1
|
Perrotti E, L'Episcopia M, Menegon M, Soares IS, Rosas-Aguirre A, Speybroeck N, LLanos-Cuentas A, Menard D, Ferreira MU, Severini C. Reduced polymorphism of Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2. Parasit Vectors 2023; 16:238. [PMID: 37461081 DOI: 10.1186/s13071-023-05851-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND ETRAMP11.2 (PVX_003565) is a well-characterized protein with antigenic potential. It is considered to be a serological marker for diagnostic tools, and it has been suggested as a potential vaccine candidate. Despite its immunological relevance, the polymorphism of the P. vivax ETRAMP11.2 gene (pvetramp11.2) remains undefined. The genetic variability of an antigen may limit the effectiveness of its application as a serological surveillance tool and in vaccine development and, therefore, the aim of this study was to investigate the genetic diversity of pvetramp11.2 in parasite populations from Amazonian regions and worldwide. We also evaluated amino acid polymorphism on predicted B-cell epitopes. The low variability of the sequence encoding PvETRAMP11.2 protein suggests that it would be a suitable marker in prospective serodiagnostic assays for surveillance strategies or in vaccine design against P. vivax malaria. METHODS The pvetramp11.2 of P. vivax isolates collected from Brazil (n = 68) and Peru (n = 36) were sequenced and analyzed to assess nucleotide polymorphisms, allele distributions, population differentiation, genetic diversity and signature of selection. In addition, sequences (n = 104) of seven populations from different geographical regions were retrieved from the PlasmoDB database and included in the analysis to study the worldwide allele distribution. Potential linear B-cell epitopes and their polymorphisms were also explored. RESULTS The multiple alignments of 208 pvetramp11.2 sequences revealed a low polymorphism and a marked geographical variation in allele diversity. Seven polymorphic sites and 11 alleles were identified. All of the alleles were detected in isolates from the Latin American region and five alleles were detected in isolates from the Southeast Asia/Papua New Guinea (SEA/PNG) region. Three alleles were shared by all Latin American populations (H1, H6 and H7). The H1 allele (reference allele from Salvador-1 strain), which was absent in the SEA/PNG populations, was the most represented allele in populations from Brazil (54%) and was also detected at high frequencies in populations from all other Latin America countries (range: 13.0% to 33.3%). The H2 allele was the major allele in SEA/PNG populations, but was poorly represented in Latin America populations (only in Brazil: 7.3%). Plasmodium vivax populations from Latin America showed a marked inter-population genetic differentiation (fixation index [Fst]) in contrast to SEA/PNG populations. Codon bias measures (effective number of codons [ENC] and Codon bias index [CBI]) indicated preferential use of synonymous codons, suggesting selective pressure at the translation level. Only three amino acid substitutions, located in the C-terminus, were detected. Linear B-cell epitope mapping predicted two epitopes in the Sal-1 PvETRAMP11.2 protein, one of which was fully conserved in all of the parasite populations analyzed. CONCLUSIONS We provide an overview of the allele distribution and genetic differentiation of ETRAMP11.2 antigen in P. vivax populations from different endemic areas of the world. The reduced polymorphism and the high degree of protein conservation supports the application of PvETRAMP11.2 protein as a reliable antigen for application in serological assays or vaccine design. Our findings provide useful information that can be used to inform future study designs.
Collapse
Affiliation(s)
- Edvige Perrotti
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy.
| | | | - Michela Menegon
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Irene S Soares
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Angel Rosas-Aguirre
- Research Institute of Health and Society (IRSS), Université Catholique de Louvain, Brussels, Belgium
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Niko Speybroeck
- Research Institute of Health and Society (IRSS), Université Catholique de Louvain, Brussels, Belgium
| | - Alejandro LLanos-Cuentas
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Didier Menard
- Laboratoire de Parasitologie Et Mycologie Médicale, Les Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Parasitologie Et Pathologie Tropicale, Université de Strasbourg, Strasbourg, France
- Malaria Genetics and Resistance Unit-INSERM U1201, Institut Pasteur, Paris, France
| | - Marcelo Urbano Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Carlo Severini
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy.
