1
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Tan Y, Yu Y, Niu H, Wang C, Mo P, Li D, Zhang Q, Feng D, Liu C. Profile of miRNA expression in the hippocampus of epileptic mice and the prediction of potential therapeutic targets. Mol Biol Rep 2024; 51:929. [PMID: 39172288 DOI: 10.1007/s11033-024-09861-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024]
Abstract
Epilepsy is a common neurological disease. Increasing evidence has highlighted the role of miRNAs in the molecular mechanisms underlying the development of neurological diseases such as epilepsy. In this study, we established a lithium chloride-pilocarpine epilepsy mouse model, performed miRNA sequencing of hippocampal tissue samples, and compared the obtained miRNA expression profile with that of normal control mice to determine differences in expression levels. We found that 55 miRNAs were differentially expressed in status epilepticus mice compared with normal control mice, with 38 upregulated and 17 downregulated miRNAs. Through subsequent analysis of the five downregulated miRNAs (mmu-let-7a-1-3p, mmu-let-7a-2-3p, mmu-let-7c-5p, mmu-let-7d-5p, and mmu-let-7e-5p) with the most significant differences in expression, the key pathways involved included the MAPK signaling pathway and focal adhesion, among others. Therefore, we believe that let-7 family miRNAs may be potential therapeutic targets for epilepsy.
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Affiliation(s)
- Yafu Tan
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yongjia Yu
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Haodong Niu
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Chunxi Wang
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Panlin Mo
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Dongqiao Li
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Qing Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Daqin Feng
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China.
- State Key Laboratory of Targeting Oncology, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Chang Liu
- Department of Neurosurgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China.
- State Key Laboratory of Targeting Oncology, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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2
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Poole RJ, Flames N, Cochella L. Neurogenesis in Caenorhabditis elegans. Genetics 2024:iyae116. [PMID: 39167071 DOI: 10.1093/genetics/iyae116] [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: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/23/2024] Open
Abstract
Animals rely on their nervous systems to process sensory inputs, integrate these with internal signals, and produce behavioral outputs. This is enabled by the highly specialized morphologies and functions of neurons. Neuronal cells share multiple structural and physiological features, but they also come in a large diversity of types or classes that give the nervous system its broad range of functions and plasticity. This diversity, first recognized over a century ago, spurred classification efforts based on morphology, function, and molecular criteria. Caenorhabditis elegans, with its precisely mapped nervous system at the anatomical level, an extensive molecular description of most of its neurons, and its genetic amenability, has been a prime model for understanding how neurons develop and diversify at a mechanistic level. Here, we review the gene regulatory mechanisms driving neurogenesis and the diversification of neuron classes and subclasses in C. elegans. We discuss our current understanding of the specification of neuronal progenitors and their differentiation in terms of the transcription factors involved and ensuing changes in gene expression and chromatin landscape. The central theme that has emerged is that the identity of a neuron is defined by modules of gene batteries that are under control of parallel yet interconnected regulatory mechanisms. We focus on how, to achieve these terminal identities, cells integrate information along their developmental lineages. Moreover, we discuss how neurons are diversified postembryonically in a time-, genetic sex-, and activity-dependent manner. Finally, we discuss how the understanding of neuronal development can provide insights into the evolution of neuronal diversity.
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Affiliation(s)
- Richard J Poole
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia 46012, Spain
| | - Luisa Cochella
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Shih M, Zou Y, Ferreira T, Suzuki N, Kim E, Chuang CF, Chang C. The kpc-1 3'UTR facilitates dendritic transport and translation efficiency of mRNAs for dendrite arborization of a mechanosensory neuron important for male courtship. PLoS Genet 2024; 20:e1011362. [PMID: 39110773 PMCID: PMC11333003 DOI: 10.1371/journal.pgen.1011362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 08/19/2024] [Accepted: 07/05/2024] [Indexed: 08/21/2024] Open
Abstract
A recently reported Schizophrenia-associated genetic variant in the 3'UTR of the human furin gene, a homolog of C. elegans kpc-1, highlights an important role of the furin 3'UTR in neuronal development. We isolate three kpc-1 mutants that display abnormal dendrite arborization in PVD neurons and defective male mating behaviors. We show that the kpc-1 3'UTR participates in dendrite branching and self-avoidance. The kpc-1 3'UTR facilitates mRNA localization to branching points and contact points between sibling dendrites and promotes translation efficiency. A predicted secondary structural motif in the kpc-1 3'UTR is required for dendrite self-avoidance. Animals with over-expression of DMA-1, a PVD dendrite receptor, exhibit similar dendrite branching and self-avoidance defects that are suppressed with kpc-1 over-expression. Our results support a model in which KPC-1 proteins are synthesized at branching points and contact points to locally down-regulate DMA-1 receptors to promote dendrite branching and self-avoidance of a mechanosensory neuron important for male courtship.
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Affiliation(s)
- Mushaine Shih
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yan Zou
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tarsis Ferreira
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Nobuko Suzuki
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Eunseo Kim
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Chiou-Fen Chuang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Chieh Chang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
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4
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Chekulaeva M. Mechanistic insights into the basis of widespread RNA localization. Nat Cell Biol 2024; 26:1037-1046. [PMID: 38956277 DOI: 10.1038/s41556-024-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/20/2024] [Indexed: 07/04/2024]
Abstract
The importance of subcellular mRNA localization is well established, but the underlying mechanisms mostly remain an enigma. Early studies suggested that specific mRNA sequences recruit RNA-binding proteins (RBPs) to regulate mRNA localization. However, despite the observation of thousands of localized mRNAs, only a handful of these sequences and RBPs have been identified. This suggests the existence of alternative, and possibly predominant, mechanisms for mRNA localization. Here I re-examine currently described mRNA localization mechanisms and explore alternative models that could account for its widespread occurrence.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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5
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Brar HK, Dey S, Singh P, Pande D, Ghosh-Roy A. Functional Recovery Associated with Dendrite Regeneration in PVD Neuron of Caenorhabditis elegans. eNeuro 2024; 11:ENEURO.0292-23.2024. [PMID: 38548333 PMCID: PMC7615967 DOI: 10.1523/eneuro.0292-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 05/02/2024] Open
Abstract
PVD neuron of Caenorhabditis elegans is a highly polarized cell with well-defined axonal, and dendritic compartments. PVD neuron operates in multiple sensory modalities including the control of both nociceptive touch sensation and body posture. Although both the axon and dendrites of this neuron show a regeneration response following laser-assisted injury, it is rather unclear how the behavior associated with this neuron is affected by the loss of these structures. It is also unclear whether neurite regrowth would lead to functional restoration in these neurons. Upon axotomy, using a femtosecond laser, we saw that harsh touch response was specifically affected leaving the body posture unperturbed. Subsequently, recovery in the touch response is highly correlated to the axon regrowth, which was dependent on DLK-1/MLK-1 MAP Kinase. Dendrotomy of both major and minor primary dendrites affected the wavelength and amplitude of sinusoidal movement without any apparent effect on harsh touch response. We further correlated the recovery in posture behavior to the type of dendrite regeneration events. We found that dendrite regeneration through the fusion and reconnection between the proximal and distal branches of the injured dendrite corresponded to improved recovery in posture. Our data revealed that the axons and dendrites of PVD neurons regulate the nociception and proprioception in worms, respectively. It also revealed that dendrite and axon regeneration lead to the restoration of these differential sensory modalities.
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Affiliation(s)
- Harjot Kaur Brar
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar 122052, Haryana, India
| | - Swagata Dey
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar 122052, Haryana, India
| | - Pallavi Singh
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar 122052, Haryana, India
| | - Devashish Pande
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar 122052, Haryana, India
| | - Anindya Ghosh-Roy
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar 122052, Haryana, India
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6
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Duan Y, Li L, Panzade GP, Piton A, Zinovyeva A, Ambros V. Modeling neurodevelopmental disorder-associated human AGO1 mutations in Caenorhabditis elegans Argonaute alg-1. Proc Natl Acad Sci U S A 2024; 121:e2308255121. [PMID: 38412125 DOI: 10.1073/pnas.2308255121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/30/2023] [Indexed: 02/29/2024] Open
Abstract
MicroRNAs (miRNA) associate with Argonaute (AGO) proteins and repress gene expression by base pairing to sequences in the 3' untranslated regions of target genes. De novo coding variants in the human AGO genes AGO1 and AGO2 cause neurodevelopmental disorders (NDD) with intellectual disability, referred to as Argonaute syndromes. Most of the altered amino acids are conserved between the miRNA-associated AGO in Homo sapiens and Caenorhabditis elegans, suggesting that the human mutations could disrupt conserved functions in miRNA biogenesis or activity. We genetically modeled four human AGO1 mutations in C. elegans by introducing identical mutations into the C. elegans AGO1 homologous gene, alg-1. These alg-1 NDD mutations cause phenotypes in C. elegans indicative of disrupted miRNA processing, miRISC (miRNA silencing complex) formation, and/or target repression. We show that the alg-1 NDD mutations are antimorphic, causing developmental and molecular phenotypes stronger than those of alg-1 null mutants, likely by sequestrating functional miRISC components into non-functional complexes. The alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles, accompanied by perturbation of downstream gene expression, including altered translational efficiency and/or messenger RNA abundance. The perturbed genes include those with human orthologs whose dysfunction is associated with NDD. These cross-clade genetic studies illuminate fundamental AGO functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Ye Duan
- Program of Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Li Li
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | | | - Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch 67 400, France
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | - Victor Ambros
- Program of Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605
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7
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Wang S, Li S. Lin28 as a therapeutic target for central nervous system regeneration and repair. Neural Regen Res 2024; 19:397-398. [PMID: 37488899 PMCID: PMC10503609 DOI: 10.4103/1673-5374.375322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 04/11/2023] [Indexed: 07/26/2023] Open
Affiliation(s)
- Shuo Wang
- Shriners Hospitals Pediatric Research Center, Department of Neural Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Shuxin Li
- Shriners Hospitals Pediatric Research Center, Department of Neural Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
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8
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Subramanian M, Mills WT, Paranjpe MD, Onuchukwu US, Inamdar M, Maytin AR, Li X, Pomerantz JL, Meffert MK. Growth-suppressor microRNAs mediate synaptic overgrowth and behavioral deficits in Fragile X mental retardation protein deficiency. iScience 2024; 27:108676. [PMID: 38235335 PMCID: PMC10792201 DOI: 10.1016/j.isci.2023.108676] [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: 06/30/2023] [Revised: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
Abnormal neuronal and synapse growth is a core pathology resulting from deficiency of the Fragile X mental retardation protein (FMRP), but molecular links underlying the excessive synthesis of key synaptic proteins remain incompletely defined. We find that basal brain levels of the growth suppressor let-7 microRNA (miRNA) family are selectively lowered in FMRP-deficient mice and activity-dependent let-7 downregulation is abrogated. Primary let-7 miRNA transcripts are not altered in FMRP-deficiency and posttranscriptional misregulation occurs downstream of MAPK pathway induction and elevation of Lin28a, a let-7 biogenesis inhibitor. Neonatal restoration of brain let-7 miRNAs corrects hallmarks of FMRP-deficiency, including dendritic spine overgrowth and social and cognitive behavioral deficits, in adult mice. Blockade of MAPK hyperactivation normalizes let-7 miRNA levels in both brain and peripheral blood plasma from Fmr1 KO mice. These results implicate dysregulated let-7 miRNA biogenesis in the pathogenesis of FMRP-deficiency, and highlight let-7 miRNA-based strategies for future biomarker and therapeutic development.
