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Abstract
Sepsis is a heterogeneous clinical syndrome that is complicated commonly by acute kidney injury (sepsis-AKI). Currently, no approved pharmacologic therapies exist to either prevent sepsis-AKI or to treat sepsis-AKI once it occurs. A growing body of evidence supports a connection between red blood cell biology and sepsis-AKI. Increased levels of circulating cell-free hemoglobin (CFH) released from red blood cells during hemolysis are common during sepsis and can contribute to sepsis-AKI through several mechanisms including tubular obstruction, nitric oxide depletion, oxidative injury, and proinflammatory signaling. A number of potential pharmacologic therapies targeting CFH in sepsis have been identified including haptoglobin, hemopexin, and acetaminophen, and early phase clinical trials have suggested that acetaminophen may have beneficial effects on lipid peroxidation and kidney function in patients with sepsis. Bedside measurement of CFH levels may facilitate predictive enrichment for future clinical trials of CFH-targeted therapeutics. However, rapid and reliable bedside tests for plasma CFH will be required for such trials to move forward.
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Affiliation(s)
- V Eric Kerchberger
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Lorraine B Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville TN.
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Finding relationships among biological entities. LOGIC AND CRITICAL THINKING IN THE BIOMEDICAL SCIENCES 2020. [PMCID: PMC7499094 DOI: 10.1016/b978-0-12-821364-3.00005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Confusion over the concepts of “relationships” and “similarities” lies at the heart of many battles over the direction and intent of research projects. Here is a short story that demonstrates the difference between the two concepts: You look up at the clouds, and you begin to see the shape of a lion. The cloud has a tail, like a lion’s tale, and a fluffy head, like a lion’s mane. With a little imagination the mouth of the lion seems to roar down from the sky. You have succeeded in finding similarities between the cloud and a lion. If you look at a cloud and you imagine a tea kettle producing a head of steam and you recognize that the physical forces that create a cloud and the physical forces that produced steam from a heated kettle are the same, then you have found a relationship. Most popular classification algorithms operate by grouping together data objects that have similar properties or values. In so doing, they may miss finding the true relationships among objects. Traditionally, relationships among data objects are discovered by an intellectual process. In this chapter, we will discuss the scientific gains that come when we classify biological entities by relationships, not by their similarities.
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Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 2019; 47:10994-11006. [PMID: 31584084 PMCID: PMC6868369 DOI: 10.1093/nar/gkz841] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with 'ready-to-use' deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
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Affiliation(s)
- Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton. CB10 1SD, UK
| | - Patryk Jarnot
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Universite Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
- Institut de Biologie Computationnelle, 34095 Montpellier, France
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678 Nicosia, Cyprus
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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54
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Uchida N, Nassehi T, Drysdale CM, Gamer J, Yapundich M, Bonifacino AC, Krouse AE, Linde N, Hsieh MM, Donahue RE, Dunbar CE, Kean LS, Tisdale JF. Busulfan Combined with Immunosuppression Allows Efficient Engraftment of Gene-Modified Cells in a Rhesus Macaque Model. Mol Ther 2019; 27:1586-1596. [PMID: 31253582 PMCID: PMC6731177 DOI: 10.1016/j.ymthe.2019.05.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 01/24/2023] Open
Abstract
Busulfan conditioning is utilized for hematopoietic stem cell (HSC) depletion in the context of HSC gene-therapy conditioning but may result in insufficient immunosuppression. In this study, we evaluated whether additional immunosuppression is required for efficient engraftment of gene-modified cells using a rhesus HSC lentiviral gene-therapy model. We transduced half of rhesus CD34+ cells with an enhanced green fluorescent protein (GFP)-encoding vector (immunogenic) and the other half with a γ-globin-encoding vector (no predicted immunogenicity). After autologous transplantation of both transduced cell populations following myeloablative busulfan conditioning (5.5 mg/kg/day for 4 days), we observed immunological rejection of GFP-transduced cells up to 3 months post-transplant and stable engraftment of γ-globin-transduced cells in two animals, demonstrating that ablative busulfan conditioning is sufficient for engraftment of gene-modified cells producing non-immunogenic proteins but insufficient to permit engraftment of immunogenic proteins. We then added immunosuppression with abatacept and sirolimus to busulfan conditioning and observed engraftment of both GFP- and γ-globin-transduced cells in two animals, demonstrating that additional immunosuppression allows for engraftment of gene-modified cells expressing immunogenic proteins. In conclusion, myeloablative busulfan conditioning should permit engraftment of gene-modified cells producing non-immunogenic proteins, while additional immunosuppression is required to prevent immunological rejection of a neoantigen.
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Affiliation(s)
- Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Tina Nassehi
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Claire M Drysdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Jackson Gamer
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Morgan Yapundich
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | | | - Allen E Krouse
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
| | - Nathaniel Linde
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
| | - Matthew M Hsieh
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Robert E Donahue
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
| | - Leslie S Kean
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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55
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Biswas S, Ray R, Roy K, Bandyopadhyay A, Ghosh K, Bhattacharyya M. Alpha Globin Gene Mutation: A Major Determinant of Hydroxyurea Response in Transfusion-Dependent HbE-β-Thalassaemia. Acta Haematol 2019; 142:132-141. [PMID: 31352439 DOI: 10.1159/000495453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022]
Abstract
Thalassaemias are the most common inherited autosomal recessive single gene disorders characterised by chronic hereditary haemolytic anaemia due to absence or reduced synthesis of one or more of the globin chains. Haemoglobin E (HbE)-β-thalassaemia is the genotype responsible for approximately one-half of all cases of severe β-thalassaemia worldwide. This study proposes to evaluate response of hydroxyurea in reducing transfusion requirements of severe HbE-β-thalassaemia patients, and its correlation with foetal haemoglobin (HbF) level and α-mutation. Hydroxyurea was started at a baseline dose in 82 transfusion-dependent HbE-β-thalassaemia patients. HbF levels and %F-cells were measured. β-Thalassaemia mutations and α-globin gene deletions and triplications were detected by amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR) and Gap-PCR, respectively. Patients were categorised as good (41.5%), moderate (31.7%), and poor responders (26.8%) based on their decrease in transfusion requirements. Nine patients were excellent responders who became transfusion independent. The mean increase in HbF levels and %F-cells after therapy was correlated with decrease in transfusion requirements. Patients having a deletion of the α-globin gene were better responders. The response was proportional to the number of α-globin gene deletions. We conclude that hydroxyurea treatment decreases transfusion requirements, and the response correlates with α-globin gene deletions.
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Affiliation(s)
- Sujana Biswas
- Institute of Haematology and Transfusion Medicine, Medical College, Kolkata, India
| | - Rudra Ray
- Institute of Haematology and Transfusion Medicine, Medical College, Kolkata, India
| | | | | | - Kanjaksha Ghosh
- National Institute of Immunohaematology (ICMR), Mumbai, India
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56
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Signore AV, Paijmans JLA, Hofreiter M, Fago A, Weber RE, Springer MS, Campbell KL. Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia. Mol Biol Evol 2019; 36:1134-1147. [PMID: 30828717 PMCID: PMC6526914 DOI: 10.1093/molbev/msz044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller’s sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb–O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb–O2 affinity in (sub)Arctic Steller’s sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.
