1
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Luo D, Ottesen E, Lee JH, Singh R. Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. RESEARCH SQUARE 2024:rs.3.rs-3818622. [PMID: 38464174 PMCID: PMC10925445 DOI: 10.21203/rs.3.rs-3818622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Spinal muscular atrophy (SMA) genes, SMN1 and SMN2, produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2. These fifindings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/SMN2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
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Baldassarro VA, Cescatti M, Rocco ML, Aloe L, Lorenzini L, Giardino L, Calzà L. Nerve growth factor promotes differentiation and protects the oligodendrocyte precursor cells from in vitro hypoxia/ischemia. Front Neurosci 2023; 17:1111170. [PMID: 36875668 PMCID: PMC9978228 DOI: 10.3389/fnins.2023.1111170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction Nerve growth factor (NGF) is a pleiotropic molecule acting on different cell types in physiological and pathological conditions. However, the effect of NGF on the survival, differentiation and maturation of oligodendrocyte precursor cells (OPCs) and oligodendrocytes (OLs), the cells responsible for myelin formation, turnover, and repair in the central nervous system (CNS), is still poorly understood and heavily debated. Methods Here we used mixed neural stem cell (NSC)-derived OPC/astrocyte cultures to clarify the role of NGF throughout the entire process of OL differentiation and investigate its putative role in OPC protection under pathological conditions. Results We first showed that the gene expression of all the neurotrophin receptors (TrkA, TrkB, TrkC, and p75NTR ) dynamically changes during the differentiation. However, only TrkA and p75NTR expression depends on T3-differentiation induction, as Ngf gene expression induction and protein secretion in the culture medium. Moreover, in the mixed culture, astrocytes are the main producer of NGF protein, and OPCs express both TrkA and p75NTR . NGF treatment increases the percentage of mature OLs, while NGF blocking by neutralizing antibody and TRKA antagonist impairs OPC differentiation. Moreover, both NGF exposure and astrocyte-conditioned medium protect OPCs exposed to oxygenglucose deprivation (OGD) from cell death and NGF induces an increase of AKT/pAKT levels in OPCs nuclei by TRKA activation. Discussion This study demonstrated that NGF is implicated in OPC differentiation, maturation, and protection in the presence of metabolic challenges, also suggesting implications for the treatment of demyelinating lesions and diseases.
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Affiliation(s)
| | | | | | | | - Luca Lorenzini
- Department of Veterinary Medical Science, University of Bologna, Bologna, Italy
| | - Luciana Giardino
- Department of Veterinary Medical Science, University of Bologna, Bologna, Italy.,IRET Foundation, Bologna, Italy
| | - Laura Calzà
- Health Science and Technologies - Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Bologna, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Montecatone Rehabilitation Institute, Bologna, Italy
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3
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Herrera-Úbeda C, Garcia-Fernàndez J. New Genes Born-In or Invading Vertebrate Genomes. Front Cell Dev Biol 2021; 9:713918. [PMID: 34295903 PMCID: PMC8290160 DOI: 10.3389/fcell.2021.713918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/15/2021] [Indexed: 12/02/2022] Open
Abstract
Which is the origin of genes is a fundamental question in Biology, indeed a question older than the discovery of genes itself. For more than a century, it was uneven to think in origins other than duplication and divergence from a previous gene. In recent years, however, the intersection of genetics, embryonic development, and bioinformatics, has brought to light that de novo generation from non-genic DNA, horizontal gene transfer and, noticeably, virus and transposon invasions, have shaped current genomes, by integrating those newcomers into old gene networks, helping to shape morphological and physiological innovations. We here summarized some of the recent research in the field, mostly in the vertebrate lineage with a focus on protein-coding novelties, showing that the placenta, the adaptative immune system, or the highly developed neocortex, among other innovations, are linked to de novo gene creation or domestication of virus and transposons. We provocatively suggest that the high tolerance to virus infections by bats may also be related to previous virus and transposon invasions in the bat lineage.
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Affiliation(s)
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
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4
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Dokaneheifard S, Soltani BM. Implication of TrkC-miR2 in neurotrophin signalling pathway regulation through NGFR transcript targeting. J Cell Mol Med 2021; 25:3381-3390. [PMID: 33675128 PMCID: PMC8034437 DOI: 10.1111/jcmm.16415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
TrkC and NGFR neurotrophin receptors are associated with cell death, cancer and differentiation. TrkC-miR2, which is located in TrkC gene, is known to regulate Wnt signalling pathway, and its influence on other signalling pathways is under investigation. Here, through RT-qPCR, dual-luciferase assay and Western blotting we reveal that TrkC-miR2 targets NGFR. Overexpression of TrkC-miR2 also affected TrkA, TrkC, NFKB, BCL2 and Akt2 expressions involved in neurotrophin signalling pathway, and elevated survival rate of HEK293t and U87 cells was distinguished by flow cytometry and MTT assay. Consistently, an opposite expression correlation was obtained between TrkC-miR2 and NGFR or TrkC for the duration of NT2 differentiation. Meanwhile, TrkC-miR2 down-regulation attenuated NT2 differentiation into neural-like cells. Overall, here we present in silico and experimental evidence showing TrkC-miR2 as a new controller in regulation of neurotrophin signalling pathway.