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Affiliation(s)
- Megha Subramanian
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William T. Mills
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manish D. Paranjpe
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Uche S. Onuchukwu
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manasi Inamdar
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amanda R. Maytin
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinbei Li
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joel L. Pomerantz
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mollie K. Meffert
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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9
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Li X, Morgan C, Nadar‐Ponniah PT, Kolanus W, Doetzlhofer A. TRIM71 reactivation enhances the mitotic and hair cell-forming potential of cochlear supporting cells. EMBO Rep 2023; 24:e56562. [PMID: 37492931 PMCID: PMC10481673 DOI: 10.15252/embr.202256562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
Cochlear hair cell loss is a leading cause of deafness in humans. Neighboring supporting cells have some capacity to regenerate hair cells. However, their regenerative potential sharply declines as supporting cells undergo maturation (postnatal day 5 in mice). We recently reported that reactivation of the RNA-binding protein LIN28B restores the hair cell-regenerative potential of P5 cochlear supporting cells. Here, we identify the LIN28B target Trim71 as a novel and equally potent enhancer of supporting cell plasticity. TRIM71 is a critical regulator of stem cell behavior and cell reprogramming; however, its role in cell regeneration is poorly understood. Employing an organoid-based assay, we show that TRIM71 re-expression increases the mitotic and hair cell-forming potential of P5 cochlear supporting cells by facilitating their de-differentiation into progenitor-like cells. Our mechanistic work indicates that TRIM71's RNA-binding activity is essential for such ability, and our transcriptomic analysis identifies gene modules that are linked to TRIM71 and LIN28B-mediated supporting cell reprogramming. Furthermore, our study uncovers that the TRIM71-LIN28B target Hmga2 is essential for supporting cell self-renewal and hair cell formation.
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Affiliation(s)
- Xiao‐Jun Li
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Present address:
Frontier Institute of Science and TechnologyXi'an Jiaotong UniversityXi'an710054China
| | - Charles Morgan
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Prathamesh T Nadar‐Ponniah
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES)University of BonnBonnGermany
| | - Angelika Doetzlhofer
- The Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of Otolaryngology and Center for Hearing and BalanceJohns Hopkins University School of MedicineBaltimoreMDUSA
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10
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Sun H, Hobert O. Temporal transitions in the postembryonic nervous system of the nematode Caenorhabditis elegans: Recent insights and open questions. Semin Cell Dev Biol 2023; 142:67-80. [PMID: 35688774 DOI: 10.1016/j.semcdb.2022.05.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
After the generation, differentiation and integration into functional circuitry, post-mitotic neurons continue to change certain phenotypic properties throughout postnatal juvenile stages until an animal has reached a fully mature state in adulthood. We will discuss such changes in the context of the nervous system of the nematode C. elegans, focusing on recent descriptions of anatomical and molecular changes that accompany postembryonic maturation of neurons. We summarize the characterization of genetic timer mechanisms that control these temporal transitions or maturational changes, and discuss that many but not all of these transitions relate to sexual maturation of the animal. We describe how temporal, spatial and sex-determination pathways are intertwined to sculpt the emergence of cell-type specific maturation events. Finally, we lay out several unresolved questions that should be addressed to move the field forward, both in C. elegans and in vertebrates.
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Affiliation(s)
- Haosheng Sun
- Department of Cell, Developmental, and Integrative Biology. University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, USA
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11
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Duan Y, Li L, Panzade GP, Piton A, Zinovyeva A, Ambros V. Modeling neurodevelopmental disorder-associated hAGO1 mutations in C. elegans Argonaute ALG-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535748. [PMID: 37066388 PMCID: PMC10104039 DOI: 10.1101/2023.04.06.535748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
MicroRNAs (miRNA) are endogenous non-coding RNAs important for post-transcriptional regulation of gene expression. miRNAs associate with Argonaute proteins to bind to the 3' UTR of target genes and confer target repression. Recently, multiple de novo coding variants in the human Argonaute gene AGO1 ( hAGO1 ) have been reported to cause a neurodevelopmental disorder (NDD) with intellectual disability (ID). Most of the altered amino acids are conserved between the miRNA-associated Argonautes in H. sapiens and C. elegans , suggesting the hAGO1 mutations could disrupt evolutionarily conserved functions in the miRNA pathway. To investigate how the hAGO1 mutations may affect miRNA biogenesis and/or functions, we genetically modeled four of the hAGO1 de novo variants (referred to as NDD mutations) by introducing the identical mutations to the C. elegans hAGO1 homolog, alg-1 . This array of mutations caused distinct effects on C. elegans miRNA functions, miRNA populations, and downstream gene expression, indicative of profound alterations in aspects of miRNA processing and miRISC formation and/or activity. Specifically, we found that the alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles both in terms of overall abundances and association with mutant ALG-1. We also observed allele-specific profiles of gene expression with altered translational efficiency and/or mRNA abundance. The sets of perturbed genes include human homologs whose dysfunction is known to cause NDD. We anticipate that these cross-clade genetic studies may advance the understanding of fundamental Argonaute functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.
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12
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Liu X, Zhao Y, Zou W. Molecular mechanisms of neurite regeneration and repair: insights from C. elegans and Drosophila. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:12. [PMID: 37005942 PMCID: PMC10067779 DOI: 10.1186/s13619-022-00155-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/01/2022] [Indexed: 04/04/2023]
Abstract
The difficulties of injured and degenerated neurons to regenerate neurites and regain functions are more significant than in other body tissues, making neurodegenerative and related diseases hard to cure. Uncovering the secrets of neural regeneration and how this process may be inhibited after injury will provide insights into novel management and potential treatments for these diseases. Caenorhabditis elegans and Drosophila melanogaster are two of the most widely used and well-established model organisms endowed with advantages in genetic manipulation and live imaging to explore this fundamental question about neural regeneration. Here, we review the classical models and techniques, and the involvement and cooperation of subcellular structures during neurite regeneration using these two organisms. Finally, we list several important open questions that we look forward to inspiring future research.
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Affiliation(s)
- Xiaofan Liu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Yuqing Zhao
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
- Institute of Zhejiang University and University of Edinburgh, Jiaxing, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China.
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China.
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13
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Zhao P, Mondal S, Martin C, DuPlissis A, Chizari S, Ma KY, Maiya R, Messing RO, Jiang N, Ben-Yakar A. Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing. Nat Methods 2023; 20:590-599. [PMID: 36928074 DOI: 10.1038/s41592-023-01804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/26/2023] [Indexed: 03/18/2023]
Abstract
Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single-neuron resolution in model organisms such as Caenorhabditis elegans. Existing cell isolation techniques cannot isolate neurons with specific regeneration phenotypes from C. elegans. We present femtosecond laser microdissection (fs-LM), a single-cell isolation method that dissects specific cells directly from living tissue by leveraging the micrometer-scale precision of fs-laser ablation. We show that fs-LM facilitates sensitive and specific gene expression profiling by single-cell RNA sequencing (scRNA-seq), while mitigating the stress-related transcriptional artifacts induced by tissue dissociation. scRNA-seq of fs-LM isolated regenerating neurons revealed transcriptional programs that are correlated with either successful or failed regeneration in wild-type and dlk-1 (0) animals, respectively. This method also allowed studying heterogeneity displayed by the same type of neuron and found gene modules with expression patterns correlated with axon regrowth rate. Our results establish fs-LM as a spatially resolved single-cell isolation method for phenotype-to-genotype mapping.
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Affiliation(s)
- Peisen Zhao
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Sudip Mondal
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chris Martin
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Andrew DuPlissis
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Shahab Chizari
- Deparment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Ke-Yue Ma
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Rajani Maiya
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Institute of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Department of Physiology, LSU Health Sciences Center, New Orleans, LA, USA
| | - Robert O Messing
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Institute of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Ning Jiang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Deparment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Adela Ben-Yakar
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute of Neuroscience, The University of Texas at Austin, Austin, TX, USA.
