francisco
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana R. Soares
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana Nobre
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Andreia Reis
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Sonya Neto
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Ana João Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga 4710-057, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gabriela Moura
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| | - Manuel A. S. Santos
- Institute of Biomedicine – iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro 3810-193, Portugal
| |
Collapse
|
25
|
Benraiss A, Mariani JN, Osipovitch M, Cornwell A, Windrem MS, Villanueva CB, Chandler-Militello D, Goldman SA. Cell-intrinsic glial pathology is conserved across human and murine models of Huntington's disease. Cell Rep 2021; 36:109308. [PMID: 34233199 DOI: 10.1016/j.celrep.2021.109308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/22/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Glial pathology is a causal contributor to the striatal neuronal dysfunction of Huntington's disease (HD). We investigate mutant HTT-associated changes in gene expression by mouse and human striatal astrocytes, as well as in mouse microglia, to identify commonalities in glial pathobiology across species and models. Mouse striatal astrocytes are fluorescence-activated cell sorted (FACS) from R6/2 and zQ175 mice, which respectively express exon1-only or full-length mHTT, and human astrocytes are generated either from human embryonic stem cells (hESCs) expressing full-length mHTT or from fetal striatal astrocytes transduced with exon1-only mHTT. Comparison of differential gene expression across these conditions, all with respect to normal HTT controls, reveals cell-type-specific changes in transcription common to both species, yet with differences that distinguish glia expressing truncated mHTT versus full-length mHTT. These data indicate that the differential gene expression of glia expressing truncated mHTT may differ from that of cells expressing full-length mHTT, while identifying a conserved set of dysregulated pathways in HD glia.
Collapse
Affiliation(s)
- Abdellatif Benraiss
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | - John N Mariani
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mikhail Osipovitch
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA; Center for Translational Neuromedicine, University of Copenhagen Faculty of Health, Copenhagen 2200, Denmark
| | - Adam Cornwell
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martha S Windrem
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Carlos Benitez Villanueva
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health, Copenhagen 2200, Denmark
| | - Devin Chandler-Militello
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA; Center for Translational Neuromedicine, University of Copenhagen Faculty of Health, Copenhagen 2200, Denmark; Neuroscience Center, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark.
| |
Collapse
|
26
|
Stella R, Bonadio RS, Cagnin S, Massimino ML, Bertoli A, Peggion C. Perturbations of the Proteome and of Secreted Metabolites in Primary Astrocytes from the hSOD1(G93A) ALS Mouse Model. Int J Mol Sci 2021; 22:ijms22137028. [PMID: 34209958 PMCID: PMC8268687 DOI: 10.3390/ijms22137028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 01/16/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease whose pathophysiology is largely unknown. Despite the fact that motor neuron (MN) death is recognized as the key event in ALS, astrocytes dysfunctionalities and neuroinflammation were demonstrated to accompany and probably even drive MN loss. Nevertheless, the mechanisms priming astrocyte failure and hyperactivation are still obscure. In this work, altered pathways and molecules in ALS astrocytes were unveiled by investigating the proteomic profile and the secreted metabolome of primary spinal cord astrocytes derived from transgenic ALS mouse model overexpressing the human (h)SOD1(G93A) protein in comparison with the transgenic counterpart expressing hSOD1(WT) protein. Here we show that ALS primary astrocytes are depleted of proteins-and of secreted metabolites-involved in glutathione metabolism and signaling. The observed increased activation of Nf-kB, Ebf1, and Plag1 transcription factors may account for the augmented expression of proteins involved in the proteolytic routes mediated by proteasome or endosome-lysosome systems. Moreover, hSOD1(G93A) primary astrocytes also display altered lipid metabolism. Our results provide novel insights into the altered molecular pathways that may underlie astrocyte dysfunctionalities and altered astrocyte-MN crosstalk in ALS, representing potential therapeutic targets to abrogate or slow down MN demise in disease pathogenesis.
Collapse
Affiliation(s)
- Roberto Stella
- Department of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
| | - Raphael Severino Bonadio
- Department of Biology and CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy; (R.S.B.); (S.C.)
| | - Stefano Cagnin
- Department of Biology and CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy; (R.S.B.); (S.C.)
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
| | | | - Alessandro Bertoli
- CNR—Neuroscience Institute, 35131 Padova, Italy;
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Correspondence: (A.B.); (C.P.)
| | - Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Correspondence: (A.B.); (C.P.)
| |
Collapse
|
27
|
Monk R, Connor B. Cell Reprogramming to Model Huntington's Disease: A Comprehensive Review. Cells 2021; 10:cells10071565. [PMID: 34206228 PMCID: PMC8306243 DOI: 10.3390/cells10071565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Huntington’s disease (HD) is a neurodegenerative disorder characterized by the progressive decline of motor, cognitive, and psychiatric functions. HD results from an autosomal dominant mutation that causes a trinucleotide CAG repeat expansion and the production of mutant Huntingtin protein (mHTT). This results in the initial selective and progressive loss of medium spiny neurons (MSNs) in the striatum before progressing to involve the whole brain. There are currently no effective treatments to prevent or delay the progression of HD as knowledge into the mechanisms driving the selective degeneration of MSNs has been hindered by a lack of access to live neurons from individuals with HD. The invention of cell reprogramming provides a revolutionary technique for the study, and potential treatment, of neurological conditions. Cell reprogramming technologies allow for the generation of live disease-affected neurons from patients with neurological conditions, becoming a primary technique for modelling these conditions in vitro. The ability to generate HD-affected neurons has widespread applications for investigating the pathogenesis of HD, the identification of new therapeutic targets, and for high-throughput drug screening. Cell reprogramming also offers a potential autologous source of cells for HD cell replacement therapy. This review provides a comprehensive analysis of the use of cell reprogramming to model HD and a discussion on recent advancements in cell reprogramming technologies that will benefit the HD field.
