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Sansone L, Milani F, Fabrizi R, Belli M, Cristina M, Zagà V, de Iure A, Cicconi L, Bonassi S, Russo P. Nicotine: From Discovery to Biological Effects. Int J Mol Sci 2023; 24:14570. [PMID: 37834017 PMCID: PMC10572882 DOI: 10.3390/ijms241914570] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Nicotine, the primary psychoactive agent in tobacco leaves, has led to the widespread use of tobacco, with over one billion smokers globally. This article provides a historical overview of tobacco and discusses tobacco dependence, as well as the biological effects induced by nicotine on mammalian cells. Nicotine induces various biological effects, such as neoangiogenesis, cell division, and proliferation, and it affects neural and non-neural cells through specific pathways downstream of nicotinic receptors (nAChRs). Specific effects mediated by α7 nAChRs are highlighted. Nicotine is highly addictive and hazardous. Public health initiatives should prioritize combating smoking and its associated risks. Understanding nicotine's complex biological effects is essential for comprehensive research and informed health policies. While potential links between nicotine and COVID-19 severity warrant further investigation, smoking remains a significant cause of morbidity and mortality globally. Effective public health strategies are vital to promote healthier lifestyles.
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Affiliation(s)
- Luigi Sansone
- Department of Human Sciences and Quality, Life Promotion San Raffaele University, Via di Val Cannuta 247, 00166 Rome, Italy; (L.S.); (M.B.); (M.C.); (A.d.I.); (S.B.)
- MEBIC Consortium, San Raffaele University, 00166 Rome, Italy
| | - Francesca Milani
- Clinical and Molecular Epidemiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy; (F.M.); (R.F.); (L.C.)
| | - Riccardo Fabrizi
- Clinical and Molecular Epidemiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy; (F.M.); (R.F.); (L.C.)
| | - Manuel Belli
- Department of Human Sciences and Quality, Life Promotion San Raffaele University, Via di Val Cannuta 247, 00166 Rome, Italy; (L.S.); (M.B.); (M.C.); (A.d.I.); (S.B.)
- MEBIC Consortium, San Raffaele University, 00166 Rome, Italy
| | - Mario Cristina
- Department of Human Sciences and Quality, Life Promotion San Raffaele University, Via di Val Cannuta 247, 00166 Rome, Italy; (L.S.); (M.B.); (M.C.); (A.d.I.); (S.B.)
- Department of Molecular Medicine, University La Sapienza, Viale del Policlinico 155, 00161 Rome, Italy
| | - Vincenzo Zagà
- Italian Society of Tabaccology (SITAB), 00136 Bologna, Italy;
| | - Antonio de Iure
- Department of Human Sciences and Quality, Life Promotion San Raffaele University, Via di Val Cannuta 247, 00166 Rome, Italy; (L.S.); (M.B.); (M.C.); (A.d.I.); (S.B.)
- Experimental Neurophysiology IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Luca Cicconi
- Clinical and Molecular Epidemiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy; (F.M.); (R.F.); (L.C.)
| | - Stefano Bonassi
- Department of Human Sciences and Quality, Life Promotion San Raffaele University, Via di Val Cannuta 247, 00166 Rome, Italy; (L.S.); (M.B.); (M.C.); (A.d.I.); (S.B.)
- Clinical and Molecular Epidemiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy; (F.M.); (R.F.); (L.C.)
| | - Patrizia Russo
- Department of Human Sciences and Quality, Life Promotion San Raffaele University, Via di Val Cannuta 247, 00166 Rome, Italy; (L.S.); (M.B.); (M.C.); (A.d.I.); (S.B.)
- MEBIC Consortium, San Raffaele University, 00166 Rome, Italy
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Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty S, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181 Suppl 76:118-144. [PMID: 36794631 PMCID: PMC10329998 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
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Affiliation(s)
- Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Sean McGinty
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
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3
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Leonard S, Benfante R. Unanswered questions in the regulation and function of the duplicated α7 nicotinic receptor gene CHRFAM7A. Pharmacol Res 2023; 192:106783. [PMID: 37164281 DOI: 10.1016/j.phrs.2023.106783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
The α7 nicotinic receptor (α7 nAChR) is an important entry point for Ca2+ into the cell, which has broad and important effects on gene expression and function. The gene (CHRNA7), mapping to chromosome (15q14), has been genetically linked to a large number of diseases, many of which involve defects in cognition. While numerous mutations in CHRNA7 are associated with mental illness and inflammation, an important control point may be the function of a recently discovered partial duplication CHRNA7, CHRFAM7A, that negatively regulates the function of the α7 receptor, through the formation of heteropentamers; other functions cannot be excluded. The deregulation of this human specific gene (CHRFAM7A) has been linked to neurodevelopmental, neurodegenerative, and inflammatory disorders and has important copy number variations. Much effort is being made to understand its function and regulation both in healthy and pathological conditions. However, many questions remain to be answered regarding its functional role, its regulation, and its role in the etiogenesis of neurological and inflammatory disorders. Missing knowledge on the pharmacology of the heteroreceptor has limited the discovery of new molecules capable of modulating its activity. Here we review the state of the art on the role of CHRFAM7A, highlighting unanswered questions to be addressed. A possible therapeutic approach based on genome editing protocols is also discussed.
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Affiliation(s)
- Sherry Leonard
- Department of Psychiatry - University of Colorado Anschutz, Aurora, Colorado, USA
| | - Roberta Benfante
- CNR - Institute of Neuroscience, Vedano al Lambro (MB), Italy; Dept. Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy; NeuroMI - Milan Center for Neuroscience, University of Milano Bicocca, Milan, Italy.
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Giovenale AMG, Ruotolo G, Soriano AA, Turco EM, Rotundo G, Casamassa A, D’Anzi A, Vescovi AL, Rosati J. Deepening the understanding of CNVs on chromosome 15q11-13 by using hiPSCs: An overview. Front Cell Dev Biol 2023; 10:1107881. [PMID: 36684422 PMCID: PMC9852989 DOI: 10.3389/fcell.2022.1107881] [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: 11/25/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
The human α7 neuronal nicotinic acetylcholine receptor gene (CHRNA7) is widely expressed in the central and peripheral nervous systems. This receptor is implicated in both brain development and adult neurogenesis thanks to its ability to mediate acetylcholine stimulus (Ach). Copy number variations (CNVs) of CHRNA7 gene have been identified in humans and are genetically linked to cognitive impairments associated with multiple disorders, including schizophrenia, bipolar disorder, epilepsy, Alzheimer's disease, and others. Currently, α7 receptor analysis has been commonly performed in animal models due to the impossibility of direct investigation of the living human brain. But the use of model systems has shown that there are very large differences between humans and mice when researchers must study the CNVs and, in particular, the CNV of chromosome 15q13.3 where the CHRNA7 gene is present. In fact, human beings present genomic alterations as well as the presence of genes of recent origin that are not present in other model systems as well as they show a very heterogeneous symptomatology that is associated with both their genetic background and the environment where they live. To date, the induced pluripotent stem cells, obtained from patients carrying CNV in CHRNA7 gene, are a good in vitro model for studying the association of the α7 receptor to human diseases. In this review, we will outline the current state of hiPSCs technology applications in neurological diseases caused by CNVs in CHRNA7 gene. Furthermore, we will discuss some weaknesses that emerge from the overall analysis of the published articles.
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Affiliation(s)
- Angela Maria Giada Giovenale
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Giorgia Ruotolo
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Amata Amy Soriano
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Elisa Maria Turco
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giovannina Rotundo
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Alessia Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angela D’Anzi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angelo Luigi Vescovi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy,*Correspondence: Jessica Rosati, ; Angelo Luigi Vescovi,
| | - Jessica Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,*Correspondence: Jessica Rosati, ; Angelo Luigi Vescovi,
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Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae). Chromosome Res 2023; 31:9. [PMID: 36745262 PMCID: PMC9902428 DOI: 10.1007/s10577-023-09715-x] [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: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/28/2022] [Indexed: 02/07/2023]
Abstract
Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.
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Genomic Organization of Microsatellites and LINE-1-like Retrotransposons: Evolutionary Implications for Ctenomys minutus (Rodentia: Ctenomyidae) Cytotypes. Animals (Basel) 2022; 12:ani12162091. [PMID: 36009681 PMCID: PMC9405301 DOI: 10.3390/ani12162091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/28/2022] [Accepted: 08/13/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary In animals, several species contain substantial chromosomal and genomic variation among their populations, but as to what could have driven such diversification is still a puzzle for most cases. Here, we used molecular cytogenetic analysis to expose the main genomic elements involved in the population variation observed in the Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae), which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoint regions (EBRs) and highlight their direct impact in promoting chromosomal rearrangements. Abstract The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among which, seven parental ones, named A to G, are parapatrically distributed in the coastal plains of Southern Brazil. Looking for possible causes that led to such extensive karyotype diversification, we performed chromosomal mapping of different repetitive DNAs, including microsatellites and long interspersed element-1 (LINE-1) retrotransposons in the seven parental cytotypes. Although microsatellites were found mainly in the centromeric and telomeric regions of the chromosomes, different patterns occur for each cytotype, thus revealing specific features. Likewise, the LINE-1-like retrotransposons also showed a differential distribution for each cytotype, which may be linked to stochastic loss of LINE-1 in some populations. Here, microsatellite motifs (A)30, (C)30, (CA)15, (CAC)10, (CAG)10, (CGG)10, (GA)15, and (GAG)10 could be mapped to fusion of chromosomes 20/17, fission and inversion in the short arm of chromosome 2, fusion of chromosomes 23/19, and different combinations of centric and tandem fusions of chromosomes 22/24/16. These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoints and highlight their direct impact in promoting chromosomal rearrangements.