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14
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Massively parallel identification of mRNA localization elements in primary cortical neurons. Nat Neurosci 2023; 26:394-405. [PMID: 36646877 PMCID: PMC9991926 DOI: 10.1038/s41593-022-01243-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/01/2022] [Indexed: 01/18/2023]
Abstract
Cells adopt highly polarized shapes and form distinct subcellular compartments in many cases due to the localization of many mRNAs to specific areas, where they are translated into proteins with local functions. This mRNA localization is mediated by specific cis-regulatory elements in mRNAs, commonly called 'zipcodes'. Although there are hundreds of localized mRNAs, only a few zipcodes have been characterized. Here we describe a novel neuronal zipcode identification protocol (N-zip) that can identify zipcodes across hundreds of 3' untranslated regions. This approach combines a method of separating the principal subcellular compartments of neurons-cell bodies and neurites-with a massively parallel reporter assay. N-zip identifies the let-7 binding site and (AU)n motif as de novo zipcodes in mouse primary cortical neurons. Our analysis also provides, to our knowledge, the first demonstration of an miRNA affecting mRNA localization and suggests a strategy for detecting many more zipcodes.
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15
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Li XJ, Morgan C, Nadar-Ponniah PT, Kolanus W, Doetzlhofer A. Reactivation of the progenitor gene Trim71 enhances the mitotic and hair cell-forming potential of cochlear supporting cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523802. [PMID: 36711735 PMCID: PMC9882147 DOI: 10.1101/2023.01.12.523802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cochlear hair cell loss is a leading cause of deafness in humans. Neighboring supporting cells have some capacity to regenerate hair cells. However, their regenerative potential sharply declines as supporting cells undergo maturation (postnatal day 5 in mice). We recently reported that reactivation of the RNA-binding protein LIN28B restores the hair cell-regenerative potential of P5 cochlear supporting cells. Here, we identify the LIN28B target Trim71 as a novel and equally potent enhancer of supporting cell plasticity. TRIM71 is a critical regulator of stem cell behavior and cell reprogramming, however, its role in cell regeneration is poorly understood. Employing an organoid-based assay, we show that TRIM71 reactivation increases the mitotic and hair cell-forming potential of P5 cochlear supporting cells by facilitating their de-differentiation into progenitor-like cells. Our mechanistic work indicates that TRIM71’s RNA-binding activity is essential for such ability, and our transcriptomic analysis identifies gene modules that are linked to TRIM71 and LIN28B-mediated supporting cell reprogramming. Furthermore, our study uncovers that the TRIM71-LIN28B target Hmga2 is essential for supporting cell self-renewal and hair cell formation.
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16
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Li X, Jin DS, Eadara S, Caterina MJ, Meffert MK. Regulation by noncoding RNAs of local translation, injury responses, and pain in the peripheral nervous system. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2023; 13:100119. [PMID: 36798094 PMCID: PMC9926024 DOI: 10.1016/j.ynpai.2023.100119] [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: 12/12/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Neuropathic pain is a chronic condition arising from damage to somatosensory pathways that results in pathological hypersensitivity. Persistent pain can be viewed as a consequence of maladaptive plasticity which, like most enduring forms of cellular plasticity, requires altered expression of specific gene programs. Control of gene expression at the level of protein synthesis is broadly utilized to directly modulate changes in activity and responsiveness in nociceptive pathways and provides an effective mechanism for compartmentalized regulation of the proteome in peripheral nerves through local translation. Levels of noncoding RNAs (ncRNAs) are commonly impacted by peripheral nerve injury leading to persistent pain. NcRNAs exert spatiotemporal regulation of local proteomes and affect signaling cascades supporting altered sensory responses that contribute to hyperalgesia. This review discusses ncRNAs found in the peripheral nervous system (PNS) that are dysregulated following nerve injury and the current understanding of their roles in pathophysiological pain-related responses including neuroimmune interactions, neuronal survival and axon regeneration, Schwann cell dedifferentiation and proliferation, intercellular communication, and the generation of ectopic action potentials in primary afferents. We review progress in the field beyond cataloging, with a focus on the relevant target transcripts and mechanisms underlying pain modulation by ncRNAs.
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Affiliation(s)
- Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
| | - Daniel S. Jin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
| | - Sreenivas Eadara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
| | - Michael J. Caterina
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
- Department of Neurosurgery and Neurosurgery Pain Research Institute, Johns Hopkins University School of Medicine, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, United States
| | - Mollie K. Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, United States
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17
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Wang SY, Xu Y, Hong Q, Chen XM, Cai GY. Mesenchymal stem cells ameliorate cisplatin-induced acute kidney injury via let-7b-5p. Cell Tissue Res 2022; 392:517-533. [PMID: 36543894 DOI: 10.1007/s00441-022-03729-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
Acute kidney injury (AKI) is a clinically common kidney disease. Age is an important factor that contributes to the susceptibility to AKI. Mesenchymal stem cells (MSCs) are a promising therapy for AKI, and miRNAs in exosomes (Exos) derived from MSCs are an important aspect of MSC treatment. However, the therapeutic effect of miRNA from MSC-derived Exos on AKI and the related mechanism have not been fully clarified. Whether there is a relationship between the mechanisms of senescence for AKI susceptibility and the therapeutic effect of MSCs has not been studied. We compared the degree of cisplatin-induced AKI injury in young and elderly mice and investigated changes in the expression of p53 and markers of DNA damage and apoptosis, which are important in both senescence and AKI. Ageing mice exhibited increased expression of p53 and pro-apoptosis markers. Upregulation of the senescence-associated DNA damage/p53 pathway may be an important susceptibility factor for cisplatin-induced AKI. Treatment with MSCs can reduce the degree of DNA damage and suppress p53 expression and apoptosis. Upon screening for differentially expressed miRNAs, let-7b-5p levels were found to be lower in aged mice than in young mice, and MSC treatment increased let-7b-5p levels. The presence of let-7b-5p in MSC-derived Exos alleviates tubular epithelial cell apoptosis by inhibiting p53, which reduces DNA damage and apoptosis pathway activity. Let-7b-5p downregulation may lead to increased renal AKI susceptibility, thus indicating that this miRNA is a potential driver of the MSC treatment response in AKI.
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18
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Intrinsic heterogeneity in axon regeneration. Biochem Soc Trans 2022; 50:1753-1762. [DOI: 10.1042/bst20220624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
The nervous system is composed of a variety of neurons and glial cells with different morphology and functions. In the mammalian peripheral nervous system (PNS) or the lower vertebrate central nervous system (CNS), most neurons can regenerate extensively after axotomy, while the neurons in the mammalian CNS possess only limited regenerative ability. This heterogeneity is common within and across species. The studies about the transcriptomes after nerve injury in different animal models have revealed a series of molecular and cellular events that occurred in neurons after axotomy. However, responses of various types of neurons located in different positions of individuals were different remarkably. Thus, researchers aim to find the key factors that are conducive to regeneration, so as to provide the molecular basis for solving the regeneration difficulties after CNS injury. Here we review the heterogeneity of axonal regeneration among different cell subtypes in different animal models or the same organ, emphasizing the importance of comparative studies within and across species.
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19
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Costa G, Ribeiro FF, Sebastião AM, Muir EM, Vaz SH. Bridging the gap of axonal regeneration in the central nervous system: A state of the art review on central axonal regeneration. Front Neurosci 2022; 16:1003145. [PMID: 36440273 PMCID: PMC9682039 DOI: 10.3389/fnins.2022.1003145] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/19/2022] [Indexed: 08/26/2023] Open
Abstract
Neuronal regeneration in the central nervous system (CNS) is an important field of research with relevance to all types of neuronal injuries, including neurodegenerative diseases. The glial scar is a result of the astrocyte response to CNS injury. It is made up of many components creating a complex environment in which astrocytes play various key roles. The glial scar is heterogeneous, diverse and its composition depends upon the injury type and location. The heterogeneity of the glial scar observed in different situations of CNS damage and the consequent implications for axon regeneration have not been reviewed in depth. The gap in this knowledge will be addressed in this review which will also focus on our current understanding of central axonal regeneration and the molecular mechanisms involved. The multifactorial context of CNS regeneration is discussed, and we review newly identified roles for components previously thought to solely play an inhibitory role in central regeneration: astrocytes and p75NTR and discuss their potential and relevance for deciding therapeutic interventions. The article ends with a comprehensive review of promising new therapeutic targets identified for axonal regeneration in CNS and a discussion of novel ways of looking at therapeutic interventions for several brain diseases and injuries.
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Affiliation(s)
- Gonçalo Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Filipa F. Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana M. Sebastião
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Elizabeth M. Muir
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Sandra H. Vaz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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20
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Suzuki N, Zou Y, Sun H, Eichel K, Shao M, Shih M, Shen K, Chang C. Two intrinsic timing mechanisms set start and end times for dendritic arborization of a nociceptive neuron. Proc Natl Acad Sci U S A 2022; 119:e2210053119. [PMID: 36322763 PMCID: PMC9659368 DOI: 10.1073/pnas.2210053119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
Choreographic dendritic arborization takes place within a defined time frame, but the timing mechanism is currently not known. Here, we report that the precisely timed lin-4-lin-14 regulatory circuit triggers an initial dendritic growth activity, whereas the precisely timed lin-28-let-7-lin-41 regulatory circuit signals a subsequent developmental decline in dendritic growth ability, hence restricting dendritic arborization within a set time frame. Loss-of-function mutations in the lin-4 microRNA gene cause limited dendritic outgrowth, whereas loss-of-function mutations in its direct target, the lin-14 transcription factor gene, cause precocious and excessive outgrowth. In contrast, loss-of-function mutations in the let-7 microRNA gene prevent a developmental decline in dendritic growth ability, whereas loss-of-function mutations in its direct target, the lin-41 tripartite motif protein gene, cause further decline. lin-4 and let-7 regulatory circuits are expressed in the right place at the right time to set start and end times for dendritic arborization. Replacing the lin-4 upstream cis-regulatory sequence at the lin-4 locus with a late-onset let-7 upstream cis-regulatory sequence delays dendrite arborization, whereas replacing the let-7 upstream cis-regulatory sequence at the let-7 locus with an early-onset lin-4 upstream cis-regulatory sequence causes a precocious decline in dendritic growth ability. Our results indicate that the lin-4-lin-14 and the lin-28-let-7-lin-41 regulatory circuits control the timing of dendrite arborization through antagonistic regulation of the DMA-1 receptor level on dendrites. The LIN-14 transcription factor likely directly represses dma-1 gene expression through a transcriptional means, whereas the LIN-41 tripartite motif protein likely indirectly promotes dma-1 gene expression through a posttranscriptional means.
