37 results on '"Galina Erikson"'
Search Results
2. Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder
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Debha N. Amatya, Sara B. Linker, Ana P.D. Mendes, Renata Santos, Galina Erikson, Maxim N. Shokhirev, Yuansheng Zhou, Tatyana Sharpee, Fred H. Gage, Maria C. Marchetto, and Yeni Kim
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Medicine (General) ,R5-920 ,Biology (General) ,QH301-705.5 - Abstract
Summary: Neuronal activity can be modeled as a nonlinear dynamical system to yield measures of neuronal state and dysfunction. The electrical recordings of stem cell-derived neurons from individuals with autism spectrum disorder (ASD) and controls were analyzed using minimum embedding dimension (MED) analysis to characterize their dynamical complexity. MED analysis revealed a significant reduction in dynamical complexity in ASD neurons during differentiation, which was correlated to bursting and spike interval measures. MED was associated with clinical endpoints, such as nonverbal intelligence, and was correlated with 53 differentially expressed genes, which were overrepresented with ASD risk genes related to neurodevelopment, cell morphology, and cell migration. Spatiotemporal analysis also showed a prenatal temporal enrichment in cortical and deep brain structures. Together, we present dynamical analysis as a paradigm that can be used to distinguish disease-associated cellular electrophysiological and transcriptional signatures, while taking into account patient variability in neuropsychiatric disorders. : Marchetto, Kim, and colleagues describe the application of dynamical analysis to stem cell-derived neuronal recordings from patients with ASD. They find that dynamical complexity is reduced in ASD electrical activity, as measured by minimum embedding dimension (MED). They go on to describe the gene expression, biological pathway, and neurodevelopmental correlates of the MED signature, supporting findings in the literature. Keywords: autism spectrum disorder, multielectrode array, minimum embedding dimension, dynamical complexity, neurodevelopmental disorder models
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- 2019
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3. Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells
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Renata Santos, Krishna C. Vadodaria, Baptiste N. Jaeger, Arianna Mei, Sabrina Lefcochilos-Fogelquist, Ana P.D. Mendes, Galina Erikson, Maxim Shokhirev, Lynne Randolph-Moore, Callie Fredlender, Sonia Dave, Ruth Oefner, Conor Fitzpatrick, Monique Pena, Jerika J. Barron, Manching Ku, Ahmet M. Denli, Bilal E. Kerman, Patrick Charnay, John R. Kelsoe, Maria C. Marchetto, and Fred H. Gage
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astrocytes ,iPSCs ,neuroinflammation ,disease modeling ,stem cell ,co-culture ,neuropsychiatric disorders ,neurodegenerative disorders ,Medicine (General) ,R5-920 ,Biology (General) ,QH301-705.5 - Abstract
Astrocyte dysfunction and neuroinflammation are detrimental features in multiple pathologies of the CNS. Therefore, the development of methods that produce functional human astrocytes represents an advance in the study of neurological diseases. Here we report an efficient method for inflammation-responsive astrocyte generation from induced pluripotent stem cells (iPSCs) and embryonic stem cells. This protocol uses an intermediate glial progenitor stage and generates functional astrocytes that show levels of glutamate uptake and calcium activation comparable with those observed in human primary astrocytes. Stimulation of stem cell-derived astrocytes with interleukin-1β or tumor necrosis factor α elicits a strong and rapid pro-inflammatory response. RNA-sequencing transcriptome profiling confirmed that similar gene expression changes occurred in iPSC-derived and primary astrocytes upon stimulation with interleukin-1β. This protocol represents an important tool for modeling in-a-dish neurological diseases with an inflammatory component, allowing for the investigation of the role of diseased astrocytes in neuronal degeneration.
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- 2017
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4. Reprogramming pancreatic stellate cells via p53 activation: A putative target for pancreatic cancer therapy.
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Maya Saison-Ridinger, Kathleen E DelGiorno, Tejia Zhang, Annabelle Kraus, Randall French, Dawn Jaquish, Crystal Tsui, Galina Erikson, Benjamin T Spike, Maxim N Shokhirev, Christopher Liddle, Ruth T Yu, Michael Downes, Ronald M Evans, Alan Saghatelian, Andrew M Lowy, and Geoffrey M Wahl
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Medicine ,Science - Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extremely dense fibrotic stroma, which contributes to tumor growth, metastasis, and drug resistance. During tumorigenesis, quiescent pancreatic stellate cells (PSCs) are activated and become major contributors to fibrosis, by increasing growth factor signaling and extracellular matrix deposition. The p53 tumor suppressor is known to restrict tumor initiation and progression through cell autonomous mechanisms including apoptosis, cell cycle arrest, and senescence. There is growing evidence that stromal p53 also exerts anti-tumor activity by paracrine mechanisms, though a role for stromal p53 in PDAC has not yet been described. Here, we demonstrate that activation of stromal p53 exerts anti-tumor effects in PDAC. We show that primary cancer-associated PSCs (caPSCs) isolated from human PDAC express wild-type p53, which can be activated by the Mdm2 antagonist Nutlin-3a. Our work reveals that p53 acts as a major regulator of PSC activation and as a modulator of PDAC fibrosis. In vitro, p53 activation by Nutlin-3a induces profound transcriptional changes, which reprogram activated PSCs to quiescence. Using immunofluorescence and lipidomics, we have also found that p53 activation induces lipid droplet accumulation in both normal and tumor-associated fibroblasts, revealing a previously undescribed role for p53 in lipid storage. In vivo, treatment of tumor-bearing mice with the clinical form of Nutlin-3a induces stromal p53 activation, reverses caPSCs activation, and decreases fibrosis. All together our work uncovers new functions for stromal p53 in PDAC.
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- 2017
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5. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
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Ariel D Chipman, David E K Ferrier, Carlo Brena, Jiaxin Qu, Daniel S T Hughes, Reinhard Schröder, Montserrat Torres-Oliva, Nadia Znassi, Huaiyang Jiang, Francisca C Almeida, Claudio R Alonso, Zivkos Apostolou, Peshtewani Aqrawi, Wallace Arthur, Jennifer C J Barna, Kerstin P Blankenburg, Daniela Brites, Salvador Capella-Gutiérrez, Marcus Coyle, Peter K Dearden, Louis Du Pasquier, Elizabeth J Duncan, Dieter Ebert, Cornelius Eibner, Galina Erikson, Peter D Evans, Cassandra G Extavour, Liezl Francisco, Toni Gabaldón, William J Gillis, Elizabeth A Goodwin-Horn, Jack E Green, Sam Griffiths-Jones, Cornelis J P Grimmelikhuijzen, Sai Gubbala, Roderic Guigó, Yi Han, Frank Hauser, Paul Havlak, Luke Hayden, Sophie Helbing, Michael Holder, Jerome H L Hui, Julia P Hunn, Vera S Hunnekuhl, LaRonda Jackson, Mehwish Javaid, Shalini N Jhangiani, Francis M Jiggins, Tamsin E Jones, Tobias S Kaiser, Divya Kalra, Nathan J Kenny, Viktoriya Korchina, Christie L Kovar, F Bernhard Kraus, François Lapraz, Sandra L Lee, Jie Lv, Christigale Mandapat, Gerard Manning, Marco Mariotti, Robert Mata, Tittu Mathew, Tobias Neumann, Irene Newsham, Dinh N Ngo, Maria Ninova, Geoffrey Okwuonu, Fiona Ongeri, William J Palmer, Shobha Patil, Pedro Patraquim, Christopher Pham, Ling-Ling Pu, Nicholas H Putman, Catherine Rabouille, Olivia Mendivil Ramos, Adelaide C Rhodes, Helen E Robertson, Hugh M Robertson, Matthew Ronshaugen, Julio Rozas, Nehad Saada, Alejandro Sánchez-Gracia, Steven E Scherer, Andrew M Schurko, Kenneth W Siggens, DeNard Simmons, Anna Stief, Eckart Stolle, Maximilian J Telford, Kristin Tessmar-Raible, Rebecca Thornton, Maurijn van der Zee, Arndt von Haeseler, James M Williams, Judith H Willis, Yuanqing Wu, Xiaoyan Zou, Daniel Lawson, Donna M Muzny, Kim C Worley, Richard A Gibbs, Michael Akam, and Stephen Richards
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Biology (General) ,QH301-705.5 - Abstract
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
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- 2014
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6. Aging compromises human islet beta cell function and identity by decreasing transcription factor activity and inducing ER stress
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Shristi Shrestha, Galina Erikson, James Lyon, Aliya F. Spigelman, Austin Bautista, Jocelyn E. Manning Fox, Cristiane dos Santos, Maxim Shokhirev, Jean-Philippe Cartailler, Martin W. Hetzer, Patrick E. MacDonald, and Rafael Arrojo e Drigo
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Multidisciplinary - Abstract
Pancreatic islet beta cells are essential for maintaining glucose homeostasis. To understand the impact of aging on beta cells, we performed meta-analysis of single-cell RNA sequencing datasets, transcription factor (TF) regulon analysis, high-resolution confocal microscopy, and measured insulin secretion from nondiabetic donors spanning most of the human life span. This revealed the range of molecular and functional changes that occur during beta cell aging, including the transcriptional deregulation that associates with cellular immaturity and reorganization of beta cell TF networks, increased gene transcription rates, and reduced glucose-stimulated insulin release. These alterations associate with activation of endoplasmic reticulum (ER) stress and autophagy pathways. We propose that a chronic state of ER stress undermines old beta cell structure function to increase the risk of beta cell failure and type 2 diabetes onset as humans age.
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- 2022
7. Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq
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Graham McVicker, Yi Fu, Sélène T. Tyndale, Arya R. Massarat, Galina Erikson, Arko Sen, and Jeff Jaureguy
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AcademicSubjects/SCI00010 ,Sequencing data ,ATAC-seq ,Computational biology ,Regulatory Sequences, Nucleic Acid ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Cell Line ,Jurkat Cells ,Mice ,03 medical and health sciences ,0302 clinical medicine ,INDEL Mutation ,Cell Line, Tumor ,Genetics ,Animals ,Humans ,Overall performance ,Indel ,De novo mutations ,Narese/7 ,030304 developmental biology ,0303 health sciences ,Genome, Human ,Genetic variants ,Reproducibility of Results ,Computational Biology ,Narese/24 ,Chromatin Immunoprecipitation Sequencing ,Single-Cell Analysis ,030217 neurology & neurosurgery - Abstract
Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost ‘capture’ method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels within ATAC-seq peak regions with at least 10 reads. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.