| |
Collapse
|
2
|
Kalla R, Adams AT, Nowak JK, Bergemalm D, Vatn S, Ventham NT, Kennedy NA, Ricanek P, Lindstrom J, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjørn C, Richmond R, Relton C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome. J Crohns Colitis 2023; 17:170-184. [PMID: 36029471 PMCID: PMC10024547 DOI: 10.1093/ecco-jcc/jjac127] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Epigenetic alterations may provide valuable insights into gene-environment interactions in the pathogenesis of inflammatory bowel disease [IBD]. METHODS Genome-wide methylation was measured from peripheral blood using the Illumina 450k platform in a case-control study in an inception cohort (295 controls, 154 Crohn's disease [CD], 161 ulcerative colitis [UC], 28 IBD unclassified [IBD-U)] with covariates of age, sex and cell counts, deconvoluted by the Houseman method. Genotyping was performed using Illumina HumanOmniExpressExome-8 BeadChips and gene expression using the Ion AmpliSeq Human Gene Expression Core Panel. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. RESULTS A total of 137 differentially methylated positions [DMPs] were identified in IBD, including VMP1/MIR21 [p = 9.11 × 10-15] and RPS6KA2 [6.43 × 10-13], with consistency seen across Scandinavia and the UK. Dysregulated loci demonstrate strong genetic influence, notably VMP1 [p = 1.53 × 10-15]. Age acceleration is seen in IBD [coefficient 0.94, p < 2.2 × 10-16]. Several immuno-active genes demonstrated highly significant correlations between methylation and gene expression in IBD, in particular OSM: IBD r = -0.32, p = 3.64 × 10-7 vs non-IBD r = -0.14, p = 0.77]. Multi-omic integration of the methylome, genome and transcriptome also implicated specific pathways that associate with immune activation, response and regulation at disease inception. At follow-up, a signature of three DMPs [TAP1, TESPA1, RPTOR] were associated with treatment escalation to biological agents or surgery (hazard ratio of 5.19 [CI: 2.14-12.56], logrank p = 9.70 × 10-4). CONCLUSION These data demonstrate consistent epigenetic alterations at diagnosis in European patients with IBD, providing insights into the pathogenetic importance and translational potential of epigenetic mapping in complex disease.
Collapse
Affiliation(s)
- Rahul Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Alex T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jan K Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simen Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, Exeter, UK
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Johan Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marie Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - Mauro D’Amato
- CIC bioGUNE – BRTA, Derio, SpainIKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Christine Olbjørn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Rebecca Richmond
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jack Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| |
Collapse
|
3
|
Ishihara H, Alseekh S, Feil R, Perera P, George GM, Niedźwiecki P, Arrivault S, Zeeman SC, Fernie AR, Lunn JE, Smith AM, Stitt M. Rising rates of starch degradation during daytime and trehalose 6-phosphate optimize carbon availability. Plant Physiol 2022; 189:1976-2000. [PMID: 35486376 PMCID: PMC9342969 DOI: 10.1093/plphys/kiac162] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 05/06/2023]
Abstract
Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the light and remobilize it to support maintenance and growth at night. Starch synthesis and degradation are usually viewed as temporally separate processes. Recently, we reported that starch is also degraded in the light. Degradation rates are generally low early in the day but rise with time. Here, we show that the rate of degradation in the light depends on time relative to dawn rather than dusk. We also show that degradation in the light is inhibited by trehalose 6-phosphate, a signal for sucrose availability. The observed responses of degradation in the light can be simulated by a skeletal model in which the rate of degradation is a function of starch content divided by time remaining until dawn. The fit is improved by extension to include feedback inhibition of starch degradation by trehalose 6-phosphate. We also investigate possible functions of simultaneous starch synthesis and degradation in the light, using empirically parameterized models and experimental approaches. The idea that this cycle buffers growth against falling rates of photosynthesis at twilight is supported by data showing that rates of protein and cell wall synthesis remain high during a simulated dusk twilight. Degradation of starch in the light may also counter over-accumulation of starch in long photoperiods and stabilize signaling around dusk. We conclude that starch degradation in the light is regulated by mechanisms similar to those that operate at night and is important for stabilizing carbon availability and signaling, thus optimizing growth in natural light conditions.
