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Haidar L, Georgescu M, Drăghici GA, Bănățean-Dunea I, Nica DV, Șerb AF. DNA Methylation Machinery in Gastropod Mollusks. Life (Basel) 2024; 14:537. [PMID: 38672807 PMCID: PMC11050768 DOI: 10.3390/life14040537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.
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Affiliation(s)
- Laura Haidar
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - Marius Georgescu
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - George Andrei Drăghici
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Ioan Bănățean-Dunea
- Biology and Plant Protection Department, Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timișoara, Calea Aradului 119, 300645 Timișoara, Romania;
| | - Dragoș Vasile Nica
- The National Institute of Research—Development for Machines and Installations Designed for Agriculture and Food Industry (INMA), Bulevardul Ion Ionescu de la Brad 6, 077190 București, Romania
| | - Alina-Florina Șerb
- Department of Biochemistry and Pharmacology, Biochemistry Discipline, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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Hamanaka Y, Shiga S. Unique morphology and photoperiodically regulated activity of neurosecretory canopy cells in the pond snail Lymnaea stagnalis. Cell Tissue Res 2023; 393:547-558. [PMID: 37418027 PMCID: PMC10484813 DOI: 10.1007/s00441-023-03799-x] [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: 03/15/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023]
Abstract
The pond snail Lymnaea stagnalis exhibits clear photoperiodism in egg laying; it lays more eggs in long-day conditions than in medium-day conditions. A key regulator of egg laying is neurosecretory caudo-dorsal cells (CDCs) producing an ovulation hormone in the cerebral ganglia. Paired small budding structures of the cerebral ganglia (viz. the lateral lobe) also promote egg laying in addition to spermatogenesis and maturation of female accessory sex organs. However, it remains unknown which cells in the lateral lobe are responsible for these. Previous anatomical and physiological studies prompted us to hypothesize that canopy cells in the lateral lobe modulate activity of CDCs. However, double labeling of the canopy cell and CDCs revealed no sign of direct neural connections, suggesting that activity of CDCs is regulated either humorally or through a neural pathway independent of canopy cells. In addition, our detailed anatomical re-evaluation confirmed previous observations that the canopy cell bears fine neurites along the ipsilateral axon and extensions from the plasma membrane of the cell body, although the function of these extensions remains unexplored. Furthermore, comparison of electrophysiological properties between long-day and medium-day conditions indicated that the canopy cell's activity is moderately under photoperiodic regulation: resting membrane potentials of long-day snails are shallower than those of medium-day snails, and spontaneously spiking neurons are only observed in long-day conditions. Thus, canopy cells appear to receive photoperiodic information and regulate photoperiod-dependent phenomena, but not provide direct neural inputs to CDCs.
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Affiliation(s)
- Yoshitaka Hamanaka
- Laboratory of Comparative Neurobiology, Graduate School of Science, Osaka University, Machikaneyama-Cho 1-1, Toyonaka, Osaka, 560-0043, Japan.
| | - Sakiko Shiga
- Laboratory of Comparative Neurobiology, Graduate School of Science, Osaka University, Machikaneyama-Cho 1-1, Toyonaka, Osaka, 560-0043, Japan
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4
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Kron NS, Fieber LA. Aplysia Neurons as a Model of Alzheimer's Disease: Shared Genes and Differential Expression. J Mol Neurosci 2021; 72:287-302. [PMID: 34664226 PMCID: PMC8840921 DOI: 10.1007/s12031-021-01918-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/18/2021] [Indexed: 11/19/2022]
Abstract
Although Alzheimer’s disease (AD) is the most common form of dementia in the United States, development of therapeutics has proven difficult. Invertebrate alternatives to current mammalian AD models have been successfully employed to study the etiology of the molecular hallmarks of AD. The marine snail Aplysia californica offers a unique and underutilized system in which to study the physiological, behavioral, and molecular impacts of AD. Mapping of the Aplysia proteome to humans and cross-referencing with two databases of genes of interest in AD research identified 898 potential orthologs of interest in Aplysia. Included among these orthologs were alpha, beta and gamma secretases, amyloid-beta, and tau. Comparison of age-associated differential expression in Aplysia sensory neurons with that of late-onset AD in the frontal lobe identified 59 ortholog with concordant differential expression across data sets. The 21 concordantly upregulated genes suggested increased cellular stress and protein dyshomeostasis. The 47 concordantly downregulated genes included important components of diverse neuronal processes, including energy metabolism, mitochondrial homeostasis, synaptic signaling, Ca++ regulation, and cellular cargo transport. Compromised functions in these processes are known hallmarks of both human aging and AD, the ramifications of which are suggested to underpin cognitive declines in aging and neurodegenerative disease.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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6
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Györi J, Kohn AB, Romanova DY, Moroz LL. ATP signaling in the integrative neural center of Aplysia californica. Sci Rep 2021; 11:5478. [PMID: 33750901 PMCID: PMC7943599 DOI: 10.1038/s41598-021-84981-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/23/2021] [Indexed: 11/22/2022] Open
Abstract
ATP and its ionotropic P2X receptors are components of the most ancient signaling system. However, little is known about the distribution and function of purinergic transmission in invertebrates. Here, we cloned, expressed, and pharmacologically characterized the P2X receptors in the sea slug Aplysia californica—a prominent neuroscience model. AcP2X receptors were successfully expressed in Xenopus oocytes and displayed activation by ATP with two-phased kinetics and Na+-dependence. Pharmacologically, they were different from other P2X receptors. The ATP analog, Bz-ATP, was a less effective agonist than ATP, and PPADS was a more potent inhibitor of the AcP2X receptors than the suramin. AcP2X were uniquely expressed within the cerebral F-cluster, the multifunctional integrative neurosecretory center. AcP2X receptors were also detected in the chemosensory structures and the early cleavage stages. Therefore, in molluscs, rapid ATP-dependent signaling can be implicated both in development and diverse homeostatic functions. Furthermore, this study illuminates novel cellular and systemic features of P2X-type ligand-gated ion channels for deciphering the evolution of neurotransmitters.