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Affiliation(s)
- Anthony V Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada.,School of Biological Sciences, University of Nebraska, Lincoln, NE
| | | | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, Germany
| | - Angela Fago
- Department of Bioscience, Zoophysiology, Aarhus University, Denmark
| | - Roy E Weber
- Department of Bioscience, Zoophysiology, Aarhus University, Denmark
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
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57
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Klei TRL, Kheradmand Kia S, Veldthuis M, Dehbozorgian J, Karimi M, Geissler J, Sellink E, Thiel-Valkhof M, Burger P, van Alphen F, Meijer AB, van Bruggen R, van Zwieten R. A Homozygous Mutation on the HBA1 Gene Coding for Hb Charlieu (HBA1: c.320T>C) Together with β-Thalassemia Trait Results in Severe Hemolytic Anemia. Hemoglobin 2019; 43:77-82. [PMID: 31190578 DOI: 10.1080/03630269.2019.1601107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A 4-year-old boy, a β-thalassemia (β-thal) carrier, with an unexplained severe chronic microcytic anemia was referred to us. Sequencing of the α-globin genes revealed a Hb Charlieu [α106(G13)Leu→Pro, HBA1: c.320T>C, p.Leu107Pro] mutation present on both HBA1 genes. Quantitative polymerase chain reaction (qPCR) confirmed αCharlieu mRNA in the proband and his parents, showing that the mutation does not affect mRNA stability. However, we were unable to detect the Hb Charlieu protein by capillary electrophoresis (CE), reverse phase electrophoresis, cation exchange electrophoresis or isoelectric focusing. Mass spectrometry (MS) allowed us to confirm the presence of the Hb Charlieu peptide in erythrocyte progenitors. These findings suggest that the mutation affects the stability of αCharlieu. As hemoglobin (Hb) heat stability tests showed no abnormalities in erythrocytes, we speculated that αCharlieu is already degraded during red blood cell (RBC) development. The clinical severity in the proband and the presence of new methylene blue-stained aggregates in his reticulocytes indicates that incorporation of αCharlieu destabilizes Hb. This, combined with an excess of unstable free α-globins as the result of β-thal minor, results in severely impaired erythropoiesis and, as a consequence, severe and chronic microcytic anemia in the proband.
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Affiliation(s)
- Thomas R L Klei
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands
| | - Sima Kheradmand Kia
- b Laboratory for Red Blood Cell Diagostics , Sanquin , Amsterdam , The Netherlands.,c Department of Hematology , PeyvandLab Complex , Shiraz , Iran
| | - Martijn Veldthuis
- b Laboratory for Red Blood Cell Diagostics , Sanquin , Amsterdam , The Netherlands
| | | | - Mehran Karimi
- d Hematology Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
| | - Judy Geissler
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands
| | - Erica Sellink
- e Department of Hematopoiesis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , The Netherlands
| | - Marijke Thiel-Valkhof
- e Department of Hematopoiesis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , The Netherlands
| | - Patrick Burger
- e Department of Hematopoiesis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , The Netherlands
| | - Floris van Alphen
- f Department of Molecular and Cellular Hemostasis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , The Netherlands
| | - Alexander B Meijer
- f Department of Molecular and Cellular Hemostasis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , The Netherlands.,g Department of Biomolecular Mass Spectrometry and Proteomics , Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University , Utrecht 3584 CS , The Netherlands
| | - Robin van Bruggen
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands
| | - Rob van Zwieten
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands.,b Laboratory for Red Blood Cell Diagostics , Sanquin , Amsterdam , The Netherlands
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58
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Developmental validation of an enhanced mRNA-based multiplex system for body fluid and cell type identification. Sci Justice 2019; 59:217-227. [DOI: 10.1016/j.scijus.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/16/2018] [Accepted: 01/20/2019] [Indexed: 12/14/2022]
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59
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Smith RD, Kinser TJ, Smith GDC, Puzey JR. A likelihood ratio test for changes in homeolog expression bias. BMC Bioinformatics 2019; 20:149. [PMID: 30894122 PMCID: PMC6427896 DOI: 10.1186/s12859-019-2709-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may retain their ancestral function, sub- or neofunctionalize, or be lost entirely. A primary way that duplicate genes evolve new functions is by altering their expression patterns. Comparing the expression patterns of duplicate genes gives clues as to whether any of these evolutionary processes have occurred. RESULTS We develop a likelihood ratio test for the analysis of the expression ratios of duplicate genes across two conditions (e.g., tissues). We demonstrate an application of this test by comparing homeolog expression patterns of 1448 homeologous gene pairs using RNA-seq data generated from leaves and petals of an allotetraploid monkeyflower (Mimulus luteus). We assess the sensitivity of this test to different levels of homeolog expression bias and compare the method to several alternatives. CONCLUSIONS The likelihood ratio test derived here is a direct, transparent, and easily implemented method for detecting changes in homeolog expression bias that outperforms alternative approaches. While our method was derived with homeolog analysis in mind, this method can be used to analyze changes in the ratio of expression levels between any two genes in any two conditions.
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Affiliation(s)
- Ronald D Smith
- Department of Applied Science, The College of William & Mary, Williamsburg, 23187, VA, USA
| | - Taliesin J Kinser
- Department of Biology, The College of William & Mary, Williamsburg, 23187, VA, USA
| | | | - Joshua R Puzey
- Department of Biology, The College of William & Mary, Williamsburg, 23187, VA, USA.
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60
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Hunt von Herbing I, Schroeder-Spain K. Hemoglobin Polymerization in Red Blood Cells of Marine Fishes: A Case of Adaptive Phenotypic Plasticity? THE BIOLOGICAL BULLETIN 2019; 236:29-42. [PMID: 30707608 DOI: 10.1086/700832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigated the occurrence of the unusual phenomenon of hemoglobin polymerization in a 10-year survey of 47 species of fishes. Similar to human sickle cell disease, hemoglobin polymers in fish red blood cells can cause distortion or sickling under low oxygen and low pH. We sampled fish from three geographic areas, including the east and west coasts of the Atlantic Ocean and the Gulf of Mexico. Fifteen species spanning five orders and nine families exhibited hemoglobin polymerization in vitro, with a majority in or related to Gadiformes, as well as species within Notocanthiformes, Perciformes, and Scorpianiformes. Atlantic cod, Gadus morhua, also showed the trait in vivo. Light and transmission electron microscopy confirmed the presence of hemoglobin polymers at the cellular level, but the morphology of hemoglobin polymers and rates of polymerization varied across species. Hemoglobin polymerization in red blood cells in vitro was pH dependent and reversible. For two species, G. morhua and Opsanus tau, >60% and >40% of all red blood cells contained hemoglobin polymers at pH 7.6, while 100% and 90% of red blood cells polymerized at pH 6.96, respectively. In both species, recovery of 60%-70% of red blood cells occurred within 45 minutes when pH increased from 6.96 to 7.99. From these results we conclude that hemoglobin polymerization is present in a broad range of fish taxa occupying wide biogeographical ranges and habitats and that it is oxygen and pH sensitive. The physiology and adaptive significance of hemoglobin polymerization in fishes remain unclear, but as oceans and coastal environments become more hypoxic and hypercapnic, this trait may have the potential to affect fish survival.
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61
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Gu L, Xia C. Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 2019; 19:9. [PMID: 30621595 PMCID: PMC6325677 DOI: 10.1186/s12862-018-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
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Affiliation(s)
- Langyu Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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62
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Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S. Long-read sequence capture of the haemoglobin gene clusters across codfish species. Mol Ecol Resour 2018; 19:245-259. [PMID: 30329222 PMCID: PMC7379720 DOI: 10.1111/1755-0998.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 11/30/2022]
Abstract
Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.