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Di Lascio S, Fornasari D, Benfante R. The Human-Restricted Isoform of the α7 nAChR, CHRFAM7A: A Double-Edged Sword in Neurological and Inflammatory Disorders. Int J Mol Sci 2022; 23:ijms23073463. [PMID: 35408823 PMCID: PMC8998457 DOI: 10.3390/ijms23073463] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/13/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
CHRFAM7A is a relatively recent and exclusively human gene arising from the partial duplication of exons 5 to 10 of the α7 neuronal nicotinic acetylcholine receptor subunit (α7 nAChR) encoding gene, CHRNA7. CHRNA7 is related to several disorders that involve cognitive deficits, including neuropsychiatric, neurodegenerative, and inflammatory disorders. In extra-neuronal tissues, α7nAChR plays an important role in proliferation, differentiation, migration, adhesion, cell contact, apoptosis, angiogenesis, and tumor progression, as well as in the modulation of the inflammatory response through the “cholinergic anti-inflammatory pathway”. CHRFAM7A translates the dupα7 protein in a multitude of cell lines and heterologous systems, while maintaining processing and trafficking that are very similar to the full-length form. It does not form functional ion channel receptors alone. In the presence of CHRNA7 gene products, dupα7 can assemble and form heteromeric receptors that, in order to be functional, should include at least two α7 subunits to form the agonist binding site. When incorporated into the receptor, in vitro and in vivo data showed that dupα7 negatively modulated α7 activity, probably due to a reduction in the number of ACh binding sites. Very recent data in the literature report that the presence of the duplicated gene may be responsible for the translational gap in several human diseases. Here, we will review the studies that have been conducted on CHRFAM7A in different pathologies, with the intent of providing evidence regarding when and how the expression of this duplicated gene may be beneficial or detrimental in the pathogenesis, and eventually in the therapeutic response, to CHRNA7-related neurological and non-neurological diseases.
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Affiliation(s)
- Simona Di Lascio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
| | - Diego Fornasari
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
- CNR Institute of Neuroscience, 20845 Vedano al Lambro, Italy
| | - Roberta Benfante
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
- CNR Institute of Neuroscience, 20845 Vedano al Lambro, Italy
- NeuroMi, Milan Center for Neuroscience, University of Milano Bicocca, 20126 Milan, Italy
- Correspondence:
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Kolodziej MA, Gött H, Kopischke B, Bender MK, Weigand MA, Di Fazio P, Schwarm FP, Uhle F. Antiproliferative effect of GTS-21 in glioblastoma cells. Oncol Lett 2021; 22:759. [PMID: 34539863 PMCID: PMC8436335 DOI: 10.3892/ol.2021.13020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most common malignant brain tumour in adults. The poor prognosis and short median overall survival of patients with GBM is associated with resistance to therapy after surgical and adjuvant treatment. The expression of various acetylcholine receptors (AChR) in GBM has been widely reported. The present study aimed to investigate the expression of cholinergic system-related genes in primary GBM and to explore the antiproliferative effect of 3-(2,4-dimethoxybenzylidene) anabaseine (GTS-21) in GBM cell lines. Therefore, the expression of 28 genes associated with the cholinergic system was detected using a customized RT2 Profiler PCR Array in 44 GBM and 5 healthy control brain tissue samples. In addition, the activity of GTS-21, an alpha 7 subunit nicotinic AChR (α7 nAChR) agonist, and that of α-bungarotoxin (α-BTX), an α7 nAChR antagonist, was determined in primary and established GBM cells. Therefore, the A172, U87 and G28 cell lines and primary GBM cells were treated with GTS-21, ACh or nicotine. Cell viability was evaluated using MTT assay at 24, 48 and 72 h following cell treatment with the corresponding compounds. The results revealed that the expression of cholinergic system-related components was notably downregulated, except that of cholinergic receptor nicotinic alpha 7 subunit (CHRNA7), in primary GBM and U87 cells. However, the dominant-negative duplicate form of CHRNA7 was also downregulated. Furthermore, A172 and G28 cells exhibited a heterogeneous gene expression pattern. Additionally, GTS-21 inhibited the proliferation of GBM cells in a dose- and time-dependent manner. Interestingly, treatment with α-BTX restored the proliferation of U87 cells, but not that of A172 and G28 cells. Collectively, the findings of the present study suggested that GTS-21 may inhibit the proliferation of GBM cells and may therefore serve as a novel therapeutic approach to the treatment of GBM, which warrants further investigation.
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Affiliation(s)
- Malgorzata A. Kolodziej
- Department of Neurosurgery, Justus-Liebig University Giessen, D-35392 Giessen, Germany
- Correspondence to: Dr Malgorzata Anna Kolodziej, Department of Neurosurgery, Justus-Liebig University Giessen, Klinikstrasse 33, D-35392 Giessen, Germany, E-mail:
| | - Hanna Gött
- Department of Neurosurgery, Justus-Liebig University Giessen, D-35392 Giessen, Germany
| | - Benjamin Kopischke
- Department of Neurosurgery, Justus-Liebig University Giessen, D-35392 Giessen, Germany
| | - Michael K.F. Bender
- Department of Neurosurgery, Justus-Liebig University Giessen, D-35392 Giessen, Germany
| | - Markus A. Weigand
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Pietro Di Fazio
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, D-35033 Marburg, Germany
| | - Frank P. Schwarm
- Department of Neurosurgery, Justus-Liebig University Giessen, D-35392 Giessen, Germany
| | - Florian Uhle
- Department of Anaesthesiology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
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Martín-Sánchez C, Alés E, Balseiro-Gómez S, Atienza G, Arnalich F, Bordas A, Cedillo JL, Extremera M, Chávez-Reyes A, Montiel C. The human-specific duplicated α7 gene inhibits the ancestral α7, negatively regulating nicotinic acetylcholine receptor-mediated transmitter release. J Biol Chem 2021; 296:100341. [PMID: 33515545 PMCID: PMC7949125 DOI: 10.1016/j.jbc.2021.100341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/13/2021] [Accepted: 01/21/2021] [Indexed: 12/31/2022] Open
Abstract
Gene duplication generates new functions and traits, enabling evolution. Human-specific duplicated genes in particular are primary sources of innovation during our evolution although they have very few known functions. Here we examine the brain function of one of these genes (CHRFAM7A) and its product (dupα7 subunit). This gene results from a partial duplication of the ancestral CHRNA7 gene encoding the α7 subunit that forms the homopentameric α7 nicotinic acetylcholine receptor (α7-nAChR). The functions of α7-nAChR in the brain are well defined, including the modulation of synaptic transmission and plasticity underlying normal attention, cognition, learning, and memory processes. However, the role of the dupα7 subunit remains unexplored at the neuronal level. Here, we characterize that role by combining immunoblotting, quantitative RT-PCR and FRET techniques with functional assays of α7-nAChR activity using human neuroblastoma SH-SY5Y cell variants with different dupα7 expression levels. Our findings reveal a physical interaction between dupα7 and α7 subunits in fluorescent protein-tagged dupα7/α7 transfected cells that negatively affects normal α7-nAChR activity. Specifically, in both single cells and cell populations, the [Ca2+]i signal and the exocytotic response induced by selective stimulation of α7-nAChR were either significantly inhibited by stable dupα7 overexpression or augmented after silencing dupα7 gene expression with specific siRNAs. These findings identify a new role for the dupα7 subunit as a negative regulator of α7-nAChR-mediated control of exocytotic neurotransmitter release. If this effect is excessive, it would result in an impaired synaptic transmission that could underlie the neurocognitive and neuropsychiatric disorders associated with α7-nAChR dysfunction.
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Affiliation(s)
- Carolina Martín-Sánchez
- Department of Pharmacology and Therapeutics, Medical School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eva Alés
- Department of Medical Physiology and Biophysics, Medical School, Universidad de Sevilla, Sevilla, Spain
| | - Santiago Balseiro-Gómez
- Department of Medical Physiology and Biophysics, Medical School, Universidad de Sevilla, Sevilla, Spain
| | - Gema Atienza
- Department of Pharmacology and Therapeutics, Medical School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Arnalich
- Internal Medicine Service, University Hospital La Paz-IdiPAZ, Madrid, Spain
| | - Anna Bordas
- Department of Pharmacology and Therapeutics, Medical School, Universidad Autónoma de Madrid, Madrid, Spain
| | - José L Cedillo
- Department of Pharmacology and Therapeutics, Medical School, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Extremera
- Department of Pharmacology and Therapeutics, Medical School, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Carmen Montiel
- Department of Pharmacology and Therapeutics, Medical School, Universidad Autónoma de Madrid, Madrid, Spain.
