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Efficient Gene Expression in Human Stem Cell Derived-Cortical Organoids Using Adeno Associated Virus. Cells 2022; 11:cells11203194. [PMID: 36291062 PMCID: PMC9601198 DOI: 10.3390/cells11203194] [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: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/25/2022] Open
Abstract
Cortical organoids are 3D structures derived either from human embryonic stem cells or human induced pluripotent stem cells with their use exploding in recent years due to their ability to better recapitulate the human brain in vivo in respect to organization; differentiation; and polarity. Adeno-associated viruses (AAVs) have emerged in recent years as the vectors of choice for CNS-targeted gene therapy. Here; we compare the use of AAVs as a mode of gene expression in cortical organoids; over traditional methods such as lipofectamine and electroporation and demonstrate its ease-of-use in generating quick disease models through expression of different variants of the central gene—TDP-43—implicated in amyotrophic lateral sclerosis and frontotemporal dementia.
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van der Linden RJ, Gerritsen JS, Liao M, Widomska J, Pearse RV, White FM, Franke B, Young-Pearse TL, Poelmans G. RNA-binding protein ELAVL4/HuD ameliorates Alzheimer's disease-related molecular changes in human iPSC-derived neurons. Prog Neurobiol 2022; 217:102316. [PMID: 35843356 PMCID: PMC9912016 DOI: 10.1016/j.pneurobio.2022.102316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/18/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022]
Abstract
The RNA binding protein ELAVL4/HuD regulates the translation and splicing of multiple Alzheimer's disease (AD) candidate genes. We generated ELAVL4 knockout (KO) human induced pluripotent stem cell-derived neurons to study the effect that ELAVL4 has on AD-related cellular phenotypes. ELAVL4 KO significantly increased the levels of specific APP isoforms and intracellular phosphorylated tau, molecular changes that are related to the pathological hallmarks of AD. Overexpression of ELAVL4 in wild-type neurons and rescue experiments in ELAVL4 KO cells showed opposite effects and also led to a reduction of the extracellular amyloid-beta (Aβ)42/40 ratio. All these observations were made in familial AD (fAD) and fAD-corrected neurons. To gain insight into the molecular cascades involved in neuronal ELAVL4 signaling, we conducted pathway and upstream regulator analyses of transcriptomic and proteomic data from the generated neurons. These analyses revealed that ELAVL4 affects multiple biological pathways linked to AD, including those involved in synaptic function, as well as gene expression downstream of APP and tau signaling. The analyses also suggest that ELAVL4 expression is regulated by insulin receptor-FOXO1 signaling in neurons. Taken together, ELAVL4 expression ameliorates AD-related molecular changes in neurons and affects multiple synaptic pathways, making it a promising target for novel drug development.
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Affiliation(s)
- Robert J van der Linden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Meichen Liao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joanna Widomska
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands; Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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Ideno H, Imaizumi K, Shimada H, Sanosaka T, Nemoto A, Kohyama J, Okano H. Human PSCs determine the competency of cerebral organoid differentiation via FGF signaling and epigenetic mechanisms. iScience 2022; 25:105140. [PMID: 36185382 PMCID: PMC9523398 DOI: 10.1016/j.isci.2022.105140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/06/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Hirosato Ideno
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kent Imaizumi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Corresponding author
| | - Hiroko Shimada
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akisa Nemoto
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Corresponding author
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Hofmann B, Zinöcker S, Holm S, Lewis J, Kavouras P. Organoids in the Clinic: A Systematic Review of Outcomes. Cells Tissues Organs 2022; 212:499-511. [PMID: 36170843 PMCID: PMC10906541 DOI: 10.1159/000527237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/02/2022] [Indexed: 11/19/2022] Open
Abstract
Research on organoids has undergone significant advances during the last decade. However, outcomes from the use of organoids in clinical trials have not yet been documented. Therefore, there is an urgent need to assess the reporting of clinically relevant outcomes from organoid research in the scientific literature. This article presents a systematic review and appraisal of the published literature in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, together with a synopsis of recent relevant reviews. Surprisingly, no randomized controlled trials have reported clinical outcomes with any types of organoids. We found very few ongoing and registered studies that may provide clinically relevant results within this decade. Our screening and interpretation of the literature, including review articles, indicate a focus on technical and preclinical aspects of organoid research. This is the first systematic review of clinical trials involving organoids. Few clinical studies are planned or already underway, and, so far, no high-quality evidence relating to the clinical outcomes of organoid research has been published. The many promises of organoid research still need to be translated from bench to bed.