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- 2021
8. m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin
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Megumi Onishi-Seebacher, Galina Erikson, Katharina Fritz, Thomas Jenuwein, Philip Knuckles, Valentina Perrera, Mark Helm, Reagan W. Ching, Katarzyna J Duda, Marc Bühler, Gerhard Mittler, Bettina Engist, Florian Richter, Nicholas Shukeir, and Lisa Jerabek
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Adenosine ,AcademicSubjects/SCI00010 ,Heterochromatin ,RNA methylation ,Methylation ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Gene expression ,Genetics ,Animals ,030304 developmental biology ,0303 health sciences ,biology ,Methyltransferase complex ,Gene regulation, Chromatin and Epigenetics ,RNA ,Mouse Embryonic Stem Cells ,DNA ,Chromatin ,Cell biology ,Histone ,chemistry ,Tandem Repeat Sequences ,biology.protein ,030217 neurology & neurosurgery - Abstract
Heterochromatin has essential functions in maintaining chromosome structure, in protecting genome integrity and in stabilizing gene expression programs. Heterochromatin is often nucleated by underlying DNA repeat sequences, such as major satellite repeats (MSR) and long interspersed nuclear elements (LINE). In order to establish heterochromatin, MSR and LINE elements need to be transcriptionally competent and generate non-coding repeat RNA that remain chromatin associated. We explored whether these heterochromatic RNA, similar to DNA and histones, may be methylated, particularly for 5-methylcytosine (5mC) or methyl-6-adenosine (m6A). Our analysis in mouse ES cells identifies only background level of 5mC but significant enrichment for m6A on heterochromatic RNA. Moreover, MSR transcripts are a novel target for m6A RNA modification, and their m6A RNA enrichment is decreased in ES cells that are mutant for Mettl3 or Mettl14, which encode components of a central RNA methyltransferase complex. Importantly, MSR transcripts that are partially deficient in m6A RNA methylation display impaired chromatin association and have a reduced potential to form RNA:DNA hybrids. We propose that m6A modification of MSR RNA will enhance the functions of MSR repeat transcripts to stabilize mouse heterochromatin.
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- 2021
9. Altered Neuronal Support and Inflammatory Response in Bipolar Disorder Patient-Derived Astrocytes
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Michael McCarthy, Maria C. Marchetto, Renata Santos, Maxim N. Shokhirev, Arianna Mei, Kelly J. Heard, Ruth Oefner, Galina Erikson, Krishna C. Vadodaria, Vipula Racha, Lisa T. Eyler, John R. Kelsoe, Ana P.D. Mendes, Fred H. Gage, The Salk Institute for Biological Studies, University of California [San Diego] (UC San Diego), University of California, Institut de psychiatrie et neurosciences de Paris (IPNP - U1266 Inserm), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), University of California (UC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), and Martinez Rico, Clara
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0301 basic medicine ,Bipolar Disorder ,glia ,medicine.medical_treatment ,[SDV.MHEP.PSM] Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health ,Interleukin-1beta ,Biochemistry ,neuronal activity ,Transcriptome ,0302 clinical medicine ,cytokine ,Premovement neuronal activity ,Induced pluripotent stem cell ,Neurons ,iPSC ,biology ,Phenotype ,mood disorders ,psychiatry ,3. Good health ,Cytokine ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,medicine.symptom ,Neuroglia ,medicine.medical_specialty ,Clinical Sciences ,Induced Pluripotent Stem Cells ,Inflammation ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Neuropathology ,Article ,03 medical and health sciences ,Internal medicine ,Genetics ,medicine ,Humans ,[SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,Interleukin 6 ,[SDV.BC] Life Sciences [q-bio]/Cellular Biology ,IL-6 ,Interleukin-6 ,astrocytes ,Cell Biology ,Coculture Techniques ,IL-6 Stem Cell Reports ,030104 developmental biology ,Endocrinology ,inflammation ,[SDV.MHEP.PSM]Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health ,biology.protein ,Biochemistry and Cell Biology ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Summary Bipolar disorder (BD) is characterized by cyclical mood shifts. Studies indicate that BD patients have a peripheral pro-inflammatory state and alterations in glial populations in the brain. We utilized an in vitro model to study inflammation-related phenotypes of astrocytes derived from induced pluripotent stem cells (iPSCs) generated from BD patients and healthy controls. BD astrocytes showed changes in transcriptome and induced a reduction in neuronal activity when co-cultured with neurons. IL-1β-stimulated BD astrocytes displayed a unique inflammatory gene expression signature and increased secretion of IL-6. Conditioned medium from stimulated BD astrocytes reduced neuronal activity, and this effect was partially blocked by IL-6 inactivating antibody. Our results suggest that BD astrocytes are functionally less supportive of neuronal excitability and this effect is partially mediated by IL-6. We confirmed higher IL-6 in blood in a distinct cohort of BD patients, highlighting the potential role of astrocyte-mediated inflammatory signaling in BD neuropathology., Highlights • Bipolar disorder astrocytes are functionally less supportive of neuronal activity • Bipolar disorder astrocytes response to IL-1β is transcriptionally distinct • IL-6 secretion in bipolar disorder astrocytes reduces neuronal activity • Bipolar disorder patients show higher circulating levels of IL-6 in blood, In this article, Gage and collaborators show that astrocytes differentiated from induced pluripotent stem cells generated from bipolar disorder patients are functionally less supportive of neuronal activity. Bipolar disorder astrocytes' response to pro-inflammatory cytokines is characterized by a unique transcriptional response and increased IL-6 secretion that directly and negatively impacted on neuronal activity. Increased peripheral IL-6 was confirmed in a distinct clinical cohort highlighting the potential role of astrocyte-mediated inflammatory signaling in the neuropathology of bipolar disorder.
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- 2021
10. Activity-dependent modulation of synapse-regulating genes in astrocytes
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Cari Dowling, Hanqing Liu, Galina Erikson, Chen Farhy, Nicola J. Allen, Joseph R. Ecker, Matthew M. Boisvert, Isabella Farhy-Tselnicker, Elena Blanco-Suarez, and Maxim N. Shokhirev
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Male ,Mouse ,QH301-705.5 ,Science ,Presynaptic Terminals ,Glutamic Acid ,Biology ,synaptic terminals ,General Biochemistry, Genetics and Molecular Biology ,neuronal activity ,Synapse ,Rats, Sprague-Dawley ,Mice ,Gene expression ,medicine ,Premovement neuronal activity ,Animals ,Humans ,Biology (General) ,Gene ,Visual Cortex ,Neurons ,General Immunology and Microbiology ,General Neuroscience ,Glutamate receptor ,astrocytes ,General Medicine ,Rats ,Mice, Inbred C57BL ,medicine.anatomical_structure ,Visual cortex ,Neurodevelopmental Disorders ,visual development ,Synapses ,gene expression ,Medicine ,Female ,Developmental biology ,Neuroscience ,Astrocyte ,Research Article ,Developmental Biology - Abstract
Astrocytes regulate the formation and function of neuronal synapses via multiple signals; however, what controls regional and temporal expression of these signals during development is unknown. We determined the expression profile of astrocyte synapse-regulating genes in the developing mouse visual cortex, identifying astrocyte signals that show differential temporal and layer-enriched expression. These patterns are not intrinsic to astrocytes, but regulated by visually evoked neuronal activity, as they are absent in mice lacking glutamate release from thalamocortical terminals. Consequently, synapses remain immature. Expression of synapse-regulating genes and synaptic development is also altered when astrocyte signaling is blunted by diminishing calcium release from astrocyte stores. Single-nucleus RNA sequencing identified groups of astrocytic genes regulated by neuronal and astrocyte activity, and a cassette of genes that show layer-specific enrichment. Thus, the development of cortical circuits requires coordinated signaling between astrocytes and neurons, highlighting astrocytes as a target to manipulate in neurodevelopmental disorders.
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- 2021
11. Author response: Activity-dependent modulation of synapse-regulating genes in astrocytes
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Nicola J. Allen, Cari Dowling, Hanqing Liu, Maxim N. Shokhirev, Joseph R. Ecker, Isabella Farhy-Tselnicker, Galina Erikson, Chen Farhy, Matthew M. Boisvert, and Elena Blanco-Suarez
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Synapse ,Modulation ,Biology ,Gene ,Neuroscience - Published
- 2021
12. Complete loss of H3K9 methylation dissolves mouse heterochromatin organization
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Alexandra Graff Meyer, Megumi Onishi-Seebacher, Thomas Jenuwein, Yaarub Musa, Thomas Montavon, Nicholas Shukeir, Devon Ryan, Bettina Engist, Galina Erikson, Christel Genoud, and Gerhard Mittler
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Methyltransferase ,General Physics and Astronomy ,Mass Spectrometry ,Epigenesis, Genetic ,Histones ,Mice ,0302 clinical medicine ,Heterochromatin ,RNA-Seq ,Heterochromatin organization ,In Situ Hybridization, Fluorescence ,0303 health sciences ,Multidisciplinary ,Gene silencing ,Methylation ,Chromatin ,Cell biology ,Histone ,Chromatin Immunoprecipitation Sequencing ,General Biochemistry, Genetics and Molecular Biology ,General Chemistry ,Signal Transduction ,Retroelements ,Science ,Biology ,Article ,03 medical and health sciences ,Histone H3 ,Microscopy, Electron, Transmission ,Transferases ,Animals ,Epigenetics ,Repetitive Sequences, Nucleic Acid ,030304 developmental biology ,Lysine ,fungi ,Histone-Lysine N-Methyltransferase ,Fibroblasts ,Demethylation ,Mutation ,biology.protein ,CRISPR-Cas Systems ,Protein Processing, Post-Translational ,Gene Deletion ,030217 neurology & neurosurgery ,Chromatography, Liquid - Abstract
Histone H3 lysine 9 (H3K9) methylation is a central epigenetic modification that defines heterochromatin from unicellular to multicellular organisms. In mammalian cells, H3K9 methylation can be catalyzed by at least six distinct SET domain enzymes: Suv39h1/Suv39h2, Eset1/Eset2 and G9a/Glp. We used mouse embryonic fibroblasts (MEFs) with a conditional mutation for Eset1 and introduced progressive deletions for the other SET domain genes by CRISPR/Cas9 technology. Compound mutant MEFs for all six SET domain lysine methyltransferase (KMT) genes lack all H3K9 methylation states, derepress nearly all families of repeat elements and display genomic instabilities. Strikingly, the 6KO H3K9 KMT MEF cells no longer maintain heterochromatin organization and have lost electron-dense heterochromatin. This is a compelling analysis of H3K9 methylation-deficient mammalian chromatin and reveals a definitive function for H3K9 methylation in protecting heterochromatin organization and genome integrity., Histone H3K9 methylation (H3K9me) states define repressed chromatin in eukaryotic cells. Here the authors reveal complete loss of all H3K9me in mammalian cells through successive deletion of H3K9 methyltransferase genes that results in the dissolution of heterochromatin and the derepression of nearly all repeat families.