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Affiliation(s)
- Nobuko Suzuki
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Yan Zou
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - HaoSheng Sun
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Kelsie Eichel
- HHMI, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Meiyu Shao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mushaine Shih
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Kang Shen
- HHMI, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Chieh Chang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
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21
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Wang Y, Zhao J, Chen S, Li D, Yang J, Zhao X, Qin M, Guo M, Chen C, He Z, Zhou Y, Xu L. Let-7 as a Promising Target in Aging and Aging-Related Diseases: A Promise or a Pledge. Biomolecules 2022; 12:biom12081070. [PMID: 36008964 PMCID: PMC9406090 DOI: 10.3390/biom12081070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
The abnormal regulation and expression of microRNA (miRNA) are closely related to the aging process and the occurrence and development of aging-related diseases. Lethal-7 (let-7) was discovered in Caenorhabditis elegans (C. elegans) and plays an important role in development by regulating cell fate regulators. Accumulating evidence has shown that let-7 is elevated in aging tissues and participates in multiple pathways that regulate the aging process, including affecting tissue stem cell function, body metabolism, and various aging-related diseases (ARDs). Moreover, recent studies have found that let-7 plays an important role in the senescence of B cells, suggesting that let-7 may also participate in the aging process by regulating immune function. Therefore, these studies show the diversity and complexity of let-7 expression and regulatory functions during aging. In this review, we provide a detailed overview of let-7 expression regulation as well as its role in different tissue aging and aging-related diseases, which may provide new ideas for enriching the complex expression regulation mechanism and pathobiological function of let-7 in aging and related diseases and ultimately provide help for the development of new therapeutic strategies.
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Affiliation(s)
- Ya Wang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Shipeng Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Dongmei Li
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Jing Yang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Xu Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Ming Qin
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Zhixu He
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi 563000, China;
| | - Ya Zhou
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Medical Physics, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (L.X.)
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (L.X.)
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22
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Reprogramming neurons for regeneration: The fountain of youth. Prog Neurobiol 2022; 214:102284. [PMID: 35533809 DOI: 10.1016/j.pneurobio.2022.102284] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/03/2022] [Accepted: 05/02/2022] [Indexed: 01/22/2023]
Abstract
Neurons in the central nervous system (CNS) are terminally differentiated cells that gradually lose their ability to support regeneration during maturation due to changes in transcriptomic and chromatin landscape. Similar transcriptomic changes also occur during development when stem cells differentiate into different types of somatic cells. Importantly, differentiated cells can be reprogrammed back to induced pluripotent stems cells (iPSCs) via global epigenetic remodeling by combined overexpression of pluripotent reprogramming factors, including Oct4, Sox2, Klf4, c-Myc, Nanog, and/or Lin28. Moreover, recent findings showed that many proneural transcription factors were able to convert non-neural somatic cells into neurons bypassing the pluripotent stage via direct reprogramming. Interestingly, many of these factors have recently been identified as key regulators of CNS neural regeneration. Recent studies indicated that these factors could rejuvenate mature CNS neurons back to a younger state through cellular state reprogramming, thus favoring regeneration. Here we will review some recent findings regarding the roles of genetic cellular state reprogramming in regulation of neural regeneration and explore the potential underlying molecular mechanisms. Moreover, by using newly emerging techniques, such as multiomics sequencing with big data analysis and Crispr-based gene editing, we will discuss future research directions focusing on better revealing cellular state reprogramming-induced remodeling of chromatin landscape and potential translational application.
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23
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Brar HK, Dey S, Bhardwaj S, Pande D, Singh P, Dey S, Ghosh-Roy A. Dendrite regeneration in C. elegans is controlled by the RAC GTPase CED-10 and the RhoGEF TIAM-1. PLoS Genet 2022; 18:e1010127. [PMID: 35344539 PMCID: PMC8989329 DOI: 10.1371/journal.pgen.1010127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 04/07/2022] [Accepted: 02/28/2022] [Indexed: 01/30/2023] Open
Abstract
Neurons are vulnerable to physical insults, which compromise the integrity of both dendrites and axons. Although several molecular pathways of axon regeneration are identified, our knowledge of dendrite regeneration is limited. To understand the mechanisms of dendrite regeneration, we used the PVD neurons in C. elegans with stereotyped branched dendrites. Using femtosecond laser, we severed the primary dendrites and axon of this neuron. After severing the primary dendrites near the cell body, we observed sprouting of new branches from the proximal site within 6 hours, which regrew further with time in an unstereotyped manner. This was accompanied by reconnection between the proximal and distal dendrites, and fusion among the higher-order branches as reported before. We quantified the regeneration pattern into three aspects–territory length, number of branches, and fusion phenomena. Axonal injury causes a retraction of the severed end followed by a Dual leucine zipper kinase-1 (DLK-1) dependent regrowth from the severed end. We tested the roles of the major axon regeneration signalling hubs such as DLK-1-RPM-1, cAMP elevation, let-7 miRNA, AKT-1, Phosphatidylserine (PS) exposure/PS in dendrite regeneration. We found that neither dendrite regrowth nor fusion was affected by the axon injury pathway molecules. Surprisingly, we found that the RAC GTPase, CED-10 and its upstream GEF, TIAM-1 play a cell-autonomous role in dendrite regeneration. Additionally, the function of CED-10 in epidermal cell is critical for post-dendrotomy fusion phenomena. This work describes a novel regulatory mechanism of dendrite regeneration and provides a framework for understanding the cellular mechanism of dendrite regeneration using PVD neuron as a model system. The knowledge of the repair of injured neural circuits comes from the study of the regeneration of injured axons. The information receiving neurites, namely dendrites, are also vulnerable to physical insult during stroke and trauma. However, little knowledge is available on the mechanism of dendrite regeneration since the study of Cajal. In order to get insight into this process, we severed both axon and dendrites of PVD neuron in C. elegans using laser. By comparing the roles of axon regeneration pathways in both dendrite and axon regeneration in this neuron, we found that dendrite regeneration is independent of molecular mechanisms involving axon regrowth. We discovered that dendrite regeneration is dependent on the RAC GTPase CED-10 and GEF TIAM-1. Moreover, we found that CED-10 plays roles within both neuron and in the surrounding epithelia for mounting regeneration response to dendrite injury. This work provides mechanistic insight into the process of dendrite repair after physical injury.
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Affiliation(s)
- Harjot Kaur Brar
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Haryana, India
| | - Swagata Dey
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Haryana, India
| | - Smriti Bhardwaj
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Haryana, India
| | - Devashish Pande
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Haryana, India
| | - Pallavi Singh
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Haryana, India
| | - Shirshendu Dey
- Fluorescence Microscopy Division, Bruker India Scientific Pvt. Ltd., International Trade Tower, Nehru Place, New Delhi, India
| | - Anindya Ghosh-Roy
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Haryana, India
- * E-mail:
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24
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Panzade G, Li L, Hebbar S, Veksler-Lublinsky I, Zinovyeva A. Global profiling and annotation of templated isomiRs dynamics across Caenorhabditis elegans development. RNA Biol 2022; 19:928-942. [PMID: 35848953 PMCID: PMC9298154 DOI: 10.1080/15476286.2022.2099646] [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] [Indexed: 11/11/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through translational repression and mRNA destabilization. During canonical miRNA biogenesis, several miRNA isoforms, or isomiRs, are produced from a single precursor miRNA. Templated isomiRs are generated through Drosha or Dicer cleavage at alternate positions on either the primary or the precursor miRNAs, generating truncated or extended 5’ and/or 3’ miRNA ends. As changes to the mature miRNA sequence can alter miRNA gene target repertoire, we investigated the extent of templated isomiR prevalence, providing a profiling map for templated isomiRs across stages of C. elegans development. While most miRNA loci did not produce abundant templated isomiRs, a substantial number of miRNA loci produced isomiRs were just as, or more, abundant than their annotated canonical mature miRNAs. 3’ end miRNA alterations were more frequent than the seed-altering 5’ end extensions or truncations. However, we identified several miRNA loci that produced a considerable amount of isomiRs with 5’ end alterations, predicted to target new, distinct sets of genes. Overall, the presented annotation of templated isomiR dynamics across C. elegans developmental stages provides a basis for further studies into miRNA biogenesis and the intriguing potential of functional miRNA diversification through isomiR production.
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Affiliation(s)
- Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Li Li
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-sheva, Israel
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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25
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Kulkarni SS, Sabharwal V, Sheoran S, Basu A, Matsumoto K, Hisamoto N, Ghosh-Roy A, Koushika SP. UNC-16 alters DLK-1 localization and negatively regulates actin and microtubule dynamics in Caenorhabditis elegans regenerating neurons. Genetics 2021; 219:6359182. [PMID: 34740241 DOI: 10.1093/genetics/iyab139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Neuronal regeneration after injury depends on the intrinsic growth potential of neurons. Our study shows that UNC-16, a Caenorhabditis elegans JIP3 homolog, inhibits axonal regeneration by regulating initiation and rate of regrowth. This occurs through the inhibition of the regeneration-promoting activity of the long isoform of DLK-1 and independently of the inhibitory short isoform of DLK-1. We show that UNC-16 promotes DLK-1 punctate localization in a concentration-dependent manner limiting the availability of the long isoform of DLK-1 at the cut site, minutes after injury. UNC-16 negatively regulates actin dynamics through DLK-1 and microtubule dynamics partially via DLK-1. We show that post-injury cytoskeletal dynamics in unc-16 mutants are also partially dependent on CEBP-1. The faster regeneration seen in unc-16 mutants does not lead to functional recovery. Our data suggest that the inhibitory control by UNC-16 and the short isoform of DLK-1 balances the intrinsic growth-promoting function of the long isoform of DLK-1 in vivo. We propose a model where UNC-16's inhibitory role in regeneration occurs through both a tight temporal and spatial control of DLK-1 and cytoskeletal dynamics.