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Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution. Genome Res 2020; 30:1680-1693. [PMID: 33093070 PMCID: PMC7605249 DOI: 10.1101/gr.265322.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.
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11
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Santoro A, Tomino C, Prinzi G, Lamonaca P, Cardaci V, Fini M, Russo P. Tobacco Smoking: Risk to Develop Addiction, Chronic Obstructive Pulmonary Disease, and Lung Cancer. Recent Pat Anticancer Drug Discov 2019; 14:39-52. [PMID: 30605063 DOI: 10.2174/1574892814666190102122848] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/11/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND The morbidity and mortality associated with tobacco smoking is well established. Nicotine is the addictive component of tobacco. Nicotine, through the non-neuronal α7nicotinic receptor, induces cell proliferation, neo-angiogenesis, epithelial to mesenchymal transition, and inhibits drug-induced apoptosis. OBJECTIVE To understand the genetic, molecular and cellular biology of addiction, chronic obstructive pulmonary disease and lung cancer. METHODS The search for papers to be included in the review was performed during the months of July- September 2018 in the following databases: PubMed (http://www.ncbi.nlm.nih.gov), Scopus (http://www.scopus.com), EMBASE (http://www.elsevier.com/online-tools/embase), and ISI Web of Knowledge (http://apps.webofknowledge.com/). The following searching terms: "nicotine", "nicotinic receptor", and "addiction" or "COPD" or "lung cancer" were used. Patents were retrieved in clinicaltrials.gov (https://clinicaltrials.gov/). All papers written in English were evaluated. The reference list of retrieved articles was also reviewed to identify other eligible studies that were not indexed by the above-mentioned databases. New experimental data on the ability of nicotine to promote transformation of human bronchial epithelial cells, exposed for one hour to Benzo[a]pyrene-7,8-diol-9-10-epoxide, are reported. RESULTS Nicotinic receptors variants and nicotinic receptors upregulation are involved in addiction, chronic obstructive pulmonary disease and/or lung cancer. Nicotine through α7nicotinic receptor upregulation induces complete bronchial epithelial cells transformation. CONCLUSION Genetic studies highlight the involvement of nicotinic receptors variants in addiction, chronic obstructive pulmonary disease and/or lung cancer. A future important step will be to translate these genetic findings to clinical practice. Interventions able to help smoking cessation in nicotine dependence subjects, under patent, are reported.
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Affiliation(s)
- Alessia Santoro
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Carlo Tomino
- Scientific Direction, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Giulia Prinzi
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Palma Lamonaca
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Vittorio Cardaci
- Pulmonary Rehabilitation, IRCCS San Raffaele Pisana, Via della Pisana, 235, I-00163 Rome, Italy
| | - Massimo Fini
- Scientific Direction, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Patrizia Russo
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
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12
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Cedillo JL, Bordas A, Arnalich F, Esteban-Rodríguez I, Martín-Sánchez C, Extremera M, Atienza G, Rios JJ, Arribas RL, Montiel C. Anti-tumoral activity of the human-specific duplicated form of α7-nicotinic receptor subunit in tobacco-induced lung cancer progression. Lung Cancer 2018; 128:134-144. [PMID: 30642446 DOI: 10.1016/j.lungcan.2018.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 01/17/2023]
Abstract
OBJECTIVES Tobacco smoking is strongly correlated with the onset and progression of non-small cell lung cancer (NSCLC). By activating α7 nicotinic acetylcholine receptors (α7-nAChRs) in these tumors nicotine and its tobacco-derived nitrosamine, NNK, contribute to these oncogenic processes. Here, we investigated whether the human-specific duplicated form of the α7-nAChR subunit (dupα7) behaves as an endogenous negative regulator of α7-nAChR-mediated tumorigenic activity induced by tobacco in NSCLC cells, similarly to its influence on other α7-nAChR-controlled functions in non-tumor cells. METHODS Two human NSCLC cell lines, lung adenocarcinoma (A549) and squamous cell carcinoma of the lung (SK-MES-1), both wild-type or with stable overexpression of dupα7 (A549dupα7 or SK-MES-1dupα7), were used to investigate in vitro anti-tumor activity of dupα7 on nicotine- or NNK-induced tumor progression. For this purpose, migration, proliferation or epithelial-mesenchymal transition (EMT) were examined. The anti-tumor effect of dupα7 on nicotine-promoted tumor growth, proliferation or angiogenesis was also assessed in vivo in an athymic mouse model implanted with A549dupα7 or A549 xenografts. RESULTS Overexpression of dupα7 in both cell lines almost completely suppresses the in vitro tumor-promoting effects induced by nicotine (1 μM) or NNK (100 nM) in wild-type cells. Furthermore, in mice receiving nicotine, A549dupα7 xenografts show: (i) a significant reduction of tumor growth, and (ii) decreased expression of cell markers for proliferation (Ki67) or angiogenesis (VEGF) compared to A549 xenografts. CONCLUSION Our study demonstrates, for the first time, the in vitro and in vivo anti-tumor capacity of dupα7 to block the α7-nAChR-mediated tumorigenic effects of tobacco in NSCLC, suggesting that up-regulation of dupα7 expression in these tumors could offer a potential new therapeutic target in smoking-related cancers.
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Affiliation(s)
- José Luis Cedillo
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain
| | - Anna Bordas
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain
| | - Francisco Arnalich
- Internal Medicine Service, University Hospital La Paz of Madrid-IdiPAZ, Madrid, Spain.
| | | | - Carolina Martín-Sánchez
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain
| | - María Extremera
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain
| | - Gema Atienza
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain
| | - Juan J Rios
- Internal Medicine Service, University Hospital La Paz of Madrid-IdiPAZ, Madrid, Spain
| | - Raquel L Arribas
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain
| | - Carmen Montiel
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid-IdiPAZ, Madrid, Spain.
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13
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Kapun M, Flatt T. The adaptive significance of chromosomal inversion polymorphisms inDrosophila melanogaster. Mol Ecol 2018; 28:1263-1282. [DOI: 10.1111/mec.14871] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Martin Kapun
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
| | - Thomas Flatt
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
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14
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Maldifassi MC, Martín-Sánchez C, Atienza G, Cedillo JL, Arnalich F, Bordas A, Zafra F, Giménez C, Extremera M, Renart J, Montiel C. Interaction of the α7-nicotinic subunit with its human-specific duplicated dupα7 isoform in mammalian cells: Relevance in human inflammatory responses. J Biol Chem 2018; 293:13874-13888. [PMID: 30006348 DOI: 10.1074/jbc.ra118.003443] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/11/2018] [Indexed: 01/19/2023] Open
Abstract
The α7 nicotinic receptor subunit and its partially duplicated human-specific dupα7 isoform are coexpressed in neuronal and non-neuronal cells. In these cells, α7 subunits form homopentameric α7 nicotinic acetylcholine receptors (α7-nAChRs) implicated in numerous pathologies. In immune cells, α7-nAChRs are essential for vagal control of inflammatory response in sepsis. Recent studies show that the dupα7 subunit is a dominant-negative regulator of α7-nAChR activity in Xenopus oocytes. However, its biological significance in mammalian cells, particularly immune cells, remains unexplored, as the duplicated form is indistinguishable from the original subunit in standard tests. Here, using immunocytochemistry, confocal microscopy, coimmunoprecipitation, FRET, flow cytometry, and ELISA, we addressed this challenge in GH4C1 rat pituitary cells and RAW264.7 murine macrophages transfected with epitope- and fluorescent protein-tagged α7 or dupα7. We used quantitative RT-PCR of dupα7 gene expression levels in peripheral blood mononuclear cells (PBMCs) from patients with sepsis to analyze its relationship with PBMC α7 mRNA levels and with serum concentrations of inflammatory markers. We found that a physical interaction between dupα7 and α7 subunits in both cell lines generates heteromeric nAChRs that remain mainly trapped in the endoplasmic reticulum. The dupα7 sequestration of α7 subunits reduced membrane expression of functional α7-nAChRs, attenuating their anti-inflammatory capacity in lipopolysaccharide-stimulated macrophages. Moreover, the PBMC's dupα7 levels correlated inversely with their α7 levels and directly with the magnitude of the patients' inflammatory state. These results indicate that dupα7 probably reduces human vagal anti-inflammatory responses and suggest its involvement in other α7-nAChR-mediated pathophysiological processes.