Collapse
Affiliation(s)
- Hirofumi Ishihara
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Regina Feil
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Pumi Perera
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gavin M George
- Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland
| | - Piotr Niedźwiecki
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Stephanie Arrivault
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - John E Lunn
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Alison M Smith
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | |
Collapse
|
4
|
Pagliazzo L, Caby S, Lancelot J, Salomé-Desnoulez S, Saliou JM, Heimburg T, Chassat T, Cailliau K, Sippl W, Vicogne J, Pierce RJ. Histone deacetylase 8 interacts with the GTPase SmRho1 in Schistosoma mansoni. PLoS Negl Trop Dis 2021; 15:e0009503. [PMID: 34843489 PMCID: PMC8670706 DOI: 10.1371/journal.pntd.0009503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/14/2021] [Accepted: 10/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Schistosoma mansoni histone deacetylase 8 (SmHDAC8) has elicited considerable interest as a target for drug discovery. Invalidation of its transcripts by RNAi leads to impaired survival of the worms in infected mice and its inhibition causes cell apoptosis and death. To determine why it is a promising therapeutic target the study of the currently unknown cellular signaling pathways involving this enzyme is essential. Protein partners of SmHDAC8 were previously identified by yeast two-hybrid (Y2H) cDNA library screening and by mass spectrometry (MS) analysis. Among these partners we characterized SmRho1, the schistosome orthologue of human RhoA GTPase, which is involved in the regulation of the cytoskeleton. In this work, we validated the interaction between SmHDAC8 and SmRho1 and explored the role of the lysine deacetylase in cytoskeletal regulation. Methodology/principal findings We characterized two isoforms of SmRho1, SmRho1.1 and SmRho1.2. Co- immunoprecipitation (Co-IP)/Mass Spectrometry (MS) analysis identified SmRho1 partner proteins and we used two heterologous expression systems (Y2H assay and Xenopus laevis oocytes) to study interactions between SmHDAC8 and SmRho1 isoforms. To confirm SmHDAC8 and SmRho1 interaction in adult worms and schistosomula, we performed Co-IP experiments and additionally demonstrated SmRho1 acetylation using a Nano LC-MS/MS approach. A major impact of SmHDAC8 in cytoskeleton organization was documented by treating adult worms and schistosomula with a selective SmHDAC8 inhibitor or using RNAi followed by confocal microscopy. Conclusions/significance Our results suggest that SmHDAC8 is involved in cytoskeleton organization via its interaction with the SmRho1.1 isoform. The SmRho1.2 isoform failed to interact with SmHDAC8, but did specifically interact with SmDia suggesting the existence of two distinct signaling pathways regulating S. mansoni cytoskeleton organization via the two SmRho1 isoforms. A specific interaction between SmHDAC8 and the C-terminal moiety of SmRho1.1 was demonstrated, and we showed that SmRho1 is acetylated on K136. SmHDAC8 inhibition or knockdown using RNAi caused extensive disruption of schistosomula actin cytoskeleton. Schistosoma mansoni is the major parasitic platyhelminth species causing intestinal schistosomiasis. Currently one drug, praziquantel, is the treatment of choice but its use in mass treatment programs means that the development of resistance is likely and renders imperative the development of new therapeutic agents. As new potential targets we have focused on lysine deacetylases, and in particular S. mansoni histone deacetylase 8 (SmHDAC8). Previous studies showed that reduction in the level of transcripts of SmHDAC8 by RNAi led to the impaired survival of the worms after the infection of mice. The analysis of the 3D structure of SmHDAC8 by X-ray crystallography showed that the catalytic domain structure diverges significantly from that of human HDAC8 and this was exploited to develop novel potential anti-schistosomal drugs. The biological roles of SmHDAC8 are unknown. For this reason, we previously characterized its protein binding partners and identified the schistosome orthologue of the human RhoA GTPase, suggesting the involvement of SmHDAC8 in the modulation of cytoskeleton organization. Here we investigated the interaction between SmHDAC8 and SmRho1 and identified two SmRho1 isoforms (SmRho1.1 and SmRho1.2). Our study showed that SmHDAC8 is involved in schistosome cytoskeleton organization.