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Affiliation(s)
- János Györi
- Department of Experimental Zoology, Centre for Ecological Research, Balaton Limnological Institute, 8237, Tihany, Hungary.,Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, 32080, USA
| | - Andrea B Kohn
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, 32080, USA
| | - Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, 117485, Russia
| | - Leonid L Moroz
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, 32080, USA. .,Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
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Kron NS, Schmale MC, Fieber LA. Changes in Metabolism and Proteostasis Drive Aging Phenotype in Aplysia californica Sensory Neurons. Front Aging Neurosci 2020; 12:573764. [PMID: 33101008 PMCID: PMC7522570 DOI: 10.3389/fnagi.2020.573764] [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: 06/17/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022] Open
Abstract
Aging is associated with cognitive declines that originate in impairments of function in the neurons that make up the nervous system. The marine mollusk Aplysia californica (Aplysia) is a premier model for the nervous system uniquely suited to investigation of neuronal aging due to uniquely identifiable neurons and molecular techniques available in this model. This study describes the molecular processes associated with aging in two populations of sensory neurons in Aplysia by applying RNA sequencing technology across the aging process (age 6-12 months). Differentially expressed genes clustered into four to five coherent expression patterns across the aging time series in the two neuron populations. Enrichment analysis of functional annotations in these neuron clusters revealed decreased expression of pathways involved in energy metabolism and neuronal signaling, suggesting that metabolic and signaling pathways are intertwined. Furthermore, increased expression of pathways involved in protein processing and translation suggests that proteostatic stress also occurs in aging. Temporal overlap of enrichment for energy metabolism, proteostasis, and neuronal function suggests that cognitive impairments observed in advanced age result from the ramifications of broad declines in energy metabolism.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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8
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Winters GC, Polese G, Di Cosmo A, Moroz LL. Mapping of neuropeptide Y expression in Octopus brains. J Morphol 2020; 281:790-801. [PMID: 32384206 DOI: 10.1002/jmor.21141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/22/2020] [Accepted: 04/25/2020] [Indexed: 12/31/2022]
Abstract
Neuropeptide Y (NPY) is an evolutionarily conserved neurosecretory molecule implicated in a diverse complement of functions across taxa and in regulating feeding behavior and reproductive maturation in Octopus. However, little is known about the precise molecular circuitry of NPY-mediated behaviors and physiological processes, which likely involve a complex interaction of multiple signal molecules in specific brain regions. Here, we examined the expression of NPY throughout the Octopus central nervous system. The sequence analysis of Octopus NPY precursor confirmed the presence of both, signal peptide and putative active peptides, which are highly conserved across bilaterians. In situ hybridization revealed distinct expression of NPY in specialized compartments, including potential "integration centers," where visual, tactile, and other behavioral circuitries converge. These centers integrating separate circuits may maintain and modulate learning and memory or other behaviors not yet attributed to NPY-dependent modulation in Octopus. Extrasomatic localization of NPY mRNA in the neurites of specific neuron populations in the brain suggests a potential demand for immediate translation at synapses and a crucial temporal role for NPY in these cell populations. We also documented the presence of NPY mRNA in a small cell population in the olfactory lobe, which is a component of the Octopus feeding and reproductive control centers. However, the molecular mapping of NPY expression only partially overlapped with that produced by immunohistochemistry in previous studies. Our study provides a precise molecular map of NPY mRNA expression that can be used to design and test future hypotheses about molecular signaling in various Octopus behaviors.
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Affiliation(s)
- Gabrielle C Winters
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Gianluca Polese
- Department of Biology, Di Cosmo Laboratory, University of Napoli Federico II, Naples, Italy
| | - Anna Di Cosmo
- Department of Biology, Di Cosmo Laboratory, University of Napoli Federico II, Naples, Italy
| | - Leonid L Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA.,Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, Florida, USA
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Pende M, Vadiwala K, Schmidbaur H, Stockinger AW, Murawala P, Saghafi S, Dekens MPS, Becker K, Revilla-i-Domingo R, Papadopoulos SC, Zurl M, Pasierbek P, Simakov O, Tanaka EM, Raible F, Dodt HU. A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. SCIENCE ADVANCES 2020; 6:eaba0365. [PMID: 32523996 PMCID: PMC7259959 DOI: 10.1126/sciadv.aba0365] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.