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Affiliation(s)
- Sadat Dokaneheifard
- Department of Molecular GeneticsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
- Medical Biology Research CenterKermanshah University of Medical SciencesKermanshahIran
| | - Bahram M. Soltani
- Department of Molecular GeneticsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
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5
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Vastagh C, Csillag V, Solymosi N, Farkas I, Liposits Z. Gonadal Cycle-Dependent Expression of Genes Encoding Peptide-, Growth Factor-, and Orphan G-Protein-Coupled Receptors in Gonadotropin- Releasing Hormone Neurons of Mice. Front Mol Neurosci 2021; 13:594119. [PMID: 33551743 PMCID: PMC7863983 DOI: 10.3389/fnmol.2020.594119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 12/30/2022] Open
Abstract
Rising serum estradiol triggers the surge release of gonadotropin-releasing hormone (GnRH) at late proestrus leading to ovulation. We hypothesized that proestrus evokes alterations in peptidergic signaling onto GnRH neurons inducing a differential expression of neuropeptide-, growth factor-, and orphan G-protein-coupled receptor (GPCR) genes. Thus, we analyzed the transcriptome of GnRH neurons collected from intact, proestrous and metestrous GnRH-green fluorescent protein (GnRH-GFP) transgenic mice using Affymetrix microarray technique. Proestrus resulted in a differential expression of genes coding for peptide/neuropeptide receptors including Adipor1, Prokr1, Ednrb, Rtn4r, Nmbr, Acvr2b, Sctr, Npr3, Nmur1, Mc3r, Cckbr, and Amhr2. In this gene cluster, Adipor1 mRNA expression was upregulated and the others were downregulated. Expression of growth factor receptors and their related proteins was also altered showing upregulation of Fgfr1, Igf1r, Grb2, Grb10, and Ngfrap1 and downregulation of Egfr and Tgfbr2 genes. Gpr107, an orphan GPCR, was upregulated during proestrus, while others were significantly downregulated (Gpr1, Gpr87, Gpr18, Gpr62, Gpr125, Gpr183, Gpr4, and Gpr88). Further affected receptors included vomeronasal receptors (Vmn1r172, Vmn2r-ps54, and Vmn1r148) and platelet-activating factor receptor (Ptafr), all with marked downregulation. Patch-clamp recordings from mouse GnRH-GFP neurons carried out at metestrus confirmed that the differentially expressed IGF-1, secretin, and GPR107 receptors were operational, as their activation by specific ligands evoked an increase in the frequency of miniature postsynaptic currents (mPSCs). These findings show the contribution of certain novel peptides, growth factors, and ligands of orphan GPCRs to regulation of GnRH neurons and their preparation for the surge release.
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Affiliation(s)
- Csaba Vastagh
- Laboratory of Endocrine Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Veronika Csillag
- Laboratory of Endocrine Neurobiology, Institute of Experimental Medicine, Budapest, Hungary.,Faculty of Information Technology and Bionics, Roska Tamás Doctoral School of Sciences and Technology, Pázmány Péter Catholic University, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Imre Farkas
- Laboratory of Endocrine Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Zsolt Liposits
- Laboratory of Endocrine Neurobiology, Institute of Experimental Medicine, Budapest, Hungary.,Department of Neuroscience, Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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6
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Martín-Rodríguez C, Song M, Anta B, González-Calvo FJ, Deogracias R, Jing D, Lee FS, Arevalo JC. TrkB deubiquitylation by USP8 regulates receptor levels and BDNF-dependent neuronal differentiation. J Cell Sci 2020; 133:jcs247841. [PMID: 33288548 PMCID: PMC7774901 DOI: 10.1242/jcs.247841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitylation of receptor tyrosine kinases (RTKs) regulates both the levels and functions of these receptors. The neurotrophin receptor TrkB (also known as NTRK2), a RTK, is ubiquitylated upon activation by brain-derived neurotrophic factor (BDNF) binding. Although TrkB ubiquitylation has been demonstrated, there is a lack of knowledge regarding the precise repertoire of proteins that regulates TrkB ubiquitylation. Here, we provide mechanistic evidence indicating that ubiquitin carboxyl-terminal hydrolase 8 (USP8) modulates BDNF- and TrkB-dependent neuronal differentiation. USP8 binds to the C-terminus of TrkB using its microtubule-interacting domain (MIT). Immunopurified USP8 deubiquitylates TrkB in vitro, whereas knockdown of USP8 results in enhanced ubiquitylation of TrkB upon BDNF treatment in neurons. As a consequence of USP8 depletion, TrkB levels and its activation are reduced. Moreover, USP8 protein regulates the differentiation and correct BDNF-dependent dendritic formation of hippocampal neurons in vitro and in vivo We conclude that USP8 positively regulates the levels and activation of TrkB, modulating BDNF-dependent neuronal differentiation.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Carlos Martín-Rodríguez
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca, 37007 Salamanca, Spain
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
| | - Begoña Anta
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca, 37007 Salamanca, Spain
| | - Francisco J González-Calvo
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Rubén Deogracias
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Deqiang Jing
- Department of Psychiatry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Francis S Lee
- Department of Psychiatry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Juan Carlos Arevalo
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca, 37007 Salamanca, Spain
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7