Collapse
|
28
|
Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
Collapse
Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| |
Collapse
|
29
|
Huntington's disease brain-derived small RNAs recapitulate associated neuropathology in mice. Acta Neuropathol 2021; 141:565-584. [PMID: 33547932 DOI: 10.1007/s00401-021-02272-9] [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: 01/12/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Progressive motor alterations and selective death of striatal medium spiny neurons (MSNs) are key pathological hallmarks of Huntington's disease (HD), a neurodegenerative condition caused by a CAG trinucleotide repeat expansion in the coding region of the huntingtin (HTT) gene. Most research has focused on the pathogenic effects of the resultant protein product(s); however, growing evidence indicates that expanded CAG repeats within mutant HTT mRNA and derived small CAG repeat RNAs (sCAG) participate in HD pathophysiology. The individual contribution of protein versus RNA toxicity to HD pathophysiology remains largely uncharacterized and the role of other classes of small RNAs (sRNA) that are strongly perturbed in HD is uncertain. Here, we demonstrate that sRNA produced in the putamen of HD patients (HD-sRNA-PT) are sufficient to induce HD pathology in vivo. Mice injected with HD-sRNA-PT show motor abnormalities, decreased levels of striatal HD-related proteins, disruption of the indirect pathway, and strong transcriptional abnormalities, paralleling human HD pathology. Importantly, we show that the specific blockage of sCAG mitigates HD-sRNA-PT neurotoxicity only to a limited extent. This observation prompted us to identify other sRNA species enriched in HD putamen with neurotoxic potential. We detected high levels of tRNA fragments (tRFs) in HD putamen, and we validated the neurotoxic potential of an Alanine derived tRF in vitro. These results highlight that HD-sRNA-PT are neurotoxic, and suggest that multiple sRNA species contribute to striatal dysfunction and general transcriptomic changes, favoring therapeutic strategies based on the blockage of sRNA-mediated toxicity.
Collapse
|
30
|
Elorza A, Márquez Y, Cabrera JR, Sánchez-Trincado JL, Santos-Galindo M, Hernández IH, Picó S, Díaz-Hernández JI, García-Escudero R, Irimia M, Lucas JJ. Huntington's disease-specific mis-splicing unveils key effector genes and altered splicing factors. Brain 2021; 144:2009-2023. [PMID: 33725094 PMCID: PMC8370404 DOI: 10.1093/brain/awab087] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 12/31/2022] Open
Abstract
Correction of mis-splicing events is a growing therapeutic approach for neurological diseases such as spinal muscular atrophy or neuronal ceroid lipofuscinosis 7, which are caused by splicing-affecting mutations. Mis-spliced effector genes that do not harbour mutations are also good candidate therapeutic targets in diseases with more complex aetiologies such as cancer, autism, muscular dystrophies or neurodegenerative diseases. Next-generation RNA sequencing (RNA-seq) has boosted investigation of global mis-splicing in diseased tissue to identify such key pathogenic mis-spliced genes. Nevertheless, while analysis of tumour or dystrophic muscle biopsies can be informative on early stage pathogenic mis-splicing, for neurodegenerative diseases, these analyses are intrinsically hampered by neuronal loss and neuroinflammation in post-mortem brains. To infer splicing alterations relevant to Huntington’s disease pathogenesis, here we performed intersect-RNA-seq analyses of human post-mortem striatal tissue and of an early symptomatic mouse model in which neuronal loss and gliosis are not yet present. Together with a human/mouse parallel motif scan analysis, this approach allowed us to identify the shared mis-splicing signature triggered by the Huntington’s disease-causing mutation in both species and to infer upstream deregulated splicing factors. Moreover, we identified a plethora of downstream neurodegeneration-linked mis-spliced effector genes that—together with the deregulated splicing factors—become new possible therapeutic targets. In summary, here we report pathogenic global mis-splicing in Huntington’s disease striatum captured by our new intersect-RNA-seq approach that can be readily applied to other neurodegenerative diseases for which bona fide animal models are available.
Collapse
Affiliation(s)
- Ainara Elorza
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Yamile Márquez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
| | - Jorge R Cabrera
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - José Luis Sánchez-Trincado
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - María Santos-Galindo
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Ivó H Hernández
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain.,Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Sara Picó
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Juan I Díaz-Hernández
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT, Madrid 28040, Spain.,Biomedical Research Institute i+12, Hospital 12 de Octubre, Madrid 28041, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - José J Lucas
- Center for Molecular Biology 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid 28049, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| |
Collapse
|
31
|
Choi HJ, Jin SD, Rengaraj D, Kim JH, Pain B, Han JY. Differential transcriptional regulation of the NANOG gene in chicken primordial germ cells and embryonic stem cells. J Anim Sci Biotechnol 2021; 12:40. [PMID: 33658075 PMCID: PMC7931612 DOI: 10.1186/s40104-021-00563-5] [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: 09/21/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023] Open
Abstract
Background NANOG is a core transcription factor (TF) in embryonic stem cells (ESCs) and primordial germ cells (PGCs). Regulation of the NANOG gene by TFs, epigenetic factors, and autoregulatory factors is well characterized in ESCs, and transcriptional regulation of NANOG is well established in these cells. Although NANOG plays a key role in germ cells, the molecular mechanism underlying its transcriptional regulation in PGCs has not been studied. Therefore, we investigated the mechanism that regulates transcription of the chicken NANOG (cNANOG) gene in PGCs and ESCs. Results We first identified the transcription start site of cNANOG by 5′-rapid amplification of cDNA ends PCR analysis. Then, we measured the promoter activity of various 5′ flanking regions of cNANOG in chicken PGCs and ESCs using the luciferase reporter assay. cNANOG expression required transcriptional regulatory elements, which were positively regulated by POU5F3 (OCT4) and SOX2 and negatively regulated by TP53 in PGCs. The proximal region of the cNANOG promoter contains a positive transcriptional regulatory element (CCAAT/enhancer-binding protein (CEBP)-binding site) in ESCs. Furthermore, small interfering RNA-mediated knockdown demonstrated that POU5F3, SOX2, and CEBP played a role in cell type-specific transcription of cNANOG. Conclusions We show for the first time that different trans-regulatory elements control transcription of cNANOG in a cell type-specific manner. This finding might help to elucidate the mechanism that regulates cNANOG expression in PGCs and ESCs.