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Affiliation(s)
- Marko Pende
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hannah Schmidbaur
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander W. Stockinger
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Marcus P. S. Dekens
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Sofia-Christina Papadopoulos
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Martin Zurl
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Elly M. Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Florian Raible
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proc Natl Acad Sci U S A 2019; 116:26980-26990. [PMID: 31806754 PMCID: PMC6936480 DOI: 10.1073/pnas.1911413116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Single-cell transcriptional profiling has become a widespread tool in cell identification, particularly in the nervous system, based on the notion that genomic information determines cell identity. However, many cell-type classification studies are unconstrained by other cellular attributes (e.g., morphology, physiology). Here, we systematically test how accurately transcriptional profiling can assign cell identity to well-studied anatomically and functionally identified neurons in 2 small neuronal networks. While these neurons clearly possess distinct patterns of gene expression across cell types, their expression profiles are not sufficient to unambiguously confirm their identity. We suggest that true cell identity can only be determined by combining gene expression data with other cellular attributes such as innervation pattern, morphology, or physiology. Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
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Fallet M, Luquet E, David P, Cosseau C. Epigenetic inheritance and intergenerational effects in mollusks. Gene 2019; 729:144166. [PMID: 31678264 DOI: 10.1016/j.gene.2019.144166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023]
Abstract
Recent insights in evolutionary biology have shed light on epigenetic variation that interacts with genetic variation to convey heritable information. An important characteristic of epigenetic changes is that they can be produced in response to environmental cues and passed on to later generations, potentially facilitating later genetic adaptation. While our understanding of epigenetic mechanisms in vertebrates is rapidly growing, our knowledge about invertebrates remains lower, or is restricted to model organisms. Mollusks in particular, are a large group of invertebrates, with several species important for ecosystem function, human economy and health. In this review, we attempt to summarize the literature on epigenetic and intergenerational studies in mollusk species, with potential importance for adaptive evolution. Our review highlights that two molecular bearers of epigenetic information, DNA methylation and histone modifications, are key features for development in mollusk species, and both are sensitive to environmental conditions to which developing individuals are exposed. Further, although studies are still scarce, various environmental factors (e.g. predator cues, chemicals, parasites) can induce intergenerational effects on the phenotype (life-history traits, morphology, behaviour) of several mollusk taxa. More work is needed to better understand whether environmentally-induced changes in DNA methylation and histone modifications have phenotypic impacts, whether they can be inherited through generations and their role in intergenerational effects on phenotype. Such work may bring insights into the potential role of epigenetic in adaptation and evolution in mollusks.
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Affiliation(s)
- Manon Fallet
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Emilien Luquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, F-69622 Villeurbanne, France
| | - Patrice David
- CEFE, UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, IRD, EPHE, Montpellier, France
| | - Céline Cosseau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France.
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12
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Zhang L, Liu M, Li Q, Shen B, Hu C, Fu R, Liu M, Deng J, Cao Q, Wang Y, Wang Y. Identification of differential gene expression in endothelial cells from young and aged mice using RNA-Seq technique. Am J Transl Res 2019; 11:6553-6560. [PMID: 31737206 PMCID: PMC6834518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
Aging is a complex phenomenon. Endothelial cell senescence is regarded as a vital characteristic of cardiovascular diseases. This study aims to identify differentially expressed genes in vascular endothelial cells (ECs) of different age groups by RNA sequencing (RNA-Seq) technique, and to explore which molecular pathways differentially expressed genes (DEGs) may enrich in. In this study, we used RNA-Seq to analyze DEGs in primary endothelial cells of young and old mice, and further analyzed them by gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Our results showed that in total identified 229 of the DEGs, 104 were upregulated and 125 were downregulated in endothelial cells of aged mice compared with young mice. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the involvement of these DEGs in the regulation of morphogenesis of a branching structure, angiogenesis, upregulation of cell proliferation, and extracellular matrix (ECM)-receptor interaction. These results provided a novel insight to understand the molecular mechanisms underlying aortic endothelial cell senescence, and some of the novel candidate genes identified in this study may be valuable in elucidating the molecular mechanisms underlying endothelial cell senescence.
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Affiliation(s)
- Liang Zhang
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Manli Liu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Qing Li
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
- The Central Laboratory of Medical Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefei 230001, Anhui, PR China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical UniversityHefei 230032, Anhui, PR China
| | - Chaojie Hu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
- The Central Laboratory of Medical Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefei 230001, Anhui, PR China
| | - Rui Fu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Mengdie Liu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Jie Deng
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Qi Cao
- The Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of SydneySydney, NSW, Australia
| | - Yiping Wang
- The Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of SydneySydney, NSW, Australia
| | - Yuanmin Wang
- Centre for Kidney Research, Children’s Hospital at WestmeadSydney, NSW, Australia
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13
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Zverkov OA, Mikhailov KV, Isaev SV, Rusin LY, Popova OV, Logacheva MD, Penin AA, Moroz LL, Panchin YV, Lyubetsky VA, Aleoshin VV. Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. Front Genet 2019; 10:443. [PMID: 31178892 PMCID: PMC6543705 DOI: 10.3389/fgene.2019.00443] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 04/29/2019] [Indexed: 01/22/2023] Open
Abstract
Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.