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Affiliation(s)
- Sucheta S Kulkarni
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Vidur Sabharwal
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Seema Sheoran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Atrayee Basu
- Department of Biotechnology National Brain Research Centre, Manesar 122052, India
| | - Kunihiro Matsumoto
- Department of Molecular Biology, Nagoya University, Nagoya 4648601, Japan
| | - Naoki Hisamoto
- Department of Molecular Biology, Nagoya University, Nagoya 4648601, Japan
| | - Anindya Ghosh-Roy
- Department of Biotechnology National Brain Research Centre, Manesar 122052, India
| | - Sandhya P Koushika
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
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Shih M, Chang C. Brain-wide identification of LIN-41 (TRIM71) protein-expressing neurons by NeuroPAL. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000472. [PMID: 35622497 PMCID: PMC9015712 DOI: 10.17912/micropub.biology.000472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/10/2022]
Abstract
LIN-41 (TRIM71), an ancient protein best known for its role in timing mitotic stem cell lineages, has been recently shown to be involved in postmitotic neurons to time their differentiation and post-differentiation. Here, we report the identification of 276 LIN-41 protein-expressing neurons in the C. elegans nervous system by NeuroPAL and a CRISPR-engineered mNG::LIN-41 reporter, which represents 91% of all hermaphrodite neurons and includes 87 neurons that were not previously reported by CeNGEN using single-cell RNA-seq. Broad lin-41 protein expression in C. elegans neurons suggests a widespread role of LIN-41 (TRIM71) in timing neuronal assembly, plasticity, and maintenance.
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Affiliation(s)
- Mushaine Shih
- Department of Biological Sciences, University of Illinois at Chicago
| | - Chieh Chang
- Department of Biological Sciences, University of Illinois at Chicago
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27
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Basu A, Behera S, Bhardwaj S, Dey S, Ghosh-Roy A. Regulation of UNC-40/DCC and UNC-6/Netrin by DAF-16 promotes functional rewiring of the injured axon. Development 2021; 148:268990. [PMID: 34109380 DOI: 10.1242/dev.198044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/04/2021] [Indexed: 01/02/2023]
Abstract
The adult nervous system has a limited capacity to regenerate after accidental damage. Post-injury functional restoration requires proper targeting of the injured axon to its postsynaptic cell. Although the initial response to axonal injury has been studied in great detail, it is rather unclear what controls the re-establishment of a functional connection. Using the posterior lateral microtubule neuron in Caenorhabditis elegans, we found that after axotomy, the regrowth from the proximal stump towards the ventral side and accumulation of presynaptic machinery along the ventral nerve cord correlated to the functional recovery. We found that the loss of insulin receptor DAF-2 promoted 'ventral targeting' in a DAF-16-dependent manner. We further showed that coordinated activities of DAF-16 in neuron and muscle promoted 'ventral targeting'. In response to axotomy, expression of the Netrin receptor UNC-40 was upregulated in the injured neuron in a DAF-16-dependent manner. In contrast, the DAF-2-DAF-16 axis contributed to the age-related decline in Netrin expression in muscle. Therefore, our study revealed an important role for insulin signaling in regulating the axon guidance molecules during the functional rewiring process.
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Affiliation(s)
- Atrayee Basu
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Nainwal Mode, Gurgaon, Haryana 122051, India
| | - Sibaram Behera
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Nainwal Mode, Gurgaon, Haryana 122051, India
| | - Smriti Bhardwaj
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Nainwal Mode, Gurgaon, Haryana 122051, India
| | - Shirshendu Dey
- Fluorescence Microscopy Division, Bruker India Scientific PvT Ltd, International Trade Tower, Nehru Place, New Delhi 110019, India
| | - Anindya Ghosh-Roy
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Nainwal Mode, Gurgaon, Haryana 122051, India
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28
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van Erp S, van Berkel AA, Feenstra EM, Sahoo PK, Wagstaff LJ, Twiss JL, Fawcett JW, Eva R, Ffrench-Constant C. Age-related loss of axonal regeneration is reflected by the level of local translation. Exp Neurol 2021; 339:113594. [PMID: 33450233 PMCID: PMC8024785 DOI: 10.1016/j.expneurol.2020.113594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/07/2020] [Accepted: 12/17/2020] [Indexed: 01/08/2023]
Abstract
Regeneration capacity is reduced as CNS axons mature. Using laser-mediated axotomy, proteomics and puromycin-based tagging of newly-synthesized proteins in a human embryonic stem cell-derived neuron culture system that allows isolation of axons from cell bodies, we show here that efficient regeneration in younger axons (d45 in culture) is associated with local axonal protein synthesis (local translation). Enhanced regeneration, promoted by co-culture with human glial precursor cells, is associated with increased axonal synthesis of proteins, including those constituting the translation machinery itself. Reduced regeneration, as occurs with the maturation of these axons by d65 in culture, correlates with reduced levels of axonal proteins involved in translation and an inability to respond by increased translation of regeneration promoting axonal mRNAs released from stress granules. Together, our results provide evidence that, as in development and in the PNS, local translation contributes to CNS axon regeneration.
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Affiliation(s)
- Susan van Erp
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK.
| | - Annemiek A van Berkel
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands
| | - Eline M Feenstra
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
| | - Pabitra K Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia 29208, SC, USA
| | - Laura J Wagstaff
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
| | - Jeffery L Twiss
- Department of Biological Sciences, University of South Carolina, Columbia 29208, SC, USA
| | - James W Fawcett
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Centre for Reconstructive Neuroscience, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Richard Eva
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Charles Ffrench-Constant
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
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Shimizu T, Hisamoto N. Factors regulating axon regeneration via JNK MAP kinase in Caenorhabditis elegans. J Biochem 2021; 167:433-439. [PMID: 32091576 DOI: 10.1093/jb/mvaa020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/23/2020] [Indexed: 12/25/2022] Open
Abstract
Axon regeneration following nerve injury is a highly conserved process in animals. The nematode Caenorhabditis elegans is an excellent model for investigating the molecular mechanisms of axon regeneration. Recent studies using C. elegans have shown that the c-Jun N-terminal kinase (JNK) plays the important role in axon regeneration. Furthermore, many factors have been identified that act upstream of the JNK cascade after axotomy. This review introduces these factors and describes their roles during the regulation of axon regeneration.
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Affiliation(s)
- Tatsuhiro Shimizu
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Naoki Hisamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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Comprehensive Analysis of Age-related Changes in Lipid Metabolism and Myelin Sheath Formation in Sciatic Nerves. J Mol Neurosci 2021; 71:2310-2323. [PMID: 33492614 DOI: 10.1007/s12031-020-01768-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
To investigate the molecular changes related to myelin formation and lipid metabolism in the sciatic nerve in Sprague Dawley (SD) rats during aging. Thirty-six healthy male SD rats were divided into five groups according to age: 1 week, 1 month, 6 months, 12 months, and 24 months. Sciatic nerves were collected from 1-month-old and 24-month-old SD rats (n = 3) to perform next-generation sequencing (NGS) and bioinformatics analysis. Specimens from each group were harvested and analyzed by qPCR, Western blotting, and transmission electron microscopy (TEM). Protein-protein interaction (PPI) networks of differentially expressed mRNAs (DEmRNAs) related to myelin and lipid metabolism were constructed. DEmRNAs in subnetworks were verified using qPCR. A total of 4580 DEmRNAs were found during aging. The top enriched GO biological processes were primarily clustered in cholesterol and lipid metabolism, including the cholesterol biosynthetic process (RF = 3.16), sterol biosynthetic process (RF = 3.03), cholesterol metabolic process (RF = 2.15), sterol metabolic process (RF = 2.11), fatty acid biosynthetic process (RF = 2.09), and lipid biosynthetic process (RF = 1.79). The mRNA levels of MBP, PMP22, and MPZ were downregulated during aging, while the protein expression of MBP showed an increasing trend. The TEM results showed thin myelin sheaths and an increased number of unmyelinated axons in the 1-week-old rats, and the sheaths became thickened with degenerated axons appearing in older animals. Forty PPI subnetworks related to lipid metabolism were constructed, including one primary subnetwork and two smaller subnetworks. The hub genes were mTOR in sub-network 1, Akt1 in sub-network 2, and SIRT1 in sub-network 3. No gene expression was found consistent with the sequencing results, while in the downregulated genes, AKT1, CEBPA, LIPE, LRP5, PHB, and Rara were significantly downregulated in 24-month-old rats. Lipid metabolism might play an important role in maintaining the structure and physiological function in sciatic nerves during aging and could be candidates for nerve aging research.
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31
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Varela-Rodríguez H, Abella-Quintana DG, Espinal-Centeno A, Varela-Rodríguez L, Gomez-Zepeda D, Caballero-Pérez J, García-Medel PL, Brieba LG, Ordaz-Ortiz JJ, Cruz-Ramirez A. Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming. Front Cell Dev Biol 2020; 8:562940. [PMID: 33330447 PMCID: PMC7710800 DOI: 10.3389/fcell.2020.562940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their associated implications, remain unexplored. However, a circuit with a potential role as a modulator of cellular metabolism along regeneration is that formed by Lin28/let-7. In this study, we report two Lin28 paralogs and eight mature let-7 microRNAs encoded in the axolotl genome. Particularly, in the proliferative blastema stage amxLin28B is more abundant in the nuclei of blastemal cells, while the microRNAs amx-let-7c and amx-let-7a are most downregulated. Functional inhibition of Lin28 factors increase the levels of most mature let-7 microRNAs, consistent with an increment of intermediary metabolites of the Krebs cycle, and phenotypic alterations in the outgrowth of the blastema. In summary, we describe the primary components of the Lin28/let-7 circuit and their function during axolotl regeneration, acting upstream of metabolic reprogramming events.