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Affiliation(s)
- María C Maldifassi
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and.,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Carolina Martín-Sánchez
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and.,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Gema Atienza
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and.,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - José L Cedillo
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and.,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Francisco Arnalich
- the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain.,the Servicio de Medicina Interna, Hospital Universitario La Paz de Madrid, 28046 Madrid
| | - Anna Bordas
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and.,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Francisco Zafra
- the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain.,the Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, and
| | - Cecilio Giménez
- the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain.,the Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, and
| | - María Extremera
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and.,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Jaime Renart
- the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28029 Madrid
| | - Carmen Montiel
- From the Departamento de Farmacología y Terapéutica, Facultad de Medicina and .,the Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28046 Madrid, Spain
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15
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Kretschmer R, de Oliveira TD, de Oliveira Furo I, Oliveira Silva FA, Gunski RJ, Del Valle Garnero A, de Bello Cioffi M, de Oliveira EHC, de Freitas TRO. Repetitive DNAs and shrink genomes: A chromosomal analysis in nine Columbidae species (Aves, Columbiformes). Genet Mol Biol 2018; 41:98-106. [PMID: 29473932 PMCID: PMC5901494 DOI: 10.1590/1678-4685-gmb-2017-0048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/16/2017] [Indexed: 12/02/2022] Open
Abstract
An extensive karyotype variation is found among species belonging to the
Columbidae family of birds (Columbiformes), both in diploid number and
chromosomal morphology. Although clusters of repetitive DNA sequences play an
important role in chromosomal instability, and therefore in chromosomal
rearrangements, little is known about their distribution and amount in avian
genomes. The aim of this study was to analyze the distribution of 11 distinct
microsatellite sequences, as well as clusters of 18S rDNA, in nine different
Columbidae species, correlating their distribution with the occurrence of
chromosomal rearrangements. We found 2n values ranging from 76 to 86 and nine
out of 11 microsatellite sequences showed distinct hybridization signals among
the analyzed species. The accumulation of microsatellite repeats was found
preferentially in the centromeric region of macro and microchromosomes, and in
the W chromosome. Additionally, pair 2 showed the accumulation of several
microsatellites in different combinations and locations in the distinct species,
suggesting the occurrence of intrachromosomal rearrangements, as well as a
possible fission of this pair in Geotrygon species. Therefore,
although birds have a smaller amount of repetitive sequences when compared to
other Tetrapoda, these seem to play an important role in the karyotype evolution
of these species.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
| | - Thays Duarte de Oliveira
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Ivanete de Oliveira Furo
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Ricardo José Gunski
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-Graduação em Ciências Biológicas, PPGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA, Brazil.,Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Thales Renato Ochotorena de Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
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16
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Expression patterns for nicotinic acetylcholine receptor subunit genes in smoking-related lung cancers. Oncotarget 2017; 8:67878-67890. [PMID: 28978081 PMCID: PMC5620221 DOI: 10.18632/oncotarget.18948] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/17/2017] [Indexed: 01/03/2023] Open
Abstract
Cigarette smoking is associated with increased risk for all histologic types of lung cancer, but why the strength of this association is stronger for squamous cell carcinoma than adenocarcinoma of the lung (SQC-L, ADC-L) is not fully understood. Because nicotine and tobacco-specific nitrosamines contribute to carcinogenesis by activating nicotinic acetylcholine receptors (nAChRs) on lung tumors and epithelial cells, we investigated whether differential expression of nAChR subtypes in these tumors could explain their different association with smoking. Expression of nAChR subunit genes in paired tumor and non-tumor lung specimens from 40 SQC-L and 38 ADC-L patients was analyzed by quantitative PCR. Compared to normal lung, both tumors share: i) transcriptional dysregulation of CHRNA3/CHRNA5/CHRNB4 (α3, α5, β4 subunits) at the chromosomal locus that predisposes to lung cancer; and ii) decreased expression of CHRFAM7A (dupα7 subunit); this last subunit negatively modulates α7-nAChR activity in oocytes. In contrast, CHRNA7 (α7 subunit) expression was increased in SQC-L, particularly in smokers and non-survivors, while CHRNA4 (α4 subunit) expression was decreased in ADC-L. Thus, over-representation of cancer-stimulating α7-nAChR in SQC-L, also potentiated by smoking, and under-representation of cancer-inhibiting α4β2-nAChR in ADC-L could explain the different tobacco influences on the tumorigenic process in each cancer type.
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17
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Ortiz JF, Rokas A. CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes. Mol Biol Evol 2016; 34:215-229. [DOI: 10.1093/molbev/msw227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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18
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Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome. Cytogenet Genome Res 2015; 145:42-9. [PMID: 25926034 DOI: 10.1159/000381764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (Hylobates lar, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
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Affiliation(s)
- Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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19
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Costantini TW, Dang X, Yurchyshyna MV, Coimbra R, Eliceiri BP, Baird A. A Human-Specific α7-Nicotinic Acetylcholine Receptor Gene in Human Leukocytes: Identification, Regulation and the Consequences of CHRFAM7A Expression. Mol Med 2015; 21:323-36. [PMID: 25860877 DOI: 10.2119/molmed.2015.00018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/02/2015] [Indexed: 12/30/2022] Open
Abstract
The human genome contains a variant form of the α7-nicotinic acetylcholine receptor (α7nAChR) gene that is uniquely human. This CHRFAM7A gene arose during human speciation and recent data suggests that its expression alters ligand tropism of the normally homopentameric human α7-AChR ligand-gated cell surface ion channel that is found on the surface of many different cell types. To understand its possible significance in regulating inflammation in humans, we investigated its expression in normal human leukocytes and leukocyte cell lines, compared CHRFAM7A expression to that of the CHRNA7 gene, mapped its promoter and characterized the effects of stable CHRFAM7A overexpression. We report here that CHRFAM7A is highly expressed in human leukocytes but that the levels of both CHRFAM7A and CHRNA7 mRNAs were independent and varied widely. To this end, mapping of the CHRFAM7A promoter in its 5'-untranslated region (UTR) identified a unique 1-kb sequence that independently regulates CHRFAM7A gene expression. Because overexpression of CHRFAM7A in THP1 cells altered the cell phenotype and modified the expression of genes associated with focal adhesion (for example, FAK, P13K, Akt, rho, GEF, Elk1, CycD), leukocyte transepithelial migration (Nox, ITG, MMPs, PKC) and cancer (kit, kitL, ras, cFos cyclinD1, Frizzled and GPCR), we conclude that CHRFAM7A is biologically active. Most surprisingly however, stable CHRFAM7A overexpression in THP1 cells upregulated CHRNA7, which, in turn, led to increased binding of the specific α7nAChR ligand, bungarotoxin, on the THP1 cell surface. Taken together, these data confirm the close association between CHRFAM7A and CHRNA7 expression, establish a biological consequence to CHRFAM7A expression in human leukocytes and support the possibility that this human-specific gene might contribute to, and/or gauge, a human-specific response to inflammation.
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Affiliation(s)
- Todd W Costantini
- Department of Surgery, University of California San Diego Health Sciences, San Diego, California, United States of America
| | - Xitong Dang
- Department of Surgery, University of California San Diego Health Sciences, San Diego, California, United States of America.,Cardiovascular Research Center, Luzhou Medical College, Luzhou, Sichuan, China
| | - Maryana V Yurchyshyna
- Department of Surgery, University of California San Diego Health Sciences, San Diego, California, United States of America
| | - Raul Coimbra
- Department of Surgery, University of California San Diego Health Sciences, San Diego, California, United States of America
| | - Brian P Eliceiri
- Department of Surgery, University of California San Diego Health Sciences, San Diego, California, United States of America
| | - Andrew Baird
- Department of Surgery, University of California San Diego Health Sciences, San Diego, California, United States of America
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20
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Shorey-Kendrick LE, Ford MM, Allen DC, Kuryatov A, Lindstrom J, Wilhelm L, Grant KA, Spindel ER. Nicotinic receptors in non-human primates: Analysis of genetic and functional conservation with humans. Neuropharmacology 2015; 96:263-73. [PMID: 25661700 PMCID: PMC4486519 DOI: 10.1016/j.neuropharm.2015.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 01/18/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are highly conserved between humans and non-human primates. Conservation exists at the level of genomic structure, protein structure and epigenetics. Overall homology of nAChRs at the protein level is 98% in macaques versus 89% in mice, which is highly relevant for evaluating subtype-specific ligands that have different affinities in humans versus rodents. In addition to conservation at the protein level, there is high conservation of genomic structure in terms of intron and exon size and placement of CpG sites that play a key role in epigenetic regulation. Analysis of single nucleotide polymorphisms (SNPs) shows that while the majority of SNPs are not conserved between humans and macaques, some functional polymorphisms are. Most significantly, cynomolgus monkeys express a similar α5 nAChR Asp398Asn polymorphism to the human α5 Asp398Asn polymorphism that has been linked to greater nicotine addiction and smoking related disease. Monkeys can be trained to readily self-administer nicotine, and in an initial study we have demonstrated that cynomolgus monkeys bearing the α5 D398N polymorphism show a reduced behavioral sensitivity to oral nicotine and tend to consume it in a different pattern when compared to wild-type monkeys. Thus the combination of highly homologous nAChR, higher cortical functions and capacity for complex training makes non-human primates a unique model to study in vivo functions of nicotinic receptors. In particular, primate studies on nicotine addiction and evaluation of therapies to prevent or overcome nicotine addiction are likely to be highly predictive of treatment outcomes in humans.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Matthew M Ford
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Daicia C Allen
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Alexander Kuryatov
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jon Lindstrom
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Larry Wilhelm
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
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21
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Costantini TW, Dang X, Coimbra R, Eliceiri BP, Baird A. CHRFAM7A, a human-specific and partially duplicated α7-nicotinic acetylcholine receptor gene with the potential to specify a human-specific inflammatory response to injury. J Leukoc Biol 2014; 97:247-57. [PMID: 25473097 DOI: 10.1189/jlb.4ru0814-381r] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conventional wisdom presumes that the α7nAChR product of CHRNA7 expression mediates the ability of the vagus nerve to regulate the inflammatory response to injury and infection. Yet, 15 years ago, a 2nd structurally distinct and human-specific α7nAChR gene was discovered that has largely escaped attention of the inflammation research community. The gene, originally called dupα7nAChR but now known as CHRFAM7A, has been studied exhaustively in psychiatric research because of its association with mental illness. However, dupα7nAChR/CHRFAM7A expression is relatively low in human brain but elevated in human leukocytes. Furthermore, α7nAChR research in human tissues has been confounded by cross-reacting antibodies and nonspecific oligonucleotide primers that crossreact in immunoblotting, immunohistochemistry, and RT-PCR. Yet, 3 independent reports show the human-specific CHRFAM7A changes cell responsiveness to the canonical α7nAChR/CHRNA7 ion-gated channel. Because of its potential for the injury research community, its possible significance to human leukocyte biology, and its relevance to human inflammation, we review the discovery and structure of the dupα7nAChR/CHRFAM7A gene, the distribution of its mRNA, and its biologic activities and then discuss its possible role(s) in specifying human inflammation and injury. In light of emerging concepts that point to a role for human-specific genes in complex human disease, the existence of a human-specific α7nAChR regulating inflammatory responses in injury underscores the need for caution in extrapolating findings in the α7nAChR literature to man. To this end, we discuss the translational implications of a uniquely human α7nAChR-like gene on new drug target discovery and therapeutics development for injury, infection, and inflammation.