Collapse
Affiliation(s)
- Hee Jung Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Dam Jin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin Hwa Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Bertrand Pain
- Univ Lyon, Universite ́Lyon 1, INSERM, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, 69500, Bron, France
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea. .,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan.
| |
Collapse
|
32
|
Alcalá‐Vida R, Garcia‐Forn M, Castany‐Pladevall C, Creus‐Muncunill J, Ito Y, Blanco E, Golbano A, Crespí‐Vázquez K, Parry A, Slater G, Samarajiwa S, Peiró S, Di Croce L, Narita M, Pérez‐Navarro E. Neuron type-specific increase in lamin B1 contributes to nuclear dysfunction in Huntington's disease. EMBO Mol Med 2021; 13:e12105. [PMID: 33369245 PMCID: PMC7863407 DOI: 10.15252/emmm.202012105] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/08/2023] Open
Abstract
Lamins are crucial proteins for nuclear functionality. Here, we provide new evidence showing that increased lamin B1 levels contribute to the pathophysiology of Huntington's disease (HD), a CAG repeat-associated neurodegenerative disorder. Through fluorescence-activated nuclear suspension imaging, we show that nucleus from striatal medium-sized spiny and CA1 hippocampal neurons display increased lamin B1 levels, in correlation with altered nuclear morphology and nucleocytoplasmic transport disruption. Moreover, ChIP-sequencing analysis shows an alteration of lamin-associated chromatin domains in hippocampal nuclei, accompanied by changes in chromatin accessibility and transcriptional dysregulation. Supporting lamin B1 alterations as a causal role in mutant huntingtin-mediated neurodegeneration, pharmacological normalization of lamin B1 levels in the hippocampus of the R6/1 mouse model of HD by betulinic acid administration restored nuclear homeostasis and prevented motor and cognitive dysfunction. Collectively, our work points increased lamin B1 levels as a new pathogenic mechanism in HD and provides a novel target for its intervention.
Collapse
Affiliation(s)
- Rafael Alcalá‐Vida
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
- Present address:
Laboratory of Cognitive and Adaptive NeuroscienceUMR 7364 (CNRS/Strasbourg University)StrasbourgFrance
| | - Marta Garcia‐Forn
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
- Present address:
Seaver Autism Center for Research and TreatmentIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Carla Castany‐Pladevall
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Jordi Creus‐Muncunill
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Yoko Ito
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Arantxa Golbano
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Kilian Crespí‐Vázquez
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Aled Parry
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUK
| | - Guy Slater
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Shamith Samarajiwa
- MRC Cancer UnitHutchison/MRC Research CentreUniversity of CambridgeCambridgeUK
| | - Sandra Peiró
- Vall d'Hebron Institute of OncologyBarcelonaSpain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Esther Pérez‐Navarro
- Departament de BiomedicinaFacultat de Medicina i Ciències de la SalutInstitut de NeurociènciesUniversitat de BarcelonaBarcelonaCatalonia
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaCatalonia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| |
Collapse
|
33
|
Islam MR, Lbik D, Sakib MS, Maximilian Hofmann R, Berulava T, Jiménez Mausbach M, Cha J, Goldberg M, Vakhtang E, Schiffmann C, Zieseniss A, Katschinski DM, Sananbenesi F, Toischer K, Fischer A. Epigenetic gene expression links heart failure to memory impairment. EMBO Mol Med 2021; 13:e11900. [PMID: 33471428 PMCID: PMC7933944 DOI: 10.15252/emmm.201911900] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
In current clinical practice, care of diseased patients is often restricted to separated disciplines. However, such an organ-centered approach is not always suitable. For example, cognitive dysfunction is a severe burden in heart failure patients. Moreover, these patients have an increased risk for age-associated dementias. The underlying molecular mechanisms are presently unknown, and thus, corresponding therapeutic strategies to improve cognition in heart failure patients are missing. Using mice as model organisms, we show that heart failure leads to specific changes in hippocampal gene expression, a brain region intimately linked to cognition. These changes reflect increased cellular stress pathways which eventually lead to loss of neuronal euchromatin and reduced expression of a hippocampal gene cluster essential for cognition. Consequently, mice suffering from heart failure exhibit impaired memory function. These pathological changes are ameliorated via the administration of a drug that promotes neuronal euchromatin formation. Our study provides first insight to the molecular processes by which heart failure contributes to neuronal dysfunction and point to novel therapeutic avenues to treat cognitive defects in heart failure patients.