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Affiliation(s)
- Oleg A. Zverkov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Kirill V. Mikhailov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V. Isaev
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Leonid Y. Rusin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V. Popova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey A. Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Leonid L. Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Yuri V. Panchin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vassily A. Lyubetsky
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V. Aleoshin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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14
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Kasozi KI, Bukenya A, Eze ED, Kasolo J, Tayebwa DS, Ssempijja F, Suubo J, Tamale A, Echoru I, Ntulume I, Onkoba SK, Micheni LN, Ayikobua ET, Asiimwe OH, Kalange M. Low concentrations of Lactobacillus rhamnosus GG (Yoba ®) are safe in male Drosophila melanogaster. BMC Res Notes 2019; 12:269. [PMID: 31088517 PMCID: PMC6518721 DOI: 10.1186/s13104-019-4297-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE The purpose of the study was to generate information on the safety of probiotics, thus the study objectives were to evaluate the effects of Yoba® on basic physiochemical properties. The study assessed male w1118 Drosophila melanogaster which were provided food supplemented with Yoba® at 1%, 3%, 6%, and 12% on motor function, total protein, catalase activity, and hydrogen peroxide scavenging activity and lifespan. RESULTS Yoba® at high concentration (≥ 6%) increased locomotor activity in Drosophila melanogaster, however, total protein, catalase, and hydrogen peroxide scavenging activity were significantly higher at 1% Yoba® compared to 3%, 6%, and 12% Yoba®. Yoba consumed at 1% was associated with greater physiological benefits in Drosophila melanogaster. Findings in the study offer a rationale for the consumption of Yoba® at 1% in humans as is currently being promoted by the Yoba for Life consortium, however, high concentrations of Yoba® would disrupt physiological function as shown by this study.
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Affiliation(s)
- Keneth Iceland Kasozi
- Department of Physiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Aisha Bukenya
- School of Pharmacy, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Ejike Daniel Eze
- Department of Physiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
- Department of Biomedical Sciences, School of Medicine, Kabale University, Kabale, Uganda
| | - Josephine Kasolo
- Department of Physiology, College of Health Sciences, Makerere University, Box 7062, Kampala, Uganda
| | - Dickson Stuart Tayebwa
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Box 7062, Kampala, Uganda
| | - Fred Ssempijja
- Department of Anatomy, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Joy Suubo
- Department of Physiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Andrew Tamale
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Box 7062, Kampala, Uganda
| | - Isaac Echoru
- Department of Anatomy, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Ibrahim Ntulume
- Department of Microbiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Sarah Kemuma Onkoba
- Department of Microbiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Lisa Nkatha Micheni
- Department of Microbiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Emmanuel Tiyo Ayikobua
- Department of Physiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Oscar Hilary Asiimwe
- Department of Biochemistry, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Muhamudu Kalange
- Department of Physiology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
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15
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Yang Q, Antonov I, Castillejos D, Nagaraj A, Bostwick C, Kohn A, Moroz LL, Hawkins RD. Intermediate-term memory in Aplysia involves neurotrophin signaling, transcription, and DNA methylation. ACTA ACUST UNITED AC 2018; 25:620-628. [PMID: 30442770 PMCID: PMC6239133 DOI: 10.1101/lm.047977.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/16/2018] [Indexed: 12/14/2022]
Abstract
Long-term but not short-term memory and synaptic plasticity in many brain areas require neurotrophin signaling, transcription, and epigenetic mechanisms including DNA methylation. However, it has been difficult to relate these cellular mechanisms directly to behavior because of the immense complexity of the mammalian brain. To address that problem, we and others have examined numerically simpler systems such as the hermaphroditic marine mollusk Aplysia californica. As a further simplification, we have used a semi-intact preparation of the Aplysia siphon withdrawal reflex in which it is possible to relate cellular plasticity directly to behavioral learning. We find that inhibitors of neurotrophin signaling, transcription, and DNA methylation block sensitization and classical conditioning beginning ∼1 h after the start of training, which is in the time range of an intermediate-term stage of plasticity that combines elements of short- and long-term plasticity and may form a bridge between them. Injection of decitabine (an inhibitor of DNA methylation that may have other actions in these experiments) into an LE sensory neuron blocks the neural correlates of conditioning in the same time range. In addition, we found that both DNA and RNA methylation in the abdominal ganglion are correlated with learning in the same preparations. These results begin to suggest the functions and integration of these different molecular mechanisms during behavioral learning.