Collapse
Affiliation(s)
- Lucile Pagliazzo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Stéphanie Caby
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Julien Lancelot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
| | | | - Jean-Michel Saliou
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Tino Heimburg
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Thierry Chassat
- Institut Pasteur de Lille - PLEHTA (Plateforme d’expérimentation et de Haute Technologie Animale), Lille, France
| | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Jérôme Vicogne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
- * E-mail: (JV); (RJP)
| | - Raymond J. Pierce
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, - Centre d’Infection et d’Immunité de Lille, Lille, France
- * E-mail: (JV); (RJP)
| |
Collapse
|
5
|
Gershony LC, Belanger JM, Short AD, Le M, Hytönen MK, Lohi H, Famula TR, Kennedy LJ, Oberbauer AM. DLA class II risk haplotypes for autoimmune diseases in the bearded collie offer insight to autoimmunity signatures across dog breeds. Canine Genet Epidemiol 2019; 6:2. [PMID: 30783534 PMCID: PMC6376674 DOI: 10.1186/s40575-019-0070-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/24/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Primary hypoadrenocorticism (Addison's disease, AD) and symmetrical lupoid onychodystrophy (SLO) are two clinical conditions with an autoimmune etiology that occur in multiple dog breeds. In man, autoimmunity is associated with polymorphisms in immune-related genes that result in a reduced threshold for, or defective regulation of, T cell activation. The major histocompatibility complex (MHC) class II genes encode molecules that participate in these functions, and polymorphisms within these genes have been associated with autoimmune conditions in dogs and humans. Bearded collies have a relatively high prevalence of autoimmune diseases, particularly AD and SLO. Our study assessed the relationship between particular MHC (dog leukocyte antigen, DLA) class II haplotypes and the two autoimmune diseases most common in this breed. Moreover, five unrelated breeds at increased risk for AD were studied for comparative purposes and analyzed in the context of extant literature. RESULTS A single DLA class II three-locus haplotype, determined by sequence-based typing, was associated with increased risk for AD (DLA-DRB1*009:01/DQA1*001:01/DQB1*008:02) in bearded collies. Comparative analysis with the five additional breeds showed limited allele sharing, with DQA1*001:01 and DQB1*002:01 being the only alleles observed in all breeds. A distinct three-locus risk haplotype (DLA-DRB1*001:01/DQA1*001:01/DQB1*002:01) was associated with AD in the West Highland white terrier and Leonberger. Two different risk haplotypes were associated with increased risk for SLO in the bearded collie (DLA-DRB1*018:01/DQA1*001:01/DQB1*002:01 and DLA-DRB1*018:01/DQA1*001:01/ DQB1*008:02). CONCLUSION Two-locus DQ haplotypes composed of DLA-DQA1*001:01 in association with DLA-DQB1*002:01 or DLA-DQB1*008:02 make up the four risk haplotypes identified in the present study and are also found in other risk haplotypes previously associated with diabetes mellitus and hypothyroidism across different dog breeds. Our findings build upon previously published data to suggest that this two-locus (DQ) model serves as a good indicator for susceptibility to multiple organ-specific autoimmune diseases in the canine population. However, it is also clear that additional loci are necessary for actual disease expression. Investigation of affected and unaffected dogs carrying these predisposing DQ haplotype signatures may allow for the identification of those additional genetic components that determine autoimmune disease expression and organ specificity.