Collapse
Affiliation(s)
- Md Rezaul Islam
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Dawid Lbik
- Clinic of Cardiology and Pneumology, Georg-August-University, Göttingen, Germany
| | - M Sadman Sakib
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | | | - Tea Berulava
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Martí Jiménez Mausbach
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Julia Cha
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Maria Goldberg
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Elerdashvili Vakhtang
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Christian Schiffmann
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Anke Zieseniss
- German Center for Cardiovascular Research (DZHK), Göttingen, Germany.,Institute for Cardiovascular Physiology, University Medical Center, Georg-August University Göttingen, Göttingen, Germany
| | - Dörthe Magdalena Katschinski
- German Center for Cardiovascular Research (DZHK), Göttingen, Germany.,Institute for Cardiovascular Physiology, University Medical Center, Georg-August University Göttingen, Göttingen, Germany
| | - Farahnaz Sananbenesi
- Genome Dynamics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Karl Toischer
- Clinic of Cardiology and Pneumology, Georg-August-University, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Göttingen, Germany
| | - Andre Fischer
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| |
Collapse
|
34
|
Alcalá-Vida R, Seguin J, Lotz C, Molitor AM, Irastorza-Azcarate I, Awada A, Karasu N, Bombardier A, Cosquer B, Skarmeta JLG, Cassel JC, Boutillier AL, Sexton T, Merienne K. Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice. Nat Commun 2021; 12:364. [PMID: 33441541 PMCID: PMC7807045 DOI: 10.1038/s41467-020-20605-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
Temporal dynamics and mechanisms underlying epigenetic changes in Huntington's disease (HD), a neurodegenerative disease primarily affecting the striatum, remain unclear. Using a slowly progressing knockin mouse model, we profile the HD striatal chromatin landscape at two early disease stages. Data integration with cell type-specific striatal enhancer and transcriptomic databases demonstrates acceleration of age-related epigenetic remodelling and transcriptional changes at neuronal- and glial-specific genes from prodromal stage, before the onset of motor deficits. We also find that 3D chromatin architecture, while generally preserved at neuronal enhancers, is altered at the disease locus. Specifically, we find that the HD mutation, a CAG expansion in the Htt gene, locally impairs the spatial chromatin organization and proximal gene regulation. Thus, our data provide evidence for two early and distinct mechanisms underlying chromatin structure changes in the HD striatum, correlating with transcriptional changes: the HD mutation globally accelerates age-dependent epigenetic and transcriptional reprogramming of brain cell identities, and locally affects 3D chromatin organization.
Collapse
Affiliation(s)
- Rafael Alcalá-Vida
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Jonathan Seguin
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Caroline Lotz
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Anne M Molitor
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Ibai Irastorza-Azcarate
- Berlin Institute of Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ali Awada
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Nezih Karasu
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Aurélie Bombardier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Brigitte Cosquer
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Jose Luis Gomez Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Jean-Christophe Cassel
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Anne-Laurence Boutillier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France
- CNRS UMR 7364, 67000, Strasbourg, France
| | - Thomas Sexton
- Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), 67404, Illkirch, France
- CNRS UMR7104, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- University of Strasbourg, 67000, Strasbourg, France
| | - Karine Merienne
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), University of Strasbourg, 67000, Strasbourg, France.
- CNRS UMR 7364, 67000, Strasbourg, France.
| |
Collapse
|
35
|
Kim HT, Ohn T, Jeong SG, Song A, Jang CH, Cho GW. Oxidative stress-induced aberrant G9a activation disturbs RE-1-containing neuron-specific genes expression, leading to degeneration in human SH-SY5Y neuroblastoma cells. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2021; 25:51-58. [PMID: 33361537 PMCID: PMC7756531 DOI: 10.4196/kjpp.2021.25.1.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 11/15/2022]
Abstract
Oxidative stress-induced neurodegeneration is one of several etiologies underlying neurodegenerative disease. In the present study, we investigated the functional role of histone methyltransferase G9a in oxidative stress-induced degeneration in human SH-SY5Y neuroblastoma cells. Cell viability significantly decreased on H2O2 treatment; however, treatment with the G9a inhibitor BIX01294 partially attenuated this effect. The expression of neuron-specific genes also decreased in H2O2- treated cells; however, it recovered on G9a inhibition. H2O2-treated cells showed high levels of H3K9me2 (histone H3 demethylated at the lysine 9 residue), which is produced by G9a activation; BIX01294 treatment reduced aberrant activation of G9a. H3K9me2 occupancy of the RE-1 site in neuron-specific genes was significantly increased in H2O2-treated cells, whereas it was decreased in BIX01294-treated cells. The differentiation of H2O2-treated cells also recovered on G9a inhibition by BIX01294. Consistent results were observed when used another G9a inhibitor UCN0321. These results demonstrate that oxidative stress induces aberrant activation of G9a, which disturbs the expression of neuron-specific genes and progressively mediates neuronal cell death. Moreover, a G9a inhibitor can lessen aberrant G9a activity and prevent neuronal damage. G9a inhibition may therefore contribute to the prevention of oxidative stress-induced neurodegeneration.