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- 2021
13. Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia
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Megumi Onishi-Seebacher, Zoe Sawitzki, Gabriele Greve, Thomas Jenuwein, Michael Lübbert, Galina Erikson, and Devon Ryan
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Myeloid leukemia ,Retrotransposon ,QH426-470 ,Biology ,RC31-1245 ,Leukemia, Myeloid, Acute ,Gene expression ,Genetics ,Cancer research ,Biomarker (medicine) ,Human genome ,Epigenetics ,DNA microarray ,Internal medicine ,Gene ,Genetics (clinical) ,Research Article - Abstract
Background Repeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcription of endogenous retrotransposons is often suppressed to attenuate an anti-tumor immune response, whereas aberrant expression of heterochromatin-derived satellite RNA has been identified as a tumor driver. These insights demonstrate separate functions for the dysregulation of distinct repeat subclasses in either the attenuation or progression of human solid tumors. For hematopoietic malignancies, such as Acute Myeloid Leukemia (AML), only very few studies on the expression/dysregulation of repeat elements were done. Methods To study the expression of repeat elements in AML, we performed total-RNA sequencing of healthy CD34 + cells and of leukemic blast cells from primary AML patient material. We also developed an integrative bioinformatic approach that can quantify the expression of repeat transcripts from all repeat subclasses (SINE/ALU, LINE, ERV and satellites) in relation to the expression of gene and other non-repeat transcripts (i.e. R/G ratio). This novel approach can be used as an instructive signature for repeat element expression and has been extended to the analysis of poly(A)-RNA sequencing datasets from Blueprint and TCGA consortia that together comprise 120 AML patient samples. Results We identified that repeat element expression is generally down-regulated during hematopoietic differentiation and that relative changes in repeat to gene expression can stratify risk prediction of AML patients and correlate with overall survival probabilities. A high R/G ratio identifies AML patient subgroups with a favorable prognosis, whereas a low R/G ratio is prevalent in AML patient subgroups with a poor prognosis. Conclusions We developed an integrative bioinformatic approach that defines a general model for the analysis of repeat element dysregulation in physiological and pathological development. We find that changes in repeat to gene expression (i.e. R/G ratios) correlate with hematopoietic differentiation and can sub-stratify AML patients into low-risk and high-risk subgroups. Thus, the definition of a R/G ratio can serve as a valuable biomarker for AML and could also provide insights into differential patient response to epigenetic drug treatment.
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- 2021
14. Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder
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Renata Santos, Galina Erikson, Yeni Kim, Sara B. Linker, Fred H. Gage, Maxim N. Shokhirev, Debha Amatya, Maria C. Marchetto, Tatyana O. Sharpee, Ana P.D. Mendes, and Yuansheng Zhou
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Adult ,0301 basic medicine ,Adolescent ,multielectrode array ,Autism Spectrum Disorder ,Induced Pluripotent Stem Cells ,Neuronal differentiation ,neurodevelopmental disorder models ,dynamical complexity ,Biology ,Cell morphology ,Biochemistry ,Article ,Nonlinear dynamical systems ,Young Adult ,03 medical and health sciences ,Bursting ,Spatio-Temporal Analysis ,0302 clinical medicine ,Cell Movement ,mental disorders ,Genetics ,medicine ,Humans ,Premovement neuronal activity ,Child ,lcsh:QH301-705.5 ,Neurons ,lcsh:R5-920 ,minimum embedding dimension ,Spatiotemporal Analysis ,Brain ,Cell Differentiation ,Cell Biology ,Middle Aged ,medicine.disease ,Electrophysiological Phenomena ,Electrophysiology ,030104 developmental biology ,Gene Expression Regulation ,lcsh:Biology (General) ,Autism spectrum disorder ,Case-Control Studies ,lcsh:Medicine (General) ,Neuroscience ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Summary Neuronal activity can be modeled as a nonlinear dynamical system to yield measures of neuronal state and dysfunction. The electrical recordings of stem cell-derived neurons from individuals with autism spectrum disorder (ASD) and controls were analyzed using minimum embedding dimension (MED) analysis to characterize their dynamical complexity. MED analysis revealed a significant reduction in dynamical complexity in ASD neurons during differentiation, which was correlated to bursting and spike interval measures. MED was associated with clinical endpoints, such as nonverbal intelligence, and was correlated with 53 differentially expressed genes, which were overrepresented with ASD risk genes related to neurodevelopment, cell morphology, and cell migration. Spatiotemporal analysis also showed a prenatal temporal enrichment in cortical and deep brain structures. Together, we present dynamical analysis as a paradigm that can be used to distinguish disease-associated cellular electrophysiological and transcriptional signatures, while taking into account patient variability in neuropsychiatric disorders., Graphical Abstract, Highlights • Electrical recordings of iPSC-derived neurons can be modeled as a dynamical system • Dynamical complexity is characterized by minimum embedding dimension (MED) • MED is reduced in ASD neuronal lines during differentiation • MED is correlated to gene expression changes relevant to prenatal neurodevelopment, Marchetto, Kim, and colleagues describe the application of dynamical analysis to stem cell-derived neuronal recordings from patients with ASD. They find that dynamical complexity is reduced in ASD electrical activity, as measured by minimum embedding dimension (MED). They go on to describe the gene expression, biological pathway, and neurodevelopmental correlates of the MED signature, supporting findings in the literature.
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- 2019
15. Targeting LIF-mediated paracrine interaction for pancreatic cancer therapy and monitoring
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Ruijun Tian, Mathias Leblanc, Tony Pawson, Kathleen E. DelGiorno, Corina E. Antal, Yu Shi, Peiwu Huang, Elena Terenziani, Uri Manor, Michael A. Hollingsworth, Miriam Scadeng, Tony Hunter, Sarah E. Umetsu, Paul M. Grandgenett, Jill Meisenhelder, Galina Erikson, Timothy R. Donahue, Thom P. Santisakultarm, Ronald M. Evans, Xiao Yuan, Huaiyu Sun, Maya Ridinger-Saison, Geoffrey M. Wahl, Gyunghwi Woo, Daniel D. Von Hoff, Nikki K. Lytle, Andrew M. Lowy, Eric A. Collisson, Carlos Becerra, Linjing Fang, Michael Downes, Amanda M. Dann, Annette R. Atkins, Ruilian Xu, Weina Gao, Gaoyang Liang, Erkut Borazanci, and Tannishtha Reya
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0301 basic medicine ,Male ,endocrine system diseases ,Carcinogenesis ,Drug Resistance ,Leukemia inhibitory factor receptor ,medicine.disease_cause ,Leukemia Inhibitory Factor ,Mass Spectrometry ,OSM-LIF ,Metastasis ,Mice ,0302 clinical medicine ,Monoclonal ,Receptors ,Tumor Microenvironment ,2.1 Biological and endogenous factors ,Aetiology ,Cancer ,screening and diagnosis ,Tumor ,Multidisciplinary ,Antibodies, Monoclonal ,Cell Differentiation ,3. Good health ,Detection ,Pancreatic Ductal ,5.1 Pharmaceuticals ,030220 oncology & carcinogenesis ,Disease Progression ,Female ,Development of treatments and therapeutic interventions ,Carcinoma, Pancreatic Ductal ,Epithelial-Mesenchymal Transition ,Receptors, OSM-LIF ,General Science & Technology ,Antibodies ,Article ,Cell Line ,Pancreatic Cancer ,03 medical and health sciences ,Paracrine signalling ,Rare Diseases ,Pancreatic cancer ,Cell Line, Tumor ,Paracrine Communication ,medicine ,Animals ,Humans ,Epithelial–mesenchymal transition ,Tumor microenvironment ,business.industry ,Carcinoma ,medicine.disease ,4.1 Discovery and preclinical testing of markers and technologies ,Pancreatic Neoplasms ,Orphan Drug ,030104 developmental biology ,Drug Resistance, Neoplasm ,Cancer cell ,Cancer research ,Neoplasm ,Digestive Diseases ,business - Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis largely owing to inefficient diagnosis and tenacious drug resistance. Activation of pancreatic stellate cells (PSCs) and consequent development of dense stroma are prominent features accounting for this aggressive biology1,2. The reciprocal interplay between PSCs and pancreatic cancer cells (PCCs) not only enhances tumour progression and metastasis but also sustains their own activation, facilitating a vicious cycle to exacerbate tumorigenesis and drug resistance3-7. Furthermore, PSC activation occurs very early during PDAC tumorigenesis8-10, and activated PSCs comprise a substantial fraction of the tumour mass, providing a rich source of readily detectable factors. Therefore, we hypothesized that the communication between PSCs and PCCs could be an exploitable target to develop effective strategies for PDAC therapy and diagnosis. Here, starting with asystematic proteomic investigation of secreted disease mediators and underlying molecular mechanisms, we reveal that leukaemia inhibitory factor (LIF) is a key paracrine factor from activated PSCs acting on cancer cells. Both pharmacologic LIF blockade and genetic Lifr deletion markedly slow tumour progression and augment theefficacy of chemotherapy to prolong survival of PDAC mouse models, mainly by modulating cancer cell differentiation and epithelial-mesenchymal transition status. Moreover, in both mouse models and human PDAC, aberrant production of LIF in the pancreas is restricted to pathological conditions and correlates with PDAC pathogenesis, and changes in the levels ofcirculating LIF correlate well with tumour response to therapy. Collectively, these findings reveal a function of LIF in PDAC tumorigenesis, and suggest its translational potential as an attractive therapeutic target and circulating marker. Our studies underscore how a better understanding of cell-cell communication within the tumour microenvironment can suggest novel strategies for cancer therapy.