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Affiliation(s)
- Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Helle T Baalsrud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Morten Skage
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | | | - Ole Kristian Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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63
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Abstract
During infection, bacteria must steal metals, including iron, from the host tissue. Therefore, pathogenic bacteria have evolved metal acquisition systems to overcome the elaborate processes mammals use to withhold metal from pathogens. Staphylococcus aureus uses IsdB, a hemoglobin receptor, to thieve iron-containing heme from hemoglobin within human blood. We find evidence that primate hemoglobin has undergone rapid evolution at protein surfaces contacted by IsdB. Additionally, variation in the hemoglobin sequences among primates, or variation in IsdB of related staphylococci, reduces bacterial hemoglobin capture. Together, these data suggest that S. aureus has evolved to recognize human hemoglobin in the face of rapid evolution at the IsdB binding interface, consistent with repeated evolutionary conflicts in the battle for iron during host-pathogen interactions. Metals are a limiting resource for pathogenic bacteria and must be scavenged from host proteins. Hemoglobin provides the most abundant source of iron in the human body and is required by several pathogens to cause invasive disease. However, the consequences of hemoglobin evolution for bacterial nutrient acquisition remain unclear. Here we show that the α- and β-globin genes exhibit strikingly parallel signatures of adaptive evolution across simian primates. Rapidly evolving sites in hemoglobin correspond to binding interfaces of IsdB, a bacterial hemoglobin receptor harbored by pathogenic Staphylococcus aureus. Using an evolution-guided experimental approach, we demonstrate that the divergence between primates and staphylococcal isolates governs hemoglobin recognition and bacterial growth. The reintroduction of putative adaptive mutations in α- or β-globin proteins was sufficient to impair S. aureus binding, providing a mechanism for the evolution of disease resistance. These findings suggest that bacterial hemoprotein capture has driven repeated evolutionary conflicts with hemoglobin during primate descent.
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64
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Genetic determinants related to pharmacological induction of foetal haemoglobin in transfusion-dependent HbE-β thalassaemia. Ann Hematol 2018; 98:289-299. [PMID: 30413899 DOI: 10.1007/s00277-018-3536-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/23/2018] [Indexed: 10/27/2022]
Abstract
Thalassaemia are the most common inherited autosomal recessive single gene disorders characterized by chronic hereditary haemolytic anaemia due to the absence or reduced synthesis of one or more of the globin chains. Haemoglobin E-β thalassaemia is the genotype responsible for approximately one half of all severe beta-thalassaemia worldwide. This study proposes to evaluate the effect of various molecular parameters on the response of hydroxyurea. Hydroxyurea was started at an initial dose of 10 mg/kg of body weight/day on 110 transfusion-dependent HbE-β thalassaemia patients. HbF level was measured by HPLC analysis. β-Thalassaemia mutations, XmnI and five other SNPs, and α-globin gene deletions and triplications were detected by ARMS-PCR, RFLP-PCR and Gap-PCR, respectively. Based on the factors for evaluating hydroxyurea-response, 42 patients were responders as they showed an increment of Hb from a mean baseline value of 6.45 g/dl (± 0.70) to 7.78 g/dl (± 0.72) post-therapy. Based on increase in HbF above the median value (14.72%) post-therapy, 78 patients were found to be responders. All the 78 responders showed mean decrease in transfusion of 74.26% (± 8.32) with a maximum decrease of 98.43%. There was a significant correlation between decrease in transfusion and increase in HbF level for all 78 responders. XmnI polymorphism showed the strongest association (p < 0.0001) with increase in HbF levels and Hb levels. Patients with α-globin gene deletions were better responders. It was concluded that hydroxyurea treatment is effective in transfusion-dependent HbE-β thalassaemia patients and the response is best in patients having both XmnI polymorphism and α-deletion.
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65
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Hoffmann FG, Vandewege MW, Storz JF, Opazo JC. Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates. Genome Biol Evol 2018; 10:344-358. [PMID: 29340581 PMCID: PMC5786229 DOI: 10.1093/gbe/evy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2018] [Indexed: 11/24/2022] Open
Abstract
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | | | - Jay F Storz
- School of Biological Sciences, University of Nebraska
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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66
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Keller JI, Schmidt JO, Schmoker AM, Ballif BA, Stevens L. Protein mass spectrometry extends temporal blood meal detection over polymerase chain reaction in mouse-fed Chagas disease vectors. Mem Inst Oswaldo Cruz 2018; 113:e180160. [PMID: 30277492 PMCID: PMC6167943 DOI: 10.1590/0074-02760180160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/03/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Chagas disease is highly prevalent in Latin America, and vector control is the most effective control strategy to date. We have previously shown that liquid chromatography tandem mass spectrometry (LC-MS/MS) is a valuable tool for identifying triatomine vector blood meals. OBJECTIVES The purpose of this study was to determine blood meal detection ability as a function of method [polymerase chain reaction (PCR) vs. LC-MS/MS], time since feeding, and the effect of molting in mouse-fed triatomine insect vectors targeting hemoglobin and albumin proteins with LC-MS/MS and short interspersed nuclear elements (SINE)-based PCR. METHODS We experimentally fed Triatoma protracta on mice and used LC-MS/MS to detect hemoglobin and albumin peptides over time post-feeding and post-molting (≤ 12 weeks). We compared LC-MS/MS results with those of a standard PCR method based on SINEs. FINDINGS Hemoglobin-based LC-MS/MS detected blood meals most robustly at all time points post-feeding. Post-molting, no blood meals were detected with PCR, whereas LC-MS/MS detected mouse hemoglobin and albumin up to 12 weeks. MAIN CONCLUSIONS In our study, the hemoglobin signature in the insect abdomen lasted longer than that of albumin and DNA. LC-MS/MS using hemoglobin shows promise for identifying triatomine blood meals over long temporal scales and even post-molting. Clarifying the frequency of blood-feeding on different hosts can foster our understanding of vector behavior and may help devise sounder disease-control strategies, including Ecohealth (community based ecosystem management) approaches.
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Affiliation(s)
- Judith I Keller
- University of Vermont, Department of Biology, Burlington, VT, United States of America
| | - Justin O Schmidt
- Southwestern Biological Institute, Tucson, AZ, United States of America
| | - Anna M Schmoker
- University of Vermont, Department of Biology, Burlington, VT, United States of America
| | - Bryan A Ballif
- University of Vermont, Department of Biology, Burlington, VT, United States of America
| | - Lori Stevens
- University of Vermont, Department of Biology, Burlington, VT, United States of America
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67
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Diepstraten ST, Hart AH. Modelling human haemoglobin switching. Blood Rev 2018; 33:11-23. [PMID: 30616747 DOI: 10.1016/j.blre.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Genetic lesions of the β-globin gene result in haemoglobinopathies such as β-thalassemia and sickle cell disease. To discover and test new molecular medicines for β-haemoglobinopathies, cell-based and animal models are now being widely utilised. However, multiple in vitro and in vivo models are required due to the complex structure and regulatory mechanisms of the human globin gene locus, subtle species-specific differences in blood cell development, and the influence of epigenetic factors. Advances in genome sequencing, gene editing, and precision medicine have enabled the first generation of molecular therapies aimed at reactivating, repairing, or replacing silenced or damaged globin genes. Here we compare and contrast current animal and cell-based models, highlighting their complementary strengths, reflecting on how they have informed the scope and direction of the field, and describing some of the novel molecular and precision medicines currently under development or in clinical trial.
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Affiliation(s)
- Sarah T Diepstraten
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Adam H Hart
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
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68
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Abstract
Sickle cell disease is the most prevalent monogenic disorder worldwide and curative therapies are limited to hematopoietic stem cell transplant to the few with matched donors. Gene therapy has curative potential, whereby autologous hematopoietic stem cells are genetically modified and transplanted, which would not be limited by matched donors, resulting in 1-time, life-long correction devoid of immune side effects. Significant progress has been made to clinically translate gene therapy for sickle cell disease using lentivirus vectors carrying antisickling genes. This review focuses on the current state of the field, factors that determine clinical success, gene editing, and future prospects.