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Affiliation(s)
- Bjørn Hofmann
- Centre for Medical Ethics, University of Oslo, Oslo, Norway
- Department of Health Sciences, Norwegian University of Science and Technology (NTNU), Gjøvik, Norway
| | - Severin Zinöcker
- Centre for Medical Ethics, University of Oslo, Oslo, Norway
- Norwegian Institute of Public Health, Oslo, Norway
| | - Søren Holm
- Centre for Medical Ethics, University of Oslo, Oslo, Norway
- Centre for Social Ethics and Policy, Department of Law, School of Social Sciences, The University of Manchester, Manchester, UK
| | - Jonathan Lewis
- Centre for Social Ethics and Policy, Department of Law, School of Social Sciences, The University of Manchester, Manchester, UK
| | - Panagiotis Kavouras
- RNanoLab, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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Zhou B, Xu Q, Guo J, Chen Q, Lv Q, Xiao K, Zhu H, Zhao J, Liu Y. Necroptosis Contributes to LPS-Induced Activation of the Hypothalamic-Pituitary-Adrenal Axis in a Piglet Model. Int J Mol Sci 2022; 23:ijms231911218. [PMID: 36232518 PMCID: PMC9569845 DOI: 10.3390/ijms231911218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Stressors cause activation of the hypothalamic-pituitary-adrenal (HPA) axis and a systemic inflammatory response. As a newly proposed cell death manner in recent years, necroptosis occurs in a variety of tissue damage and inflammation. However, the role of necroptosis in HPA axis activation remains to be elucidated. The aim of this study was to investigate the occurrence of necroptosis and its role in HPA activation in a porcine stress model induced by Escherichia coli lipopolysaccharide (LPS). Several typical stress behaviors like fever, anorexia, shivering and vomiting were observed in piglets after LPS injection. HPA axis was activated as shown by increased plasma cortisol concentration and mRNA expression of pituitary corticotropin-releasing hormone receptor 1 (CRHR1) and adrenal steroidogenic acute regulatory protein (StAR). The mRNA expression of tumor necrosis factor α (TNF-α), interleukin-1β (IL-1β) and IL-6 in the hypothalamus, pituitary gland and adrenal gland was elevated by LPS, accompanied by the activation of necroptosis indicated by higher mRNA expression of necroptosis signals including receptor-interacting protein kinase (RIP) 1, RIP3, and phosphorylated mixed-lineage kinase domain-like protein (MLKL). Furthermore, necrostatin-1 (Nec-1), an inhibitor of necroptosis, inhibited necroptosis indicated by decreased mRNA levels of RIP1, RIP3, MLKL, and phosphoglycerate mutase family member 5 (PGAM5) in the hypothalamus, pituitary gland and adrenal gland. Nec-1 also decreased the mRNA expression of TNF-α and IL-β and inhibited the activation of the HPA axis indicated by lower plasma cortisol concentration and mRNA expression of adrenal type 2 melanocortin receptor (MC2R) and StAR. These findings suggest that necroptosis is present and contributes to HPA axis activation induced by LPS. These findings provide a potential possibility for necroptosis as an intervention target for alleviating HPA axis activation and stress responses.
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Affiliation(s)
- Bei Zhou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qilong Xu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Junjie Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qinliang Chen
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qingqing Lv
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Kan Xiao
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Huiling Zhu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yulan Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan 430023, China
- Correspondence: ; Tel./Fax: +86-027-8395-6175
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Yin L, Zhou J, Li T, Wang X, Xue W, Zhang J, Lin L, Wang N, Kang X, Zhou Y, Liu H, Li Y. Inhibition of the dopamine transporter promotes lysosome biogenesis and ameliorates Alzheimer's disease-like symptoms in mice. Alzheimers Dement 2022; 19:1343-1357. [PMID: 36130073 DOI: 10.1002/alz.12776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Lysosomes are degradative organelles that maintain cellular homeostasis and protein quality control. Transcription factor EB (TFEB)-mediated lysosome biogenesis enhances lysosome-dependent degradation and alleviates neurodegenerative diseases, but the mechanisms underlying TFEB regulation and modification are still poorly understood. METHODS By screening novel small-molecule compounds, we identified a group of lysosome-enhancing compounds (LYECs) that promote TFEB activation and lysosome biogenesis. RESULTS One of these compounds, LH2-051, significantly inhibited the function of the dopamine transporter (DAT) and subsequently promoted lysosome biogenesis. We uncovered cyclin-dependent kinase 9 (CDK9) as a novel regulator of DAT-mediated lysosome biogenesis and identified six novel CDK9-phosphorylated sites on TFEB. We observed that signal transduction by the DAT-CDK9-TFEB axis occurs on lysosomes. Finally, we found that LH2-051 enhanced the degradation of amyloid beta plaques and improved the memory of amyloid precursor protein (APP)/Presenilin 1 (PS1) mice. DISCUSSION We identified the DAT-CDK9-TFEB signaling axis as a novel regulator of lysosome biogenesis. Our study sheds light on the mechanisms of protein quality control under pathophysiological conditions.