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- 2019
16. Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3
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Ian Maze, Kelly J. Heard, Natalia Alenina, Henrik Molina, Bradley J. Lukasak, Ryan M. Bastle, Fred H. Gage, Michael Bader, Tom W. Muir, Krishna C. Vadodaria, Baichao Zhang, Robert E. Thompson, Natarajan V. Bhanu, Robert G. Roeder, Shuai Zhao, Tomoyoshi Nakadai, Yang Lyu, Aarthi Ramakrishnan, Olivier Berton, Lorna A. Farrelly, Li Shen, Henry Zebroski, Haitao Li, Benjamin A. Garcia, Ashley E. Lepack, Galina Erikson, and Yong-Hwee E. Loh
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0301 basic medicine ,Regulation of gene expression ,Multidisciplinary ,biology ,Chemistry ,Cellular differentiation ,Serotonylation ,Cell biology ,03 medical and health sciences ,Histone H3 ,030104 developmental biology ,0302 clinical medicine ,Histone ,biology.protein ,H3K4me3 ,Nucleosome ,Epigenetics ,030217 neurology & neurosurgery - Abstract
Chemical modifications of histones can mediate diverse DNA-templated processes, including gene transcription1–3. Here we provide evidence for a class of histone post-translational modification, serotonylation of glutamine, which occurs at position 5 (Q5ser) on histone H3 in organisms that produce serotonin (also known as 5-hydroxytryptamine (5-HT)). We demonstrate that tissue transglutaminase 2 can serotonylate histone H3 tri-methylated lysine 4 (H3K4me3)-marked nucleosomes, resulting in the presence of combinatorial H3K4me3Q5ser in vivo. H3K4me3Q5ser displays a ubiquitous pattern of tissue expression in mammals, with enrichment observed in brain and gut, two organ systems responsible for the bulk of 5-HT production. Genome-wide analyses of human serotonergic neurons, developing mouse brain and cultured serotonergic cells indicate that H3K4me3Q5ser nucleosomes are enriched in euchromatin, are sensitive to cellular differentiation and correlate with permissive gene expression, phenomena that are linked to the potentiation of TFIID4–6 interactions with H3K4me3. Cells that ectopically express a H3 mutant that cannot be serotonylated display significantly altered expression of H3K4me3Q5ser-target loci, which leads to deficits in differentiation. Taken together, these data identify a direct role for 5-HT, independent from its contributions to neurotransmission and cellular signalling, in the mediation of permissive gene expression. In serotonin-rich tissues, tissue transglutaminase 2 is able to attach serotonin to a glutamine residue in histone H3; this modification mediates permissive gene expression in these tissues.
- Published
- 2019
17. Single-Dose CRISPR/Cas9 Therapy Extends Lifespan of Mice with Hutchinson-Gilford Progeria Syndrome
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Pradeep Reddy, Mako Yamamoto, Reyna Hernández-Benítez, Hsin-Kai Liao, Galina Erikson, Yunpeng Fu, Juan Carlos Izpisua Belmonte, and Ergin Beyret
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0301 basic medicine ,congenital, hereditary, and neonatal diseases and abnormalities ,Genetic enhancement ,Longevity ,Biology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Progeria ,medicine ,Animals ,Protein Isoforms ,Mutation ,integumentary system ,Point mutation ,Genetic disorder ,nutritional and metabolic diseases ,General Medicine ,Genetic Therapy ,medicine.disease ,Progerin ,Lamin Type A ,Phenotype ,Disease Models, Animal ,030104 developmental biology ,030220 oncology & carcinogenesis ,embryonic structures ,Cancer research ,CRISPR-Cas Systems ,Lamin - Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is a rare lethal genetic disorder characterized by symptoms reminiscent of accelerated aging. The major underlying genetic cause is a substitution mutation in the gene coding for lamin A, causing the production of a toxic isoform called progerin. Here we show that reduction of lamin A/progerin by a single-dose systemic administration of adeno-associated virus-delivered CRISPR–Cas9 components suppresses HGPS in a mouse model. AAV-mediated CRISPR–Cas9 therapy extends lifespan and ameliorates disease-related phenotypes in a mouse model of Hutchinson–Gilford progeria syndrome.
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- 2019
18. Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq
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Jeff Jaureguy, Yi Fu, Sélène T. Tyndale, Arya R. Massarat, Arko Sen, Galina Erikson, and Graham McVicker
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chemistry.chemical_classification ,chemistry ,Computer science ,Regulatory sequence ,Genetic variants ,Nucleotide ,ATAC-seq ,Computational biology ,Indel ,Genome ,De novo mutations ,Chromatin - Abstract
Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost ‘capture’ method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.
- Published
- 2021
19. Deficient LEF1 expression is associated with lithium resistance and hyperexcitability in neurons derived from bipolar disorder patients
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Yeni Kim, John R. Kelsoe, Maria C. Marchetto, Ana P.D. Mendes, Maxim N. Shokhirev, Galina Erikson, Martin Alda, Lynne Randolph-Moore, Sara B. Linker, Fred H. Gage, Renata Santos, Anne G. Bang, Shani Stern, Vipula Racha, The Salk Institute for Biological Studies, Institut de psychiatrie et neurosciences de Paris (IPNP - U1266 Inserm), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), University of Haifa [Haifa], Dongguk University (DU), Department of Psychiatry [San Diego, CA, États-Unis], University of California [San Diego] (UC San Diego), University of California-University of California, Sanford Burnham Prebys Medical Discovery Institute, Dalhousie University [Halifax], University of California, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of California (UC)-University of California (UC), University of California (UC), and Martinez Rico, Clara
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0301 basic medicine ,medicine.medical_specialty ,Lithium (medication) ,[SDV.MHEP.PSM] Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health ,Hippocampal formation ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,0302 clinical medicine ,Downregulation and upregulation ,Transcription (biology) ,Internal medicine ,medicine ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Induced pluripotent stem cell ,Molecular Biology ,Valproic Acid ,Chemistry ,Wnt signaling pathway ,3. Good health ,Psychiatry and Mental health ,030104 developmental biology ,Endocrinology ,[SDV.MHEP.PSM]Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health ,embryonic structures ,Signal transduction ,030217 neurology & neurosurgery ,medicine.drug - Abstract
International audience; Bipolar disorder (BD) is a psychiatric condition characterized by depressive and manic episodes that affect 2% of the world population. The first-line long-term treatment for mood stabilization is lithium (Li). Induced pluripotent stem cell modeling of BD using hippocampal dentate gyrus-like neurons derived from Li-responsive (LR) and Li-non-responsive (NR) patients previously showed neuronal hyperexcitability. Li treatment reversed hyperexcitability only on the LR neurons. In this study we searched for specific targets of Li resistance in NR neurons and found that the activity of Wnt/β-catenin signaling pathway was severely affected, with a significant decrease in expression of LEF1. Li targets the Wnt/βcatenin signaling pathway by inhibiting GSK-3β and releasing β-catenin that forms a nuclear complex with TCF/LEF1, activating the Wnt/β-catenin transcription program. Therefore, we propose that downregulation of LEF1 may account for Li resistance in NR neurons. Our results show that valproic acid (VPA), a drug used to treat NR patients that also acts downstream of GSK-3β, upregulated LEF1 and Wnt/β-catenin gene targets, increased transcriptional activity of complex β-catenin/TCF/LEF1 and reduced excitability in NR neurons. Additionally, decreasing LEF1 expression in control neurons using shLEF1 caused hyperexcitability, confirming that the impact of VPA on excitability in NR neurons was connected to changes in LEF1 and in the Wnt/β-catenin pathway. Our results suggest that LEF1 may be a useful target for the discovery of new drugs for BD treatment.
- Published
- 2021
20. Activity-Dependent Modulation of Synapse-Regulating Genes in Astrocytes
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Nicola J. Allen, Elena Blanco-Suarez, Joseph R. Ecker, Isabella Farhy-Tselnicker, Maxim N. Shokhirev, Galina Erikson, Cari Dowling, Hanqing Liu, Chen Farhy, and Matthew M. Boisvert
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Synapse ,Visual cortex ,medicine.anatomical_structure ,Glutamate receptor ,medicine ,RNA ,Premovement neuronal activity ,Biology ,Gene ,Nucleus ,Astrocyte ,Cell biology - Abstract
SummaryAstrocytes regulate the formation and function of neuronal synapses via multiple signals, however, what controls regional and temporal expression of these signals during development is unknown. We determined the expression profile of astrocyte synapse-regulating genes in the developing mouse visual cortex, identifying astrocyte signals that show differential temporal and layer-enriched expression. These patterns are not intrinsic to astrocytes, but regulated by visually-evoked neuronal activity, as they are absent in mice lacking glutamate release from thalamocortical terminals. Consequently, synapses remain immature. Expression of synapse-regulating genes and synaptic development are also altered when astrocyte signaling is blunted by diminishing calcium release from astrocyte stores. Single nucleus RNA sequencing identified groups of astrocytic genes regulated by neuronal and astrocyte activity, and a cassette of genes that show layer-specific enrichment. Thus, the development of cortical circuits requires coordinated signaling between astrocytes and neurons, identifying astrocytes as a target to manipulate in neurodevelopmental disorders.