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Affiliation(s)
- Rajeswari Jayavaradhan
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Mail Location 7013, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Pathobiology and Molecular Medicine Graduate Program, Mail Location: 0529, 231 Albert Sabin Way, Cincinnati, OH 45267-0529, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Mail Location 7013, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Pathobiology and Molecular Medicine Graduate Program, Mail Location: 0529, 231 Albert Sabin Way, Cincinnati, OH 45267-0529, USA.
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69
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Philipsen S, Hardison RC. Evolution of hemoglobin loci and their regulatory elements. Blood Cells Mol Dis 2018; 70:2-12. [PMID: 28811072 PMCID: PMC5807248 DOI: 10.1016/j.bcmd.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/13/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022]
Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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70
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Barts N, Greenway R, Passow CN, Arias-Rodriguez L, Kelley JL, Tobler M. Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs. Genome 2018; 61:273-286. [DOI: 10.1139/gen-2017-0051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.
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Affiliation(s)
- Nicholas Barts
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Courtney N. Passow
- Ecology, Evolution and Behavior, University of Minnesota St. Paul, 205 Cargill Building, St. Paul, MN 55108, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, 431 Heald Hall, Pullman, WA 99164, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
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71
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Esin A, Bergendahl LT, Savolainen V, Marsh JA, Warnecke T. The genetic basis and evolution of red blood cell sickling in deer. Nat Ecol Evol 2018; 2:367-376. [PMID: 29255300 PMCID: PMC5777626 DOI: 10.1038/s41559-017-0420-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/20/2017] [Indexed: 11/09/2022]
Abstract
Crescent-shaped red blood cells, the hallmark of sickle-cell disease, present a striking departure from the biconcave disc shape normally found in mammals. Characterized by increased mechanical fragility, sickled cells promote haemolytic anaemia and vaso-occlusions and contribute directly to disease in humans. Remarkably, a similar sickle-shaped morphology has been observed in erythrocytes from several deer species, without obvious pathological consequences. The genetic basis of erythrocyte sickling in deer, however, remains unknown. Here, we determine the sequences of human β-globin orthologues in 15 deer species and use protein structural modelling to identify a sickling mechanism distinct from the human disease, coordinated by a derived valine (E22V) that is unique to sickling deer. Evidence for long-term maintenance of a trans-species sickling/non-sickling polymorphism suggests that sickling in deer is adaptive. Our results have implications for understanding the ecological regimes and molecular architectures that have promoted convergent evolution of sickling erythrocytes across vertebrates.
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Affiliation(s)
- Alexander Esin
- Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, United Kingdom
| | - L Therese Bergendahl
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
- University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Joseph A Marsh
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Tobias Warnecke
- Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, United Kingdom.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, United Kingdom.
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72
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Alvarez RA, Miller MP, Hahn SA, Galley JC, Bauer E, Bachman T, Hu J, Sembrat J, Goncharov D, Mora AL, Rojas M, Goncharova E, Straub AC. Targeting Pulmonary Endothelial Hemoglobin α Improves Nitric Oxide Signaling and Reverses Pulmonary Artery Endothelial Dysfunction. Am J Respir Cell Mol Biol 2017; 57:733-744. [PMID: 28800253 PMCID: PMC5765416 DOI: 10.1165/rcmb.2016-0418oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
Pulmonary hypertension is characterized by pulmonary endothelial dysfunction. Previous work showed that systemic artery endothelial cells (ECs) express hemoglobin (Hb) α to control nitric oxide (NO) diffusion, but the role of this system in pulmonary circulation has not been evaluated. We hypothesized that up-regulation of Hb α in pulmonary ECs contributes to NO depletion and pulmonary vascular dysfunction in pulmonary hypertension. Primary distal pulmonary arterial vascular smooth muscle cells, lung tissue sections from unused donor (control) and idiopathic pulmonary artery (PA) hypertension lungs, and rat and mouse models of SU5416/hypoxia-induced pulmonary hypertension (PH) were used. Immunohistochemical, immunocytochemical, and immunoblot analyses and transfection, infection, DNA synthesis, apoptosis, migration, cell count, and protein activity assays were performed in this study. Cocultures of human pulmonary microvascular ECs and distal pulmonary arterial vascular smooth muscle cells, lung tissue from control and pulmonary hypertensive lungs, and a mouse model of chronic hypoxia-induced PH were used. Immunohistochemical, immunoblot analyses, spectrophotometry, and blood vessel myography experiments were performed in this study. We find increased expression of Hb α in pulmonary endothelium from humans and mice with PH compared with controls. In addition, we show up-regulation of Hb α in human pulmonary ECs cocultured with PA smooth muscle cells in hypoxia. We treated pulmonary ECs with a Hb α mimetic peptide that disrupts the association of Hb α with endothelial NO synthase, and found that cells treated with the peptide exhibited increased NO signaling compared with a scrambled peptide. Myography experiments using pulmonary arteries from hypoxic mice show that the Hb α mimetic peptide enhanced vasodilation in response to acetylcholine. Our findings reveal that endothelial Hb α functions as an endogenous scavenger of NO in the pulmonary endothelium. Targeting this pathway may offer a novel therapeutic target to increase endogenous levels of NO in PH.
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MESH Headings
- Animals
- Biomimetic Materials/pharmacology
- Coculture Techniques
- Disease Models, Animal
- Endothelial Cells/metabolism
- Endothelial Cells/pathology
- Female
- Hemoglobin A/biosynthesis
- Humans
- Hypertension, Pulmonary/drug therapy
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/physiopathology
- Male
- Mice
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Nitric Oxide/metabolism
- Nitric Oxide Synthase Type III/genetics
- Nitric Oxide Synthase Type III/metabolism
- Peptides/pharmacology
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/physiopathology
- Rats
- Up-Regulation/drug effects
- Vasodilation/drug effects
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Affiliation(s)
- Roger A. Alvarez
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, Florida; and
| | | | | | - Joseph C. Galley
- Heart, Lung, Blood, and Vascular Medicine Institute
- Department of Pharmacology and Chemical Biology
| | | | - Timothy Bachman
- Heart, Lung, Blood, and Vascular Medicine Institute
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian Hu
- Heart, Lung, Blood, and Vascular Medicine Institute
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John Sembrat
- Heart, Lung, Blood, and Vascular Medicine Institute
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Dmitry Goncharov
- Heart, Lung, Blood, and Vascular Medicine Institute
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ana L. Mora
- Heart, Lung, Blood, and Vascular Medicine Institute
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Mauricio Rojas
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Elena Goncharova
- Heart, Lung, Blood, and Vascular Medicine Institute
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Adam C. Straub
- Heart, Lung, Blood, and Vascular Medicine Institute
- Department of Pharmacology and Chemical Biology
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73
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Morey JS, Burek Huntington KA, Campbell M, Clauss TM, Goertz CE, Hobbs RC, Lunardi D, Moors AJ, Neely MG, Schwacke LH, Van Dolah FM. De novo transcriptome assembly and RNA-Seq expression analysis in blood from beluga whales of Bristol Bay, AK. Mar Genomics 2017; 35:77-92. [PMID: 28802692 DOI: 10.1016/j.margen.2017.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022]
Abstract
Assessing the health of marine mammal sentinel species is crucial to understanding the impacts of environmental perturbations on marine ecosystems and human health. In Arctic regions, beluga whales, Delphinapterus leucas, are upper level predators that may serve as a sentinel species, potentially forecasting impacts on human health. While gene expression profiling from blood transcriptomes has widely been used to assess health status and environmental exposures in human and veterinary medicine, its use in wildlife has been limited due to the lack of available genomes and baseline data. To this end we constructed the first beluga whale blood transcriptome de novo from samples collected during annual health assessments of the healthy Bristol Bay, AK stock during 2012-2014 to establish baseline information on the content and variation of the beluga whale blood transcriptome. The Trinity transcriptome assembly from beluga was comprised of 91,325 transcripts that represented a wide array of cellular functions and processes and was extremely similar in content to the blood transcriptome of another cetacean, the bottlenose dolphin. Expression of hemoglobin transcripts was much lower in beluga (25.6% of TPM, transcripts per million) than has been observed in many other mammals. A T12A amino acid substitution in the HBB sequence of beluga whales, but not bottlenose dolphins, was identified and may play a role in low temperature adaptation. The beluga blood transcriptome was extremely stable between sex and year, with no apparent clustering of samples by principle components analysis and <4% of genes differentially expressed (EBseq, FDR<0.05). While the impacts of season, sexual maturity, disease, and geography on the beluga blood transcriptome must be established, the presence of transcripts involved in stress, detoxification, and immune functions indicate that blood gene expression analyses may provide information on health status and exposure. This study provides a wealth of transcriptomic data on beluga whales and provides a sizeable pool of preliminary data for comparison with other studies in beluga whale.