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Affiliation(s)
- Qizong Yang
- Department of Neuroscience, Columbia University, New York, New York 10032, USA
| | - Igor Antonov
- Department of Neuroscience, Columbia University, New York, New York 10032, USA
| | - David Castillejos
- Department of Neuroscience, Columbia University, New York, New York 10032, USA
| | - Anagha Nagaraj
- Department of Neuroscience, Columbia University, New York, New York 10032, USA
| | - Caleb Bostwick
- Whitney Laboratory for Marine Biosciences, University of Florida, Saint Augustine, Florida 32080, USA.,Department of Neuroscience, University of Florida, Gainesville, Florida 32610, USA
| | - Andrea Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, Saint Augustine, Florida 32080, USA
| | - Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, Saint Augustine, Florida 32080, USA.,Department of Neuroscience, University of Florida, Gainesville, Florida 32610, USA
| | - Robert D Hawkins
- Department of Neuroscience, Columbia University, New York, New York 10032, USA.,Division of Systems Neuroscience, New York State Psychiatric Institute, New York, New York 10032, USA
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16
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Hernández HG, Sandoval-Hernández AG, Garrido-Gil P, Labandeira-Garcia JL, Zelaya MV, Bayon GF, Fernández AF, Fraga MF, Arboleda G, Arboleda H. Alzheimer's disease DNA methylome of pyramidal layers in frontal cortex: laser-assisted microdissection study. Epigenomics 2018; 10:1365-1382. [PMID: 30324800 DOI: 10.2217/epi-2017-0160] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To study DNA methylation patterns of cortical pyramidal layers susceptible to late-onset Alzheimer's disease (LOAD) neurodegeneration. METHODS Laser-assisted microdissection to select pyramidal layers' cells in frontal cortex of 32 human brains (18 LOAD) and Infinium DNA Methylation 450K analysis were performed to find differential methylated positions and regions, in addition to the corresponding gene set functional enrichment analyses. RESULTS Differential hypermethylation in several genomic regions and genes mainly in HOXA3, GSTP1, CXXC1-3 and BIN1. The functional enrichment analysis revealed genes significantly related to oxidative-stress and synapsis. CONCLUSION The present results indicate the differentially methylated genes related to neural projections, synapsis, oxidative stress and epigenetic regulator genes and represent the first epigenome of cortical pyramidal layers in LOAD.
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Affiliation(s)
- Hernán Guillermo Hernández
- PhD Program in Dentistry, Universidad Santo Tomás, Bucaramanga, Colombia.,Research Unity, Universidad Manuela Beltrán, Bucaramanga, Colombia
| | - Adrián Gabriel Sandoval-Hernández
- Grupo de Neurociencias y muerte Celular, Facultad de Medicina e instituto de Genética, Universidad Nacional de Colombia, Colombia.,Área de Bioquímica, Departamento de Química Universidad Nacional de Colombia, Colombia
| | - Pablo Garrido-Gil
- Laboratory of Neuroanatomy and Experimental Neurology, Department of Morphological Sciences, CIMUS, Faculty of Medicine, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - José Luis Labandeira-Garcia
- Laboratory of Neuroanatomy and Experimental Neurology, Department of Morphological Sciences, CIMUS, Faculty of Medicine, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.,Networking Research Center on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - María Victoria Zelaya
- Navarrabiomed Brain Bank, Navarra Institute for Health Research, Pamplona, Navarra, Spain
| | - Gustavo F Bayon
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Principado de Asturias, Spain
| | - Agustín F Fernández
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Principado de Asturias, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Spain
| | - Gonzalo Arboleda
- Grupo de Neurociencias y muerte Celular, Facultad de Medicina e instituto de Genética, Universidad Nacional de Colombia, Colombia.,Área de Bioquímica, Departamento de Química Universidad Nacional de Colombia, Colombia
| | - Humberto Arboleda
- Grupo de Neurociencias y muerte Celular, Facultad de Medicina e instituto de Genética, Universidad Nacional de Colombia, Colombia
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17
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Lee JH, Kim JH, Kim S, Cho KS, Lee SB. Chromatin Changes Associated with Neuronal Maintenance and Their Pharmacological Application. Curr Neuropharmacol 2018; 16:118-125. [PMID: 28571546 PMCID: PMC5883374 DOI: 10.2174/1570159x15666170601124220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/03/2017] [Accepted: 05/31/2017] [Indexed: 01/07/2023] Open
Abstract
Background: The transcriptional control of neuronal specification and early development has been intensively stud-ied over the past few decades. However, relatively little is known about transcriptional programs associated with the mainte-nance of terminally differentiated neuronal cells with respect to their functions, structures, and cell type-specific identity features. Methods: Notably, largely because of the recent advances in related techniques such as next generation sequencing and chromatin immunoprecipitation sequencing, the physiological implications of system-wide regulation of gene expression through changes in chromatin states have begun to be extensively studied in various contexts and systems, including the nervous system. Results: Here, we attempt to review our current understanding of the link between chromatin changes and neuronal mainte-nance in the period of life after the completion of neuronal development. Perturbations involving chromatin changes in the system-wide transcriptional control are believed to be closely associated with diverse aspects of neuronal aging and neuro-degenerative conditions. Conclusion: In this review, we focused on heterochromatin and epigenetic dysregulation in neurodegenerative conditions as well as neuronal aging, the most important risk factor leading to neuronal degeneration, in order to highlight the close association between chromatin changes and neuronal maintenance. Lastly, we reviewed the cur-rently available and potential future applications of pharmacological control of the chromatin states associated with neuronal maintenance.