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- 2020
21. Deficient LEF1 expression is associated with lithium resistance and hyperexcitability in neurons derived from bipolar disorder patients
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Renata, Santos, Sara B, Linker, Shani, Stern, Ana P D, Mendes, Maxim N, Shokhirev, Galina, Erikson, Lynne, Randolph-Moore, Vipula, Racha, Yeni, Kim, John R, Kelsoe, Anne G, Bang, M, Alda, Maria C, Marchetto, and Fred H, Gage
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Neurons ,Bipolar Disorder ,Glycogen Synthase Kinase 3 beta ,Lymphoid Enhancer-Binding Factor 1 ,Humans ,Lithium ,Wnt Signaling Pathway ,beta Catenin - Abstract
Bipolar disorder (BD) is a psychiatric condition characterized by depressive and manic episodes that affect 2% of the world population. The first-line long-term treatment for mood stabilization is lithium (Li). Induced pluripotent stem cell modeling of BD using hippocampal dentate gyrus-like neurons derived from Li-responsive (LR) and Li-non-responsive (NR) patients previously showed neuronal hyperexcitability. Li treatment reversed hyperexcitability only on the LR neurons. In this study we searched for specific targets of Li resistance in NR neurons and found that the activity of Wnt/β-catenin signaling pathway was severely affected, with a significant decrease in expression of LEF1. Li targets the Wnt/β-catenin signaling pathway by inhibiting GSK-3β and releasing β-catenin that forms a nuclear complex with TCF/LEF1, activating the Wnt/β-catenin transcription program. Therefore, we propose that downregulation of LEF1 may account for Li resistance in NR neurons. Our results show that valproic acid (VPA), a drug used to treat NR patients that also acts downstream of GSK-3β, upregulated LEF1 and Wnt/β-catenin gene targets, increased transcriptional activity of complex β-catenin/TCF/LEF1, and reduced excitability in NR neurons. In addition, decreasing LEF1 expression in control neurons using shLEF1 caused hyperexcitability, confirming that the impact of VPA on excitability in NR neurons was connected to changes in LEF1 and in the Wnt/β-catenin pathway. Our results suggest that LEF1 may be a useful target for the discovery of new drugs for BD treatment.
- Published
- 2020
22. Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling
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Kathleen E. DelGiorno, Sammy Weiser Novak, Dezhen Wang, Chi-Yeh Chung, Mauer Hc, Rajshekhar R. Giraddi, Linjing Fang, Geoffrey M. Wahl, Urade Y, Carolyn O’Connor, Maya Ridinger-Saison, Wahida H. Ali, Maxim N. Shokhirev, Leo Andrade, Ichiro Matsumoto, Makoto Ohmoto, Razia F. Naeem, Pankaj K. Singh, Vavinskaya, Nikki K. Lytle, Kenneth P. Olive, Gubbala Vb, Crystal Tsui, Uri Manor, and Galina Erikson
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0303 health sciences ,Cell type ,Stromal cell ,Pancreatic disease ,Biology ,medicine.disease ,medicine.disease_cause ,3. Good health ,03 medical and health sciences ,Paracrine signalling ,chemistry.chemical_compound ,0302 clinical medicine ,Stroma ,chemistry ,medicine ,Cancer research ,Prostaglandin D2 ,Tuft cell ,Carcinogenesis ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Despite numerous advances in our understanding of pancreatic ductal adenocarcinoma (PDA) genetics and biology, this disease is expected to become the second leading cause of cancer-related U.S. deaths within the next few years. Incomplete understanding of how it arises precludes development of early detection and interception strategies to improve therapeutic outcomes. Acinar to ductal metaplasia involving genesis of tuft cells is one early step in PDA formation, but their functional significance has remained obscure due to their rarity and a lack of methods and relevant animal models for their molecular and functional analysis. Here, we show that deletion of tuft cell master regulator Pou2f3 eliminates pancreatic tuft cells and increases fibrosis, alters immune cell activation, and accelerates disease progression. We demonstrate that tuft cell expression of the prostaglandin D2 synthase Hpgds restrains pancreatic disease progression in early stages by inhibiting stromal activation. Analyses of human data sets are consistent with mouse studies. We propose that tuft cells and, by inference, the associated metaplastic lesions, play a protective role early in pancreatic tumorigenesis.SignificanceWe find that tuft cell formation in response to oncogenic Kras is protective and restrains tumorigenesis through local production of anti-inflammatory substances, including paracrine prostaglandin D2 signaling to the stroma. Our findings establish tuft cells as a metaplasia-induced tumor suppressive cell type.
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- 2019
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23. The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain
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Galina Erikson, Nicola J. Allen, Maxim N. Shokhirev, and Matthew M. Boisvert
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0301 basic medicine ,Aging ,Mice, Transgenic ,Biology ,Synaptic Transmission ,Article ,General Biochemistry, Genetics and Molecular Biology ,Transcriptome ,Synapse ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Downregulation and upregulation ,Gene expression ,medicine ,Animals ,Cognitive decline ,lcsh:QH301-705.5 ,Gene ,Cerebral Cortex ,Neurodegeneration ,medicine.disease ,Up-Regulation ,030104 developmental biology ,medicine.anatomical_structure ,lcsh:Biology (General) ,Astrocytes ,Synapses ,Databases, Nucleic Acid ,Neuroscience ,030217 neurology & neurosurgery ,Astrocyte - Abstract
SUMMARY Aging brains undergo cognitive decline, associated with decreased neuronal synapse number and function and altered metabolism. Astrocytes regulate neuronal synapse formation and function in development and adulthood, but whether these properties change during aging, contributing to neuronal dysfunction, is unknown. We addressed this by generating aged and adult astrocyte transcriptomes from multiple mouse brain regions. These data provide a comprehensive RNA-seq database of adult and aged astrocyte gene expression, available online as a resource. We identify astrocyte genes altered by aging across brain regions and regionally unique aging changes. Aging astrocytes show minimal alteration of homeostatic and neurotransmission-regulating genes. However, aging astrocytes upregulate genes that eliminate synapses and partially resemble reactive astrocytes. We further identified heterogeneous expression of synapse-regulating genes between astrocytes from different cortical regions. We find that alterations to astrocytes in aging create an environment permissive to synapse elimination and neuronal damage, potentially contributing to aging-associated cognitive decline., In Brief The aging brain has reduced synapse number and decreased neuronal activity, functions regulated by neighboring astrocytes. Boisvert et al. investigated if aging astrocytes are contributing to these changes and found that aged astrocytes show increased expression of genes for inflammatory and synapse elimination pathways and decreased cholesterol synthesis enzymes.
- Published
- 2018
24. Author Correction: Targeting LIF-mediated paracrine interaction for pancreatic cancer therapy and monitoring
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Uri Manor, Jill Meisenhelder, Kathleen E. DelGiorno, Timothy R. Donahue, Huaiyu Sun, Eric A. Collisson, Maya Ridinger-Saison, Carlos Becerra, Tannishtha Reya, Tony Hunter, Yu Shi, Annette R. Atkins, Tony Pawson, Paul M. Grandgenett, Peiwu Huang, Galina Erikson, Miriam Scadeng, Geoffrey M. Wahl, Gyunghwi Woo, Nikki K. Lytle, Sarah E. Umetsu, Erkut Borazanci, Ruilian Xu, Corina E. Antal, Andrew M. Lowy, Mathias Leblanc, Xiao Yuan, Ruijun Tian, Weina Gao, Amanda M. Dann, Michael Downes, Gaoyang Liang, Ronald M. Evans, Thom P. Santisakultarm, Daniel D. Von Hoff, Linjing Fang, Elena Terenziani, and Michael A. Hollingsworth
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Paracrine signalling ,Multidisciplinary ,business.industry ,Pancreatic cancer ,Cancer research ,Medicine ,business ,medicine.disease - Published
- 2021
25. Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells
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Callie Fredlender, Ana P.D. Mendes, Lynne Randolph-Moore, Manching Ku, Sonia Dave, Sabrina Lefcochilos-Fogelquist, Patrick Charnay, Renata Santos, Fred H. Gage, Krishna C. Vadodaria, Maria C. Marchetto, Ruth Oefner, Ahmet M. Denli, Arianna Mei, Galina Erikson, John R. Kelsoe, Conor Fitzpatrick, Monique Pena, Maxim N. Shokhirev, Baptiste N. Jaeger, Jerika J. Barron, and Bilal E. Kerman
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0301 basic medicine ,Interleukin-1beta ,Stimulation ,Biochemistry ,Leukemia Inhibitory Factor ,Glial Progenitors Generated ,neuroinflammation ,disease modeling ,Induced pluripotent stem cell ,lcsh:QH301-705.5 ,Cells, Cultured ,Neurons ,Principal Component Analysis ,lcsh:R5-920 ,Stem Cells ,Cell Differentiation ,3. Good health ,Cell biology ,neuropsychiatric disorders ,medicine.anatomical_structure ,Hyaluronan Receptors ,neurodegenerative disorders ,medicine.symptom ,Stem cell ,lcsh:Medicine (General) ,Astrocyte ,Resource ,Pluripotent Stem Cells ,Induced Pluripotent Stem Cells ,Glutamic Acid ,iPSCs ,Inflammation ,Biology ,03 medical and health sciences ,Glial Fibrillary Acidic Protein ,Genetics ,medicine ,Humans ,Progenitor cell ,Neuroinflammation ,Embryonic Stem Cells ,Progenitor ,Sequence Analysis, RNA ,Tumor Necrosis Factor-alpha ,astrocytes ,Cell Biology ,co-culture ,Coculture Techniques ,stem cell ,030104 developmental biology ,Microscopy, Fluorescence ,lcsh:Biology (General) ,Inflammation-Responsive Astrocytes ,Immunology ,RNA ,Calcium ,Transcriptome ,Developmental Biology - Abstract
Summary Astrocyte dysfunction and neuroinflammation are detrimental features in multiple pathologies of the CNS. Therefore, the development of methods that produce functional human astrocytes represents an advance in the study of neurological diseases. Here we report an efficient method for inflammation-responsive astrocyte generation from induced pluripotent stem cells (iPSCs) and embryonic stem cells. This protocol uses an intermediate glial progenitor stage and generates functional astrocytes that show levels of glutamate uptake and calcium activation comparable with those observed in human primary astrocytes. Stimulation of stem cell-derived astrocytes with interleukin-1β or tumor necrosis factor α elicits a strong and rapid pro-inflammatory response. RNA-sequencing transcriptome profiling confirmed that similar gene expression changes occurred in iPSC-derived and primary astrocytes upon stimulation with interleukin-1β. This protocol represents an important tool for modeling in-a-dish neurological diseases with an inflammatory component, allowing for the investigation of the role of diseased astrocytes in neuronal degeneration., Graphical Abstract, Highlights • Reliable method for generation of astrocytes from human iPSCs and ESCs • Generated astrocytes are functional and inflammation-responsive • Generated astrocytes share properties with primary astrocytes in vitro • This method is a valuable tool for disease modeling of neuroinflammation, In this article, Gage and colleagues developed a reliable method for generating functional astrocytes from human pluripotent stem cells. This protocol uses an intermediate glial progenitor stage and generates inflammation-responsive astrocytes, providing an important tool to model neurological diseases in-a-dish, enabling the study of neurological disorders with an inflammatory component.