Collapse
Affiliation(s)
- Ho-Tae Kim
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea
| | - Takbum Ohn
- Department of Cellular and Molecular Medicine, College of Medicine, Chosun University, Gwangju 61452, Korea
| | - Sin-Gu Jeong
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea.,Department of Bio Research and Business Development, Biot Korea Inc., Gwangju 61001, Korea
| | - Anji Song
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea
| | - Chul Ho Jang
- Department of Otolaryngology, Chonnam National University Medical School, Gwangju 61469, Korea
| | - Gwang-Won Cho
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea
| |
Collapse
|
36
|
Gadi I, Fatima S, Elwakiel A, Nazir S, Mohanad Al-Dabet M, Rana R, Bock F, Manoharan J, Gupta D, Biemann R, Nieswandt B, Braun-Dullaeus R, Besler C, Scholz M, Geffers R, Griffin JH, Esmon CT, Kohli S, Isermann B, Shahzad K. Different DOACs Control Inflammation in Cardiac Ischemia-Reperfusion Differently. Circ Res 2020; 128:513-529. [PMID: 33353373 DOI: 10.1161/circresaha.120.317219] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RATIONALE While thrombin is the key protease in thrombus formation, other coagulation proteases, such as fXa (factor Xa) or aPC (activated protein C), independently modulate intracellular signaling via partially distinct receptors. OBJECTIVES To study the differential effects of fXa or fIIa (factor IIa) inhibition on gene expression and inflammation in myocardial ischemia-reperfusion injury. METHODS AND RESULTS Mice were treated with a direct fIIa inhibitor (fIIai) or direct fXa inhibitor (fXai) at doses that induced comparable anticoagulant effects ex vivo and in vivo (tail-bleeding assay and FeCl3-induced thrombosis). Myocardial ischemia-reperfusion injury was induced via left anterior descending ligation. We determined infarct size and in vivo aPC generation, analyzed gene expression by RNA sequencing, and performed immunoblotting and ELISA. The signaling-only 3K3A-aPC variant and inhibitory antibodies that blocked all or only the anticoagulant function of aPC were used to determine the role of aPC. Doses of fIIai and fXai that induced comparable anticoagulant effects resulted in a comparable reduction in infarct size. However, unbiased gene expression analyses revealed marked differences, including pathways related to sterile inflammation and inflammasome regulation. fXai but not fIIai inhibited sterile inflammation by reducing the expression of proinflammatory cytokines (IL [interleukin]-1β, IL-6, and TNFα [tumor necrosis factor alpha]), as well as NF-κB (nuclear factor kappa B) and inflammasome activation. This anti-inflammatory effect was associated with reduced myocardial fibrosis 28 days post-myocardial ischemia-reperfusion injury. Mechanistically, in vivo aPC generation was higher with fXai than with fIIai. Inhibition of the anticoagulant and signaling properties of aPC abolished the anti-inflammatory effect associated with fXai, while inhibiting only the anticoagulant function of aPC had no effect. Combining 3K3A-aPC with fIIai reduced the inflammatory response, mimicking the fXai-associated effect. CONCLUSIONS We showed that specific inhibition of coagulation via direct oral anticoagulants had differential effects on gene expression and inflammation, despite comparable anticoagulant effects and infarct sizes. Targeting individual coagulation proteases induces specific cellular responses unrelated to their anticoagulant effect.
Collapse
Affiliation(s)
- Ihsan Gadi
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Sameen Fatima
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Ahmed Elwakiel
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Sumra Nazir
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Moh'd Mohanad Al-Dabet
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.).,Medical Laboratories, Faculty of Health Sciences, American University of Madaba, Amman, Jordan (M.M.A.-D.)
| | - Rajiv Rana
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Fabian Bock
- Medicine, Vanderbilt University Medical Center, Nashville, TN (F.B.)
| | - Jayakumar Manoharan
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Dheerendra Gupta
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Ronald Biemann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Centre, University of Würzburg, Germany (B.N.)
| | - Ruediger Braun-Dullaeus
- Clinics of Cardiology and Angiology, Otto-von-Guericke-University, Magdeburg, Germany (R.B.-D.)
| | - Christian Besler
- Cardiology, Leipzig Heart Center (C.B.), University of Leipzig, Germany
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology (M.S.), University of Leipzig, Germany
| | - Robert Geffers
- RG Genome Analytics, Helmholtz Center for Infection Research, Braunschweig, Germany (R.G.)
| | - John H Griffin
- Molecular Medicine, The Scripps Research Institute, La Jolla, CA (J.H.G.)
| | - Charles T Esmon
- Coagulation Biology Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104 (C.T.E.)
| | - Shrey Kohli
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Khurrum Shahzad
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| |
Collapse
|
37
|
Alcalà-Vida R, Awada A, Boutillier AL, Merienne K. Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration. Neurobiol Dis 2020; 147:105155. [PMID: 33127472 DOI: 10.1016/j.nbd.2020.105155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), are progressive conditions characterized by selective, disease-dependent loss of neuronal regions and/or subpopulations. Neuronal loss is preceded by a long period of neuronal dysfunction, during which glial cells also undergo major changes, including neuroinflammatory response. Those dramatic changes affecting both neuronal and glial cells associate with epigenetic and transcriptional dysregulations, characterized by defined cell-type-specific signatures. Notably, increasing studies support the view that altered regulation of transcriptional enhancers, which are distal regulatory regions of the genome capable of modulating the activity of promoters through chromatin looping, play a critical role in transcriptional dysregulation in HD and AD. We review current knowledge on enhancers in HD and AD, and highlight challenging issues to better decipher the epigenetic code of neurodegenerative diseases.