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Affiliation(s)
- Hugo Varela-Rodríguez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Diana G Abella-Quintana
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | | | - David Gomez-Zepeda
- Mass Spectrometry and Metabolomics Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Juan Caballero-Pérez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Paola L García-Medel
- Structural Biochemistry Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Luis G Brieba
- Structural Biochemistry Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - José J Ordaz-Ortiz
- Mass Spectrometry and Metabolomics Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Alfredo Cruz-Ramirez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
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Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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33
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Vanhunsel S, Beckers A, Moons L. Designing neuroreparative strategies using aged regenerating animal models. Ageing Res Rev 2020; 62:101086. [PMID: 32492480 DOI: 10.1016/j.arr.2020.101086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/13/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022]
Abstract
In our ever-aging world population, the risk of age-related neuropathies has been increasing, representing both a social and economic burden to society. Since the ability to regenerate in the adult mammalian central nervous system is very limited, brain trauma and neurodegeneration are often permanent. As a consequence, novel scientific challenges have emerged and many research efforts currently focus on triggering repair in the damaged or diseased brain. Nevertheless, stimulating neuroregeneration remains ambitious. Even though important discoveries have been made over the past decades, they did not translate into a therapy yet. Actually, this is not surprising; while these disorders mainly manifest in aged individuals, most of the research is being performed in young animal models. Aging of neurons and their environment, however, greatly affects the central nervous system and its capacity to repair. This review provides a detailed overview of the impact of aging on central nervous system functioning and regeneration potential, both in non-regenerating and spontaneously regenerating animal models. Additionally, we highlight the need for aging animal models with regenerative capacities in the search for neuroreparative strategies.
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Affiliation(s)
- Sophie Vanhunsel
- Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology Section, Department of Biology, KU Leuven, Leuven, Belgium
| | - An Beckers
- Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology Section, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lieve Moons
- Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology Section, Department of Biology, KU Leuven, Leuven, Belgium.
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Zhang J, Zhang Y, Chen L, Rao Z, Sun Y. Ulinastatin Promotes Regeneration of Peripheral Nerves After Sciatic Nerve Injury by Targeting let-7 microRNAs and Enhancing NGF Expression. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:2695-2705. [PMID: 32753848 PMCID: PMC7358071 DOI: 10.2147/dddt.s255158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/16/2020] [Indexed: 12/14/2022]
Abstract
Background Peripheral nerve injury is characterized as a common clinical problem. Ulinastatin (UTI) is a serine protease inhibitor with many biological activities including anti-inflammatory and antioxidant effects. Nonetheless, it is unknown whether UTI has a protective effect on peripheral nerve injury. Methods Thirty rats were divided into the sham operation group, the sciatic nerve injury group (injected with normal saline), and the UTI treatment group (80mg/kg/day for two consecutive weeks). Sciatic nerve function index (SFI) was used to assess the biological functions of the sciatic nerve, and compound muscle action potential (CMAP) was measured by electrophysiology. The expressions of let-7 miRNA members were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Nerve growth factor (NGF), nerve regeneration-related proteins GAP43 and NF200, and myelin formation-related proteins MAG and PMP22 expressions were explored by Western blot. After Schwann cells were transfected with let-7 mimics, pcDNA3.1-NGF, let-7 inhibitors, NGF siRNA and their corresponding controls, 5-ethynyl-2ʹ-deoxyuridine (EdU) assay, and Transwell assays were employed to investigate the proliferation and migration of Schwann cells. H2O2 was utilized to construct oxidative injury to cells, and the contents of MDA, SOD, GSH, and CAT were determined. Results UTI treatment remarkably increased SFI of the rats and CMAP of sciatic nerve, enhanced nerve regeneration, and myelin regeneration, and raised the production of GAP43, NF200, MAG, and PMP22. Furthermore, it was found that UTI markedly reduced let-7 miRNAs’ expressions and increased NGF expression after sciatic nerve injury. The dual-luciferase reporter assay validated that let-7 miRNAs targeted NGF, and functional experiments demonstrated that low expression of let-7 miRNAs and NGF overexpression contributed to Schwann cells’ proliferation and migration. Additionally, UTI treatment repressed the oxidative stress regulated by let-7/NGF axis. Conclusion UTI modulates the let-7/NGF axis to inhibit oxidative stress, promote nerve regeneration, and facilitate function recovery after peripheral nerve injury.
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Affiliation(s)
- Jincheng Zhang
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Yingqi Zhang
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Lei Chen
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Zhitao Rao
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Yeqing Sun
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
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35
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LaBella ML, Hujber EJ, Moore KA, Rawson RL, Merrill SA, Allaire PD, Ailion M, Hollien J, Bastiani MJ, Jorgensen EM. Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin. Dev Cell 2020; 52:88-103.e18. [PMID: 31910362 DOI: 10.1016/j.devcel.2019.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 01/19/2023]
Abstract
After axon outgrowth and synapse formation, the nervous system transitions to a stable architecture. In C. elegans, this transition is marked by the appearance of casein kinase 1δ (CK1δ) in the nucleus. In CK1δ mutants, neurons continue to sprout growth cones into adulthood, leading to a highly ramified nervous system. Nervous system architecture in these mutants is completely restored by suppressor mutations in ten genes involved in transcription termination. CK1δ prevents termination by phosphorylating and inhibiting SSUP-72. SSUP-72 would normally remodel the C-terminal domain of RNA polymerase in anticipation of termination. The antitermination activity of CK1δ establishes the mature state of a neuron by promoting the expression of the long isoform of a single gene, the cytoskeleton protein Ankyrin.
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Affiliation(s)
- Matthew L LaBella
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Edward J Hujber
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Kristin A Moore
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Randi L Rawson
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sean A Merrill
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Patrick D Allaire
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Julie Hollien
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | | | - Erik M Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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36
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Chang C, Hisamoto N. Engulfment Genes Promote Neuronal Regeneration in
Caenorhabditis Elegans
: Two Divergent But Complementary Views. Bioessays 2020; 42:e1900185. [DOI: 10.1002/bies.201900185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 04/23/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Chieh Chang
- Department of Biological Sciences University of Illinois at Chicago Chicago Illinois 60607 USA
| | - Naoki Hisamoto
- Dept. of Biological Science Graduate School of Science Nagoya University Furo‐cho, Chikusa‐ku, Aichi Prefecture Nagoya 464‐8602 Japan
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37
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Li L, Zinovyeva AY. Protein Extract Preparation and Co-immunoprecipitation from Caenorhabditis elegans. J Vis Exp 2020. [PMID: 32510481 DOI: 10.3791/61243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Co-immunoprecipitation methods are frequently used to study protein-protein interactions. Confirmation of hypothesized protein-protein interactions or identification of new ones can provide invaluable information about the function of a protein of interest. Some of the traditional methods for extract preparation frequently require labor-intensive and time-consuming techniques. Here, a modified extract preparation protocol using a bead mill homogenizer and metal beads is described as a rapid alternative to traditional protein preparation methods. This extract preparation method is compatible with downstream co-immunoprecipitation studies. As an example, the method was used to successfully co-immunoprecipitate C. elegans microRNA Argonaute ALG-1 and two known ALG-1 interactors: AIN-1, and HRPK-1. This protocol includes descriptions of animal sample collection, extract preparation, extract clarification, and protein immunoprecipitation. The described protocol can be adapted to test for interactions between any two or more endogenous, endogenously tagged, or overexpressed C. elegans proteins in a variety of genetic backgrounds.
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Affiliation(s)
- Li Li
- Division of Biology, Kansas State University
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38
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Nathan FM, Ohtake Y, Wang S, Jiang X, Sami A, Guo H, Zhou FQ, Li S. Upregulating Lin28a Promotes Axon Regeneration in Adult Mice with Optic Nerve and Spinal Cord Injury. Mol Ther 2020; 28:1902-1917. [PMID: 32353321 DOI: 10.1016/j.ymthe.2020.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/16/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022] Open
Abstract
Severed CNS axons fail to regenerate in adult mammals and there are no effective regenerative strategies to treat patients with CNS injuries. Several genes, including phosphatase and tensin homolog (PTEN) and Krüppel-like factors, regulate intrinsic growth capacity of mature neurons. The Lin28 gene is essential for cell development and pluripotency in worms and mammals. In this study, we evaluated the role of Lin28a in regulating regenerative capacity of diverse populations of CNS neurons in adult mammals. Using a neuron-specific Thy1 promoter, we generated transgenic mice that overexpress Lin28a protein in multiple populations of projection neurons, including corticospinal tracts and retinal ganglion cells. We demonstrate that upregulation of Lin28a in transgenic mice induces significant long distance regeneration of both corticospinal axons and the optic nerve in adult mice. Importantly, overexpression of Lin28a by post-injury treatment with adeno-associated virus type 2 (AAV2) vector stimulates dramatic regeneration of descending spinal tracts and optic nerve axons after lesions. Upregulation of Lin28a also enhances activity of the Akt signaling pathway in mature CNS neurons. Therefore, Lin28a is critical for regulating growth capacity of multiple CNS neurons and may become an important molecular target for treating CNS injuries.
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Affiliation(s)
- Fatima M Nathan
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Yosuke Ohtake
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Shuo Wang
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Xinpei Jiang
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Armin Sami
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hua Guo
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Feng-Quan Zhou
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuxin Li
- Shriners Hospitals Pediatric Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Anatomy and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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Williams FP, Haubrich K, Perez-Borrajero C, Hennig J. Emerging RNA-binding roles in the TRIM family of ubiquitin ligases. Biol Chem 2020; 400:1443-1464. [PMID: 31120853 DOI: 10.1515/hsz-2019-0158] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
TRIM proteins constitute a large, diverse and ancient protein family which play a key role in processes including cellular differentiation, autophagy, apoptosis, DNA repair, and tumour suppression. Mostly known and studied through the lens of their ubiquitination activity as E3 ligases, it has recently emerged that many of these proteins are involved in direct RNA binding through their NHL or PRY/SPRY domains. We summarise the current knowledge concerning the mechanism of RNA binding by TRIM proteins and its biological role. We discuss how RNA-binding relates to their previously described functions such as E3 ubiquitin ligase activity, and we will consider the potential role of enrichment in membrane-less organelles.