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Affiliation(s)
- Limin Yin
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Jianhui Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tianyou Li
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Xinghua Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenlong Xue
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Jie Zhang
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Lingxi Lin
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Ning Wang
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Xinyi Kang
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Yu Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Li
- Department of Pharmacology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Science, Fudan University, Shanghai, China
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Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells 2022; 11:2803. [PMID: 36139380 PMCID: PMC9496777 DOI: 10.3390/cells11182803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 01/25/2023] Open
Abstract
The cerebral cortex forms early in development according to a series of heritable neurodevelopmental instructions. Despite deep evolutionary conservation of the cerebral cortex and its foundational six-layered architecture, significant variations in cortical size and folding can be found across mammals, including a disproportionate expansion of the prefrontal cortex in humans. Yet our mechanistic understanding of neurodevelopmental processes is derived overwhelmingly from rodent models, which fail to capture many human-enriched features of cortical development. With the advent of pluripotent stem cells and technologies for differentiating three-dimensional cultures of neural tissue in vitro, cerebral organoids have emerged as an experimental platform that recapitulates several hallmarks of human brain development. In this review, we discuss the merits and limitations of cerebral organoids as experimental models of the developing human brain. We highlight innovations in technology development that seek to increase its fidelity to brain development in vivo and discuss recent efforts to use cerebral organoids to study regeneration and brain evolution as well as to develop neurological and neuropsychiatric disease models.
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Affiliation(s)
- Tomasz J. Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sofie R. Salama
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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Generation and Characterization of Novel iPSC Lines from a Portuguese Family Bearing Heterozygous and Homozygous GRN Mutations. Biomedicines 2022; 10:biomedicines10081905. [PMID: 36009452 PMCID: PMC9405606 DOI: 10.3390/biomedicines10081905] [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: 07/06/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations in granulin (GRN) have been associated with neurodegenerative diseases, such as frontotemporal lobar degeneration (FTLD) and neuronal ceroid lipofuscinosis (NCL). In Portugal, GRN mutations account for around half of all FTLD cases with known genetic origin. Here, we describe the generation and characterization of three human-induced pluripotent stem cell (hiPSC) lines from a Portuguese family harboring heterozygous and homozygous GRN mutation. hiPSCs were reprogrammed from human dermal fibroblasts by episomal nucleofection of the Yamanaka factors. The new generated lines were positive for pluripotency markers, could be further differentiated to cells expressing all trilineage markers, and presented a normal karyotype. They were also capable of differentiating into 3D brain organoids and presented a significant decrease in progranulin protein levels. Hence, these cell lines constitute suitable new tools to elucidate the pathophysiological mechanisms associated with the GRN mutations in the context of FTLD.