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Affiliation(s)
- Todd W Costantini
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Xitong Dang
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Raul Coimbra
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Brian P Eliceiri
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Andrew Baird
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
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22
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Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet 2014; 46:1293-302. [PMID: 25326701 PMCID: PMC4244265 DOI: 10.1038/ng.3120] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 09/25/2014] [Indexed: 12/14/2022]
Abstract
Recurrent deletions of chromosome 15q13.3 associate with intellectual disability, schizophrenia, autism and epilepsy. To gain insight into its instability, we sequenced the region in patients, normal individuals and nonhuman primates. We discovered five structural configurations of the human chromosome 15q13.3 region ranging in size from 2 to 3 Mbp. These configurations arose recently (~0.5–0.9 million years ago) as a result of human-specific expansions of segmental duplications and two independent inversion events. All inversion breakpoints map near GOLGA8 core duplicons—a ~14 kbp primate-specific chromosome 15 repeat that became organized into larger palindromic structures. GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent 15q13.3 microdeletions, the expansion of chromosome 15 segmental duplications in the human lineage, and independent structural changes in apes. The significant clustering (p=0.002) of breakpoints provides mechanistic evidence for the role of this core duplicon and its palindromic architecture in promoting evolutionary and disease-related instability of chromosome 15.
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23
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Wang Y, Xiao C, Indersmitten T, Freedman R, Leonard S, Lester HA. The duplicated α7 subunits assemble and form functional nicotinic receptors with the full-length α7. J Biol Chem 2014; 289:26451-26463. [PMID: 25056953 DOI: 10.1074/jbc.m114.582858] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor gene (CHRNA7) is linked to schizophrenia. A partial duplication of CHRNA7 (CHRFAM7A) is found in humans on 15q13-14. Exon 6 of CHRFAM7A harbors a 2-bp deletion polymorphism, CHRFAM7AΔ2bp, which is also associated with schizophrenia. To understand the effects of the duplicated subunits on α7 receptors, we fused α7, dupα7, and dupΔα7 subunits with various fluorescent proteins. The duplicated subunits co-localized with full-length α7 subunits in mouse neuroblastoma cells (Neuro2a) as well as rat hippocampal neurons. We investigated the interaction between the duplicated subunits and full-length α7 by measuring Förster resonance energy transfer using donor recovery after photobleaching and fluorescence lifetime imaging microscopy. The results revealed that the duplicated proteins co-assemble with α7. In electrophysiological studies, Leu at the 9'-position in the M2 membrane-spanning segment was replaced with Cys in dupα7 or dupΔα7, and constructs were co-transfected with full-length α7 in Neuro2a cells. Exposure to ethylammonium methanethiosulfonate inhibited acetylcholine-induced currents, showing that the assembled functional nicotinic acetylcholine receptors (nAChRs) included the duplicated subunit. Incorporation of dupα7 and dupΔα7 subunits modestly changes the sensitivity of receptors to choline and varenicline. Thus, the duplicated proteins are assembled and transported to the cell membrane together with full-length α7 subunits and alter the function of the nAChRs. The characterization of dupα7 and dupΔα7 as well as their influence on α7 nAChRs may help explain the pathophysiology of schizophrenia and may suggest therapeutic strategies.
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Affiliation(s)
- Ying Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Cheng Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Tim Indersmitten
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Robert Freedman
- Department of Psychiatry, University of Colorado at Denver, Denver, Colorado 80045
| | - Sherry Leonard
- Department of Psychiatry, University of Colorado at Denver, Denver, Colorado 80045
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and.
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24
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Giannuzzi G, Migliavacca E, Reymond A. Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures. Genome Res 2014; 24:1455-68. [PMID: 24916972 PMCID: PMC4158755 DOI: 10.1101/gr.167742.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human and chimpanzee genomes are 98.8% identical within comparable sequences. However, they differ structurally in nine pericentric inversions, one fusion that originated human chromosome 2, and content and localization of heterochromatin and lineage-specific segmental duplications. The possible functional consequences of these cytogenetic and structural differences are not fully understood and their possible involvement in speciation remains unclear. We show that subtelomeric regions—regions that have a species-specific organization, are more divergent in sequence, and are enriched in genes and recombination hotspots—are significantly enriched for species-specific histone modifications that decorate transcription start sites in different tissues in both human and chimpanzee. The human lineage-specific chromosome 2 fusion point and ancestral centromere locus as well as chromosome 1 and 18 pericentric inversion breakpoints showed enrichment of human-specific H3K4me3 peaks in the prefrontal cortex. Our results reveal an association between plastic regions and potential novel regulatory elements.
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Affiliation(s)
- Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland;
| | - Eugenia Migliavacca
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland;
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25
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Molas S, Dierssen M. The role of nicotinic receptors in shaping and functioning of the glutamatergic system: a window into cognitive pathology. Neurosci Biobehav Rev 2014; 46 Pt 2:315-25. [PMID: 24879992 DOI: 10.1016/j.neubiorev.2014.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 04/13/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
The involvement of the cholinergic system in learning, memory and attention has long been recognized, although its neurobiological mechanisms are not fully understood. Recent evidence identifies the endogenous cholinergic signaling via nicotinic acetylcholine receptors (nAChRs) as key players in determining the morphological and functional maturation of the glutamatergic system. Here, we review the available experimental and clinical evidence of nAChRs contribution to the establishment of the glutamatergic system, and therefore to cognitive function. We provide some clues of the putative underlying molecular mechanisms and discuss recent human studies that associate genetic variability of the genes encoding nAChR subunits with cognitive disorders. Finally, we discuss the new avenues to therapeutically targeting nAChRs in persons with cognitive dysfunction for which the α7-nAChR subunit is an important etiological mechanism.
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Affiliation(s)
- Susanna Molas
- Systems Biology Program, Centre for Genomic Regulation (CRG), Barcelona E-08003, Spain; University Pompeu Fabra (UPF), Spain; CIBER de Enfermedades Raras (CIBERER), Barcelona E-08003, Spain
| | - Mara Dierssen
- Systems Biology Program, Centre for Genomic Regulation (CRG), Barcelona E-08003, Spain; University Pompeu Fabra (UPF), Spain; CIBER de Enfermedades Raras (CIBERER), Barcelona E-08003, Spain.
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26
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Melchior L, Bertelsen B, Debes NM, Groth C, Skov L, Mikkelsen JD, Brøndum-Nielsen K, Tümer Z. Microduplication of 15q13.3 and Xq21.31 in a family with Tourette syndrome and comorbidities. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:825-31. [PMID: 23894120 DOI: 10.1002/ajmg.b.32186] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/26/2013] [Indexed: 12/31/2022]
Abstract
Tourette syndrome (TS) is a childhood onset neurodevelopmental disorder. Although it is widely accepted that genetic factors play a significant role in TS pathogenesis the etiology of this disorder is largely unknown. Identification of rare copy number variations (CNVs) as susceptibility factors in several neuropsychiatric disorders such as attention deficit-hyperactivity disorder (ADHD), autism and schizophrenia, suggests involvement of these rare structural changes also in TS etiology. In a male patient with TS, ADHD, and OCD (obsessive compulsive disorder) we identified two microduplications (at 15q13.3 and Xq21.31) inherited from a mother with subclinical ADHD. The 15q duplication included the CHRNA7 gene; while two genes, PABPC5 and PCDH11X, were within the Xq duplication. The Xq21.31 duplication was present in three brothers with TS including the proband, but not in an unaffected brother, whereas the 15q duplication was present only in the proband and his mother. The structural variations observed in this family may contribute to the observed symptoms, but further studies are necessary to investigate the possible involvement of the described variations in the TS etiology.