Collapse
Affiliation(s)
- Rafael Alcalà-Vida
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | - Ali Awada
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | | | - Karine Merienne
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France.
| |
Collapse
|
38
|
Differential Protein Expression in Striatal D1- and D2-Dopamine Receptor-Expressing Medium Spiny Neurons. Proteomes 2020; 8:proteomes8040027. [PMID: 33066078 PMCID: PMC7709116 DOI: 10.3390/proteomes8040027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Many neurological disorders and diseases including drug addiction are associated with specific neuronal cell types in the brain. The striatum, a region that plays a critically important role in the development of addictive drug-related behavior, provides a good example of the cellular heterogeneity challenges associated with analyses of specific neuronal cell types. Such studies are needed to identify the adaptive changes in neuroproteomic signaling that occur in response to diseases such as addiction. The striatum contains two major cell types, D1 and D2 type dopaminoceptive medium spiny neurons (MSNs), whose cell bodies and processes are intermingled throughout this region. Since little is known about the proteomes of these two neuronal cell populations, we have begun to address this challenge by using fluorescence-activated nuclear sorting (FANS) to isolate nuclei-containing fractions from striatum from D1 and D2 “Translating Ribosome Affinity Purification” (TRAP) mice. This approach enabled us to devise and implement a robust and reproducible workflow for preparing samples from specific MSN cell types for mass spectrometry analyses. These analyses quantified at least 685 proteins in each of four biological replicates of 50 K sorted nuclei from two D1 mice/replicate and from each of four biological replicates of 50 K sorted nuclei from two D2 mice/replicate. Proteome analyses identified 87 proteins that were differentially expressed in D1 versus D2 MSN nuclei and principal component analysis (PCA) of these proteins separated the 8 biological replicates into specific cell types. Central network analysis of the 87 differentially expressed proteins identified Hnrnpd and Hnmpa2b1 in D1 and Cct2 and Cct7 in D2 as potential central interactors. This workflow can now be used to improve our understanding of many neurological diseases including characterizing the short and long-term impact of drugs of abuse on the proteomes of these two dopaminoceptive neuronal populations.
Collapse
|
39
|
Schmauch B, Romagnoni A, Pronier E, Saillard C, Maillé P, Calderaro J, Kamoun A, Sefta M, Toldo S, Zaslavskiy M, Clozel T, Moarii M, Courtiol P, Wainrib G. A deep learning model to predict RNA-Seq expression of tumours from whole slide images. Nat Commun 2020; 11:3877. [PMID: 32747659 PMCID: PMC7400514 DOI: 10.1038/s41467-020-17678-4] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 07/13/2020] [Indexed: 02/06/2023] Open
Abstract
Deep learning methods for digital pathology analysis are an effective way to address multiple clinical questions, from diagnosis to prediction of treatment outcomes. These methods have also been used to predict gene mutations from pathology images, but no comprehensive evaluation of their potential for extracting molecular features from histology slides has yet been performed. We show that HE2RNA, a model based on the integration of multiple data modes, can be trained to systematically predict RNA-Seq profiles from whole-slide images alone, without expert annotation. Through its interpretable design, HE2RNA provides virtual spatialization of gene expression, as validated by CD3- and CD20-staining on an independent dataset. The transcriptomic representation learned by HE2RNA can also be transferred on other datasets, even of small size, to increase prediction performance for specific molecular phenotypes. We illustrate the use of this approach in clinical diagnosis purposes such as the identification of tumors with microsatellite instability. RNA-sequencing of tumour tissue can provide important diagnostic and prognostic information but this is costly and not routinely performed in all clinical settings. Here, the authors show that whole slide histology slides—part of routine care—can be used to predict RNA-sequencing data and thus reduce the need for additional analyses.
Collapse
Affiliation(s)
| | | | | | | | - Pascale Maillé
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis and Related Cancers", Créteil, France.,APHP, Department of Pathology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Julien Calderaro
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis and Related Cancers", Créteil, France.,APHP, Department of Pathology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Wilton DK, Stevens B. The contribution of glial cells to Huntington's disease pathogenesis. Neurobiol Dis 2020; 143:104963. [PMID: 32593752 DOI: 10.1016/j.nbd.2020.104963] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/07/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
Glial cells play critical roles in the normal development and function of neural circuits, but in many neurodegenerative diseases, they become dysregulated and may contribute to the development of brain pathology. In Huntington's disease (HD), glial cells both lose normal functions and gain neuropathic phenotypes. In addition, cell-autonomous dysfunction elicited by mutant huntingtin (mHTT) expression in specific glial cell types is sufficient to induce both pathology and Huntington's disease-related impairments in motor and cognitive performance, suggesting that these cells may drive the development of certain aspects of Huntington's disease pathogenesis. In support of this imaging studies in pre-symptomatic HD patients and work on mouse models have suggested that glial cell dysfunction occurs at a very early stage of the disease, prior to the onset of motor and cognitive deficits. Furthermore, selectively ablating mHTT from specific glial cells or correcting for HD-induced changes in their transcriptional profile rescues some HD-related phenotypes, demonstrating the potential of targeting these cells for therapeutic intervention. Here we review emerging research focused on understanding the involvement of different glial cell types in specific aspects of HD pathogenesis. This work is providing new insight into how HD impacts biological functions of glial cells in the healthy brain as well as how HD induced dysfunction in these cells might change the way they integrate into biological circuits.
Collapse
Affiliation(s)
- Daniel K Wilton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Beth Stevens
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center, Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
41
|
Miyazaki H, Yamanaka T, Oyama F, Kino Y, Kurosawa M, Yamada-Kurosawa M, Yamano R, Shimogori T, Hattori N, Nukina N. FACS-array-based cell purification yields a specific transcriptome of striatal medium spiny neurons in a murine Huntington disease model. J Biol Chem 2020; 295:9768-9785. [PMID: 32499373 DOI: 10.1074/jbc.ra120.012983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/21/2020] [Indexed: 12/27/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by expanded CAG repeats in the Huntingtin gene. Results from previous studies have suggested that transcriptional dysregulation is one of the key mechanisms underlying striatal medium spiny neuron (MSN) degeneration in HD. However, some of the critical genes involved in HD etiology or pathology could be masked in a common expression profiling assay because of contamination with non-MSN cells. To gain insight into the MSN-specific gene expression changes in presymptomatic R6/2 mice, a common HD mouse model, here we used a transgenic fluorescent protein marker of MSNs for purification via FACS before profiling gene expression with gene microarrays and compared the results of this "FACS-array" with those obtained with homogenized striatal samples (STR-array). We identified hundreds of differentially expressed genes (DEGs) and enhanced detection of MSN-specific DEGs by comparing the results of the FACS-array with those of the STR-array. The gene sets obtained included genes ubiquitously expressed in both MSNs and non-MSN cells of the brain and associated with transcriptional regulation and DNA damage responses. We proposed that the comparative gene expression approach using the FACS-array may be useful for uncovering the gene cascades affected in MSNs during HD pathogenesis.