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Navas-Pérez E, Vicente-García C, Mirra S, Burguera D, Fernàndez-Castillo N, Ferrán JL, López-Mayorga M, Alaiz-Noya M, Suárez-Pereira I, Antón-Galindo E, Ulloa F, Herrera-Úbeda C, Cuscó P, Falcón-Moya R, Rodríguez-Moreno A, D'Aniello S, Cormand B, Marfany G, Soriano E, Carrión ÁM, Carvajal JJ, Garcia-Fernàndez J. Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions. Genome Biol 2020; 21:267. [PMID: 33100228 PMCID: PMC7586669 DOI: 10.1186/s13059-020-02172-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood. RESULTS Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes. CONCLUSIONS We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.
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Affiliation(s)
- Enrique Navas-Pérez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Cristina Vicente-García
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Serena Mirra
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Demian Burguera
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Noèlia Fernàndez-Castillo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - José Luis Ferrán
- Department of Human Anatomy, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, 30120, Murcia, Spain
| | - Macarena López-Mayorga
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Marta Alaiz-Noya
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain.,Present Address: Instituto de Neurociencias de Alicante (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Alicante, Spain
| | - Irene Suárez-Pereira
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain.,Present Address: Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Neuropsychopharmacology and psychobiology research group, UCA, INiBICA, Cádiz, Spain
| | - Ester Antón-Galindo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Fausto Ulloa
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Pol Cuscó
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Rafael Falcón-Moya
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Antonio Rodríguez-Moreno
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Bru Cormand
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Ángel M Carrión
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Jaime J Carvajal
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain.
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.
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8
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Lin C, Bar-Joseph Z. Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. Bioinformatics 2020; 35:4707-4715. [PMID: 31038684 DOI: 10.1093/bioinformatics/btz296] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/11/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Methods for reconstructing developmental trajectories from time-series single-cell RNA-Seq (scRNA-Seq) data can be largely divided into two categories. The first, often referred to as pseudotime ordering methods are deterministic and rely on dimensionality reduction followed by an ordering step. The second learns a probabilistic branching model to represent the developmental process. While both types have been successful, each suffers from shortcomings that can impact their accuracy. RESULTS We developed a new method based on continuous-state HMMs (CSHMMs) for representing and modeling time-series scRNA-Seq data. We define the CSHMM model and provide efficient learning and inference algorithms which allow the method to determine both the structure of the branching process and the assignment of cells to these branches. Analyzing several developmental single-cell datasets, we show that the CSHMM method accurately infers branching topology and correctly and continuously assign cells to paths, improving upon prior methods proposed for this task. Analysis of genes based on the continuous cell assignment identifies known and novel markers for different cell types. AVAILABILITY AND IMPLEMENTATION Software and Supporting website: www.andrew.cmu.edu/user/chiehl1/CSHMM/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chieh Lin
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, US
| | - Ziv Bar-Joseph
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, US.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, US
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9
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Chen S, Sun X, Wu S, Jiang J, Zhu C, Xu K, Xu K. Role of identified noncoding RNA in erectile dysfunction. Andrologia 2020; 52:e13596. [PMID: 32441367 DOI: 10.1111/and.13596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
- Sixiang Chen
- Zhejiang Chinese Medical University Hangzhou China
| | | | - Suliu Wu
- Wuyi First People's Hospital Wuyi China
| | - Jing Jiang
- Zhejiang Chinese Medical University Hangzhou China
| | - Chenfeng Zhu
- Zhejiang Chinese Medical University Hangzhou China
| | - Kechen Xu
- Wuyi First People's Hospital Wuyi China
| | - Keyang Xu
- Hangzhou Xixi Hospital affiliated to Zhejiang Chinese Medical University Hangzhou China
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10
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do Amaral MJ, Araujo TS, Díaz NC, Accornero F, Polycarpo CR, Cordeiro Y, Cabral KM, Almeida MS. Phase Separation and Disorder-to-Order Transition of Human Brain Expressed X-Linked 3 (hBEX3) in the Presence of Small Fragments of tRNA. J Mol Biol 2020; 432:2319-2348. [DOI: 10.1016/j.jmb.2020.02.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/10/2020] [Accepted: 02/27/2020] [Indexed: 12/19/2022]
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11
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Mittal P, Jaiswal SK, Vijay N, Saxena R, Sharma VK. Comparative analysis of corrected tiger genome provides clues to its neuronal evolution. Sci Rep 2019; 9:18459. [PMID: 31804567 PMCID: PMC6895189 DOI: 10.1038/s41598-019-54838-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/14/2019] [Indexed: 01/01/2023] Open
Abstract
The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.