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Affiliation(s)
- Felix Preston Williams
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Kevin Haubrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Cecilia Perez-Borrajero
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, e-mail:
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40
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Sutherland TC, Geoffroy CG. The Influence of Neuron-Extrinsic Factors and Aging on Injury Progression and Axonal Repair in the Central Nervous System. Front Cell Dev Biol 2020; 8:190. [PMID: 32269994 PMCID: PMC7109259 DOI: 10.3389/fcell.2020.00190] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
In the aging western population, the average age of incidence for spinal cord injury (SCI) has increased, as has the length of survival of SCI patients. This places great importance on understanding SCI in middle-aged and aging patients. Axon regeneration after injury is an area of study that has received substantial attention and made important experimental progress, however, our understanding of how aging affects this process, and any therapeutic effort to modulate repair, is incomplete. The growth and regeneration of axons is mediated by both neuron intrinsic and extrinsic factors. In this review we explore some of the key extrinsic influences on axon regeneration in the literature, focusing on inflammation and astrogliosis, other cellular responses, components of the extracellular matrix, and myelin proteins. We will describe how each element supports the contention that axonal growth after injury in the central nervous system shows an age-dependent decline, and how this may affect outcomes after a SCI.
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Affiliation(s)
- Theresa C Sutherland
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX, United States
| | - Cédric G Geoffroy
- Department of Neuroscience and Experimental Therapeutics, Texas A&M Health Science Center, Bryan, TX, United States
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41
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Lin28 Signaling Supports Mammalian PNS and CNS Axon Regeneration. Cell Rep 2019; 24:2540-2552.e6. [PMID: 30184489 PMCID: PMC6173831 DOI: 10.1016/j.celrep.2018.07.105] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/05/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins Lin28a/b regulate cellular growth and tissue regeneration. Here, we investigated the role of Lin28 in the control of axon regeneration in postmitotic neurons. We find that Lin28a/b are both necessary and sufficient for supporting axon regeneration in mature sensory neurons through their regulatory partners, let-7 microRNAs (miRNAs). More importantly, overexpression of Lin28a in mature retinal ganglion cells (RGCs) produces robust and sustained optic nerve regeneration. Additionally, combined overexpression of Lin28a and downregulation of Pten in RGCs act additively to promote optic nerve regeneration, potentially by reducing the backward turning of regenerating RGC axons. Our findings not only reveal a vital role of Lin28 signaling in regulating mammalian axon regeneration but also identify a signaling pathway that can promote axon regeneration in the central nervous system (CNS). Axon regeneration in the mammalian CNS is a challenge. Wang et al. show that the Lin28/let-7 axis plays an important role in governing mammalian axon regeneration in the peripheral nervous system. More importantly, overexpression of Lin28a induces robust and sustained axon regeneration in the CNS.
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42
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Li L, Veksler-Lublinsky I, Zinovyeva A. HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008067. [PMID: 31584932 PMCID: PMC6795461 DOI: 10.1371/journal.pgen.1008067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/16/2019] [Accepted: 09/11/2019] [Indexed: 01/14/2023] Open
Abstract
microRNAs (miRNAs) are potent regulators of gene expression that function in diverse developmental and physiological processes. Argonaute proteins loaded with miRNAs form the miRNA Induced Silencing Complexes (miRISCs) that repress gene expression at the post-transcriptional level. miRISCs target genes through partial sequence complementarity between the miRNA and the target mRNA’s 3’ UTR. In addition to being targeted by miRNAs, these mRNAs are also extensively regulated by RNA-binding proteins (RBPs) through RNA processing, transport, stability, and translation regulation. While the degree to which RBPs and miRISCs interact to regulate gene expression is likely extensive, we have only begun to unravel the mechanisms of this functional cooperation. An RNAi-based screen of putative ALG-1 Argonaute interactors has identified a role for a conserved RNA binding protein, HRPK-1, in modulating miRNA activity during C. elegans development. Here, we report the physical and genetic interaction between HRPK-1 and ALG-1/miRNAs. Specifically, we report the genetic and molecular characterizations of hrpk-1 and its role in C. elegans development and miRNA-mediated target repression. We show that loss of hrpk-1 causes numerous developmental defects and enhances the mutant phenotypes associated with reduction of miRNA activity, including those of lsy-6, mir-35-family, and let-7-family miRNAs. In addition to hrpk-1 genetic interaction with these miRNA families, hrpk-1 is required for efficient regulation of lsy-6 target cog-1. We report that hrpk-1 plays a role in processing of some but not all miRNAs and is not required for ALG-1/AIN-1 miRISC assembly. We suggest that HRPK-1 may functionally interact with miRNAs by both affecting miRNA processing and by enhancing miRNA/miRISC gene regulatory activity and present models for its activity. microRNAs are small non-coding RNAs that regulate gene expression at the post-transcriptional level. The core microRNA Induced Silencing Complex (miRISC), composed of Argonaute, mature microRNA, and GW182 protein effector, assembles on the target messenger RNA and inhibits translation or leads to messenger RNA degradation. RNA binding proteins interface with miRNA pathways on multiple levels to coordinate gene expression regulation. Here, we report identification and characterization of HRPK-1, a conserved RNA binding protein, as a physical and functional interactor of miRNAs. We confirm the physical interaction between HRPK-1, an hnRNPK homolog, and Argonaute ALG-1. We report characterizations of hrpk-1 role in development and its functional interactions with multiple miRNA families. We suggest that HRPK-1 promotes miRNA activity on multiple levels in part by contributing to miRNA processing and by coordinating with miRISC at the level of target RNAs. This work contributes to our understanding of how RNA binding proteins and auxiliary miRNA cofactors may interface with miRNA pathways to modulate miRNA gene regulatory activity.
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Affiliation(s)
- Li Li
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-sheva, Israel
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
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Imperadore P, Uckermann O, Galli R, Steiner G, Kirsch M, Fiorito G. Nerve regeneration in the cephalopod mollusc Octopus vulgaris: label-free multiphoton microscopy as a tool for investigation. J R Soc Interface 2019; 15:rsif.2017.0889. [PMID: 29643223 DOI: 10.1098/rsif.2017.0889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 01/16/2023] Open
Abstract
Octopus and cephalopods are able to regenerate injured tissues. Recent advancements in the study of regeneration in cephalopods appear promising encompassing different approaches helping to decipher cellular and molecular machinery involved in the process. However, lack of specific markers to investigate degenerative/regenerative phenomena and inflammatory events occurring after damage is limiting these studies. Label-free multiphoton microscopy is applied for the first time to the transected pallial nerve of Octopus vulgaris Various optical contrast methods including coherent anti-Stokes Raman scattering (CARS), endogenous two-photon excited fluorescence (TPEF) and second harmonic generation (SHG) have been used. We detected cells and structures often not revealed with classical staining methods. CARS highlighted the involvement of haemocytes in building up scar tissue; CARS and TPEF facilitated the identification of degenerating fibres; SHG allowed visualization of fibrillary collagen, revealing the formation of a connective tissue bridge between the nerve stumps, likely involved in axon guidance. Using label-free multiphoton microscopy, we studied the regenerative events in octopus without using any other labelling techniques. These imaging methods provided extremely helpful morpho-chemical information to describe regeneration events. The techniques applied here are species-specific independent and should facilitate the comparison among various animal species.
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Affiliation(s)
- Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy .,Association for Cephalopod Research - CephRes, 80133 Napoli, Italy
| | - Ortrud Uckermann
- Department of Neurosurgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Roberta Galli
- Clinical Sensoring and Monitoring, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Gerald Steiner
- Clinical Sensoring and Monitoring, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Matthias Kirsch
- Department of Neurosurgery, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany.,CRTD/DFG-Center for Regenerative Therapies Dresden - Cluster of Excellence, TU Dresden, Dresden, Germany
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
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44
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Wang S, Smith GM, Selzer ME, Li S. Emerging molecular therapeutic targets for spinal cord injury. Expert Opin Ther Targets 2019; 23:787-803. [PMID: 31460807 DOI: 10.1080/14728222.2019.1661381] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introduction: Spinal cord injury (SCI) is a complicated and devastating neurological disorder. Patients with SCI usually have dramatically reduced quality of life. In recent years, numerous studies have reported advances in understanding the pathophysiology of SCI and developing preclinical therapeutic strategies for SCI, including various molecular therapies, and yet there is still no cure. Areas covered: After SCI, tissue damage, responses and repair involve interactions among many cellular components, including neurons, axons, glia, leukocytes, and other cells. Accordingly, numerous cellular genes and molecules have become therapeutic targets for neural tissue repair, circuit reconstruction, and behavioral restoration. Here, we review the major recent advances in biological and molecular strategies to enhance neuroprotection, axon regeneration, remyelination, neuroplasticity and functional recovery in preclinical studies of SCI. Expert opinion: Researchers have made tremendous progress in identifying individual and combined molecular therapies in animal studies. It is very important to identify additional highly effective treatments for early neuroprotective intervention and for functionally meaningful axon regeneration and neuronal reconnections. Because multiple mechanisms contribute to the functional loss after SCI, combining the most promising approaches that target different pathophysiological and molecular mechanisms should exhibit synergistic actions for maximal functional restoration. [Databases searched: PubMed; inclusive dates: 6/27/2019].