Collapse
Affiliation(s)
- Haruko Miyazaki
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoyuki Yamanaka
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fumitaka Oyama
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Department of Chemistry and Life Science, Kogakuin University, Tokyo, Japan
| | - Yoshihiro Kino
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Masaru Kurosawa
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Institute for Environmental and Gender-specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | | | - Risa Yamano
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan
| | - Tomomi Shimogori
- Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan .,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| |
Collapse
|
42
|
Emami-Khoyi A, Parbhu SP, Ross JG, Murphy EC, Bothwell J, Monsanto DM, Vuuren BJV, Teske PR, Paterson AM. De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums ( Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control. Genes (Basel) 2020; 11:genes11040436. [PMID: 32316496 PMCID: PMC7230921 DOI: 10.3390/genes11040436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species’ genomic diversity and population structure is hindered by a paucity of available genomic resources. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.
Collapse
Affiliation(s)
- Arsalan Emami-Khoyi
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Shilpa Pradeep Parbhu
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - James G Ross
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Elaine C Murphy
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jennifer Bothwell
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Daniela M Monsanto
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Bettine Jansen van Vuuren
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Peter R Teske
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Adrian M Paterson
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| |
Collapse
|
43
|
Harris SE, Cox SR, Bell S, Marioni RE, Prins BP, Pattie A, Corley J, Muñoz Maniega S, Valdés Hernández M, Morris Z, John S, Bronson PG, Tucker-Drob EM, Starr JM, Bastin ME, Wardlaw JM, Butterworth AS, Deary IJ. Neurology-related protein biomarkers are associated with cognitive ability and brain volume in older age. Nat Commun 2020; 11:800. [PMID: 32041957 PMCID: PMC7010796 DOI: 10.1038/s41467-019-14161-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Identifying biological correlates of late life cognitive function is important if we are to ascertain biomarkers for, and develop treatments to help reduce, age-related cognitive decline. Here, we investigated the associations between plasma levels of 90 neurology-related proteins (Olink® Proteomics) and general fluid cognitive ability in the Lothian Birth Cohort 1936 (LBC1936, N = 798), Lothian Birth Cohort 1921 (LBC1921, N = 165), and the INTERVAL BioResource (N = 4451). In the LBC1936, 22 of the proteins were significantly associated with general fluid cognitive ability (β between -0.11 and -0.17). MRI-assessed total brain volume partially mediated the association between 10 of these proteins and general fluid cognitive ability. In an age-matched subsample of INTERVAL, effect sizes for the 22 proteins, although smaller, were all in the same direction as in LBC1936. Plasma levels of a number of neurology-related proteins are associated with general fluid cognitive ability in later life, mediated by brain volume in some cases.
Collapse
Affiliation(s)
- Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. .,Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
| | - Simon R Cox
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, 300 Bath St, Glasgow, UK
| | - Steven Bell
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.,The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.,Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge Neurology Unit, Cambridge Biomedical Campus, Cambridge, CB20QQ, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Bram P Prins
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Janie Corley
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Susana Muñoz Maniega
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Brain Research Imaging Centre, Neuroimaging Sciences, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, UK.,UK Dementia Research Institute at the University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Maria Valdés Hernández
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Brain Research Imaging Centre, Neuroimaging Sciences, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, UK.,UK Dementia Research Institute at the University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Zoe Morris
- Brain Research Imaging Centre, Neuroimaging Sciences, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, UK
| | - Sally John
- Translational Biology, Biogen, Cambridge, MA, 02142, USA
| | | | - Elliot M Tucker-Drob
- Department of Psychology, University of Texas, 108 E Dean Keeton St, Austin, TX, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Mark E Bastin
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, 300 Bath St, Glasgow, UK.,Brain Research Imaging Centre, Neuroimaging Sciences, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, UK
| | - Joanna M Wardlaw
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, 300 Bath St, Glasgow, UK.,Brain Research Imaging Centre, Neuroimaging Sciences, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, UK.,UK Dementia Research Institute at the University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Adam S Butterworth
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.,The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| |
Collapse
|
44
|
Duarte Azevedo M, Sander S, Tenenbaum L. GDNF, A Neuron-Derived Factor Upregulated in Glial Cells during Disease. J Clin Med 2020; 9:jcm9020456. [PMID: 32046031 PMCID: PMC7073520 DOI: 10.3390/jcm9020456] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/20/2022] Open
Abstract
In a healthy adult brain, glial cell line-derived neurotrophic factor (GDNF) is exclusively expressed by neurons, and, in some instances, it has also been shown to derive from a single neuronal subpopulation. Secreted GDNF acts in a paracrine fashion by forming a complex with the GDNF family receptor α1 (GFRα1), which is mainly expressed by neurons and can act in cis as a membrane-bound factor or in trans as a soluble factor. The GDNF/GFRα1 complex signals through interactions with the “rearranged during transfection” (RET) receptor or via the neural cell adhesion molecule (NCAM) with a lower affinity. GDNF can also signal independently from GFRα1 by interacting with syndecan-3. RET, which is expressed by neurons involved in several pathways (nigro–striatal dopaminergic neurons, motor neurons, enteric neurons, sensory neurons, etc.), could be the main determinant of the specificity of GDNF’s pro-survival effect. In an injured brain, de novo expression of GDNF occurs in glial cells. Neuroinflammation has been reported to induce GDNF expression in activated astrocytes and microglia, infiltrating macrophages, nestin-positive reactive astrocytes, and neuron/glia (NG2) positive microglia-like cells. This disease-related GDNF overexpression can be either beneficial or detrimental depending on the localization in the brain and the level and duration of glial cell activation. Some reports also describe the upregulation of RET and GFRα1 in glial cells, suggesting that GDNF could modulate neuroinflammation.