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Glasauer SMK, Goderie SK, Rauch JN, Guzman E, Audouard M, Bertucci T, Joy S, Rommelfanger E, Luna G, Keane-Rivera E, Lotz S, Borden S, Armando AM, Quehenberger O, Temple S, Kosik KS. Human tau mutations in cerebral organoids induce a progressive dyshomeostasis of cholesterol. Stem Cell Reports 2022; 17:2127-2140. [PMID: 35985329 PMCID: PMC9481908 DOI: 10.1016/j.stemcr.2022.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Mutations in the MAPT gene that encodes tau lead to frontotemporal dementia (FTD) with pathology evident in both cerebral neurons and glia. Human cerebral organoids (hCOs) from individuals harboring pathogenic tau mutations can reveal the earliest downstream effects on molecular pathways within a developmental context, generating interacting neurons and glia. We found that in hCOs carrying the V337M and R406W tau mutations, the cholesterol biosynthesis pathway in astrocytes was the top upregulated gene set compared with isogenic controls by single-cell RNA sequencing (scRNA-seq). The 15 upregulated genes included HMGCR, ACAT2, STARD4, LDLR, and SREBF2. This result was confirmed in a homozygous R406W mutant cell line by immunostaining and sterol measurements. Cholesterol abundance in the brain is tightly regulated by efflux and cholesterol biosynthetic enzyme levels in astrocytes, and dysregulation can cause aberrant phosphorylation of tau. Our findings suggest that cholesterol dyshomeostasis is an early event in the etiology of neurodegeneration caused by tau mutations. Cerebral organoid models of tauopathy caused by MAPT mutations Upregulated cholesterol and fatty acid biosynthesis genes in MAPT mutant astrocytes Elevation of cholesterol and its precursors in MAPT mutant cerebral organoids
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Affiliation(s)
- Stella M K Glasauer
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | | | - Jennifer N Rauch
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elmer Guzman
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Morgane Audouard
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | | | - Shona Joy
- Neural Stem Cell Institute, Rensselaer, NY 12144, USA
| | - Emma Rommelfanger
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Gabriel Luna
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Erica Keane-Rivera
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Steven Lotz
- Neural Stem Cell Institute, Rensselaer, NY 12144, USA
| | - Susan Borden
- Neural Stem Cell Institute, Rensselaer, NY 12144, USA
| | - Aaron M Armando
- Department of Pharmacology, University of California, San Diego, San Diego, CA 92093, USA
| | - Oswald Quehenberger
- Department of Pharmacology, University of California, San Diego, San Diego, CA 92093, USA
| | - Sally Temple
- Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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Corsini NS, Knoblich JA. Human organoids: New strategies and methods for analyzing human development and disease. Cell 2022; 185:2756-2769. [PMID: 35868278 DOI: 10.1016/j.cell.2022.06.051] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/06/2023]
Abstract
For decades, insight into fundamental principles of human biology and disease has been obtained primarily by experiments in animal models. While this has allowed researchers to understand many human biological processes in great detail, some developmental and disease mechanisms have proven difficult to study due to inherent species differences. The advent of organoid technology more than 10 years ago has established laboratory-grown organ tissues as an additional model system to recapitulate human-specific aspects of biology. The use of human 3D organoids, as well as other advances in single-cell technologies, has revealed unprecedented insights into human biology and disease mechanisms, especially those that distinguish humans from other species. This review highlights novel advances in organoid biology with a focus on how organoid technology has generated a better understanding of human-specific processes in development and disease.
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Affiliation(s)
- Nina S Corsini
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Juergen A Knoblich
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria; Medical University of Vienna, Department of Neurology, Vienna, Austria.
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61
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Sprang M, Andrade-Navarro MA, Fontaine JF. Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality. BMC Bioinformatics 2022; 23:279. [PMID: 35836114 PMCID: PMC9284682 DOI: 10.1186/s12859-022-04775-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Background The constant evolving and development of next-generation sequencing techniques lead to high throughput data composed of datasets that include a large number of biological samples. Although a large number of samples are usually experimentally processed by batches, scientific publications are often elusive about this information, which can greatly impact the quality of the samples and confound further statistical analyzes. Because dedicated bioinformatics methods developed to detect unwanted sources of variance in the data can wrongly detect real biological signals, such methods could benefit from using a quality-aware approach. Results We recently developed statistical guidelines and a machine learning tool to automatically evaluate the quality of a next-generation-sequencing sample. We leveraged this quality assessment to detect and correct batch effects in 12 publicly available RNA-seq datasets with available batch information. We were able to distinguish batches by our quality score and used it to correct for some batch effects in sample clustering. Overall, the correction was evaluated as comparable to or better than the reference method that uses a priori knowledge of the batches (in 10 and 1 datasets of 12, respectively; total = 92%). When coupled to outlier removal, the correction was more often evaluated as better than the reference (comparable or better in 5 and 6 datasets of 12, respectively; total = 92%). Conclusions In this work, we show the capabilities of our software to detect batches in public RNA-seq datasets from differences in the predicted quality of their samples. We also use these insights to correct the batch effect and observe the relation of sample quality and batch effect. These observations reinforce our expectation that while batch effects do correlate with differences in quality, batch effects also arise from other artifacts and are more suitably corrected statistically in well-designed experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04775-y.