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Affiliation(s)
- Jang Ho Lee
- Department of Biological Sciences, Konkuk University, Seoul 05029. Korea
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon 34113, Korea
| | - Sunhong Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Biomolecular Science, University of Science and Technology, Daejeon 34113, Korea
| | - Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul 05029. Korea
| | - Sung Bae Lee
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988. Korea
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18
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Moroz LL. NeuroSystematics and Periodic System of Neurons: Model vs Reference Species at Single-Cell Resolution. ACS Chem Neurosci 2018; 9:1884-1903. [PMID: 29989789 DOI: 10.1021/acschemneuro.8b00100] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is more than one way to develop neuronal complexity, and animals frequently use different molecular toolkits to achieve similar functional outcomes (=convergent evolution). Neurons are different not only because they have different functions, but also because neurons and circuits have different genealogies, and perhaps independent origins at the broadest scale from ctenophores and cnidarians to cephalopods and primates. By combining modern phylogenomics, single-neuron sequencing (scRNA-seq), machine learning, single-cell proteomics, and metabolomic across Metazoa, it is possible to reconstruct the evolutionary histories of neurons tracing them to ancestral secretory cells. Comparative data suggest that neurons, and perhaps synapses, evolved at least 2-3 times (in ctenophore, cnidarian and bilateral lineages) during ∼600 million years of animal evolution. There were also several independent events of the nervous system centralization either from a common bilateral/cnidarian ancestor without the bona fide neurons or from the urbilaterian with diffuse, nerve-net type nervous system. From the evolutionary standpoint, (i) a neuron should be viewed as a functional rather than a genetic character, and (ii) any given neural system might be chimeric and composed of different cell lineages with distinct origins and evolutionary histories. The identification of distant neural homologies or examples of convergent evolution among 34 phyla will not only allow the reconstruction of neural systems' evolution but together with single-cell "omic" approaches the proposed synthesis would lead to the "Periodic System of Neurons" with predictive power for neuronal phenotypes and plasticity. Such a phylogenetic classification framework of Neuronal Systematics (NeuroSystematics) might be a conceptual analog of the Periodic System of Chemical Elements. scRNA-seq profiling of all neurons in an entire brain or Brain-seq is now fully achievable in many nontraditional reference species across the entire animal kingdom. Arguably, marine animals are the most suitable for the proposed tasks because the world oceans represent the greatest taxonomic and body-plan diversity.
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Affiliation(s)
- Leonid L. Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, 1149 Newell Drive, Gainesville, Florida 32611, United States
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, Florida 32080, United States
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19
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High-level dietary cadmium exposure is associated with global DNA hypermethylation in the gastropod hepatopancreas. PLoS One 2017; 12:e0184221. [PMID: 28877233 PMCID: PMC5587323 DOI: 10.1371/journal.pone.0184221] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/21/2017] [Indexed: 12/29/2022] Open
Abstract
5-methylcytosine (5mC) is a key epigenetic mark which influences gene expression and phenotype. In vertebrates, this epigenetic mark is sensitive to Cd exposure, but there is no information linking such an event with changes in global 5mC levels in terrestrial gastropods despite their importance as excellentecotoxicological bioindicators of metal contamination. Therefore, we first evaluated total 5mC content in DNA of the hepatopancreas of adult Cantareus aspersus with the aim to determine whether this epigenetic mark is responsive to Cd exposure. The experiment was conducted under laboratory conditions and involved a continuous exposure, multiple dose- and time-point (14, 28, and 56 days) study design. Hepatopancreas cadmium levels were measured using Flame Atomic Absorption Spectrometry and the percentage of 5-mC in samples using an ELISA-based colorimetric assay. Snail death rates were also assessed. Our results, for the first time, reveal the presence of 5mC in C. aspersus and provide evidence for Cd-induced changes in global 5mC levels in DNA of gastropods and mollusks. Although less sensitive than tissue accumulation, DNA methylation levels responded in a dose- and time-dependent manner to dietary cadmium, with exposure dose having a much stronger effect than exposure duration. An obvious trend of increasing 5mC levels was observed starting at 28 days of exposure to the second highest dose and this trend persisted at the two highest treatments for close to one month, when the experiment was terminated after 56 days. Moreover, a strong association was identified between Cd concentrations in the hepatopancreas and DNA methylation levels in this organ. These data indicate an overall trend towards DNA hypermethylation with elevated Cd exposure. No consistent lethal effect was observed, irrespective of time point and Cd-dosage. Overall, our findings suggest that the total 5mC content in DNA of the hepatopancreas of land snails is responsive to sublethal Cd exposure and give new insights into invertebrate environmental epigenetics.