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Affiliation(s)
- Jeanine S Morey
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA; Jardon and Howard Technologies Incorporated, 2710 Discovery Drive, Orlando, FL 32826, USA.
| | | | | | - Tonya M Clauss
- Georgia Aquarium, 225 Baker Street, Atlanta, GA 30313, USA
| | | | - Roderick C Hobbs
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way N.E., Seattle, WA 95115, USA
| | - Denise Lunardi
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
| | - Amanda J Moors
- Hollings Marine Laboratory, National Institute of Standards and Technology, 331 Fort Johnson Road, Charleston, SC 29412, USA
| | - Marion G Neely
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA; Jardon and Howard Technologies Incorporated, 2710 Discovery Drive, Orlando, FL 32826, USA
| | - Lori H Schwacke
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA
| | - Frances M Van Dolah
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA
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74
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Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Epigenetics Chromatin 2017; 10:35. [PMID: 28693562 PMCID: PMC5504709 DOI: 10.1186/s13072-017-0142-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation. RESULTS We found that, similarly to mammalian genome, the chicken genomes is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream major regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation. CONCLUSIONS Our findings demonstrate that the effects of tissue-specific transcription activation are not restricted to the host genomic locus but affect the overall chromatin structure and transcriptional output of the encompassing topologically associating domain.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| | - Aleksandra A Galitsyna
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051
| | - Ilya M Flyamer
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Arkadiy K Golov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334
| | - Ekaterina E Khrameeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia 143026.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Nezar A Abdennur
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Mikhail S Gelfand
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,Skolkovo Institute of Science and Technology, Skolkovo, Russia 143026.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia 125319
| | - Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334
| | - Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992
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76
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Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba. PLoS Genet 2017; 13:e1006795. [PMID: 28531189 PMCID: PMC5460883 DOI: 10.1371/journal.pgen.1006795] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 06/06/2017] [Accepted: 05/03/2017] [Indexed: 01/06/2023] Open
Abstract
One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this ‘gene dosage’ hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5′ and 3′ UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution. The enclosed work shows that whole gene duplications rarely affect gene expression, in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number. We further explain how tandem duplications that create shuffled gene structures can force upregulation of gene sequences, de novo gene creation, and multifold changes in transcript levels. These results show that tandem duplications can produce new genes that are a source of immediate novelty associated with more extreme expression changes than previously suggested by theory. Further, these gene expression changes are a potential source of both beneficial and pathogenic mutations, immediately relevant to clinical and medical genetics in humans and other metazoans.
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77
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Storz JF. Gene Duplication and Evolutionary Innovations in Hemoglobin-Oxygen Transport. Physiology (Bethesda) 2017; 31:223-32. [PMID: 27053736 DOI: 10.1152/physiol.00060.2015] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During vertebrate evolution, duplicated hemoglobin (Hb) genes diverged with respect to functional properties as well as the developmental timing of expression. For example, the subfamilies of genes that encode the different subunit chains of Hb are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different developmental stages. In some vertebrate taxa, functional differentiation between co-expressed Hb isoforms may also contribute to physiologically important divisions of labor.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
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78
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Saha D, Koli S, Reddy KVR. Transcriptional regulation of Hb-
α and Hb-
β through nuclear factor E2-related factor-2 (Nrf2
) activation in human vaginal cells: A novel mechanism of cellular adaptability to oxidative stress. Am J Reprod Immunol 2017; 77. [DOI: 10.1111/aji.12645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/13/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- Debarchana Saha
- Division of Molecular Immunology and Microbiology (MIM); National Institute for Research in Reproductive Health (NIRRH); Mumbai India
| | - Swanand Koli
- Division of Molecular Immunology and Microbiology (MIM); National Institute for Research in Reproductive Health (NIRRH); Mumbai India
| | - Kudumula Venkata Rami Reddy
- Division of Molecular Immunology and Microbiology (MIM); National Institute for Research in Reproductive Health (NIRRH); Mumbai India
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79
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Zaldívar-López S, Rowell JL, Fiala EM, Zapata I, Couto CG, Alvarez CE. Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. BMC Genomics 2017; 18:141. [PMID: 28178945 PMCID: PMC5299747 DOI: 10.1186/s12864-017-3513-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/25/2017] [Indexed: 12/11/2022] Open
Abstract
Background The main function of hemoglobin (Hb) is to transport oxygen in the circulation. It is among the most highly studied proteins due to its roles in physiology and disease, and most of our understanding derives from comparative research. There is great diversity in Hb gene evolution in placental mammals, mostly in the repertoire and regulation of the β-globin subunits. Dogs are an ideal model in which to study Hb genes because: 1) they are members of Laurasiatheria, our closest relatives outside of Euarchontoglires (including primates, rodents and rabbits), 2) dog breeds are isolated populations with their own Hb-associated genetics and diseases, and 3) their high level of health care allows for development of biomedical investigation and translation. Results We established that dogs have a complement of five α and five β-globin genes, all of which can be detected as spliced mRNA in adults. Strikingly, HBD, the allegedly-unnecessary adult β-globin protein in humans, is the primary adult β-globin in dogs and other carnivores; moreover, dogs have two active copies of the HBD gene. In contrast, the dominant adult β-globin of humans, HBB, has high sequence divergence and is expressed at markedly lower levels in dogs. We also showed that canine HBD and HBB genes are complex chimeras that resulted from multiple gene conversion events between them. Lastly, we showed that the strongest signal of evolutionary selection in a high-altitude breed, the Bernese Mountain Dog, lies in a haplotype block that spans the β-globin locus. Conclusions We report the first molecular genetic characterization of Hb genes in dogs. We found important distinctions between adult β-globin expression in carnivores compared to other members of Laurasiatheria. Our findings are also likely to raise new questions about the significance of human HBD. The comparative genomics of dog hemoglobin genes sets the stage for diverse research and translation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3513-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Zaldívar-López
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Present affiliation: SZL, Departamento. de Genetica, Facultad de Veterinaria, Universidad de Cordoba, Cordoba, Spain
| | - Jennie L Rowell
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,College of Nursing, The Ohio State University, Columbus, OH, USA.,Present affiliation: Center of Excellence in Critical and Complex Care, College of Nursing, The Ohio State University, Columbus, USA
| | - Elise M Fiala
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Isain Zapata
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - C Guillermo Couto
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Present affiliation: Couto Veterinary Consultants, Hilliard, OH, USA
| | - Carlos E Alvarez
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA. .,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA. .,College of Medicine, The Ohio State University, Columbus, OH, USA.