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Affiliation(s)
- Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Jean-Fred Fontaine
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
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Tubbesing K, Moskwa N, Khoo TC, Nelson DA, Sharikova A, Feng Y, Larsen M, Khmaladze A. Raman microspectroscopy fingerprinting of organoid differentiation state. Cell Mol Biol Lett 2022; 27:53. [PMID: 35764935 PMCID: PMC9238268 DOI: 10.1186/s11658-022-00347-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/24/2022] [Indexed: 12/02/2022] Open
Abstract
Background Organoids, which are organs grown in a dish from stem or progenitor cells, model the structure and function of organs and can be used to define molecular events during organ formation, model human disease, assess drug responses, and perform grafting in vivo for regenerative medicine approaches. For therapeutic applications, there is a need for nondestructive methods to identify the differentiation state of unlabeled organoids in response to treatment with growth factors or pharmacologicals. Methods Using complex 3D submandibular salivary gland organoids developed from embryonic progenitor cells, which respond to EGF by proliferating and FGF2 by undergoing branching morphogenesis and proacinar differentiation, we developed Raman confocal microspectroscopy methods to define Raman signatures for each of these organoid states using both fixed and live organoids. Results Three separate quantitative comparisons, Raman spectral features, multivariate analysis, and machine learning, classified distinct organoid differentiation signatures and revealed that the Raman spectral signatures were predictive of organoid phenotype. Conclusions As the organoids were unlabeled, intact, and hydrated at the time of imaging, Raman spectral fingerprints can be used to noninvasively distinguish between different organoid phenotypes for future applications in disease modeling, drug screening, and regenerative medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00347-3. Salivary gland organoids have unique Raman signatures detectable with a confocal-based Raman imaging approach. Raman signatures can be detected in unlabeled fixed or live organoids. Raman spectral signatures effectively predict organoid phenotypes.
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63
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Zampatti S, Peconi C, Campopiano R, Gambardella S, Caltagirone C, Giardina E. C9orf72-Related Neurodegenerative Diseases: From Clinical Diagnosis to Therapeutic Strategies. Front Aging Neurosci 2022; 14:907122. [PMID: 35754952 PMCID: PMC9226392 DOI: 10.3389/fnagi.2022.907122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Hexanucleotide expansion in C9orf72 has been related to several phenotypes to date, complicating the clinical recognition of these neurodegenerative disorders. An early diagnosis can improve the management of patients, promoting early administration of therapeutic supportive strategies. Here, we report known clinical presentations of C9orf72-related neurodegenerative disorders, pointing out suggestive phenotypes that can benefit the genetic characterization of patients. Considering the high variability of C9orf72-related disorder, frequent and rare manifestations are described, with detailed clinical, instrumental evaluation, and supportive therapeutical approaches. Furthermore, to improve the understanding of molecular pathways of the disease and potential therapeutical targets, a detailed description of the cellular mechanisms related to the pathological effect of C9orf72 is reported. New promising therapeutical strategies and ongoing studies are reported highlighting their molecular role in cellular pathological pathways of C9orf72. These therapeutic approaches are particularly promising because they seem to stop the disease before neuronal damage. The knowledge of clinical and molecular features of C9orf72-related neurodegenerative disorders improves the therapeutical application of known strategies and will lay the basis for the development of new potential therapies.
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Affiliation(s)
- Stefania Zampatti
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Cristina Peconi
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy
| | | | - Stefano Gambardella
- IRCCS Neuromed, Pozzilli, Italy.,Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy.,Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
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64
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Lange J, Zhou H, McTague A. Cerebral Organoids and Antisense Oligonucleotide Therapeutics: Challenges and Opportunities. Front Mol Neurosci 2022; 15:941528. [PMID: 35836547 PMCID: PMC9274522 DOI: 10.3389/fnmol.2022.941528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
The advent of stem cell-derived cerebral organoids has already advanced our understanding of disease mechanisms in neurological diseases. Despite this, many remain without effective treatments, resulting in significant personal and societal health burden. Antisense oligonucleotides (ASOs) are one of the most widely used approaches for targeting RNA and modifying gene expression, with significant advancements in clinical trials for epilepsy, neuromuscular disorders and other neurological conditions. ASOs have further potential to address the unmet need in other neurological diseases for novel therapies which directly target the causative genes, allowing precision treatment. Induced pluripotent stem cell (iPSC) derived cerebral organoids represent an ideal platform in which to evaluate novel ASO therapies. In patient-derived organoids, disease-causing mutations can be studied in the native genetic milieu, opening the door to test personalized ASO therapies and n-of-1 approaches. In addition, CRISPR-Cas9 can be used to generate isogenic iPSCs to assess the effects of ASOs, by either creating disease-specific mutations or correcting available disease iPSC lines. Currently, ASO therapies face a number of challenges to wider translation, including insufficient uptake by distinct and preferential cell types in central nervous system and inability to cross the blood brain barrier necessitating intrathecal administration. Cerebral organoids provide a practical model to address and improve these limitations. In this review we will address the current use of organoids to test ASO therapies, opportunities for future applications and challenges including those inherent to cerebral organoids, issues with organoid transfection and choice of appropriate read-outs.