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- 2017
26. Aging of human endocrine pancreatic cell types is heterogeneous and sex-specific
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Galina Erikson, James Lyon, Juliana Capitanio, Martin W. Hetzer, Swati Tyagi, Arrojo e Drigo R, Austin Bautista, Aliya F. Spigelman, Manning Fox Je, Patrick E. MacDonald, and Maxim N. Shokhirev
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0303 health sciences ,medicine.medical_specialty ,Cell type ,Alpha (ethology) ,030209 endocrinology & metabolism ,Biology ,medicine.disease ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,Endocrinology ,Diabetes mellitus ,Internal medicine ,medicine ,Glucose homeostasis ,Endocrine system ,Beta cell ,Pancreas ,Beta (finance) ,030304 developmental biology - Abstract
SummaryThe human endocrine pancreas must regulate glucose homeostasis throughout the human lifespan, which is generally decades. We performed meta-analysis of single-cell, RNA-sequencing datasets derived from 36 individuals, as well as functional analyses, to characterize age-associated changes to the major endocrine pancreatic cell types. Increasing age was associated with shifts in pancreatic alpha and beta cell identity and loss of nuclear integrity in non-diabetic humans. In non-diabetic individuals ≥ 50 years old, 80% of their beta cells exhibited a transcriptional signature similar to cells from type-2 diabetic (T2D) donors. Surprisingly, ∼5% of beta cells from T2D donors retained a youthful, N.D. transcriptional profile. Furthermore, beta cell function was reduced by 50% during aging in men but not women, which may explain sex-associated differences in diabetes etiology. These analyses reveal that aging of the human endocrine pancreas is sex- and cell-type specific.
- Published
- 2019
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27. BreakCA, a method to discover indels using ChIP-seq and ATAC-seq reads, finds recurrent indels in regulatory regions of neuroblastoma genomes
- Author
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Sélène T. Tyndale, Yi Fu, Galina Erikson, Graham McVicker, and Arko Sen
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Whole genome sequencing ,0303 health sciences ,ATAC-seq ,Computational biology ,Biology ,Genome ,Germline ,3. Good health ,Chromatin ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Indel ,Chromatin immunoprecipitation ,Gene ,030304 developmental biology - Abstract
Most known cancer driver mutations are within protein coding regions of the genome, however, there are several important examples of oncogenic non-coding regulatory mutations. We developed a method to identify insertions and deletions (indels) in regulatory regions using aligned reads from chromatin immunoprecipitation followed by sequencing (ChIP-seq) or the assay for transposase-accessible chromatin (ATAC-seq). Our method, which we call BreakCA for Breaks in Chromatin Accessible regions, allows non-coding indels to be discovered in the absence of whole genome sequencing data, out-performs popular variant callers such as the GATK-HaplotypeCaller and VarScan2, and detects known oncogenic regulatory mutations in T-cell acute lymphoblastic leukemia cell lines. We apply BreakCA to identify indels in H3K27ac ChIP-seq peaks in 23 neuroblastoma cell lines and, after removing common germline variants, we identify 23 rare germline or somatic indels that occur in multiple neuroblastoma cell lines. Among them, 4 indels are candidate oncogenic drivers that are present in 4 or 5 cell lines, absent from the genome aggregation database of over 15,000 whole genome sequences, and within the promoters or first introns of known genes (PHF21A, ADAMTS19, GPR85andRALGDS). In addition, we observe a rare 7bp germline deletion in two cell lines, which is associated with high expression of the histone demethylaseKDM5B. Overexpression ofKDM5Bis prognostic for many cancers and further characterization of this indel as a potential oncogenic risk factor is therefore warranted.
- Published
- 2019
28. Tuft Cells Inhibit Pancreatic Tumorigenesis in Mice by Producing Prostaglandin D2
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Leonardo R. Andrade, Chi-Yeh Chung, Rajshekhar R. Giraddi, Linjing Fang, Uri Manor, H. Carlo Maurer, Dezhen Wang, Susan M. Kaech, Nasun Hah, Maxim N. Shokhirev, Zhibo Ma, Galina Erikson, Makoto Ohmoto, Carolyn O’Connor, Pankaj K. Singh, Ichiro Matsumoto, Kenneth P. Olive, Geoffrey M. Wahl, Razia F. Naeem, Crystal Tsui, Vikas B. Gubbala, Kathleen E. DelGiorno, Sammy Weiser Novak, Yoshihiro Urade, Nikki K. Lytle, Hubert Tseng, Vera Vavinskaya, Maya Ridinger-Saison, and Wahida H. Ali
- Subjects
0301 basic medicine ,Hepatology ,Intraductal papillary mucinous neoplasm ,Gastroenterology ,Pancreatic Intraepithelial Neoplasia ,Pancreatic stellate cell ,Prostaglandin ,Inflammation ,Biology ,medicine.disease ,medicine.disease_cause ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,chemistry ,Cancer research ,medicine ,030211 gastroenterology & hepatology ,Prostaglandin D2 ,Pancreatic injury ,medicine.symptom ,Carcinogenesis - Abstract
Background & Aims Development of pancreatic ductal adenocarcinoma (PDA) involves acinar to ductal metaplasia and genesis of tuft cells. It has been a challenge to study these rare cells because of the lack of animal models. We investigated the role of tuft cells in pancreatic tumorigenesis. Methods We performed studies with LSL-KrasG12D/+;Ptf1aCre/+ mice (KC; develop pancreatic tumors), KC mice crossed with mice with pancreatic disruption of Pou2f3 (KPouC mice; do not develop tuft cells), or mice with pancreatic disruption of the hematopoietic prostaglandin D synthase gene (Hpgds, KHC mice) and wild-type mice. Mice were allowed to age or were given caerulein to induce pancreatitis; pancreata were collected and analyzed by histology, immunohistochemistry, RNA sequencing, ultrastructural microscopy, and metabolic profiling. We performed laser-capture dissection and RNA-sequencing analysis of pancreatic tissues from 26 patients with pancreatic intraepithelial neoplasia (PanIN), 19 patients with intraductal papillary mucinous neoplasms (IPMNs), and 197 patients with PDA. Results Pancreata from KC mice had increased formation of tuft cells and higher levels of prostaglandin D2 than wild-type mice. Pancreas-specific deletion of POU2F3 in KC mice (KPouC mice) resulted in a loss of tuft cells and accelerated tumorigenesis. KPouC mice had increased fibrosis and activation of immune cells after administration of caerulein. Pancreata from KPouC and KHC mice had significantly lower levels of prostaglandin D2, compared with KC mice, and significantly increased numbers of PanINs and PDAs. KPouC and KHC mice had increased pancreatic injury after administration of caerulein, significantly less normal tissue, more extracellular matrix deposition, and higher PanIN grade than KC mice. Human PanIN and intraductal papillary mucinous neoplasm had gene expression signatures associated with tuft cells and increased expression of Hpgds messenger RNA compared with PDA. Conclusions In mice with KRAS-induced pancreatic tumorigenesis, loss of tuft cells accelerates tumorigenesis and increases the severity of caerulein-induced pancreatic injury, via decreased production of prostaglandin D2. These data are consistent with the hypothesis that tuft cells are a metaplasia-induced tumor attenuating cell type.