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80
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Yoon J, Kim DJ, Sung HH, Jo YK. Analysis of Bone Mineral Density according to Hemoglobin in University Students. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2016. [DOI: 10.15324/kjcls.2016.48.4.296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Joon Yoon
- Department of Radiologic Technology, Dongnam Health University, Suwon 16328, Korea
| | - Dai-Joong Kim
- Department of Laboratory Medicine, Bundang Jesaeng Hospital, Seongnam 13590, Korea
| | - Hyun-Ho Sung
- Department of Clinical Laboratory Science, Dongnam Health University, Suwon 16328, Korea
| | - Yoon-Kyung Jo
- Department of Clinical Laboratory Science, Dongnam Health University, Suwon 16328, Korea
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81
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82
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Girling JE, Lockhart MG, Olshansky M, Paiva P, Woodrow N, Marino JL, Hickey M, Rogers PAW. Differential Gene Expression in Menstrual Endometrium From Women With Self-Reported Heavy Menstrual Bleeding. Reprod Sci 2016; 24:28-46. [PMID: 27189201 DOI: 10.1177/1933719116648217] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Heavy menstrual bleeding (HMB) is a significant social and public health issue for menstruating women. Development of targeted treatments has been limited by poor understanding of local mechanisms underlying HMB. We aimed to determine how gene expression differs in menstrual phase endometrium from women with HMB. Menstrual phase endometrial biopsies were collected from women with (n = 7) and without (n = 10) HMB (regular menstrual cycles, no known pelvic pathology), as well as women with uterine fibroids (n = 7, n = 4 had HMB). Biopsies were analyzed using Illumina Sentrix Human HT12 arrays and data analyzed using "Remove Unwanted Variation-inverse". Ingenuity Pathway Analysis and the Database for Annotation, Visualization and Integrated Discovery v6.7 were used to identify gene pathways, functional gene clusters, and upstream regulators specific to the clinical groupings. Individual genes of interest were examined using quantitative polymerase chain reaction. In total, 829 genes were differentially expressed in one or more comparisons. Significant canonical pathways and gene clusters enriched in controls relative to both HMB and fibroid groups suggest the mechanisms responsible for HMB include modifications of the endometrial inflammatory or infection response. In contrast, differentially expressed genes in women with fibroids suggest modifications of hemoglobin, antigen processing, and the major histocompatibility complex (class II, beta chain) activity. In conclusion, HMB associated with fibroids may be regulated by different endometrial mechanisms from HMB in women without fibroids and from normal menstrual bleeding. These novel data provide numerous testable hypotheses that will advance our understanding of the mechanisms responsible for HMB.
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Affiliation(s)
- Jane E Girling
- 1 Gynaecology Research Centre, The University of Melbourne Department of Obstetrics and Gynaecology and the Royal Women's Hospital, Parkville, Victoria, Australia
| | - Michelle G Lockhart
- 1 Gynaecology Research Centre, The University of Melbourne Department of Obstetrics and Gynaecology and the Royal Women's Hospital, Parkville, Victoria, Australia
| | - Moshe Olshansky
- 2 Bioinformatics Division, Walter and Elisa Hall Institute, Parkville, Victoria, Australia.,3 Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia.,Current affiliation
| | - Premila Paiva
- 1 Gynaecology Research Centre, The University of Melbourne Department of Obstetrics and Gynaecology and the Royal Women's Hospital, Parkville, Victoria, Australia
| | - Nicole Woodrow
- 4 Pauline Gandel Imaging Centre, Royal Women's Hospital, Parkville, Victoria, Australia
| | - Jennifer L Marino
- 1 Gynaecology Research Centre, The University of Melbourne Department of Obstetrics and Gynaecology and the Royal Women's Hospital, Parkville, Victoria, Australia
| | - Martha Hickey
- 1 Gynaecology Research Centre, The University of Melbourne Department of Obstetrics and Gynaecology and the Royal Women's Hospital, Parkville, Victoria, Australia
| | - Peter A W Rogers
- 1 Gynaecology Research Centre, The University of Melbourne Department of Obstetrics and Gynaecology and the Royal Women's Hospital, Parkville, Victoria, Australia
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83
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Wang X, Ma Z, Kong X, Lv Z. Effects of RNAs on chromatin accessibility and gene expression suggest RNA-mediated activation. Int J Biochem Cell Biol 2016; 79:24-32. [PMID: 27497987 DOI: 10.1016/j.biocel.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/20/2023]
Abstract
The study of the interaction between RNA and DNA sequences in activating genes has important significance for understanding the mechanisms of RNA-mediated activation. Here, we used in vitro chromatin reconstitution approach to observe whether RNAs increase DNase I digestion, plasmid transfection to observe whether RNAs promote gene expression, and bioinformatics analysis to predict the binding ability of RNAs to centromere DNA (constitutive heterochromatin). Synthetic RNAs (23nt) that were complementary to mouse albumin gene and total liver RNA increased DNase I digestion sensitivity of mouse albumin gene, suggesting that RNAs can increase chromatin accessibility. Transcribed sense-antisense tandem Alu elements activated an enhanced green fluorescent protein reporter gene after stable transfection. Bioinformatics analysis showed that the binding strength of RNA population to centromere DNAs is significantly lower than that of their flanking sequences, which suggests that the centromere is not easily affected by RNAs produced from other transcribed regions and may be the reason why centromeres consist of constitutive heterochromatin. The results in this paper illustrate that RNAs complementary to DNA sequences play roles in activating genes. Since RNA is mainly produced from the cell's own DNA, the work presented in this paper suggests that RNAs transcribed from DNA create feedback that activates DNA transcription.
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Affiliation(s)
- Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
| | - Zhihong Ma
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, The Second Hospital of Tangshan, 21 North Jianshe Road, Tangshan, Hebei Province, China.
| | - Xianglong Kong
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, Hebei Chest Hospital, 372 Shengli North Street, Shijiazhuang, Hebei Province, China.
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
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84
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The Primary Structure of β(I)-Chain of Hemoglobin from Snake Sindhi Krait (Bungarus sindanus sindanus). Protein J 2016; 35:193-201. [PMID: 27118198 DOI: 10.1007/s10930-016-9661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The amino acid sequence of β(I)-globin chain from Sindhi Krait (Bungarus sindanus sindanus) was determined to study the molecular evolution among snakes. The hemoglobin was isolated from the red blood cells and was analyzed by ion-exchange chromatography (IEX). The crude globin was subjected to reversed phased-high performance liquid chromatography (RP-HPLC) using C4 column. The N-terminal sequences of intact globin chains and tryptic peptides were determined by Edman degradation in a pulsed liquid gas phase sequencer using an online Phenylthiohydantoin analyzer. Sindhi Krait is expected to express three hemoglobin components that are composed of β(II), β(I), α(D) and α(A)-globin chains, as apparent by IEX, RP-HPLC and N-terminal sequence analyses. Sequence alignment and phylogenetic analyses of β(I) globin chain from Sindhi Krait showed closest relationship with β(I) globin chain from Rattlesnake, Water snake and Indigo snake. Interestingly, comparison of primary sequence of β(I) globin chain of Sindhi Krait with human β chain revealed 63 % similarity along with the retention of all heme contact points. Variations among the two sequences were prominent at αβ contact points and in regions directly not important for function.