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Affiliation(s)
- Shuo Wang
- Shriners Hospitals Pediatric Research Center, Temple University School of Medicine , Philadelphia , PA , USA.,Department of Anatomy and Cell Biology, Temple University School of Medicine , Philadelphia , PA , USA
| | - George M Smith
- Shriners Hospitals Pediatric Research Center, Temple University School of Medicine , Philadelphia , PA , USA.,Department of Neuroscience, Temple University School of Medicine , Philadelphia , PA , USA
| | - Michael E Selzer
- Shriners Hospitals Pediatric Research Center, Temple University School of Medicine , Philadelphia , PA , USA.,Department of Neurology, Temple University School of Medicine , Philadelphia , PA , USA
| | - Shuxin Li
- Shriners Hospitals Pediatric Research Center, Temple University School of Medicine , Philadelphia , PA , USA.,Department of Anatomy and Cell Biology, Temple University School of Medicine , Philadelphia , PA , USA
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45
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Lawson H, Vuong E, Miller RM, Kiontke K, Fitch DHA, Portman DS. The Makorin lep-2 and the lncRNA lep-5 regulate lin-28 to schedule sexual maturation of the C. elegans nervous system. eLife 2019; 8:e43660. [PMID: 31264582 PMCID: PMC6606027 DOI: 10.7554/elife.43660] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/10/2019] [Indexed: 12/30/2022] Open
Abstract
Sexual maturation must occur on a controlled developmental schedule. In mammals, Makorin3 (MKRN3) and the miRNA regulators LIN28A/B are key regulators of this process, but how they act is unclear. In C. elegans, sexual maturation of the nervous system includes the functional remodeling of postmitotic neurons and the onset of adult-specific behaviors. Here, we find that the lin-28-let-7 axis (the 'heterochronic pathway') determines the timing of these events. Upstream of lin-28, the Makorin lep-2 and the lncRNA lep-5 regulate maturation cell-autonomously, indicating that distributed clocks, not a central timer, coordinate sexual differentiation of the C. elegans nervous system. Overexpression of human MKRN3 delays aspects of C. elegans sexual maturation, suggesting the conservation of Makorin function. These studies reveal roles for a Makorin and a lncRNA in timing of sexual differentiation; moreover, they demonstrate deep conservation of the lin-28-let-7 system in controlling the functional maturation of the nervous system.
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Affiliation(s)
- Hannah Lawson
- Department of BiologyUniversity of RochesterRochesterUnited States
| | - Edward Vuong
- Department of Biomedical GeneticsUniversity of RochesterRochesterUnited States
| | - Renee M Miller
- Department of Brain and Cognitive SciencesUniversity of RochesterRochesterUnited States
| | - Karin Kiontke
- Center for Developmental Genetics, Department of BiologyNew York UniversityNew YorkUnited States
| | - David HA Fitch
- Center for Developmental Genetics, Department of BiologyNew York UniversityNew YorkUnited States
| | - Douglas S Portman
- Department of BiologyUniversity of RochesterRochesterUnited States
- Department of Biomedical GeneticsUniversity of RochesterRochesterUnited States
- Department of NeuroscienceUniversity of RochesterRochesterUnited States
- DelMonte Institute for NeuroscienceUniversity of RochesterRochesterUnited States
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46
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Regulation of Caenorhabditis elegans neuronal polarity by heterochronic genes. Proc Natl Acad Sci U S A 2019; 116:12327-12336. [PMID: 31164416 DOI: 10.1073/pnas.1820928116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many neurons display characteristic patterns of synaptic connections that are under genetic control. The Caenorhabditis elegans DA cholinergic motor neurons form synaptic connections only on their dorsal axons. We explored the genetic pathways that specify this polarity by screening for gene inactivations and mutations that disrupt this normal polarity of a DA motorneuron. A RAB-3::GFP fusion protein that is normally localized to presynaptic terminals along the dorsal axon of the DA9 motorneuron was used to screen for gene inactivations that disrupt the DA9 motorneuron polarity. This screen identified heterochronic genes as major regulators of DA neuron presynaptic polarity. In many heterochronic mutants, presynapses of this cholinergic motoneuron are mislocalized to the dendrite at the ventral side: inactivation of the blmp-1 transcription factor gene, the lin-29/Zn finger transcription factor, lin-28/RNA binding protein, and the let-7miRNA gene all disrupt the presynaptic polarity of this DA cholinergic neuron. We also show that the dre-1/F box heterochronic gene functions early in development to control maintenance of polarity at later stages, and that a mutation in the let-7 heterochronic miRNA gene causes dendritic misplacement of RAB-3 presynaptic markers that colocalize with muscle postsynaptic terminals ectopically. We propose that heterochronic genes are components in the UNC-6/Netrin pathway of synaptic polarity of these neurons. These findings highlight the role of heterochronic genes in postmitotic neuronal patterning events.
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Abstract
How the nervous system is wired has been a central question of neuroscience since the inception of the field, and many of the foundational discoveries and conceptual advances have been made through the study of invertebrate experimental organisms, including Caenorhabditis elegans and Drosophila melanogaster. Although many guidance molecules and receptors have been identified, recent experiments have shed light on the many modes of action for these pathways. Here, we summarize the recent progress in determining how the physical and temporal constraints of the surrounding environment provide instructive regulations in nervous system wiring. We use Netrin and its receptors as an example to analyze the complexity of how they guide neurite outgrowth. In neurite repair, conserved injury detection and response-signaling pathways regulate gene expression and cytoskeletal dynamics. We also describe recent developments in the research on molecular mechanisms of neurite regeneration in worms and flies.
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Affiliation(s)
- Claire E Richardson
- Department of Biology, Stanford University, Stanford, California 94305, USA;
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, California 94305, USA; .,Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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48
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Nelson C, Ambros V. Trans-splicing of the C. elegans let-7 primary transcript developmentally regulates let-7 microRNA biogenesis and let-7 family microRNA activity. Development 2019; 146:dev172031. [PMID: 30770392 PMCID: PMC6432665 DOI: 10.1242/dev.172031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/11/2019] [Indexed: 12/19/2022]
Abstract
The sequence and roles in developmental progression of the microRNA let-7 are conserved. In general, transcription of the let-7 primary transcript (pri-let-7) occurs early in development, whereas processing of the mature let-7 microRNA arises during cellular differentiation. In Caenorhabditiselegans and other animals, the RNA-binding protein LIN-28 post-transcriptionally inhibits let-7 biogenesis at early developmental stages, but the mechanisms by which LIN-28 does this are not fully understood. Nor is it understood how the developmental regulation of let-7 might influence the expression or activities of other microRNAs of the same seed family. Here, we show that pri-let-7 is trans-spliced to the SL1 splice leader downstream of the let-7 precursor stem-loop, which produces a short polyadenylated downstream mRNA, and that this trans-splicing event negatively impacts the biogenesis of mature let-7 microRNA in cis Moreover, this trans-spliced mRNA contains sequences that are complementary to multiple members of the let-7 seed family (let-7fam) and negatively regulates let-7fam function in trans Thus, this study provides evidence for a mechanism by which splicing of a microRNA primary transcript can negatively regulate said microRNA in cis as well as other microRNAs in trans.
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Affiliation(s)
- Charles Nelson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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49
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Caneo M, Julian V, Byrne AB, Alkema MJ, Calixto A. Diapause induces functional axonal regeneration after necrotic insult in C. elegans. PLoS Genet 2019; 15:e1007863. [PMID: 30640919 PMCID: PMC6347329 DOI: 10.1371/journal.pgen.1007863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 01/25/2019] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
Many neurons are unable to regenerate after damage. The ability to regenerate after an insult depends on life stage, neuronal subtype, intrinsic and extrinsic factors. C. elegans is a powerful model to test the genetic and environmental factors that affect axonal regeneration after damage, since its axons can regenerate after neuronal insult. Here we demonstrate that diapause promotes the complete morphological regeneration of truncated touch receptor neuron (TRN) axons expressing a neurotoxic MEC-4(d) DEG/ENaC channel. Truncated axons of different lengths were repaired during diapause and we observed potent axonal regrowth from somas alone. Complete morphological regeneration depends on DLK-1 but neuronal sprouting and outgrowth is DLK-1 independent. We show that TRN regeneration is fully functional since animals regain their ability to respond to mechanical stimulation. Thus, diapause induced regeneration provides a simple model of complete axonal regeneration which will greatly facilitate the study of environmental and genetic factors affecting the rate at which neurons die.
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Affiliation(s)
- Mauricio Caneo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago de Chile, Chile
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
| | - Victoria Julian
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Alexandra B. Byrne
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Mark J. Alkema
- Neurobiology Department, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Andrea Calixto
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago de Chile, Chile
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
- * E-mail: ,
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50
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Pereira L, Aeschimann F, Wang C, Lawson H, Serrano-Saiz E, Portman DS, Großhans H, Hobert O. Timing mechanism of sexually dimorphic nervous system differentiation. eLife 2019; 8:e42078. [PMID: 30599092 PMCID: PMC6312707 DOI: 10.7554/elife.42078] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/24/2018] [Indexed: 12/16/2022] Open
Abstract
The molecular mechanisms that control the timing of sexual differentiation in the brain are poorly understood. We found that the timing of sexually dimorphic differentiation of postmitotic, sex-shared neurons in the nervous system of the Caenorhabditis elegans male is controlled by the temporally regulated miRNA let-7 and its target lin-41, a translational regulator. lin-41 acts through lin-29a, an isoform of a conserved Zn finger transcription factor, expressed in a subset of sex-shared neurons only in the male. Ectopic lin-29a is sufficient to impose male-specific features at earlier stages of development and in the opposite sex. The temporal, sexual and spatial specificity of lin-29a expression is controlled intersectionally through the lin-28/let-7/lin-41 heterochronic pathway, sex chromosome configuration and neuron-type-specific terminal selector transcription factors. Two Doublesex-like transcription factors represent additional sex- and neuron-type specific targets of LIN-41 and are regulated in a similar intersectional manner.
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Affiliation(s)
- Laura Pereira
- Department of Biological Sciences, Howard Hughes Medical InstituteColumbia UniversityNew YorkUnited States
| | - Florian Aeschimann
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Chen Wang
- Department of Biological Sciences, Howard Hughes Medical InstituteColumbia UniversityNew YorkUnited States
| | - Hannah Lawson
- Department of BiologyUniversity of RochesterRochesterUnited States
| | - Esther Serrano-Saiz
- Department of Biological Sciences, Howard Hughes Medical InstituteColumbia UniversityNew YorkUnited States
| | - Douglas S Portman
- Department of BiologyUniversity of RochesterRochesterUnited States
- DelMonte Institute for Neuroscience, Department of Biomedical GeneticsUniversity of RochesterNew YorkUnited States
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical InstituteColumbia UniversityNew YorkUnited States
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