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Affiliation(s)
- Jenny Lange
- Department for Developmental Neurosciences, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Haiyan Zhou
- Genetics and Genomic Medicine Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, United Kingdom
| | - Amy McTague
- Department for Developmental Neurosciences, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, United Kingdom
- *Correspondence: Amy McTague,
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65
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Schwed-Gross A, Hamiel H, Faber GP, Angel M, Ben-Yishay R, Benichou JIC, Ishay-Ronen D, Shav-Tal Y. Glucocorticoids enhance chemotherapy-driven stress granule assembly and impair granule dynamics leading to cell death. J Cell Sci 2022; 135:276097. [PMID: 35713120 PMCID: PMC9450892 DOI: 10.1242/jcs.259629] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Stress granules (SGs) can assemble in cancer cells upon chemotoxic stress. Glucocorticoids function during stress responses and are administered with chemotherapies. The roles of glucocorticoids in SG assembly and disassembly pathways are unknown. We examined whether combining glucocorticoids such as cortisone with chemotherapies from the vinca alkaloid family, which dismantle the microtubule network, affects SG assembly and disassembly pathways and influences cell viability in cancer cells and human-derived organoids. Cortisone augmented SG formation when combined with vinorelbine (VRB). Live-cell imaging showed that cortisone increased SG assembly rates but reduced SG clearance rates after stress, by increasing protein residence times within the SGs. Mechanistically, VRB and cortisone signaled through the integrated stress response mediated by eIF2α (also known as EIF2S1), yet induced different kinases, with cortisone activating the GCN2 kinase (also known as EIF2AK4). Cortisone increased VRB-induced cell death and reduced the population of cells trapped in mitotic catastrophe. These effects were mediated by the core SG proteins G3BP1 and G3BP2. In conclusion, glucocorticoids induce SG assembly and cell death when administered with chemotherapies, suggesting that combining glucocorticoids with chemotherapies can enhance cancer cell chemosensitivity. Summary: Combining cortisone with the chemotherapy vinorelbine enhances the assembly of stress granules that are less likely to be cleared from the cells, augmenting vinorelbine-induced cell death.
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Affiliation(s)
- Avital Schwed-Gross
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hila Hamiel
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Gabriel P Faber
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Mor Angel
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Rakefet Ben-Yishay
- Oncology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Jennifer I C Benichou
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dana Ishay-Ronen
- Oncology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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66
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Cao Y. The uses of 3D human brain organoids for neurotoxicity evaluations: A review. Neurotoxicology 2022; 91:84-93. [PMID: 35561940 DOI: 10.1016/j.neuro.2022.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 05/05/2022] [Indexed: 12/22/2022]
Abstract
Neurotoxicity studies aim at understanding the toxic effects and mechanisms of toxicants to human central nervous systems (CNS). However, human brains are the most complex organs, whereas the most commonly used models, such as 2D cell cultures and animal brains, are probably too simple to predict the responses of human brains. Embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs)-based 3D human brain organoids hold unprecedented promise for the understanding of neurodevelopment and brain disease development. This review summarizes recent advances of using 3D human brain organoids for neurotoxicity studies. Comparative studies showed that 3D human brain organoids could support the findings obtained by animal or cohort studies, indicating that 3D human brain organoids are reliable models to evaluate the developmental neurotoxicity. 3D human brain organoids have been used to understand the toxicological mechanisms by using both conventional toxicological methods to investigate the signaling pathway changes as well as single cell RNA-sequencing to understand the neuron diversity. Some studies also used brain organoids carrying gene mutations or with virus infections to understand the toxicological responses of brains under diseased conditions. Although there are still limitations associated, 3D human brain organoids are promising tools for future neurotoxicity studies.