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Affiliation(s)
- Parul Mittal
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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12
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Hijazi H, Coelho FS, Gonzaga-Jauregui C, Bernardini L, Mar SS, Manning MA, Hanson-Kahn A, Naidu S, Srivastava S, Lee JA, Jones JR, Friez MJ, Alberico T, Torres B, Fang P, Cheung SW, Song X, Davis-Williams A, Jornlin C, Wight PA, Patyal P, Taube J, Poretti A, Inoue K, Zhang F, Pehlivan D, Carvalho CMB, Hobson GM, Lupski JR. Xq22 deletions and correlation with distinct neurological disease traits in females: Further evidence for a contiguous gene syndrome. Hum Mutat 2019; 41:150-168. [PMID: 31448840 DOI: 10.1002/humu.23902] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023]
Abstract
Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernanda S Coelho
- Programa de Pós-Graduação em Genética Departmento de Biologia Geral, UFMG, Belo Horizonte, Minas Gerais, Brazil.,Instituto René Rachou, FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | | | - Laura Bernardini
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Melanie A Manning
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Andrea Hanson-Kahn
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Genetics, Stanford University School of Medicine, Palo Alto, California
| | - SakkuBai Naidu
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | | | - Jennifer A Lee
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael J Friez
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Thomas Alberico
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Barbara Torres
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Ping Fang
- Clinical Genomics, WuXi NextCODE, Cambridge, Massachusetts
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angelique Davis-Williams
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Carly Jornlin
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Patricia A Wight
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Pankaj Patyal
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jennifer Taube
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Andrea Poretti
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Grace M Hobson
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
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13
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Hollern DP, Swiatnicki MR, Rennhack JP, Misek SA, Matson BC, McAuliff A, Gallo KA, Caron KM, Andrechek ER. E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration. Sci Rep 2019; 9:10718. [PMID: 31341204 PMCID: PMC6656723 DOI: 10.1038/s41598-019-47218-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 07/12/2019] [Indexed: 12/27/2022] Open
Abstract
In prior work we demonstrated that loss of E2F transcription factors inhibits metastasis. Here we address the mechanisms for this phenotype and identify the E2F regulated genes that coordinate tumor cell metastasis. Transcriptomic profiling of E2F1 knockout tumors identified a role for E2F1 as a master regulator of a suite of pro-metastatic genes, but also uncovered E2F1 target genes with an unknown role in pulmonary metastasis. High expression of one of these genes, Fgf13, is associated with early human breast cancer metastasis in a clinical dataset. Together these data led to the hypothesis that Fgf13 is critical for breast cancer metastasis, and that upregulation of Fgf13 may partially explain how E2F1 promotes breast cancer metastasis. To test this hypothesis we ablated Fgf13 via CRISPR. Deletion of Fgf13 in a MMTV-PyMT breast cancer cell line reduces colonization of the lungs in a tail vein injection. In addition, loss of Fgf13 reduced in vitro cell migration, suggesting that Fgf13 may be critical for tumor cells to escape the primary tumor and to colonize the distal sites. The significance of this work is twofold: we have both uncovered genomic features by which E2F1 regulates metastasis and we have identified new pro-metastatic functions for the E2F1 target gene Fgf13.
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Affiliation(s)
- Daniel P Hollern
- Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, United States
| | - Matthew R Swiatnicki
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Jonathan P Rennhack
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Sean A Misek
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Brooke C Matson
- University of North Carolina Department of Cell Biology, Chapel Hill, United States
| | - Andrew McAuliff
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Kathleen A Gallo
- Department of Physiology, Michigan State University, East Lansing, United States
| | - Kathleen M Caron
- Lineberger Comprehensive Cancer Center University of North Carolina, Chapel Hill, United States
| | - Eran R Andrechek
- Department of Physiology, Michigan State University, East Lansing, United States.