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Affiliation(s)
- Linea Melchior
- Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
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27
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Giannuzzi G, Pazienza M, Huddleston J, Antonacci F, Malig M, Vives L, Eichler EE, Ventura M. Hominoid fission of chromosome 14/15 and the role of segmental duplications. Genome Res 2013; 23:1763-73. [PMID: 24077392 PMCID: PMC3814877 DOI: 10.1101/gr.156240.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ape chromosomes homologous to human chromosomes 14 and 15 were generated by a fission event of an ancestral submetacentric chromosome, where the two chromosomes were joined head-to-tail. The hominoid ancestral chromosome most closely resembles the macaque chromosome 7. In this work, we provide insights into the evolution of human chromosomes 14 and 15, performing a comparative study between macaque boundary region 14/15 and the orthologous human regions. We construct a 1.6-Mb contig of macaque BAC clones in the region orthologous to the ancestral hominoid fission site and use it to define the structural changes that occurred on human 14q pericentromeric and 15q subtelomeric regions. We characterize the novel euchromatin–heterochromatin transition region (∼20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14–qter and 10. Further, we show a relationship between evolutionary hotspots and low-copy repeat loci for chromosome 15, revealing a possible role of segmental duplications not only in mediating but also in “stitching” together rearrangement breakpoints.
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Affiliation(s)
- Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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28
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Research proceedings on primate comparative genomics. Zool Res 2013; 33:108-18. [DOI: 10.3724/sp.j.1141.2012.01108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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29
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Robbe D, Carluccio A, Gloria A, Contri A, Ventura M, Catacchio CR, Straticò P, Petrizzi L. Digital Agenesia in Martina Franca Donkey Foal: A Case Report. J Equine Vet Sci 2012. [DOI: 10.1016/j.jevs.2012.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Stanyon R, Rocchi M, Bigoni F, Archidiacono N. Evolutionary molecular cytogenetics of catarrhine primates: past, present and future. Cytogenet Genome Res 2012; 137:273-84. [PMID: 22710640 DOI: 10.1159/000339381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The catarrhine primates were the first group of species studied with comparative molecular cytogenetics. Many of the fundamental techniques and principles of analysis were initially applied to comparisons in these primates, including interspecific chromosome painting, reciprocal chromosome painting and the extensive use of cloned DNA probes for evolutionary analysis. The definition and importance of chromosome syntenies and associations for a correct cladistics analysis of phylogenomic relationships were first applied to catarrhines. These early chromosome painting studies vividly illustrated a striking conservation of the genome between humans and macaques. Contemporarily, it also revealed profound differences between humans and gibbons, a group of species more closely related to humans, making it clear that chromosome evolution did not follow a molecular clock. Chromosome painting has now been applied to more that 60 primate species and the translocation history has been mapped onto the major taxonomic divisions in the tree of primate evolution. In situ hybridization of cloned DNA probes, primarily BAC-FISH, also made it possible to more precisely map breakpoints with spanning and flanking BACs. These studies established marker order and disclosed intrachromosomal rearrangements. When applied comparatively to a range of primate species, they led to the discovery of evolutionary new centromeres as an important new category of chromosome evolution. BAC-FISH studies are intimately connected to genome sequencing, and probes can usually be assigned to a precise location in the genome assembly. This connection ties molecular cytogenetics securely to genome sequencing, assuring that molecular cytogenetics will continue to have a productive future in the multidisciplinary science of phylogenomics.
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Affiliation(s)
- R Stanyon
- Department of Evolutionary Biology, University of Florence, Florence, Italy.
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31
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Stephens SH, Franks A, Berger R, Palionyte M, Fingerlin TE, Wagner B, Logel J, Olincy A, Ross RG, Freedman R, Leonard S. Multiple genes in the 15q13-q14 chromosomal region are associated with schizophrenia. Psychiatr Genet 2012; 22:1-14. [PMID: 21970977 PMCID: PMC3878876 DOI: 10.1097/ypg.0b013e32834c0c33] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The chromosomal region, 15q13-q14, including the α7 nicotinic acetylcholine receptor gene, CHRNA7, is a replicated region for schizophrenia. This study fine-mapped genes at 15q13-q14 to determine whether the association is unique to CHRNA7. METHODS Family-based and case-control association studies were performed on Caucasian-non-Hispanic and African-American individuals from 120 families as well as 468 individual patients with schizophrenia and 144 well-characterized controls. Single-nucleotide polymorphism (SNP) markers were genotyped, and association analyses carried out for the outcomes of schizophrenia, smoking, and smoking in schizophrenia. RESULTS Three genes were associated with schizophrenia in both ethnic populations: TRPM1, KLF13, and RYR3. Two SNPs in CHRNA7 were associated with schizophrenia in African-Americans, and a second SNP in CHRNA7 was significant for an association with smoking and smoking in schizophrenia in Caucasians. CONCLUSION Results of these studies support association of the 15q13-q14 region with schizophrenia. The broad positive association suggests that more than one 15q gene may be contributing to the disorder, either in combination or through a regulatory mechanism.
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Affiliation(s)
- Sarah H. Stephens
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Alexis Franks
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Ralph Berger
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Milda Palionyte
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Tasha E. Fingerlin
- Preventive Medicine and Biometrics, University of Colorado Denver, Denver, Colorado, USA
| | - Brandie Wagner
- Preventive Medicine and Biometrics, University of Colorado Denver, Denver, Colorado, USA
| | - Judith Logel
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Ann Olincy
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Randal G. Ross
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
| | - Robert Freedman
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
- Veterans Affairs Medical Research Center, Denver, Colorado, USA
| | - Sherry Leonard
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado, USA
- Veterans Affairs Medical Research Center, Denver, Colorado, USA
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32
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Araud T, Graw S, Berger R, Lee M, Neveu E, Bertrand D, Leonard S. The chimeric gene CHRFAM7A, a partial duplication of the CHRNA7 gene, is a dominant negative regulator of α7*nAChR function. Biochem Pharmacol 2011; 82:904-14. [PMID: 21718690 PMCID: PMC3162115 DOI: 10.1016/j.bcp.2011.06.018] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 06/10/2011] [Accepted: 06/13/2011] [Indexed: 12/11/2022]
Abstract
The human α7 neuronal nicotinic acetylcholine receptor gene (CHRNA7) is a candidate gene for schizophrenia and an important drug target for cognitive deficits in the disorder. Activation of the α7*nAChR, results in opening of the channel and entry of mono- and divalent cations, including Ca(2+), that presynaptically participates to neurotransmitter release and postsynaptically to down-stream changes in gene expression. Schizophrenic patients have low levels of α7*nAChR, as measured by binding of the ligand [(125)I]-α-bungarotoxin (I-BTX). The structure of the gene, CHRNA7, is complex. During evolution, CHRNA7 was partially duplicated as a chimeric gene (CHRFAM7A), which is expressed in the human brain and elsewhere in the body. The association between a 2bp deletion in CHRFAM7A and schizophrenia suggested that this duplicate gene might contribute to cognitive impairment. To examine the putative contribution of CHRFAM7A on receptor function, co-expression of α7 and the duplicate genes was carried out in cell lines and Xenopus oocytes. Expression of the duplicate alone yielded protein expression but no functional receptor and co-expression with α7 caused a significant reduction of the amplitude of the ACh-evoked currents. Reduced current amplitude was not correlated with a reduction of I-BTX binding, suggesting the presence of non-functional (ACh-silent) receptors. This hypothesis is supported by a larger increase of the ACh-evoked current by the allosteric modulator 1-(5-chloro-2,4-dimethoxy-phenyl)-3-(5-methyl-isoxazol-3-yl)-urea (PNU-120596) in cells expressing the duplicate than in the control. These results suggest that CHRFAM7A acts as a dominant negative modulator of CHRNA7 function and is critical for receptor regulation in humans.
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Affiliation(s)
- Tanguy Araud
- Department of Neurosciences Medical Faculty, University of Geneva, Geneva, Switzerland.
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33
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Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, Shendure J, Wilson RK, Eichler EE. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res 2011; 21:1640-9. [PMID: 21685127 DOI: 10.1101/gr.124461.111] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.