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85
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Wang Y, Gao A, Zhao H, Lu P, Cheng H, Dong F, Gong Y, Ma S, Zheng Y, Zhang H, Zhang Y, Xu J, Zhu X, Yuan W, Zhang X, Hao S, Cheng T. Leukemia cell infiltration causes defective erythropoiesis partially through MIP-1α/CCL3. Leukemia 2016; 30:1897-908. [PMID: 27109512 DOI: 10.1038/leu.2016.81] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/02/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
Abstract
Leukemia often results in severe anemia, which may significantly contribute to patient mortality and morbidity. However, the mechanisms underlying defective erythropoiesis in leukemia have not been fully elucidated. In this study, we demonstrated that insufficient erythropoiesis in an immunocompetent acute myeloid leukemia (AML) murine model was due to reduced proliferation of megakaryocyte erythroid progenitors and increased apoptosis of erythroblasts. Colony-forming cell assays indicated that the leukemic bone marrow (BM) plasma inhibited erythroid colony formation, whereas they had no inhibitory effect on other types of colonies. Cytokine array analysis demonstrated that the chemokine CCL3 was elevated in the plasma of AML mice and patients. CCL3 inhibited erythroid differentiation of hematopoietic stem cells, common myeloid progenitors and especially megakaryocytic-erythroid progenitors. Administration of the CCR1 antagonist partially recovered the yield of erythroid colonies in the presence of CCL3 or leukemic BM plasma. Mechanistically, we observed an increase of p38 phosphorylation and subsequent downregulation of GATA1 after CCL3 treatment. Furthermore, knockdown of CCL3 attenuated leukemic progression and alleviated anemia. Therefore, our results demonstrate that elevated CCL3 in the leukemic environment suppresses erythropoiesis via CCR1-p38 activation, suggesting a novel mechanism for the erythroid defects observed in leukemia.
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Affiliation(s)
- Y Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - A Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - H Zhao
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - P Lu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - H Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China.,Center for Stem Cell Medicine, Tianjin, China
| | - F Dong
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - Y Gong
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - S Ma
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - Y Zheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - H Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - Y Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - J Xu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China
| | - X Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China.,Center for Stem Cell Medicine, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - W Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China.,Center for Stem Cell Medicine, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - X Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - S Hao
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China.,Center for Stem Cell Medicine, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - T Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Tianjin, China.,Center for Stem Cell Medicine, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Collaborative Innovation Center for Cancer Medicine, Tianjin, China.,Tianjin Key Laboratory of Blood Cell Therapy and Technology, Tianjin, China
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Abstract
PURPOSE OF REVIEW Research into the fundamental mechanisms of erythropoiesis has provided critical insights into inherited and acquired disorders of the erythrocyte. Studies of human erythropoiesis have primarily utilized in-vitro systems, whereas murine models have provided insights from in-vivo studies. This report reviews recent insights into human and murine erythropoiesis gained from transcriptome-based analyses. RECENT FINDINGS The availability of high-throughput genomic methodologies has allowed attainment of detailed gene expression data from cells at varying developmental and differentiation stages of erythropoiesis. Transcriptome analyses of human and murine reveal both stage and species-specific similarities and differences across terminal erythroid differentiation. Erythroid-specific long noncoding RNAs exhibit poor sequence conservation between human and mouse. Genome-wide analyses of alternative splicing reveal that complex, dynamic, stage-specific programs of alternative splicing program are utilized during terminal erythroid differentiation. Transcriptome data provide a significant resource for understanding mechanisms of normal and perturbed erythropoiesis. Understanding these processes will provide innovative strategies to detect, diagnose, prevent, and treat hematologic disease. SUMMARY Understanding the shared and different mechanisms controlling human and murine erythropoiesis will allow investigators to leverage the best model system to provide insights in normal and perturbed erythropoiesis.
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87
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Genomic landscape of rat strain and substrain variation. BMC Genomics 2015; 16:357. [PMID: 25943489 PMCID: PMC4422378 DOI: 10.1186/s12864-015-1594-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 04/28/2015] [Indexed: 01/08/2023] Open
Abstract
Background Since the completion of the rat reference genome in 2003, whole-genome sequencing data from more than 40 rat strains have become available. These data represent the broad range of strains that are used in rat research including commonly used substrains. Currently, this wealth of information cannot be used to its full extent, because the variety of different variant calling algorithms employed by different groups impairs comparison between strains. In addition, all rat whole genome sequencing studies to date used an outdated reference genome for analysis (RGSC3.4 released in 2004). Results Here we present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains. We reanalyzed all primary data using a recent version of the rat reference assembly (RGSC5.0 released in 2012) and identified over 12 million genomic variants (SNVs, indels and structural variants) among the 40 strains. 28,318 SNVs are specific to individual substrains, which may be explained by introgression from other unsequenced strains and ongoing evolution by genetic drift. Substrain SNVs may have a larger predicted functional impact compared to older shared SNVs. Conclusions In summary we present a comprehensive catalog of uniformly analyzed genetic variants among 40 widely used rat inbred strains based on the RGSC5.0 assembly. This represents a valuable resource, which will facilitate rat functional genomic research. In line with previous observations, our genome-wide analyses do not show evidence for contribution of multiple ancestral founder rat subspecies to the currently used rat inbred strains, as is the case for mouse. In addition, we find that the degree of substrain variation is highly variable between strains, which is of importance for the correct interpretation of experimental data from different labs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1594-1) contains supplementary material, which is available to authorized users.
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88
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Moleirinho A, Lopes AM, Seixas S, Morales-Hojas R, Prata MJ, Amorim A. Distinctive patterns of evolution of the δ-globin gene (HBD) in primates. PLoS One 2015; 10:e0123365. [PMID: 25853817 PMCID: PMC4390247 DOI: 10.1371/journal.pone.0123365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
In most vertebrates, hemoglobin (Hb) is a heterotetramer composed of two dissimilar globin chains, which change during development according to the patterns of expression of α- and β-globin family members. In placental mammals, the β-globin cluster includes three early-expressed genes, ε(HBE)-γ(HBG)-ψβ(HBBP1), and the late expressed genes, δ (HBD) and β (HBB). While HBB encodes the major adult β-globin chain, HBD is weakly expressed or totally silent. Paradoxically, in human populations HBD shows high levels of conservation typical of genes under strong evolutionary constraints, possibly due to a regulatory role in the fetal-to-adult switch unique of Anthropoid primates. In this study, we have performed a comprehensive phylogenetic and comparative analysis of the two adult β-like globin genes in a set of diverse mammalian taxa, focusing on the evolution and functional divergence of HBD in primates. Our analysis revealed that anthropoids are an exception to a general pattern of concerted evolution in placental mammals, showing a high level of sequence conservation at HBD, less frequent and shorter gene conversion events. Moreover, this lineage is unique in the retention of a functional GATA-1 motif, known to be involved in the control of the developmental expression of the β-like globin genes. We further show that not only the mode but also the rate of evolution of the δ-globin gene in higher primates are strictly associated with the fetal/adult β-cluster developmental switch. To gain further insight into the possible functional constraints that have been shaping the evolutionary history of HBD in primates, we calculated dN/dS (ω) ratios under alternative models of gene evolution. Although our results indicate that HBD might have experienced different selective pressures throughout primate evolution, as shown by different ω values between apes and Old World Monkeys + New World Monkeys (0.06 versus 0.43, respectively), these estimates corroborated a constrained evolution for HBD in Anthropoid lineages, which is unlikely to be related to protein function. Collectively, these findings suggest that sequence change at the δ-globin gene has been under strong selective constraints over 65 Myr of primate evolution, likely due to a regulatory role in ontogenic switches of gene expression.