Collapse
Affiliation(s)
- Liza C. Gershony
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
- Brazilian National Council for Scientific and Technological Development (CNPq) fellow, Brasília, Brazil
| | - Janelle M. Belanger
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Andrea D. Short
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - Myly Le
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Marjo K. Hytönen
- Research Programs Unit, Molecular Neurology, and Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology, and Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Thomas R. Famula
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Lorna J. Kennedy
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - Anita M. Oberbauer
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| |
Collapse
|
6
|
Zienkiewicz K, Benning U, Siegler H, Feussner I. The type 2 acyl-CoA:diacylglycerol acyltransferase family of the oleaginous microalga Lobosphaera incisa. BMC Plant Biol 2018; 18:298. [PMID: 30477429 PMCID: PMC6257963 DOI: 10.1186/s12870-018-1510-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/29/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Oleaginous microalgae are promising sources of energy-rich triacylglycerols (TAGs) for direct use for food, feed and industrial applications. Lobosphaera incisa is a fresh water unicellular alga, which in response to nutrient stress accumulates a high amount of TAGs with a high proportion of arachidonic acid (ARA). The final committed step of de novo TAG biosynthesis is catalyzed by acyl-CoA:diacylglycerol acyltransferases (DGATs), which add a fatty acid (FA) to the final sn-3 position of diacylglycerol (DAG). RESULTS Genome analysis revealed the presence of five putative DGAT isoforms in L. incisa, including one DGAT of type 1, three DGATs of type 2 and a single isoform of a type 3 DGAT. For LiDGAT1, LiDGAT2.1, LiDGAT2.2 and LiDGAT2.3 enzyme activity was confirmed by expressing them in the TAG-deficient yeast strain H1246. Feeding experiments of yeast transformants with fatty acids suggest a broad substrate specificity spectrum for LiDGAT1. A significant TAG production in response to exogenous ARA was found for LiDGAT2.2. Cellular localization of the four type 1 and type 2 DGATs expressed in yeast revealed that they all localize to distinct ER domains. A prominent association of LiDGAT1 with ER domains in close proximity to forming lipid droplets (LDs) was also observed. CONCLUSIONS The data revealed a distinct molecular, functional and cellular nature of type 1 and type 2 DGATs from L. incisa, with LiDGAT1 being a major contributor to the TAG pool. LiDGATs of type 2 might be in turn involved in the incorporation of unusual fatty acids into TAG and thus regulate the composition of TAG. This report provides a valuable resource for the further research of microalgae DGATs oriented towards production of fresh-water strains with higher oil content of valuable composition, not only for oil industry but also for human and animal nutrition.
Collapse
Affiliation(s)
- Krzysztof Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Urs Benning
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Heike Siegler
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, 37077 Goettingen, Germany
- Department of Plant Biochemistry, International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, 37077 Goettingen, Germany
| |
Collapse
|
7
|
Llibre A, Shimakawa Y, Mottez E, Ainsworth S, Buivan TP, Firth R, Harrison E, Rosenberg AR, Meritet JF, Fontanet A, Castan P, Madejón A, Laverick M, Glass A, Viana R, Pol S, McClure CP, Irving WL, Miele G, Albert ML, Duffy D. Development and clinical validation of the Genedrive point-of-care test for qualitative detection of hepatitis C virus. Gut 2018; 67:2017-2024. [PMID: 29615488 PMCID: PMC6176522 DOI: 10.1136/gutjnl-2017-315783] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/09/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Recently approved direct acting antivirals provide transformative therapies for chronic hepatitis C virus (HCV) infection. The major clinical challenge remains to identify the undiagnosed patients worldwide, many of whom live in low-income and middle-income countries, where access to nucleic acid testing remains limited. The aim of this study was to develop and validate a point-of-care (PoC) assay for the qualitative detection of HCV RNA. DESIGN We developed a PoC assay for the qualitative detection of HCV RNA on the PCR Genedrive instrument. We validated the Genedrive HCV assay through a case-control study comparing results with those obtained with the Abbott RealTime HCV test. RESULTS The PoC assay identified all major HCV genotypes, with a limit of detection of 2362 IU/mL (95% CI 1966 to 2788). Using 422 patients chronically infected with HCV and 503 controls negative for anti-HCV and HCV RNA, the Genedrive HCV assay showed 98.6% sensitivity (95% CI 96.9% to 99.5%) and 100% specificity (95% CI 99.3% to 100%) to detect HCV. In addition, melting peak ratiometric analysis demonstrated proof-of-principle for semiquantification of HCV. The test was further validated in a real clinical setting in a resource-limited country. CONCLUSION We report a rapid, simple, portable and accurate PoC molecular test for HCV, with sensitivity and specificity that fulfils the recent FIND/WHO Target Product Profile for HCV decentralised testing in low-income and middle-income countries. This Genedrive HCV assay may positively impact the continuum of HCV care from screening to cure by supporting real-time treatment decisions. TRIAL REGISTRATION NUMBER NCT02992184 .