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20
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Rostom R, Svensson V, Teichmann SA, Kar G. Computational approaches for interpreting scRNA-seq data. FEBS Lett 2017; 591:2213-2225. [PMID: 28524227 PMCID: PMC5575496 DOI: 10.1002/1873-3468.12684] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/30/2017] [Accepted: 05/16/2017] [Indexed: 11/18/2022]
Abstract
The recent developments in high‐throughput single‐cell RNA sequencing technology (scRNA‐seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data analysis, building on high‐dimensional data mining techniques. Here, we consider biological questions for which scRNA‐seq data is used, both at a cell and gene level, and describe tools available for these types of analyses. This is an exciting and rapidly evolving field, where clustering, pseudotime inference, branching inference and gene‐level analyses are particularly informative areas of computational analysis.
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Affiliation(s)
| | | | | | - Gozde Kar
- The European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
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21
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Nica D, Popescu C, Draghici G, Privistirescu I, Suciu M, Stöger R. Effect of cadmium on cytosine hydroxymethylation in gastropod hepatopancreas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:15187-15195. [PMID: 28497329 DOI: 10.1007/s11356-017-9104-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
5-Hydroxymethylcytosine (5hmC) is an important, yet poorly understood epigenetic DNA modification, especially in invertebrates. Aberrant genome-wide 5hmC levels have been associated with cadmium (Cd) exposure in humans, but such information is lacking for invertebrate bioindicators. Here, we aimed to determine whether this epigenetic mark is present in DNA of the hepatopancreas of the land snail Cantareus aspersus and is responsive to Cd exposure. Adult snails were reared under laboratory conditions and exposed to graded amounts of dietary cadmium for 14 days. Weight gain was used as a sublethal endpoint, whereas survival as a lethal endpoint. Our results are the first to provide evidence for the presence of 5hmC in DNA of terrestrial mollusks; 5hmC levels are generally low with the measured values falling below 0.03%. This is also the first study to investigate the interplay of Cd with DNA hydroxymethylation levels in a non-human animal study system. Cadmium retention in the hepatopancreas of C. aspersus increased from a dietary Cd dose of 1 milligram per kilogram dry weight (mg/kg d. wt). For the same treatment, we identified the only significant elevation in percentage of samples with detectable 5hmC levels despite the lack of significant mortalities and changes in weight gain among treatment groups. These findings indicate that 5hmC is an epigenetic mark that may be responsive to Cd exposure, thereby opening a new aspect to invertebrate environmental epigenetics.
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Affiliation(s)
- Dragos Nica
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, P-ta Murgu Eftimie 2, RO 300041, Timisoara, Romania.
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania.
| | - Cristina Popescu
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania
- Faculty of Pharmacy, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania
| | - George Draghici
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, RO 310045, Arad, Romania
| | - Ionela Privistirescu
- Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, P-ta Murgu Eftimie 2, RO 300041, Timisoara, Romania
| | - Maria Suciu
- Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, P-ta Murgu Eftimie 2, RO 300041, Timisoara, Romania
- "Babes-Bolyai" University, Str. Mihail Kogalniceanu1, RO 400084, Cluj-Napoca, Romania
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
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22
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Kumar SS, Sun Y, Zou S, Hong J. 3D Holographic Observatory for Long-term Monitoring of Complex Behaviors in Drosophila. Sci Rep 2016; 6:33001. [PMID: 27605243 PMCID: PMC5015086 DOI: 10.1038/srep33001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 11/18/2022] Open
Abstract
Drosophila is an excellent model organism towards understanding the cognitive function, aging and neurodegeneration in humans. The effects of aging and other long-term dynamics on the behavior serve as important biomarkers in identifying such changes to the brain. In this regard, we are presenting a new imaging technique for lifetime monitoring of Drosophila in 3D at spatial and temporal resolutions capable of resolving the motion of limbs and wings using holographic principles. The developed system is capable of monitoring and extracting various behavioral parameters, such as ethograms and spatial distributions, from a group of flies simultaneously. This technique can image complicated leg and wing motions of flies at a resolution, which allows capturing specific landing responses from the same data set. Overall, this system provides a unique opportunity for high throughput screenings of behavioral changes in 3D over a long term in Drosophila.
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Affiliation(s)
- S. Santosh Kumar
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN 55414, USA
| | - Yaning Sun
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Jiarong Hong
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Saint Anthony Falls Laboratory, University of Minnesota, Minneapolis, MN 55414, USA
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23
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24
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Linnarsson S, Teichmann SA. Single-cell genomics: coming of age. Genome Biol 2016. [PMID: 27160975 DOI: 10.1186/s13059-016-0960-x.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Unit of Molecular Neurobiology, Scheeles väg 1, 171 77, Stockholm, Sweden.
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
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25
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Kim T, Lim CS, Kaang BK. Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq. BMB Rep 2016; 48:388-94. [PMID: 25603796 PMCID: PMC4577288 DOI: 10.5483/bmbrep.2015.48.7.218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/18/2023] Open
Abstract
The brain is an organ that consists of various cell types. As our knowledge of the structure and function of the brain progresses, cell type-specific research is gaining importance. Together with advances in sequencing technology and bioinformatics, cell type-specific transcriptome studies are providing important insights into brain cell function. In this review, we discuss 3 different cell type-specific transcriptome analyses i.e., Laser Capture Microdissection (LCM), Translating Ribosome Affinity Purification (TRAP)/RiboTag, and single cell RNA-Seq, that are widely used in the field of neuroscience.