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14
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Wen Y, Liu G, Jia L, Ji W, Li H. MicroRNA-141 binds to the nerve growth factor receptor associated protein 1 gene and restores the erectile function of diabetic rats through down-regulating the nerve growth factor/neurotrophin receptor p75 (NGF/p75NTR) signaling. J Cell Biochem 2019; 120:7940-7951. [PMID: 30426562 DOI: 10.1002/jcb.28071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Erectile dysfunction (ED) is one of the major complications in diabetes mellitus (DM). We have previously reported that the nerve growth factor (NGF)/tyrosine kinase receptor (TrkA) signaling is actively involved in DM-induced ED (DMED). Here, we investigate the effect of micro-RNA-141 (miR-141) on the NGF/p75 neurotrophin receptor (p75NTR) signaling and erectile function of diabetic rats. METHODS Sprague-Dawlay (SD) rats were used to establish a DMED model. The dual-luciferase reporter gene assay was first performed to identify the nerve growth factor receptor-associated protein 1 (NGFRAP1) gene as the target gene of miR-141. The regulatory mechanisms underlying miR-141 governing NGFRAP1 in vivo were then validated by modulating the expressions of miR-141 and knocking down NGFRAP1. RESULTS The expressions of miR-141 were decreased while the expressions of NGFRAP1, NGF, and p75NTR were increased in DMED. miR-141 and downregulation of NGFRAP1, respectively, increased the density of corpus cavernosum smooth muscle and the ratio of intracavernosal pressure (ICP)/mean arterial blood pressure (MAP) and promoted the expression of α-actin and desmin as well. miR-141 also upregulated the expressions of NGFRAP1 in DMED, and knockdown of NGFRAP1 inhibited the productions of NGF and p75NTR. Furthermore, miR-141 suppressed the NGF/p75NTR signaling via binding to NGFRAP1. CONCLUSIONS NGF/p75NTR signaling actively participates in the pathogenesis of DMED. miR-141 binds to NGFRAP1 and restores the erectile function of diabetic rats via downregulation of NGF/p75NTR signaling.
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Affiliation(s)
- Yan Wen
- Department of Endocrinology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Guohui Liu
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Linpei Jia
- Department of Nephrology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Wei Ji
- Department of Vascular Surgery, Jilin Provincial People's Hospital, Changchun, China
| | - Hai Li
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
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15
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Li Z, Rouse R. Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injury. BMC Genomics 2018; 19:297. [PMID: 29699496 PMCID: PMC5922017 DOI: 10.1186/s12864-018-4657-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
Background Co-sequencing of messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) across a time series (1, 3, 6, 24, and 48 h post injury) was used to identify potential miRNA-gene interactions during pancreatic injury, associate serum and tissue levels of candidate miRNA biomarkers of pancreatic injury, and functionally link these candidate miRNA biomarkers to observed histopathology. RNAs were derived from pancreatic tissues obtained in experiments characterizing the serum levels of candidate miRNA biomarkers in response to acute pancreatic injury in rats. Results No correlation was discovered between tissue and serum levels of the miRNAs. A combination of differential gene expression, novel delayed anti-correlation analysis and experimental database interrogation was used to identify messenger RNAs and miRNAs that experienced significant expression change across the time series, that were negatively correlated, that were complementary in sequence, and that had experimentally supported relationships. This approach yielded a complex signaling network for future investigation and a link for the specific candidate miRNA biomarkers, miR-216a-5p and miR-217-5p, to cellular processes that were in fact the prominent histopathology observations in the same experimental samples. RNA quality bias by treatment was observed in the study samples and a statistical correction was applied. The relevance and impact of that correction on significant results is discussed. Conclusion The described approach allowed extraction of miRNA function from genomic data and defined a mechanistic anchor for these miRNAs as biomarkers. Functional and mechanistic conclusions are supported by histopathology findings. Electronic supplementary material The online version of this article (10.1186/s12864-018-4657-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhihua Li
- U. S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, Division of Applied Regulatory Science, HFD-910, White Oak Federal Research Center, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Rodney Rouse
- U. S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, Division of Applied Regulatory Science, HFD-910, White Oak Federal Research Center, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
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16
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Generation and Characterization of Antibodies against Opioid Receptors from Zebrafish. Int J Mol Sci 2018; 19:ijms19010014. [PMID: 29301275 PMCID: PMC5795966 DOI: 10.3390/ijms19010014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
The opioid system is well conserved among species and plays a critical role in pain and addiction systems. The use of zebrafish as an experimental model to study development and genetics is extraordinary and has been proven to be relevant for the study of different diseases. The main drawback to its use for the analysis of different pathologies is the lack of protein tools. Antibodies that work in other models are not suitable for zebrafish due to the low degree of homology that exists among the opioid receptor protein sequences in different species. Here we report the successful generation and characterization of antibodies against the mu, delta 1 and delta 2 opioid receptors in zebrafish. The antibodies obtained, which are specific for each receptor due to the use of the C-terminus as antigens, work for Western blotting and immunohistochemistry. In addition, the antibodies against mu and delta 1 opioid receptors, but not those against delta 2, are able to immunoprecipitate the corresponding receptor from zebrafish lysates. The development of opioid receptor antibodies is an asset to the further study of the endogenous opioid system in zebrafish.