Collapse
Affiliation(s)
- Alba Llibre
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
| | - Yusuke Shimakawa
- Unité d’Epidémiologie des Maladies Emergentes, Institut Pasteur, Paris, France
| | - Estelle Mottez
- Centre for Translational Research, Institut Pasteur, Paris, France
- INSERM UMS20, Institut Pasteur, Paris, France
| | | | - Tan-Phuc Buivan
- Centre for Translational Research, Institut Pasteur, Paris, France
- INSERM UMS20, Institut Pasteur, Paris, France
| | | | | | - Arielle R Rosenberg
- Université Paris Descartes, EA4474 "Hepatitis C Virology", AP-HP, Hôpital Cochin, Service de Virologie, Paris, France
| | - Jean-François Meritet
- Université Paris Descartes, EA4474 "Hepatitis C Virology", AP-HP, Hôpital Cochin, Service de Virologie, Paris, France
| | - Arnaud Fontanet
- Unité d’Epidémiologie des Maladies Emergentes, Institut Pasteur, Paris, France
- PACRI Unit, Conservatoire National des Arts et Métiers, Paris, France
| | | | - Antonio Madejón
- Liver Unit, Hospital Universitario La Paz, CIBERehd, IdiPAZ, Madrid, Spain
| | | | | | | | - Stanislas Pol
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
- Université Paris Descartes, EA4474 "Hepatitis C Virology", AP-HP, Hôpital Cochin, Service de Virologie, Paris, France
| | - C Patrick McClure
- Gastrointestinal and Liver Disorders Theme, NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, Nottingham, UK
| | - William Lucien Irving
- Gastrointestinal and Liver Disorders Theme, NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, Nottingham, UK
| | | | - Matthew L Albert
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
- Department of Cancer Immunology, Genentech Inc, San Francisco, California, USA
| | - Darragh Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
| |
Collapse
|
8
|
Schaefer C, Mallela N, Seggewiß J, Lechtape B, Omran H, Dirksen U, Korsching E, Potratz J. Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm. PLoS One 2018; 13:e0191570. [PMID: 29385199 PMCID: PMC5792015 DOI: 10.1371/journal.pone.0191570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 01/08/2018] [Indexed: 11/28/2022] Open
Abstract
In the search for novel therapeutic targets, RNA interference screening has become a valuable tool. High-throughput technologies are now broadly accessible but their assay development from baseline remains resource-intensive and challenging. Focusing on this assay development process, we here describe a target discovery screen using pooled shRNA libraries and next-generation sequencing (NGS) deconvolution in a cell line model of Ewing sarcoma. In a strategy designed for comparative and synthetic lethal studies, we screened for targets specific to the A673 Ewing sarcoma cell line. Methods, results and pitfalls are described for the entire multi-step screening procedure, from lentiviral shRNA delivery to bioinformatics analysis, illustrating a complete model workflow. We demonstrate that successful studies are feasible from the first assay performance and independent of specialized screening units. Furthermore, we show that a resource-saving screen depth of 100-fold average shRNA representation can suffice to generate reproducible target hits despite heterogeneity in the derived datasets. Because statistical analysis methods are debatable for such datasets, we created ProFED, an analysis package designed to facilitate descriptive data analysis and hit calling using an aim-oriented profile filtering approach. In its versatile design, this open-source online tool provides fast and easy analysis of shRNA and other count-based datasets to complement other analytical algorithms.