- Published
- 2020
29. Whole-Genome Sequencing of a Healthy Aging Cohort
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Erick R. Scott, Eric J. Topol, Nathan E. Wineinger, Dale L. Bodian, Sarah E. Topol, Ashley A. Scott-Van Zeeland, Galina Erikson, Manuel Rueda, Bhuvan Molparia, John E. Niederhuber, and Ali Torkamani
- Subjects
Male ,0301 basic medicine ,Aging ,media_common.quotation_subject ,Longevity ,Genome-wide association study ,Coronary Artery Disease ,Disease ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Cohort Studies ,03 medical and health sciences ,Alzheimer Disease ,medicine ,Genetic predisposition ,Humans ,Genetic Predisposition to Disease ,Cognitive decline ,Aged ,media_common ,Aged, 80 and over ,Genetics ,Whole genome sequencing ,medicine.disease ,3. Good health ,030104 developmental biology ,Cognitive Aging ,Cohort ,Female ,Alzheimer's disease ,Genome-Wide Association Study - Abstract
Summary Studies of long-lived individuals have revealed few genetic mechanisms for protection against age-associated disease. Therefore, we pursued genome sequencing of a related phenotype—healthy aging—to understand the genetics of disease-free aging without medical intervention. In contrast with studies of exceptional longevity, usually focused on centenarians, healthy aging is not associated with known longevity variants, but is associated with reduced genetic susceptibility to Alzheimer and coronary artery disease. Additionally, healthy aging is not associated with a decreased rate of rare pathogenic variants, potentially indicating the presence of disease-resistance factors. In keeping with this possibility, we identify suggestive common and rare variant genetic associations implying that protection against cognitive decline is a genetic component of healthy aging. These findings, based on a relatively small cohort, require independent replication. Overall, our results suggest healthy aging is an overlapping but distinct phenotype from exceptional longevity that may be enriched with disease-protective genetic factors. Video Abstract
- Published
- 2016
30. A genome sequencing program for novel undiagnosed diseases
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Ronald A. Simon, Bradley A. Patay, Sarah E. Topol, Nicholas J. Schork, Nelson Hwynn, Eric J. Topol, Kelly Bethel, Jennifer Friedman, Debra Boeldt, Paul J. Pockros, Ali Torkamani, Gary W. Williams, Burcu F. Darst, Ashley A. Scott-Van Zeeland, Erick R. Scott, Cinnamon S. Bloss, Galina Erikson, and Robert L. Bjork
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Male ,clinical sequencing ,Disease ,Bioinformatics ,Genome ,Pathology ,Pathology, Molecular ,Child ,10. No inequality ,Genetics (clinical) ,Genetics & Heredity ,screening and diagnosis ,Genetic disorder ,undiagnosed diseases ,3. Good health ,genome sequencing ,Detection ,Genetic Diseases ,Child, Preschool ,Female ,Sequence Analysis ,Human ,Adult ,Adolescent ,Clinical Sciences ,MEDLINE ,rare disease ,Context (language use) ,Genomics ,Article ,DNA sequencing ,Young Adult ,Rare Diseases ,Clinical Research ,Genetics ,genomics ,medicine ,Humans ,Genetic Testing ,Preschool ,Genome, Human ,business.industry ,Human Genome ,Genetic Diseases, Inborn ,Molecular ,Infant ,DNA ,Sequence Analysis, DNA ,medicine.disease ,4.1 Discovery and preclinical testing of markers and technologies ,Inborn ,Good Health and Well Being ,business ,Rare disease - Abstract
PurposeThe Scripps Idiopathic Diseases of Man (IDIOM) study aims to discover novel gene-disease relationships and provide molecular genetic diagnosis and treatment guidance for individuals with novel diseases using genome sequencing integrated with clinical assessment and multidisciplinary case review. Here we describe the operational protocol and initial results of the IDIOM study.MethodsA total of 121 cases underwent first-tier review by the principal investigators to determine whether the primary inclusion criteria were satisfied, 59 (48.8%) underwent second-tier review by our clinician-scientist review panel, and 17 patients (14.0%) and their family members were enrolled.Results60% of cases resulted in a plausible molecular diagnosis, and 18% of cases resulted in a confirmed molecular diagnosis. Two of three confirmed cases led to the identification of novel gene-disease relationships. In the third confirmed case a previously described but unrecognized disease was revealed. In all three confirmed cases a new clinical management strategy was initiated based on the genetic findings.ConclusionGenome sequencing provides tangible clinical benefit for individuals with idiopathic genetic disease, not only in the context of molecular genetic diagnosis of known rare conditions but also in cases where prior clinical information regarding a new genetic disorder is lacking.
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- 2015
31. BART: bioinformatics array research tool
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Galina Erikson, Maxim N. Shokhirev, and Maria Luisa Amaral
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0301 basic medicine ,Microarray ,Computer science ,Interface (computing) ,Breast Neoplasms ,lcsh:Computer applications to medicine. Medical informatics ,Gene expression omnibus ,Bioinformatics ,Biochemistry ,03 medical and health sciences ,Differential expression ,0302 clinical medicine ,Structural Biology ,Databases, Genetic ,Humans ,natural sciences ,Cluster analysis ,lcsh:QH301-705.5 ,Molecular Biology ,Oligonucleotide Array Sequence Analysis ,Principal Component Analysis ,Microarray analysis techniques ,Applied Mathematics ,Graphical user Interface ,Computational Biology ,Microarray analysis ,Automated analysis ,Online tool ,Computer Science Applications ,ComputingMethodologies_PATTERNRECOGNITION ,030104 developmental biology ,lcsh:Biology (General) ,030220 oncology & carcinogenesis ,lcsh:R858-859.7 ,RNA ,Female ,DNA microarray ,Software ,Functional enrichment analysis - Abstract
Microarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and requires manual error-prone analysis and a bioinformatics background. This is due to a lack of standardization in array platform fabrication as well as the lack of a simple interactive tool for clustering, plotting, differential expression testing, and testing for functional enrichment. We introduce the Bioinformatics Array Research Tool (BART), an R Shiny web application that automates the microarray download and analysis process across diverse microarray platforms. It provides an intuitive interface, automatically downloads and parses data from GEO, suggests groupings of samples for differential expression testing, performs batch effect correction, outputs quality control plots, converts probe IDs, generates full lists of differentially expressed genes, and performs functional enrichment analysis. We show that BART enables a more comprehensive analysis of a wider range of microarray datasets on GEO by comparing it to four leading online microarray analysis tools. BART allows a scientist with no bioinformatics background to extract knowledge from their own microarray data or microarray experiments available from GEO. BART is functional on more microarray experiments and provides more comprehensive analyses than extant microarray analysis tools. BART is hosted on bart.salk.edu , includes a user tutorial, and is available for download from https://bitbucket.org/Luisa_amaral/bart .
- Published
- 2018
32. SG-ADVISER CNV: copy-number variant annotation and interpretation
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Neha Deshpande, Balachandar G. Kesavan, Ali Torkamani, and Galina Erikson
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Web server ,medicine.medical_specialty ,DNA Copy Number Variations ,Computer science ,Genomics ,Computational biology ,computer.software_genre ,Genome ,Article ,Annotation ,Databases, Genetic ,medicine ,Humans ,Copy-number variation ,Allele frequency ,Genetics (clinical) ,Genetics ,Internet ,Genome, Human ,Computational Biology ,Molecular Sequence Annotation ,Genomic Structural Variation ,Medical genetics ,DECIPHER ,computer ,Software - Abstract
Copy-number variants have been associated with a variety of diseases, especially cancer, autism, schizophrenia, and developmental delay. The majority of clinically relevant events occur de novo, necessitating the interpretation of novel events. In this light, we present the Scripps Genome ADVISER CNV annotation pipeline and Web server, which aims to fill the gap between copy number variant detection and interpretation by performing in-depth annotations and functional predictions for copy number variants. The Scripps Genome ADVISER CNV suite includes a Web server interface to a high-performance computing environment for calculations of annotations and a table-based user interface that allows for the execution of numerous annotation-based variant filtration strategies and statistics. The annotation results include details regarding location, impact on the coding portion of genes, allele frequency information (including allele frequencies from the Scripps Wellderly cohort), and overlap information with other reference data sets (including ClinVar, DGV, DECIPHER). A summary variant classification is produced (ADVISER score) based on the American College of Medical Genetics and Genomics scoring guidelines. We demonstrate >90% sensitivity/specificity for detection of pathogenic events. Scripps Genome ADVISER CNV is designed to allow users with no prior bioinformatics expertise to manipulate large volumes of copy-number variant data. Scripps Genome ADVISER CNV is available at http://genomics.scripps.edu/ADVISER/ . Genet Med 17 9, 714–718.
- Published
- 2015
33. The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding
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Giorgia Benegiamo, Hiep D. Le, Steven A. Brown, Ermanno Moriggi, Satchidananda Panda, Galina Erikson, Ludovic S. Mure, University of Zurich, and Brown, Steven A
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0301 basic medicine ,Physiology ,Circadian clock ,10050 Institute of Pharmacology and Toxicology ,RNA-binding protein ,610 Medicine & health ,Biology ,Models, Biological ,Energy homeostasis ,1307 Cell Biology ,03 medical and health sciences ,Gene expression ,1312 Molecular Biology ,Animals ,Homeostasis ,RNA, Messenger ,RNA Processing, Post-Transcriptional ,Molecular Biology ,Gene ,Adiposity ,2. Zero hunger ,Cell Nucleus ,Liver cell ,Body Weight ,RNA-Binding Proteins ,Paraspeckle ,Cell Biology ,Metabolism ,1314 Physiology ,Feeding Behavior ,Adaptation, Physiological ,Introns ,Cell biology ,DNA-Binding Proteins ,Mice, Inbred C57BL ,030104 developmental biology ,Glucose ,Gene Expression Regulation ,Liver ,Hepatocytes ,570 Life sciences ,biology ,Protein Binding - Abstract
The mechanisms by which feeding and fasting drive rhythmic gene expression for physiological adaptation to daily rhythm in nutrient availability are not well understood. Here we show that, upon feeding, the RNA-binding protein NONO accumulates within speckle-like structures in liver cell nuclei. Combining RNA-immunoprecipitation and sequencing (RIP-seq), we find that an increased number of RNAs are bound by NONO after feeding. We further show that NONO binds and regulates the rhythmicity of genes involved in nutrient metabolism post-transcriptionally. Finally, we show that disrupted rhythmicity of NONO target genes has profound metabolic impact. Indeed, NONO-deficient mice exhibit impaired glucose tolerance and lower hepatic glycogen and lipids. Accordingly, these mice shift from glucose storage to fat oxidation, and therefore remain lean throughout adulthood. In conclusion, our study demonstrates that NONO post-transcriptionally coordinates circadian mRNA expression of metabolic genes with the feeding/fasting cycle, thereby playing a critical role in energy homeostasis.