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17
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Zhao D, Lin M, Pedrosa E, Lachman HM, Zheng D. Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis. BMC Genomics 2017; 18:860. [PMID: 29126398 PMCID: PMC5681780 DOI: 10.1186/s12864-017-4261-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/01/2017] [Indexed: 12/24/2022] Open
Abstract
Background Monoallelic expression of autosomal genes has been implicated in human psychiatric disorders. However, there is a paucity of allelic expression studies in human brain cells at the single cell and genome wide levels. Results In this report, we reanalyzed a previously published single-cell RNA-seq dataset from several postmortem human brains and observed pervasive monoallelic expression in individual cells, largely in a random manner. Examining single nucleotide variants with a predicted functional disruption, we found that the “damaged” alleles were overall expressed in fewer brain cells than their counterparts, and at a lower level in cells where their expression was detected. We also identified many brain cell type-specific monoallelically expressed genes. Interestingly, many of these cell type-specific monoallelically expressed genes were enriched for functions important for those brain cell types. In addition, function analysis showed that genes displaying monoallelic expression and correlated expression across neuronal cells from different individual brains were implicated in the regulation of synaptic function. Conclusions Our findings suggest that monoallelic gene expression is prevalent in human brain cells, which may play a role in generating cellular identity and neuronal diversity and thus increasing the complexity and diversity of brain cell functions. Electronic supplementary material The online version of this article (10.1186/s12864-017-4261-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dejian Zhao
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Present address: Department of Neuroscience, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu, 21166, China
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA. .,Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA. .,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.
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18
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Shirai K, Higashi Y, Shimojima K, Yamamoto T. An Xq22.1q22.2 nullisomy in a male patient with severe neurological impairment. Am J Med Genet A 2017; 173:1124-1127. [PMID: 28328133 DOI: 10.1002/ajmg.a.38134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/03/2016] [Accepted: 12/24/2016] [Indexed: 12/19/2022]
Abstract
The proteolipid protein 1 gene (PLP1) is located on chromosome Xq22.2 and is related to X-linked recessive leukoencephalopathy (Pelizaeus-Merzbacher disease: PMD). Compared to PLP1 duplications, which are a major contributor to PMD, chromosomal deletions in this region are rare and only a few PMD patients with small deletions have been reported, suggesting that large deletions of this region would cause embryonic lethality. Previously, we have reported female patients, with chromosomal deletions in this region, who showed severe developmental delays and behavioral abnormalities. In this study, we identified the first case of a male patient associated with an Xq22 nullisomy in a region proximal to PLP1. The patient showed severe neurological impairment and was bedridden. Brain magnetic resonance imaging revealed a severely reduced cerebral volume. The chromosomal region proximal to PLP1 was considered to be significantly important for brain development.
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Affiliation(s)
- Kentaro Shirai
- Department of Pediatrics, Tsuchiura Kyodo Hospital, Tsuchiura, Ibaraki, Japan
| | - Yuya Higashi
- Department of Neonatology, Tsuchiura Kyodo Hospital, Tsuchiura, Ibaraki, Japan
| | - Keiko Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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19
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Gao W, Li JZ, Chen S, Chu C, Chan JY, Wong T. BEX3 contributes to cisplatin chemoresistance in nasopharyngeal carcinoma. Cancer Med 2017; 6:439-451. [PMID: 28083995 PMCID: PMC5313644 DOI: 10.1002/cam4.982] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) can develop cisplatin‐resistant phenotype. Research has revealed that enriched in cancer stem cell population is involved in developing cisplatin‐resistant phenotype. CD271 is a candidate stem cell maker in head and neck cancers. The CD receptor does not possess any enzymatic property. Signal transduction function of CD271 is mediated by the cellular receptor‐associated protein. Our data showed that Brain‐expressed X‐linked 3 (BEX3), a CD271 receptor‐associated protein, was overexpressed in NPC. BEX3 overexpression was a unique event in cancer developed in the head and neck regions, especially NPC. BEX3 expression was inducible by cisplatin in NPC. In cisplatin‐resistant NPC xenograft, treatment with nontoxic level of cisplatin led to a remarkable increase in BEX3 level. High BEX3 expression was accompanied with high octamer‐binding transcription factor 4 (OCT4) expression in cisplatin‐resistant NPC. To confirm the inducing role of BEX3 on OCT4 expression, we knockdown BEX3 using siRNA and compared the expression of OCT4 with mock transfectants. Suppressing BEX3 transcripts led to a significant reduction in OCT4. In addition, targeting BEX3 using shRNA could increase the sensitivity of NPC cells to cisplatin. In summary, our results indicated a unique functional role of BEX3 in mediating the sensitivity of NPC cells to cisplatin. Targeting or blocking BEX3 activity might be useful in reversing the cisplatin‐resistant phenotype in NPC.