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Affiliation(s)
- Yi Cao
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
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67
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Wareham LK, Liddelow SA, Temple S, Benowitz LI, Di Polo A, Wellington C, Goldberg JL, He Z, Duan X, Bu G, Davis AA, Shekhar K, Torre AL, Chan DC, Canto-Soler MV, Flanagan JG, Subramanian P, Rossi S, Brunner T, Bovenkamp DE, Calkins DJ. Solving neurodegeneration: common mechanisms and strategies for new treatments. Mol Neurodegener 2022; 17:23. [PMID: 35313950 PMCID: PMC8935795 DOI: 10.1186/s13024-022-00524-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Across neurodegenerative diseases, common mechanisms may reveal novel therapeutic targets based on neuronal protection, repair, or regeneration, independent of etiology or site of disease pathology. To address these mechanisms and discuss emerging treatments, in April, 2021, Glaucoma Research Foundation, BrightFocus Foundation, and the Melza M. and Frank Theodore Barr Foundation collaborated to bring together key opinion leaders and experts in the field of neurodegenerative disease for a virtual meeting titled "Solving Neurodegeneration". This "think-tank" style meeting focused on uncovering common mechanistic roots of neurodegenerative disease and promising targets for new treatments, catalyzed by the goal of finding new treatments for glaucoma, the world's leading cause of irreversible blindness and the common interest of the three hosting foundations. Glaucoma, which causes vision loss through degeneration of the optic nerve, likely shares early cellular and molecular events with other neurodegenerative diseases of the central nervous system. Here we discuss major areas of mechanistic overlap between neurodegenerative diseases of the central nervous system: neuroinflammation, bioenergetics and metabolism, genetic contributions, and neurovascular interactions. We summarize important discussion points with emphasis on the research areas that are most innovative and promising in the treatment of neurodegeneration yet require further development. The research that is highlighted provides unique opportunities for collaboration that will lead to efforts in preventing neurodegeneration and ultimately vision loss.
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Affiliation(s)
- Lauren K Wareham
- Department of Ophthalmology and Visual Sciences, Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA
| | - Sally Temple
- Neural Stem Cell Institute, NY, 12144, Rensselaer, USA
| | - Larry I Benowitz
- Department of Neurosurgery and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adriana Di Polo
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada
| | - Cheryl Wellington
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey L Goldberg
- Spencer Center for Vision Research, Byers Eye Institute, Stanford University, CA, Palo Alto, USA
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, MA, Boston, USA
| | - Xin Duan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Albert A Davis
- Department of Neurology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering and Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California Davis, Davis, CA, USA
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, CA, 91125, Pasadena, USA
| | - M Valeria Canto-Soler
- CellSight Ocular Stem Cell and Regeneration Research Program, Department of Ophthalmology, Sue Anschutz-Rodgers Eye Center, University of Colorado, Aurora, CO, USA
| | - John G Flanagan
- Herbert Wertheim School of Optometry and Vision Science, University of California Berkeley, Berkeley, CA, USA
| | | | | | | | | | - David J Calkins
- Department of Ophthalmology and Visual Sciences, Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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68
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Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
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Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
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69
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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70
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Liu E, Karpf L, Bohl D. Neuroinflammation in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia and the Interest of Induced Pluripotent Stem Cells to Study Immune Cells Interactions With Neurons. Front Mol Neurosci 2022; 14:767041. [PMID: 34970118 PMCID: PMC8712677 DOI: 10.3389/fnmol.2021.767041] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Inflammation is a shared hallmark between amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). For long, studies were conducted on tissues of post-mortem patients and neuroinflammation was thought to be only bystander result of the disease with the immune system reacting to dying neurons. In the last two decades, thanks to improving technologies, the identification of causal genes and the development of new tools and models, the involvement of inflammation has emerged as a potential driver of the diseases and evolved as a new area of intense research. In this review, we present the current knowledge about neuroinflammation in ALS, ALS-FTD, and FTD patients and animal models and we discuss reasons of failures linked to therapeutic trials with immunomodulator drugs. Then we present the induced pluripotent stem cell (iPSC) technology and its interest as a new tool to have a better immunopathological comprehension of both diseases in a human context. The iPSC technology giving the unique opportunity to study cells across differentiation and maturation times, brings the hope to shed light on the different mechanisms linking neurodegeneration and activation of the immune system. Protocols available to differentiate iPSC into different immune cell types are presented. Finally, we discuss the interest in studying monocultures of iPS-derived immune cells, co-cultures with neurons and 3D cultures with different cell types, as more integrated cellular approaches. The hope is that the future work with human iPS-derived cells helps not only to identify disease-specific defects in the different cell types but also to decipher the synergistic effects between neurons and immune cells. These new cellular tools could help to find new therapeutic approaches for all patients with ALS, ALS-FTD, and FTD.