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Affiliation(s)
- Ana Moleirinho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail:
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ramiro Morales-Hojas
- Genetics and Genomics Group, The Pirbright Institute, Compton Laboratory, Compton, Berkshire, United Kingdom
| | - Maria J. Prata
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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89
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Opazo JC, Hoffmann FG, Natarajan C, Witt CC, Berenbrink M, Storz JF. Gene turnover in the avian globin gene families and evolutionary changes in hemoglobin isoform expression. Mol Biol Evol 2015; 32:871-87. [PMID: 25502940 PMCID: PMC4379397 DOI: 10.1093/molbev/msu341] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α2β2 protein responsible for blood-O2 transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during approximately 100 My of avian evolution. Most interspecific variation in gene content is attributable to multiple independent inactivations of the α(D)-globin gene, which encodes the α-chain subunit of a functionally distinct Hb isoform (HbD) that is expressed in both embryonic and definitive erythrocytes. Due to consistent differences in O2-binding properties between HbD and the major adult-expressed Hb isoform, HbA (which incorporates products of the α(A)-globin gene), recurrent losses of α(D)-globin contribute to among-species variation in blood-O2 affinity. Analysis of HbA/HbD expression levels in the red blood cells of 122 bird species revealed high variability among lineages and strong phylogenetic signal. In comparison with the homologous gene clusters in mammals, the low retention rate for lineage-specific gene duplicates in the avian globin gene clusters suggests that the developmental regulation of Hb synthesis in birds may be more highly conserved, with orthologous genes having similar stage-specific expression profiles and similar functional properties in disparate taxa.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | | | - Christopher C Witt
- Department of Biology, University of New Mexico Museum of Southwestern Biology, University of New Mexico
| | - Michael Berenbrink
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
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90
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Götting M, Nikinmaa M. More than hemoglobin - the unexpected diversity of globins in vertebrate red blood cells. Physiol Rep 2015; 3:3/2/e12284. [PMID: 25649247 PMCID: PMC4393193 DOI: 10.14814/phy2.12284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In many multicellular organisms, oxygen is transported by respiratory proteins, which are globins in vertebrates, between respiratory organs and tissues. In jawed vertebrates, eight globins are known which are expressed in a highly tissue-specific manner. Until now, hemoglobin (Hb) had been agreed to be the only globin expressed in vertebrate erythrocytes. Here, we investigate for the first time the mRNA expression of globin genes in nucleated and anucleated erythrocytes of model vertebrate species by quantitative real-time reverse transcription PCR (qRT-PCR). Surprisingly, we found transcripts of the whole gnathostome globin superfamily in RBCs. The mRNA expression levels varied among species, with Hb being by far the dominant globin. Only in stickleback, a globin previously thought to be neuron-specific, neuroglobin, had higher mRNA expression. We furthermore show that in birds transcripts of globin E, which was earlier reported to be transcribed only in the eye, are also present in RBCs. Even in anucleated RBCs of mammals, we found transcripts of myoglobin, neuroglobin, and cytoglobin. Our findings add new aspects to the current knowledge on the expression of globins in vertebrate tissues. However, whether or not the mRNA expression of these globin genes has any functional significance in RBCs has to be investigated in future studies.
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Affiliation(s)
- Miriam Götting
- Zoological Institute and Zoological Museum, Biocenter Grindel, University of Hamburg, Hamburg, Germany
| | - Mikko Nikinmaa
- Department of Biology, Laboratory of Animal Physiology, University of Turku, Turku, Finland
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91
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Gaudry MJ, Storz JF, Butts GT, Campbell KL, Hoffmann FG. Repeated evolution of chimeric fusion genes in the β-globin gene family of laurasiatherian mammals. Genome Biol Evol 2014; 6:1219-34. [PMID: 24814285 PMCID: PMC4041002 DOI: 10.1093/gbe/evu097] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 12/13/2022] Open
Abstract
The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB "Lepore" deletion mutant in humans. Here, we report a comparative genomic analysis of the mammalian β-globin gene cluster, which revealed that chimeric HBB/HBD fusion genes originated independently in four separate lineages of laurasiatherian mammals: Eulipotyphlans (shrews, moles, and hedgehogs), carnivores, microchiropteran bats, and cetaceans. In cases where an independently derived "anti-Lepore" duplication mutant has become fixed, the parental HBD and/or HBB genes have typically been inactivated or deleted, so that the newly created HBB/HBD fusion gene is primarily responsible for synthesizing the β-type subunits of adult and fetal hemoglobin (Hb). Contrary to conventional wisdom that the HBD gene is a vestigial relict that is typically inactivated or expressed at negligible levels, we show that HBD-like genes often encode a substantial fraction (20-100%) of β-chain Hbs in laurasiatherian taxa. Our results indicate that the ascendancy or resuscitation of genes with HBD-like coding sequence requires the secondary acquisition of HBB-like promoter sequence via unequal crossing-over or interparalog gene conversion.
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Affiliation(s)
- Michael J Gaudry
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln
| | - Gary Tyler Butts
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State UniversityInstitute for Genomics, Biocomputing and Biotechnology, Mississippi State University
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92
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Abstract
We recently developed fluorescence-activated cell sorting (FACS)-based methods to purify morphologically and functionally discrete populations of cells, each representing specific stages of terminal erythroid differentiation. We used these techniques to obtain pure populations of both human and murine erythroblasts at distinct developmental stages. RNA was prepared from these cells and subjected to RNA sequencing analyses, creating unbiased, stage-specific transcriptomes. Tight clustering of transcriptomes from differing stages, even between biologically different replicates, validated the utility of the FACS-based assays. Bioinformatic analyses revealed that there were marked differences between differentiation stages, with both shared and dissimilar gene expression profiles defining each stage within transcriptional space. There were vast temporal changes in gene expression across the differentiation stages, with each stage exhibiting unique transcriptomes. Clustering and network analyses revealed that varying stage-specific patterns of expression observed across differentiation were enriched for genes of differing function. Numerous differences were present between human and murine transcriptomes, with significant variation in the global patterns of gene expression. These data provide a significant resource for studies of normal and perturbed erythropoiesis, allowing a deeper understanding of mechanisms of erythroid development in various inherited and acquired erythroid disorders.
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93
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Abstract
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.
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94
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Katsumura KR, DeVilbiss AW, Pope NJ, Johnson KD, Bresnick EH. Transcriptional mechanisms underlying hemoglobin synthesis. Cold Spring Harb Perspect Med 2013; 3:a015412. [PMID: 23838521 PMCID: PMC3753722 DOI: 10.1101/cshperspect.a015412] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The physiological switch in expression of the embryonic, fetal, and adult β-like globin genes has garnered enormous attention from investigators interested in transcriptional mechanisms and the molecular basis of hemoglobinopathies. These efforts have led to the discovery of cell type-specific transcription factors, unprecedented mechanisms of transcriptional coregulator function, genome biology principles, unique contributions of nuclear organization to transcription and cell function, and promising therapeutic targets. Given the vast literature accrued on this topic, this article will focus on the master regulator of erythroid cell development and function GATA-1, its associated proteins, and its frontline role in controlling hemoglobin synthesis. GATA-1 is a crucial regulator of genes encoding hemoglobin subunits and heme biosynthetic enzymes. GATA-1-dependent mechanisms constitute an essential regulatory core that nucleates additional mechanisms to achieve the physiological control of hemoglobin synthesis.
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Affiliation(s)
- Koichi R Katsumura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Wisconsin Institute for Medical Research, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
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