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Affiliation(s)
- TaeHyun Kim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Chae-Seok Lim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
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26
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Michel M, Lyons LC. Unraveling the complexities of circadian and sleep interactions with memory formation through invertebrate research. Front Syst Neurosci 2014; 8:133. [PMID: 25136297 PMCID: PMC4120776 DOI: 10.3389/fnsys.2014.00133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/07/2014] [Indexed: 12/14/2022] Open
Abstract
Across phylogeny, the endogenous biological clock has been recognized as providing adaptive advantages to organisms through coordination of physiological and behavioral processes. Recent research has emphasized the role of circadian modulation of memory in generating peaks and troughs in cognitive performance. The circadian clock along with homeostatic processes also regulates sleep, which itself impacts the formation and consolidation of memory. Thus, the circadian clock, sleep and memory form a triad with ongoing dynamic interactions. With technological advances and the development of a global 24/7 society, understanding the mechanisms underlying these connections becomes pivotal for development of therapeutic treatments for memory disorders and to address issues in cognitive performance arising from non-traditional work schedules. Invertebrate models, such as Drosophila melanogaster and the mollusks Aplysia and Lymnaea, have proven invaluable tools for identification of highly conserved molecular processes in memory. Recent research from invertebrate systems has outlined the influence of sleep and the circadian clock upon synaptic plasticity. In this review, we discuss the effects of the circadian clock and sleep on memory formation in invertebrates drawing attention to the potential of in vivo and in vitro approaches that harness the power of simple invertebrate systems to correlate individual cellular processes with complex behaviors. In conclusion, this review highlights how studies in invertebrates with relatively simple nervous systems can provide mechanistic insights into corresponding behaviors in higher organisms and can be used to outline possible therapeutic options to guide further targeted inquiry.
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Affiliation(s)
- Maximilian Michel
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine Nashville, TN, USA
| | - Lisa C Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University Tallahassee, FL, USA
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27
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Liu N, Liu L, Pan X. Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos. Cell Mol Life Sci 2014; 71:2707-15. [PMID: 24652479 PMCID: PMC11113295 DOI: 10.1007/s00018-014-1601-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/16/2014] [Accepted: 02/03/2014] [Indexed: 12/17/2022]
Abstract
Cellular heterogeneity within a cell population is a common phenomenon in multicellular organisms, tissues, cultured cells, and even FACS-sorted subpopulations. Important information may be masked if the cells are studied as a mass. Transcriptome profiling is a parameter that has been intensively studied, and relatively easier to address than protein composition. To understand the basis and importance of heterogeneity and stochastic aspects of the cell function and its mechanisms, it is essential to examine transcriptomes of a panel of single cells. High-throughput technologies, starting from microarrays and now RNA-seq, provide a full view of the expression of transcriptomes but are limited by the amount of RNA for analysis. Recently, several new approaches for amplification and sequencing the transcriptome of single cells or a limited low number of cells have been developed and applied. In this review, we summarize these major strategies, such as PCR-based methods, IVT-based methods, phi29-DNA polymerase-based methods, and several other methods, including their principles, characteristics, advantages, and limitations, with representative applications in cancer stem cells, early development, and embryonic stem cells. The prospects for development of future technology and application of transcriptome analysis in a single cell are also discussed.
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Affiliation(s)
- Na Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Science, Nankai University, Tianjin, 300071, China,
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28
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The ctenophore genome and the evolutionary origins of neural systems. Nature 2014; 510:109-14. [PMID: 24847885 PMCID: PMC4337882 DOI: 10.1038/nature13400] [Citation(s) in RCA: 455] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 04/23/2014] [Indexed: 12/31/2022]
Abstract
The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores, or comb jellies, have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here, we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well-recognized in ctenophores, many bilaterian neuron-specific genes and genes of “classical” neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.
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Abstract
RNA-seq or transcriptome analysis of individual cells and small-cell populations is essential for virtually any biomedical field. It is especially critical for developmental, aging, and cancer biology as well as neuroscience where the enormous heterogeneity of cells present a significant methodological and conceptual challenge. Here we present two methods that allow for fast and cost-efficient transcriptome sequencing from ultra-small amounts of tissue or even from individual cells using semiconductor sequencing technology (Ion Torrent, Life Technologies). The first method is a reduced representation sequencing which maximizes capture of RNAs and preserves transcripts' directionality. The second, a template-switch protocol, is designed for small mammalian neurons. Both protocols, from cell/tissue isolation to final sequence data, take up to 4 days. The efficiency of these protocols has been validated with single hippocampal neurons and various invertebrate tissues including individually identified neurons within a simpler memory-forming circuit of Aplysia californica and early (1-, 2-, 4-, 8-cells) embryonic and developmental stages from basal metazoans.
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Affiliation(s)
- Andrea B Kohn
- The Whitney Laboratory for Marine Biosciences, University of Florida, Saint Augustine, FL, USA
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