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Affiliation(s)
- Mario Ventura
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
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34
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de Lucas-Cerrillo AM, Maldifassi MC, Arnalich F, Renart J, Atienza G, Serantes R, Cruces J, Sánchez-Pacheco A, Andrés-Mateos E, Montiel C. Function of partially duplicated human α77 nicotinic receptor subunit CHRFAM7A gene: potential implications for the cholinergic anti-inflammatory response. J Biol Chem 2010; 286:594-606. [PMID: 21047781 DOI: 10.1074/jbc.m110.180067] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The neuronal α7 nicotinic receptor subunit gene (CHRNA7) is partially duplicated in the human genome forming a hybrid gene (CHRFAM7A) with the novel FAM7A gene. The hybrid gene transcript, dupα7, has been identified in brain, immune cells, and the HL-60 cell line, although its translation and function are still unknown. In this study, dupα7 cDNA has been cloned and expressed in GH4C1 cells and Xenopus oocytes to study the pattern and functional role of the expressed protein. Our results reveal that dupα7 transcript was natively translated in HL-60 cells and heterologously expressed in GH4C1 cells and oocytes. Injection of dupα7 mRNA into oocytes failed to generate functional receptors, but when co-injected with α7 mRNA at α7/dupα7 ratios of 5:1, 2:1, 1:1, 1:5, and 1:10, it reduced the nicotine-elicited α7 current generated in control oocytes (α7 alone) by 26, 53, 75, 93, and 94%, respectively. This effect is mainly due to a reduction in the number of functional α7 receptors reaching the oocyte membrane, as deduced from α-bungarotoxin binding and fluorescent confocal assays. Two additional findings open the possibility that the dominant negative effect of dupα7 on α7 receptor activity observed in vitro could be extrapolated to in vivo situations. (i) Compared with α7 mRNA, basal dupα7 mRNA levels are substantial in human cerebral cortex and higher in macrophages. (ii) dupα7 mRNA levels in macrophages are down-regulated by IL-1β, LPS, and nicotine. Thus, dupα7 could modulate α7 receptor-mediated synaptic transmission and cholinergic anti-inflammatory response.
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35
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Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Res 2010; 20:1613-22. [PMID: 20805290 DOI: 10.1101/gr.106344.110] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in the human genome. While in the past CNVs have been detected based on array CGH data, recent studies have shown that depth-of-coverage information from HTS technologies can also be used for the reliable identification of large copy-variable regions. Such methods, however, are hindered by sequencing biases that lead certain regions of the genome to be over- or undersampled, lowering their resolution and ability to accurately identify the exact breakpoints of the variants. In this work, we develop a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where mate pairs mapping discordantly to the reference serve to indicate the presence of variation. Our algorithm, called CNVer, combines this information within a unified computational framework called the donor graph, allowing us to better mitigate the sequencing biases that cause uneven local coverage and accurately predict CNVs. We use CNVer to detect 4879 CNVs in the recently described genome of a Yoruban individual. Most of the calls (77%) coincide with previously known variants within the Database of Genomic Variants, while 81% of deletion copy number variants previously known for this individual coincide with one of our loss calls. Furthermore, we demonstrate that CNVer can reconstruct the absolute copy counts of segments of the donor genome and evaluate the feasibility of using CNVer with low coverage datasets.
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Affiliation(s)
- Paul Medvedev
- Department of Computer Science, University of Toronto, Toronto, Ontario M5R 3G4, Canada
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36
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Liu GE, Ventura M, Cellamare A, Chen L, Cheng Z, Zhu B, Li C, Song J, Eichler EE. Analysis of recent segmental duplications in the bovine genome. BMC Genomics 2009; 10:571. [PMID: 19951423 PMCID: PMC2796684 DOI: 10.1186/1471-2164-10-571] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 12/01/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (>or= 1 kb in length, >or= 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes. RESULTS In this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction. CONCLUSION Our results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research.
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Affiliation(s)
- George E Liu
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA.
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37
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Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009; 6:S13-20. [PMID: 19844226 DOI: 10.1038/nmeth.1374] [Citation(s) in RCA: 362] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions.
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Marques-Bonet T, Ryder OA, Eichler EE. Sequencing primate genomes: what have we learned? Annu Rev Genomics Hum Genet 2009; 10:355-86. [PMID: 19630567 DOI: 10.1146/annurev.genom.9.081307.164420] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.
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Affiliation(s)
- Tomas Marques-Bonet
- Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98105, USA.
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Sinkus ML, Lee MJ, Gault J, Logel J, Short M, Freedman R, Christian SL, Lyon J, Leonard S. A 2-base pair deletion polymorphism in the partial duplication of the alpha7 nicotinic acetylcholine gene (CHRFAM7A) on chromosome 15q14 is associated with schizophrenia. Brain Res 2009; 1291:1-11. [PMID: 19631623 DOI: 10.1016/j.brainres.2009.07.041] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 07/13/2009] [Accepted: 07/14/2009] [Indexed: 11/27/2022]
Abstract
Multiple genetic linkage studies support the hypothesis that the 15q13-14 chromosomal region contributes to the etiology of schizophrenia. Among the putative candidate genes in this area are the alpha7 nicotinic acetylcholine receptor gene (CHRNA7) and its partial duplication, CHRFAM7A. A large chromosomal segment including the CHRFAM7A gene locus, but not the CHRNA7 locus, is deleted in some individuals. The CHRFAM7A gene contains a polymorphism consisting of a 2 base pair (2 bp) deletion at position 497-498 bp of exon 6. We employed PCR-based methods to quantify the copy number of CHRFAM7A and the presence of the 2 bp polymorphism in a large, multi-ethnic population. The 2 bp polymorphism was associated with schizophrenia in African Americans (genotype p=0.005, allele p=0.015), and in Caucasians (genotype p=0.015, allele p=0.009). We conclude that the presence of the 2 bp polymorphism at the CHRFAM7A locus may have a functional significance in schizophrenia.
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Affiliation(s)
- Melissa L Sinkus
- Department of Psychiatry, University of Colorado at Denver, Denver, CO 80045, USA
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40
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Lee J, Han K, Meyer TJ, Kim HS, Batzer MA. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLoS One 2008; 3:e4047. [PMID: 19112500 PMCID: PMC2603318 DOI: 10.1371/journal.pone.0004047] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 11/22/2008] [Indexed: 02/02/2023] Open
Abstract
The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution.
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Affiliation(s)
- Jungnam Lee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Kyudong Han
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Thomas J. Meyer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Heui-Soo Kim
- PBBRC, Interdisciplinary Research Program of Bioinformatics, College of Natural Sciences, Pusan National University, Busan, Korea
- Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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Construction, characterization, and chromosomal mapping of a fosmid library of the white-cheeked gibbon (Nomascus leucogenys). GENOMICS PROTEOMICS & BIOINFORMATICS 2008; 5:207-15. [PMID: 18267302 PMCID: PMC5054230 DOI: 10.1016/s1672-0229(08)60008-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gibbons have experienced extensive karyotype rearrangements during evolution and represent an ideal model for studying the underlying molecular mechanism of evolutionary chromosomal rearrangements. It is anticipated that the cloning and sequence characterization of evolutionary chromosomal breakpoints will provide vital insights into the molecular force that has driven such a radical karyotype reshuffle in gibbons. We constructed and characterized a high-quality fosmid library of the white-cheeked gibbon (Nomascus leucogenys) containing 192,000 non-redundant clones with an average insert size of 38 kb and 2.5-fold genome coverage. By end sequencing of 100 randomly selected fosmid clones, we generated 196 sequence tags for the library. These end-sequenced fosmid clones were then mapped onto the chromosomes of the white-cheeked gibbon by fluorescence in situ hybridization, and no spurious chimeric clone was detected. BLAST search against the human genome showed a good correlation between the number of hit clones and the number of chromosomes, an indication of unbiased chromosomal distribution of the fosmid library. The chromosomal distribution of the mapped clones is also consistent with the BLAST search result against human and white-cheeked gibbon genomes. The fosmid library and the mapped clones will serve as a valuable resource for further studying gibbons’ chromosomal rearrangements and the underlying molecular mechanism as well as for comparative genomic study in the lesser apes.
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Flomen RH, Davies AF, Di Forti M, Cascia CL, Mackie-Ogilvie C, Murray R, Makoff AJ. The copy number variant involving part of the α7 nicotinic receptor gene contains a polymorphic inversion. Eur J Hum Genet 2008; 16:1364-71. [DOI: 10.1038/ejhg.2008.112] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Louzada S, Paço A, Kubickova S, Adega F, Guedes-Pinto H, Rubes J, Chaves R. Different evolutionary trails in the related genomes Cricetus cricetus and Peromyscus eremicus (Rodentia, Cricetidae) uncovered by orthologous satellite DNA repositioning. Micron 2008; 39:1149-55. [PMID: 18602266 DOI: 10.1016/j.micron.2008.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 05/23/2008] [Accepted: 05/24/2008] [Indexed: 11/26/2022]
Abstract
Constitutive heterochromatin comprises a substantial fraction of the eukaryotic genomes and is mainly composed of tandemly arrayed satellite DNAs (satDNA). These repetitive sequences represent a very dynamic and fast evolving component of genomes. In the present work we report the isolation of Cricetus cricetus (CCR, Cricetidae, Rodentia) centromeric repetitive sequences from chromosome 4 (CCR4/10sat), using the laser microdissection and laser pressure catapulting procedure, followed by DOP-PCR amplification and labelling. Physical mapping by fluorescent in situ hybridisation of these sequences onto C. cricetus and another member of Cricetidae, Peromyscus eremicus, displayed quite interesting patterns. Namely, the centromeric sequences showed to be present in another C. cricetus chromosome (CCR10) besides CCR4. Moreover, these almost chromosome-specific sequences revealed to be present in the P. eremicus genome, and most interestingly, displaying a ubiquitous scattered distribution throughout this karyotype. Finally and in both species, a co-localisation of CCR4/10sat with constitutive heterochromatin was found, either by classical C-banding or C-banding sequential to in situ endonuclease restriction. The presence of these orthologous sequences in both genomes is suggestive of a phylogenetic proximity. Furthermore, the existence of common repetitive DNA sequences with a different chromosomal location foresees the occurrence of an extensive process of karyotype restructuring somehow related with intragenomic movements of these repetitive sequences during the evolutionary process of C. cricetus and P. eremicus species.