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Affiliation(s)
- Wei Gao
- Department of SurgeryThe University of Hong KongHong Kong SARChina
| | - John Zeng‐Hong Li
- Department of SurgeryThe University of Hong KongHong Kong SARChina
- Department of OtolaryngologyThe First People's Hospital of FoshanGuangdong ProvinceChina
| | - Si‐Qi Chen
- Department of SurgeryThe University of Hong KongHong Kong SARChina
| | - Chiao‐Yun Chu
- Department of SurgeryThe University of Hong KongHong Kong SARChina
| | | | - Thian‐Sze Wong
- Department of SurgeryThe University of Hong KongHong Kong SARChina
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20
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Anta B, Martín-Rodríguez C, Gomis-Perez C, Calvo L, López-Benito S, Calderón-García AA, Vicente-García C, Villarroel Á, Arévalo JC. Ubiquitin-specific Protease 36 (USP36) Controls Neuronal Precursor Cell-expressed Developmentally Down-regulated 4-2 (Nedd4-2) Actions over the Neurotrophin Receptor TrkA and Potassium Voltage-gated Channels 7.2/3 (Kv7.2/3). J Biol Chem 2016; 291:19132-45. [PMID: 27445338 DOI: 10.1074/jbc.m116.722637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/06/2022] Open
Abstract
Ubiquitination of the TrkA neurotrophin receptor in response to NGF is critical in the regulation of TrkA activation and functions. TrkA is ubiquitinated, among other E3 ubiquitin ligases, by Nedd4-2. To understand mechanistically how TrkA ubiquitination is regulated, we performed a siRNA screening to identify deubiquitinating enzymes and found that USP36 acts as an important regulator of TrkA activation kinetics and ubiquitination. However, USP36 action on TrkA was indirect because it does not deubiquitinate TrkA. Instead, USP36 binds to Nedd4-2 and regulates the association of TrkA and Nedd4-2. In addition, depletion of USP36 increases TrkA·Nedd4-2 complex formation, whereas USP36 expression disrupts the complex, resulting in an enhancement or impairment of Nedd4-2-dependent TrkA ubiquitination, respectively. Moreover, USP36 depletion leads to enhanced total and surface TrkA expression that results in increased NGF-mediated TrkA activation and signaling that augments PC12 cell differentiation. USP36 actions extend beyond TrkA because the presence of USP36 interferes with Nedd4-2-dependent Kv7.2/3 channel regulation. Our results demonstrate that USP36 binds to and regulates the actions of Nedd4-2 over different substrates affecting their expression and functions.
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Affiliation(s)
- Begoña Anta
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Carlos Martín-Rodríguez
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Carolina Gomis-Perez
- the Unidad de Biofísica, Consejo Superior de Investigaciones Científicas, CSIC, UPV/EHU, Universidad del País Vasco, barrio Sarriena s/n, 48940 Leoia, Spain
| | - Laura Calvo
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Saray López-Benito
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Andrés A Calderón-García
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Cristina Vicente-García
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Álvaro Villarroel
- the Unidad de Biofísica, Consejo Superior de Investigaciones Científicas, CSIC, UPV/EHU, Universidad del País Vasco, barrio Sarriena s/n, 48940 Leoia, Spain
| | - Juan C Arévalo
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
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21
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López-Benito S, Lillo C, Hernández-Hernández Á, Chao MV, Arévalo JC. ARMS/Kidins220 and synembryn-B levels regulate NGF-mediated secretion. J Cell Sci 2016; 129:1866-77. [PMID: 26966186 DOI: 10.1242/jcs.184168] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/05/2016] [Indexed: 01/22/2023] Open
Abstract
Proper development of the nervous system requires a temporally and spatially orchestrated set of events including differentiation, synapse formation and neurotransmission. Nerve growth factor (NGF) acting through the TrkA neurotrophin receptor (also known as NTRK1) regulates many of these events. However, the molecular mechanisms responsible for NGF-regulated secretion are not completely understood. Here, we describe a new signaling pathway involving TrkA, ARMS (also known as Kidins220), synembryn-B and Rac1 in NGF-mediated secretion in PC12 cells. Whereas overexpression of ARMS blocked NGF-mediated secretion, without affecting basal secretion, a decrease in ARMS resulted in potentiation. Similar effects were observed with synembryn-B, a protein that interacts directly with ARMS. Downstream of ARMS and synembryn-B are Gαq and Trio proteins, which modulate the activity of Rac1 in response to NGF. Expression of dominant-negative Rac1 rescued the secretion defects of cells overexpressing ARMS or synembryn-B. Thus, this neurotrophin pathway represents a new mechanism responsible for NGF-regulated secretion.