- Published
- 2017
34. Reprogramming pancreatic stellate cells via p53 activation: A putative target for pancreatic cancer therapy
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Christopher Liddle, Geoffrey M. Wahl, Randall French, Andrew M. Lowy, Michael Downes, Maxim N. Shokhirev, Crystal Tsui, Tejia Zhang, Annabelle Kraus, Galina Erikson, Dawn Jaquish, Ronald M. Evans, Kathleen E. DelGiorno, Ruth T. Yu, Maya Saison-Ridinger, Alan Saghatelian, and Benjamin T. Spike
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Male ,0301 basic medicine ,Cell cycle checkpoint ,Transcription, Genetic ,Cancer Treatment ,Gene Expression ,lcsh:Medicine ,Tumor initiation ,Molecular biology assays and analysis techniques ,medicine.disease_cause ,Biochemistry ,Mice ,Animal Cells ,Fibrosis ,Tumor Cells, Cultured ,Medicine and Health Sciences ,Macromolecular Structure Analysis ,Cell Cycle and Cell Division ,lcsh:Science ,Connective Tissue Cells ,Mice, Knockout ,Lipid Analysis ,Multidisciplinary ,Nucleic acid analysis ,biology ,Chemistry ,Transcriptional Control ,Pancreatic Stellate Cells ,RNA analysis ,Cellular Reprogramming ,Lipids ,3. Good health ,Oncology ,Connective Tissue ,Cell Processes ,Mdm2 ,Cholesterol Esters ,Cellular Types ,Anatomy ,Carcinoma, Pancreatic Ductal ,Research Article ,Stromal cell ,Pancreatic Cancer ,03 medical and health sciences ,Pancreatic cancer ,Gastrointestinal Tumors ,Genetics ,medicine ,Animals ,Humans ,Gene Regulation ,Molecular Biology ,Triglycerides ,lcsh:R ,Biology and Life Sciences ,Cancers and Neoplasms ,Cell Biology ,Fibroblasts ,Genes, p53 ,medicine.disease ,Mice, Inbred C57BL ,Pancreatic Neoplasms ,Research and analysis methods ,Biological Tissue ,Molecular biology techniques ,030104 developmental biology ,biology.protein ,Cancer research ,Hepatic stellate cell ,lcsh:Q ,Carcinogenesis - Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extremely dense fibrotic stroma, which contributes to tumor growth, metastasis, and drug resistance. During tumorigenesis, quiescent pancreatic stellate cells (PSCs) are activated and become major contributors to fibrosis, by increasing growth factor signaling and extracellular matrix deposition. The p53 tumor suppressor is known to restrict tumor initiation and progression through cell autonomous mechanisms including apoptosis, cell cycle arrest, and senescence. There is growing evidence that stromal p53 also exerts anti-tumor activity by paracrine mechanisms, though a role for stromal p53 in PDAC has not yet been described. Here, we demonstrate that activation of stromal p53 exerts anti-tumor effects in PDAC. We show that primary cancer-associated PSCs (caPSCs) isolated from human PDAC express wild-type p53, which can be activated by the Mdm2 antagonist Nutlin-3a. Our work reveals that p53 acts as a major regulator of PSC activation and as a modulator of PDAC fibrosis. In vitro, p53 activation by Nutlin-3a induces profound transcriptional changes, which reprogram activated PSCs to quiescence. Using immunofluorescence and lipidomics, we have also found that p53 activation induces lipid droplet accumulation in both normal and tumor-associated fibroblasts, revealing a previously undescribed role for p53 in lipid storage. In vivo, treatment of tumor-bearing mice with the clinical form of Nutlin-3a induces stromal p53 activation, reverses caPSCs activation, and decreases fibrosis. All together our work uncovers new functions for stromal p53 in PDAC.
- Published
- 2017
35. ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma
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J K Lee, Rajesh Belani, W J Shipman, M S Schechter, Galina Erikson, Glenn Oliveira, S M Haaser, S Ra, and Ali Torkamani
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Whole genome sequencing ,Genetics ,0303 health sciences ,Cancer Research ,Candidate gene ,Mutation ,Thymoma ,Point mutation ,Biology ,medicine.disease ,medicine.disease_cause ,Myasthenia gravis ,3. Good health ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,hemic and lymphatic diseases ,medicine ,Original Article ,Carcinogenesis ,Molecular Biology ,Exome sequencing ,030304 developmental biology - Abstract
The molecular drivers of thymoma are poorly understood. Outside of the identification of rarely occurring epidermal growth factor receptor and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog mutations via candidate gene sequencing, mutations in common cancer genes have yet to be observed. Only a single thymoma genome sequence has been previously reported, with no mutations in known cancer genes identified. Thus, we attempted to identify somatic driver mutations in a cytogenetically normal thymoma. A stage IVB type B3 thymoma from a 47-year-old male of Asian descent with no history of myasthenia gravis or other autoimmune condition was genomically evaluated. Exome sequencing and low-pass whole-genome sequencing was performed to identify somatic point mutations, copy number changes and structural variants. Mutations in known tumor suppressors DNMT3A (p.G728D) and ASXL1 (p.E657fs), consistent with mutations of known consequence in acute myeloid leukemia, were identified. Contrary to a previous report, this finding suggests the genetic etiology of thymomas may not be fundamentally distinct from other tumor types. Rather, these findings suggest that further sequencing of cytogenetically normal thymoma samples should reveal the specific molecular drivers of thymoma.
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- 2014
36. Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver
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William J. Shipman, Nicholas J. Schork, Phillip Pham, Galina Erikson, and Ali Torkamani
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Computer science ,lcsh:Medicine ,Genomics ,Human genomics ,Genome ,Genomic databases ,User-Computer Interface ,03 medical and health sciences ,Annotation ,Inheritance (object-oriented programming) ,0302 clinical medicine ,Databases, Genetic ,microRNA ,Humans ,Genomic medicine ,lcsh:Science ,030304 developmental biology ,Genetics ,Internet ,0303 health sciences ,Multidisciplinary ,Information retrieval ,Genome, Human ,lcsh:R ,Computational Biology ,Genome project ,lcsh:Q ,Human genome ,Software ,030217 neurology & neurosurgery ,Research Article - Abstract
Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER) suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease – without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER.
- Published
- 2015
37. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
- Author
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Shobha Patil, Tobias Neumann, Julio Rozas, William J. Gillis, Nicholas H. Putman, Elizabeth A. Goodwin-Horn, Jerome H.L. Hui, Andrew M. Schurko, Jiaxin Qu, François Lapraz, Peshtewani K. Aqrawi, DeNard Simmons, Michael Holder, Maria Ninova, Sam Griffiths-Jones, Dieter Ebert, Huaiyang Jiang, Jack E. Green, Shalini N. Jhangiani, Sai Gubbala, Zivkos Apostolou, Luke Hayden, Wallace Arthur, Liezl Francisco, Kim C. Worley, Marcus Coyle, Claudio R. Alonso, Peter D. Evans, Viktoriya Korchina, Montserrat Torres-Oliva, Ling-Ling Pu, Sophie Helbing, Eckart Stolle, Judith H. Willis, Christopher Pham, Pedro Patraquim, Nehad Saada, Yuanqing Wu, Christie Kovar, David E. K. Ferrier, Nathan J. Kenny, Dinh Ngoc Ngo, James M Williams, Cornelius Eibner, Kenneth W. Siggens, Tittu Mathew, Ariel D. Chipman, Robert Mata, Vera S. Hunnekuhl, Cornelis J. P. Grimmelikhuijzen, Tamsin E. M. Jones, Kristin Tessmar-Raible, Olivia Mendivil Ramos, Xiaoyan Zou, Divya Kalra, Stephen Richards, Louis Du Pasquier, Marco Mariotti, Hugh M. Robertson, Jennifer C. J. Barna, Michael Akam, Geoffrey Okwuonu, Matthew Ronshaugen, Arndt von Haeseler, Julia P. Hunn, Francisca C. Almeida, Daniela Brites, Maximilian J. Telford, Galina Erikson, William J. Palmer, Francis M. Jiggins, Kerstin P. Blankenburg, Tobias S. Kaiser, Toni Gabaldón, Helen E. Robertson, Maurijn van der Zee, Rebecca Thornton, Donna M. Muzny, Peter K. Dearden, Richard A. Gibbs, Gerard Manning, Elizabeth J. Duncan, LaRonda Jackson, Daniel S.T. Hughes, Steven E. Scherer, Reinhard Schröder, Paul Havlak, Daniel Lawson, Carlo Brena, Fiona Ongeri, Frank Hauser, Anna Stief, Mehwish Javaid, Salvador Capella-Gutierrez, Jie Lv, F. Bernhard Kraus, Irene Newsham, Roderic Guigó, Alejandro Sánchez-Gracia, Sandra L. Lee, Nadia Znassi, Yi Han, Catherine Rabouille, Adelaide C. Rhodes, Christigale Mandapat, Cassandra G. Extavour, Jiggins, Francis [0000-0001-7470-8157], Akam, Michael [0000-0003-0063-2297], Apollo - University of Cambridge Repository, Hubrecht Institute for Developmental Biology and Stem Cell Research, University of St Andrews. School of Biology, University of St Andrews. Marine Alliance for Science & Technology Scotland, and University of St Andrews. Scottish Oceans Institute
- Subjects
Evolutionary Genetics ,Male ,0106 biological sciences ,RNA, Untranslated ,Gene family evolution ,Lydia Becker Institute ,Animal Evolution ,QH301 Biology ,Biología ,Receptors, Odorant ,01 natural sciences ,Genome ,purl.org/becyt/ford/1 [https] ,Genética y Herencia ,Genome Sequencing ,Biology (General) ,Selenoproteins ,Genome Evolution ,R2C ,Phylogeny ,Genetics ,0303 health sciences ,Phylogenetic analysis ,Sex Chromosomes ,biology ,Myriapoda ,Circadian Rhythm Signaling Peptides and Proteins ,General Neuroscience ,~DC~ ,Gene content ,Genomics ,Insects ,Drosophila melanogaster ,Multigene Family ,QH0426 ,Female ,BDC ,General Agricultural and Biological Sciences ,CIENCIAS NATURALES Y EXACTAS ,Research Article ,Genome evolution ,Evolutionary Immunology ,Arthropoda ,QH301-705.5 ,Genome Complexity ,Synteny ,010603 evolutionary biology ,General Biochemistry, Genetics and Molecular Biology ,Ciencias Biológicas ,Evolution, Molecular ,QH301 ,Invertebrate genomics ,03 medical and health sciences ,ResearchInstitutes_Networks_Beacons/lydia_becker_institute_of_immunology_and_inflammation ,Homeobox ,Animals ,Gene family ,purl.org/becyt/ford/1.6 [https] ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,Arthropods ,Gene ,Institut für Biochemie und Biologie ,030304 developmental biology ,Comparative genomics ,Evolutionary Biology ,Polymorphism, Genetic ,General Immunology and Microbiology ,Genètica animal ,Human evolutionary genetics ,fungi ,Biology and Life Sciences ,Computational Biology ,Genètica evolutiva ,DNA Methylation ,Comparative Genomics ,biology.organism_classification ,Hormones ,Organismal Evolution ,Genome, Mitochondrial ,Arthropod ,Protein Kinases ,Transcription Factors - Abstract
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history., Author Summary Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
- Published
- 2014
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