Collapse
Affiliation(s)
- Christiane Schaefer
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Nikhil Mallela
- Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jochen Seggewiß
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Birgit Lechtape
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Heymut Omran
- General Pediatrics, University Hospital Münster, Münster, Germany
| | - Uta Dirksen
- Department of Hematology and Oncology, Pediatrics III, West German Cancer Center, German Cancer Consortium (DKTK) Center Essen, University Hospital Essen, Essen, Germany
| | - Eberhard Korsching
- Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jenny Potratz
- Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
- General Pediatrics, University Hospital Münster, Münster, Germany
- * E-mail:
| |
Collapse
|
9
|
Klosin A, Reis K, Hidalgo-Carcedo C, Casas E, Vavouri T, Lehner B. Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory. Sci Adv 2017; 3:e1701143. [PMID: 28835928 PMCID: PMC5559210 DOI: 10.1126/sciadv.1701143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
Impaired DNA replication is a hallmark of cancer and a cause of genomic instability. We report that, in addition to causing genetic change, impaired DNA replication during embryonic development can have major epigenetic consequences for a genome. In a genome-wide screen, we identified impaired DNA replication as a cause of increased expression from a repressed transgene in Caenorhabditis elegans. The acquired expression state behaved as an "epiallele," being inherited for multiple generations before fully resetting. Derepression was not restricted to the transgene but was caused by a global reduction in heterochromatin-associated histone modifications due to the impaired retention of modified histones on DNA during replication in the early embryo. Impaired DNA replication during development can therefore globally derepress chromatin, creating new intergenerationally inherited epigenetic expression states.
Collapse
Affiliation(s)
- Adam Klosin
- European Molecular Biology Laboratory–Centre for Genomic Regulation (EMBL-CRG) Systems Biology Unit, CRG, the Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Kadri Reis
- European Molecular Biology Laboratory–Centre for Genomic Regulation (EMBL-CRG) Systems Biology Unit, CRG, the Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Cristina Hidalgo-Carcedo
- European Molecular Biology Laboratory–Centre for Genomic Regulation (EMBL-CRG) Systems Biology Unit, CRG, the Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Eduard Casas
- Program of Predictive and Personalized Medicine of Cancer–Institute Germans Trias i Pujol, Can Ruti Campus, Ctra de Can Ruti, Camí de les Escoles s/n, Badalona, 08916 Barcelona, Spain
| | - Tanya Vavouri
- Program of Predictive and Personalized Medicine of Cancer–Institute Germans Trias i Pujol, Can Ruti Campus, Ctra de Can Ruti, Camí de les Escoles s/n, Badalona, 08916 Barcelona, Spain
- Josep Carreras Leukaemia Research Institute (IJC), Can Ruti Campus, Ctra de Can Ruti, Camí de les Escoles s/n, Badalona, 08916 Barcelona, Spain
| | - Ben Lehner
- European Molecular Biology Laboratory–Centre for Genomic Regulation (EMBL-CRG) Systems Biology Unit, CRG, the Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| |
Collapse
|
10
|
Chatzimichali EA, Bessant C. Novel application of heuristic optimisation enables the creation and thorough evaluation of robust support vector machine ensembles for machine learning applications. Metabolomics 2016; 12:16. [PMID: 26617479 PMCID: PMC4655007 DOI: 10.1007/s11306-015-0894-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 08/15/2015] [Indexed: 11/03/2022]
Abstract
Today's researchers have access to an unprecedented range of powerful machine learning tools with which to build models for classifying samples according to their metabolomic profile (e.g. separating diseased samples from healthy controls). However, such powerful tools need to be used with caution and the diagnostic performance of models produced by them should be rigorously evaluated if their output is to be believed. This involves considerable processing time, and has hitherto required expert knowledge in machine learning. By adopting a constrained nonlinear simplex optimisation for the tuning of support vector machines (SVMs) we have reduced SVM training times more than tenfold compared to a traditional grid search, allowing us to implement a high performance R package that makes it possible for a typical bench scientist to produce powerful SVM ensemble classifiers within a reasonable timescale, with automated bootstrapped training and rigorous permutation testing. This puts a state-of-the-art open source multivariate classification pipeline into the hands of every metabolomics researcher, allowing them to build robust classification models with realistic performance metrics.
Collapse
Affiliation(s)
| | - Conrad Bessant
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| |
Collapse
|