Collapse
|
45
|
Hirbec H, Déglon N, Foo LC, Goshen I, Grutzendler J, Hangen E, Kreisel T, Linck N, Muffat J, Regio S, Rion S, Escartin C. Emerging technologies to study glial cells. Glia 2020; 68:1692-1728. [PMID: 31958188 DOI: 10.1002/glia.23780] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022]
Abstract
Development, physiological functions, and pathologies of the brain depend on tight interactions between neurons and different types of glial cells, such as astrocytes, microglia, oligodendrocytes, and oligodendrocyte precursor cells. Assessing the relative contribution of different glial cell types is required for the full understanding of brain function and dysfunction. Over the recent years, several technological breakthroughs were achieved, allowing "glio-scientists" to address new challenging biological questions. These technical developments make it possible to study the roles of specific cell types with medium or high-content workflows and perform fine analysis of their mutual interactions in a preserved environment. This review illustrates the potency of several cutting-edge experimental approaches (advanced cell cultures, induced pluripotent stem cell (iPSC)-derived human glial cells, viral vectors, in situ glia imaging, opto- and chemogenetic approaches, and high-content molecular analysis) to unravel the role of glial cells in specific brain functions or diseases. It also illustrates the translation of some techniques to the clinics, to monitor glial cells in patients, through specific brain imaging methods. The advantages, pitfalls, and future developments are discussed for each technique, and selected examples are provided to illustrate how specific "gliobiological" questions can now be tackled.
Collapse
Affiliation(s)
- Hélène Hirbec
- Institute for Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Nicole Déglon
- Laboratory of Neurotherapies and Neuromodulation, Department of Clinical Neuroscience, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.,Laboratory of Neurotherapies and Neuromodulation, Neuroscience Research Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Lynette C Foo
- Neuroimmunology and Neurodegeneration Section, The Neuroscience and Rare Diseases Discovery and Translational Area, F. Hoffman-La Roche, Basel, Switzerland
| | - Inbal Goshen
- Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jaime Grutzendler
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emilie Hangen
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de la Recherche Fondamentale, Institut de Biologie François Jacob, MIRCen, Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique, Neurodegenerative Diseases Laboratory, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Fontenay-aux-Roses, France
| | - Tirzah Kreisel
- Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nathalie Linck
- Institute for Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, and Department of Molecular Genetics, The University of Toronto, Toronto, Canada
| | - Sara Regio
- Laboratory of Neurotherapies and Neuromodulation, Department of Clinical Neuroscience, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.,Laboratory of Neurotherapies and Neuromodulation, Neuroscience Research Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sybille Rion
- Neuroimmunology and Neurodegeneration Section, The Neuroscience and Rare Diseases Discovery and Translational Area, F. Hoffman-La Roche, Basel, Switzerland
| | - Carole Escartin
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de la Recherche Fondamentale, Institut de Biologie François Jacob, MIRCen, Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique, Neurodegenerative Diseases Laboratory, Université Paris-Sud, Université Paris-Saclay, UMR 9199, Fontenay-aux-Roses, France
| |
Collapse
|
46
|
Creus-Muncunill J, Ehrlich ME. Cell-Autonomous and Non-cell-Autonomous Pathogenic Mechanisms in Huntington's Disease: Insights from In Vitro and In Vivo Models. Neurotherapeutics 2019; 16:957-978. [PMID: 31529216 PMCID: PMC6985401 DOI: 10.1007/s13311-019-00782-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Huntington's disease (HD) is an autosomal dominant disorder caused by an expansion in the trinucleotide CAG repeat in exon-1 in the huntingtin gene, located on chromosome 4. When the number of trinucleotide CAG exceeds 40 repeats, disease invariably is manifested, characterized by motor, cognitive, and psychiatric symptoms. The huntingtin (Htt) protein and its mutant form (mutant huntingtin, mHtt) are ubiquitously expressed but although multiple brain regions are affected, the most vulnerable brain region is the striatum. Striatal medium-sized spiny neurons (MSNs) preferentially degenerate, followed by the cortical pyramidal neurons located in layers V and VI. Proposed HD pathogenic mechanisms include, but are not restricted to, excitotoxicity, neurotrophic support deficits, collapse of the protein degradation mechanisms, mitochondrial dysfunction, transcriptional alterations, and disorders of myelin. Studies performed in cell type-specific and regionally selective HD mouse models implicate both MSN cell-autonomous properties and cell-cell interactions, particularly corticostriatal but also with non-neuronal cell types. Here, we review the intrinsic properties of MSNs that contribute to their selective vulnerability and in addition, we discuss how astrocytes, microglia, and oligodendrocytes, together with aberrant corticostriatal connectivity, contribute to HD pathophysiology. In addition, mHtt causes cell-autonomous dysfunction in cell types other than MSNs. These findings have implications in terms of therapeutic strategies aimed at preventing neuronal dysfunction and degeneration.
Collapse
Affiliation(s)
- Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA.
| |
Collapse
|