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Affiliation(s)
- Elise Liu
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Léa Karpf
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
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71
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Assessment of Normal Tissue Radiosensitivity by Evaluating DNA Damage and Repair Kinetics in Human Brain Organoids. Int J Mol Sci 2021; 22:ijms222413195. [PMID: 34947991 PMCID: PMC8709464 DOI: 10.3390/ijms222413195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/04/2022] Open
Abstract
DNA-double strand break (DSB), detected by immunostaining of key proteins orchestrating repair, like γH2AX and 53BP1, is well established as a surrogate for tissue radiosensitivity. We hypothesized that the generation of normal brain 3D organoids (“mini-brains”) from human induced pluripotent stem cells (hiPSC) combined with detection of DNA damage repair (DDR) may hold the promise towards developing personalized models for the determination of normal tissue radiosensitivity. In this study, cerebral organoids, an in vitro model that stands in its complexity between 2D cellular system and an organ, have been used. To quantify radiation-induced response, immunofluorescent staining with γH2AX and 53BP1 were applied at early (30 min, initial damage), and late time points (18 and 72 h, residual damage), following clinical standard 2 Gy irradiation. Based on our findings, assessment of DDR kinetics as a surrogate for radiosensitivity in hiPSC derived cerebral organoids is feasible. Further development of mini-brains recapitulating mature adult neuronal tissue and implementation of additional signaling and toxicity surrogates may pave the way towards development of next-generation personalized assessment of radiosensitivity in healthy neuronal tissue.
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72
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Kühn R, Mahajan A, Canoll P, Hargus G. Human Induced Pluripotent Stem Cell Models of Frontotemporal Dementia With Tau Pathology. Front Cell Dev Biol 2021; 9:766773. [PMID: 34858989 PMCID: PMC8631302 DOI: 10.3389/fcell.2021.766773] [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: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 12/04/2022] Open
Abstract
Neurodegenerative dementias are the most common group of neurodegenerative diseases affecting more than 40 million people worldwide. One of these diseases is frontotemporal dementia (FTD), an early onset dementia and one of the leading causes of dementia in people under the age of 60. FTD is a heterogeneous group of neurodegenerative disorders with pathological accumulation of particular proteins in neurons and glial cells including the microtubule-associated protein tau, which is deposited in its hyperphosphorylated form in about half of all patients with FTD. As for other patients with dementia, there is currently no cure for patients with FTD and thus several lines of research focus on the characterization of underlying pathogenic mechanisms with the goal to identify therapeutic targets. In this review, we provide an overview of reported disease phenotypes in induced pluripotent stem cell (iPSC)-derived neurons and glial cells from patients with tau-associated FTD with the aim to highlight recent progress in this fast-moving field of iPSC disease modeling. We put a particular focus on genetic forms of the disease that are linked to mutations in the gene encoding tau and summarize mutation-associated changes in FTD patient cells related to tau splicing and tau phosphorylation, microtubule function and cell metabolism as well as calcium homeostasis and cellular stress. In addition, we discuss challenges and limitations but also opportunities using differentiated patient-derived iPSCs for disease modeling and biomedical research on neurodegenerative diseases including FTD.
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Affiliation(s)
- Rebekka Kühn
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Gunnar Hargus
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States
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73
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Zaghi M, Banfi F, Bellini E, Sessa A. Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era. Biomolecules 2021; 11:1713. [PMID: 34827709 PMCID: PMC8616022 DOI: 10.3390/biom11111713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
The advent of next-generation sequencing (NGS) is heavily changing both the diagnosis of human conditions and basic biological research. It is now possible to dig deep inside the genome of hundreds of thousands or even millions of people and find both common and rare genomic variants and to perform detailed phenotypic characterizations of both physiological organs and experimental models. Recent years have seen the introduction of multiple techniques using NGS to profile transcription, DNA and chromatin modifications, protein binding, etc., that are now allowing us to profile cells in bulk or even at a single-cell level. Although rare and ultra-rare diseases only affect a few people, each of these diseases represent scholarly cases from which a great deal can be learned about the pathological and physiological function of genes, pathways, and mechanisms. Therefore, for rare diseases, state-of-the-art investigations using NGS have double valence: their genomic cause (new variants) and the characterize the underlining the mechanisms associated with them (discovery of gene function) can be found. In a non-exhaustive manner, this review will outline the main usage of NGS-based techniques for the diagnosis and characterization of neurodevelopmental disorders (NDDs), under whose umbrella many rare and ultra-rare diseases fall.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
- CNR Institute of Neuroscience, 20129 Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
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74
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Abstract
Greater understanding of the events preceding neurodegeneration is needed to design effective preventive and therapeutic strategies. In this issue of Cell, Bowles et al. (2021) report cerebral organoids that reveal early events in frontotemporal dementia pathogenesis due to mutations in microtubule-associated protein tau (MAPT), shedding light on a novel mechanism involving abnormal splicing and glutamate signaling.
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Affiliation(s)
- Laura Pellegrini
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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