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Affiliation(s)
- Saray López-Benito
- Department of Cell Biology and Pathology, Instituto de Neurociencias de Castilla y León (INCyL), University of Salamanca, Salamanca 37007, Spain Institute of Biomedical Research of Salamanca (IBSAL), Salamanca 37007, Spain
| | - Concepción Lillo
- Department of Cell Biology and Pathology, Instituto de Neurociencias de Castilla y León (INCyL), University of Salamanca, Salamanca 37007, Spain Institute of Biomedical Research of Salamanca (IBSAL), Salamanca 37007, Spain
| | - Ángel Hernández-Hernández
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca 37007, Spain Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca 37007, Spain
| | - Moses V Chao
- Molecular Neurobiology Program, Skirball Institute of Biomolecular Medicine, Departments of Cell Biology, Physiology and Neuroscience, Psychiatry, and Neural Sciences, New York University School of Medicine, New York, NY 10016, USA
| | - Juan C Arévalo
- Department of Cell Biology and Pathology, Instituto de Neurociencias de Castilla y León (INCyL), University of Salamanca, Salamanca 37007, Spain Institute of Biomedical Research of Salamanca (IBSAL), Salamanca 37007, Spain
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22
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Urnukhsaikhan E, Cho H, Mishig-Ochir T, Seo YK, Park JK. Pulsed electromagnetic fields promote survival and neuronal differentiation of human BM-MSCs. Life Sci 2016; 151:130-138. [PMID: 26898125 DOI: 10.1016/j.lfs.2016.02.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 12/11/2022]
Abstract
Pulsed electromagnetic fields (PEMF) are known to affect biological properties such as differentiation, regulation of transcription factor and cell proliferation. However, the cell-protective effect of PEMF exposure is largely unknown. The aim of this study is to understand the mechanisms underlying PEMF-mediated suppression of apoptosis and promotion of survival, including PEMF-induced neuronal differentiation. Treatment of induced human BM-MSCs with PEMF increased the expression of neural markers such as NF-L, NeuroD1 and Tau. Moreover, treatment of induced human BM-MSCs with PEMF greatly decreased cell death in a dose- and time-dependent manner. There is evidence that Akt and Ras are involved in neuronal survival and protection. Activation of Akt and Ras results in the regulation of survival proteins such as Bad and Bcl-xL. Thus, the Akt/Ras signaling pathway may be a desirable target for enhancing cell survival and treatment of neurological disease. Our analyses indicated that PEMF exposure dramatically increased the activity of Akt, Rsk, Creb, Erk, Bcl-xL and Bad via phosphorylation. PEMF-dependent cell protection was reversed by pretreatment with LY294002, a specific inhibitor of phosphatidylinositol 3-kinase (PI3K). Our data suggest that the PI3K/Akt/Bad signaling pathway may be a possible mechanism for the cell-protective effects of PEMF.
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Affiliation(s)
| | - Hyunjin Cho
- Dongguk University Research Institute of Biotechnology, Republic of Korea
| | | | - Young-Kwon Seo
- Department of Medical Biotechnology, Dongguk University, Seoul, Republic of Korea
| | - Jung-Kueg Park
- Department of Medical Biotechnology, Dongguk University, Seoul, Republic of Korea
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23
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Kazi JU, Kabir NN, Rönnstrand L. Brain-Expressed X-linked (BEX) proteins in human cancers. Biochim Biophys Acta Rev Cancer 2015; 1856:226-33. [PMID: 26408910 DOI: 10.1016/j.bbcan.2015.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/20/2015] [Accepted: 09/22/2015] [Indexed: 01/08/2023]
Abstract
The Brain-Expressed X-linked (BEX) family proteins are comprised of five human proteins including BEX1, BEX2, BEX3, BEX4 and BEX5. BEX family proteins are expressed in a wide range of tissues and are known to play a role in neuronal development. Recent studies suggest a role of BEX family proteins in cancers. BEX1 expression is lost in a subgroup of patients with acute myeloid leukemia (AML) and chronic myeloid leukemia (CML). Expression of BEX1 controls cell surface receptor signaling and restores imatinib response in resistant cells. BEX2 is overexpressed in a group of breast cancer patients and also in gliomas. Increased BEX2 expression led to enhanced NF-κB signaling as well as cell proliferation. Although BEX2 acts as tumor promoter in a subset of breast cancer, BEX3 expression displayed an opposite role. Overexpression of BEX3 resulted in inhibition of tumor formation in breast cancer mouse xenograft models. The role of BEX4 and BEX5 in cancer has not yet been defined. Collectively this suggests that BEX family members have distinct roles in cancers. While BEX1 and BEX3 act as tumor suppressors, BEX2 seems to act as an oncogene.
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Affiliation(s)
- Julhash U Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village 404 ,Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden; Laboratory of Computational Biochemistry, KN Biomedical Research Institute, Barisal, Bangladesh.
| | - Nuzhat N Kabir
- Laboratory of Computational Biochemistry, KN Biomedical Research Institute, Barisal, Bangladesh
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village 404 ,Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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