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Affiliation(s)
- Sandra Louzada
- Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD), Apdo 1013, 5001-801 Vila Real, Portugal
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44
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Kehrer-Sawatzki H, Cooper DN. Molecular mechanisms of chromosomal rearrangement during primate evolution. Chromosome Res 2008; 16:41-56. [PMID: 18293104 DOI: 10.1007/s10577-007-1207-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Breakpoint analysis of the large chromosomal rearrangements which have occurred during primate evolution promises to yield new insights into the underlying mechanisms of mutagenesis. Comparison of these evolutionary breakpoints with those that are disease-associated in humans, and which occur during either meiotic or mitotic cell division, should help to identify basic mechanistic similarities as well as differences. It has recently become clear that segmental duplications (SDs) have had a very significant impact on genome plasticity during primate evolution. In comparisons of the human and chimpanzee genomes, SDs have been found in flanking regions of 70-80% of inversions and approximately 40% of deletions/duplications. A strong spatial association between primate-specific breakpoints and SDs has also become evident from comparisons of human with other mammalian genomes. The lineage-specific hyperexpansion of certain SDs observed in the genomes of human, chimpanzee, gorilla and gibbon is indicative of the intrinsic instability of some SDs in primates. However, since many primate-specific breakpoints map to regions lacking SDs, but containing interspersed high-copy repetitive sequence elements such as SINEs, LINEs, LTRs, alpha-satellites and (AT)( n ) repeats, we may infer that a range of different molecular mechanisms have probably been involved in promoting chromosomal breakage during the evolution of primate genomes.
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45
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Abstract
In 1992 the Japanese macaque was the first species for which the homology of the entire karyotype was established by cross-species chromosome painting. Today, there are chromosome painting data on more than 50 species of primates. Although chromosome painting is a rapid and economical method for tracking translocations, it has limited utility for revealing intrachromosomal rearrangements. Fortunately, the use of BAC-FISH in the last few years has allowed remarkable progress in determining marker order along primate chromosomes and there are now marker order data on an array of primate species for a good number of chromosomes. These data reveal inversions, but also show that centromeres of many orthologous chromosomes are embedded in different genomic contexts. Even if the mechanisms of neocentromere formation and progression are just beginning to be understood, it is clear that these phenomena had a significant impact on shaping the primate genome and are fundamental to our understanding of genome evolution. In this report we complete and integrate the dataset of BAC-FISH marker order for human syntenies 1, 2, 4, 5, 8, 12, 17, 18, 19, 21, 22 and the X. These results allowed us to develop hypotheses about the content, marker order and centromere position in ancestral karyotypes at five major branching points on the primate evolutionary tree: ancestral primate, ancestral anthropoid, ancestral platyrrhine, ancestral catarrhine and ancestral hominoid. Current models suggest that between-species structural rearrangements are often intimately related to speciation. Comparative primate cytogenetics has become an important tool for elucidating the phylogeny and the taxonomy of primates. It has become increasingly apparent that molecular cytogenetic data in the future can be fruitfully combined with whole-genome assemblies to advance our understanding of primate genome evolution as well as the mechanisms and processes that have led to the origin of the human genome.
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46
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Darai-Ramqvist E, Sandlund A, Müller S, Klein G, Imreh S, Kost-Alimova M. Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. Genome Res 2008; 18:370-9. [PMID: 18230801 DOI: 10.1101/gr.7010208] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 ( approximately 75 Mb position) and 3q21.3-q22.1 ( approximately 130 Mb position) (six lines). All locations are shown based on NCBI Build 36.1 human genome sequence. The last two regions participated in three of four chromosome 3 inversions during primate evolution. Regions at 75, 127, and 131 Mb positions carry a large ( approximately 250 kb) segmental duplication (tumor break-prone segmental duplication [TBSD]). TBSD homologous sequences were found at 15 sites on different chromosomes. They were located within bands frequently involved in carcinoma-associated breaks. Thirteen of them have been involved in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from specific organization of the chromosomal region, associated with location at a boundary between different CG-content isochores and with the presence of TBSDs and "instability elements," including satellite repeats and retroviral sequences.
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Affiliation(s)
- Eva Darai-Ramqvist
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-171 77, Sweden
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47
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Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM. Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol 2007; 5:e152. [PMID: 17550304 PMCID: PMC1885836 DOI: 10.1371/journal.pbio.0050152] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 04/02/2007] [Indexed: 12/19/2022] Open
Abstract
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance. The organization of genes on chromosomes changes over evolutionary time. In some organisms, such as fruit flies and mosquitoes, inversions of chromosome regions are widespread. This has been associated with adaptation to environmental pressures and speciation. However, the mechanisms by which inversions are generated at the molecular level are poorly understood. The prevailing view involves the interactions of sequences that are moderately repeated in the genome. Here, we use molecular and computational methods to study 29 inversions that differentiate the chromosomes of three closely related fruit fly species. We find little support for a causal role of repetitive sequences in the origin of inversions and, instead, detect the presence of inverted duplications of ancestrally unique sequences (generally protein-coding genes) in the breakpoint regions of many inversions. This leads us to propose an alternative model in which the generation of inversions is coupled with the generation of duplications of flanking sequences. Additionally, we find evidence for genomic regions that are prone to breakage, being associated with inversions generated independently during the evolution of the ancestors of existing species. Chromosomal inversion breakpoints were compared between three closely related Drosophila species. Many are associated with inverted gene duplications, suggesting that the prevalent mechanism for their generation involves staggered breakpoints.
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Affiliation(s)
- José M Ranz
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
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Szamalek JM, Cooper DN, Hoegel J, Hameister H, Kehrer-Sawatzki H. Chromosomal speciation of humans and chimpanzees revisited: studies of DNA divergence within inverted regions. Cytogenet Genome Res 2007; 116:53-60. [PMID: 17268178 DOI: 10.1159/000097417] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 08/10/2006] [Indexed: 11/19/2022] Open
Abstract
The human and chimpanzee karyotypes are distinguishable in terms of nine pericentric inversions. According to the recombination suppression model of speciation, these inversions could have promoted the process of parapatric speciation between hominoid populations ancestral to chimpanzees and humans. Were recombination suppression to have occurred in inversion heterozygotes, gene flow would have been reduced, resulting in the accumulation of genetic incompatibilities leading to reproductive isolation and eventual speciation. In an attempt to detect the molecular signature of such events, the sequence divergence of non-coding DNA was compared between humans and chimpanzees. Precise knowledge of the locations of the inversion breakpoints permitted accurate discrimination between inverted and non-inverted regions. Contrary to the predictions of the recombination suppression model, sequence divergence was found to be lower in inverted chromosomal regions as compared to non-inverted regions, albeit with borderline statistical significance. Thus, no signature of recombination suppression resulting from inversion heterozygosity appears to be detectable by analysis of extant human and chimpanzee non-coding DNA. The precise delineation of the inversion breakpoints may nevertheless still prove helpful in identifying potential speciation-relevant genes within the inverted regions.
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Affiliation(s)
- J M Szamalek
- Department of Human Genetics, University of Ulm, Ulm, Germany
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49
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Kehrer-Sawatzki H, Cooper DN. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons. Hum Mutat 2007; 28:99-130. [PMID: 17024666 DOI: 10.1002/humu.20420] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.
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Abstract
Chromosome deletions do abound in cancer and are detected in certain regions in a non-random manner. Although their relevance remains elusive, it is a general agreement that segmental losses provide the cell with selective growth advantage. Consequently these may contain genes and/or regulatory sequences that control normal growth and inhibit malignancy. We have developed a monochromosomal hybrid based experimental model for the generation and functional analysis of deletions, that is called "elimination test" (Et). Focused on human chromosome 3 - that was known to carry multiple 3p deletions - the Et was expected to restrict a 3p tumor suppressor region to a sufficiently small segment that permits the selection of a critically important candidate gene. Surprisingly, we detected three regions that were lost in all or majority of tumors: CER1 (3p21.3, Mb: 43.32-45.74), CER2 (3p22, Mb: 37.83-39.06) and FER (3p14.3-p21.2, Mb: 50.12-58.03). In contrast a 3q26-qter region (CRR) was regularly retained. CER1 - our main focus - contains multiple genes that may inhibit tumor growth, but 3 genes, RIS1, LF (LTF) and LIMD1 have already the necessary experimental support to be considered bona fide tumor suppressors. Tumor suppressor region borders display instability features including: (1) they break in evolution and in tumors, (2) they evolve horizontally, and (3) they are enriched with pseudogene insertions. The most remarkable features at the breakpoint cluster regions were segmental duplications that drive horizontal evolution and contribute to cancer associated instability.
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Affiliation(s)
- Maria Kost-Alimova
- Karolinska Institutet, Microbiology Tumor and Cell Biology Center (MTC), Box 280, 171 77 Stockholm, Sweden
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