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Charras A, Haldenby S, Smith EMD, Egbivwie N, Olohan L, Kenny JG, Schwarz K, Roberts C, Al-Abadi E, Armon K, Bailey K, Ciurtin C, Gardner-Medwin J, Haslam K, Hawley DP, Leahy A, Leone V, McErlane F, Modgil G, Pilkington C, Ramanan AV, Rangaraj S, Riley P, Sridhar A, Beresford MW, Hedrich CM. Panel sequencing links rare, likely damaging gene variants with distinct clinical phenotypes and outcomes in juvenile-onset SLE. Rheumatology (Oxford) 2023; 62:SI210-SI225. [PMID: 35532072 PMCID: PMC9949710 DOI: 10.1093/rheumatology/keac275] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Juvenile-onset systemic lupus erythematosus (jSLE) affects 15-20% of lupus patients. Clinical heterogeneity between racial groups, age groups and individual patients suggests variable pathophysiology. This study aimed to identify highly penetrant damaging mutations in genes associated with SLE/SLE-like disease in a large national cohort (UK JSLE Cohort Study) and compare demographic, clinical and laboratory features in patient sub-cohorts with 'genetic' SLE vs remaining SLE patients. METHODS Based on a sequencing panel designed in 2018, target enrichment and next-generation sequencing were performed in 348 patients to identify damaging gene variants. Findings were integrated with demographic, clinical and treatment related datasets. RESULTS Damaging gene variants were identified in ∼3.5% of jSLE patients. When compared with the remaining cohort, 'genetic' SLE affected younger children and more Black African/Caribbean patients. 'Genetic' SLE patients exhibited less organ involvement and damage, and neuropsychiatric involvement developed over time. Less aggressive first line treatment was chosen in 'genetic' SLE patients, but more second and third line agents were used. 'Genetic' SLE associated with anti-dsDNA antibody positivity at diagnosis and reduced ANA, anti-LA and anti-Sm antibody positivity at last visit. CONCLUSION Approximately 3.5% of jSLE patients present damaging gene variants associated with younger age at onset, and distinct clinical features. As less commonly observed after treatment induction, in 'genetic' SLE, autoantibody positivity may be the result of tissue damage and explain reduced immune complex-mediated renal and haematological involvement. Routine sequencing could allow for patient stratification, risk assessment and target-directed treatment, thereby increasing efficacy and reducing toxicity.
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Affiliation(s)
- Amandine Charras
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences
| | - Sam Haldenby
- Centre for Genomic Research, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool
| | - Eve M D Smith
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences
- Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK
| | - Naomi Egbivwie
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences
- Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK
| | - Lisa Olohan
- Centre for Genomic Research, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool
| | - John G Kenny
- Centre for Genomic Research, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
| | - Klaus Schwarz
- Institut for Transfusion Medicine, University Ulm, Ulm
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg—Hessen, Ulm, Germany
| | - Carla Roberts
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences
| | - Eslam Al-Abadi
- Department of Rheumatology, Birmingham Children’s Hospital, Birmingham
| | - Kate Armon
- Department of Paediatric Rheumatology, Cambridge University Hospitals, Cambridge
| | - Kathryn Bailey
- Department of Paediatric Rheumatology, Oxford University Hospitals NHS Foundation Trust, Oxford
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology, University College London, London
| | | | - Kirsty Haslam
- Department of Paediatrics, Bradford Royal Infirmary, Bradford
| | - Daniel P Hawley
- Department of Paediatric Rheumatology, Sheffield Children’s Hospital, Sheffield
| | - Alice Leahy
- Department of Paediatric Rheumatology, Southampton General Hospital, Southampton
| | - Valentina Leone
- Department of Paediatric Rheumatology, Leeds Children Hospital, Leeds
| | - Flora McErlane
- Paediatric Rheumatology, Great North Children’s Hospital, Royal Victoria Infirmary, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne
| | - Gita Modgil
- Department of Paediatrics, Musgrove Park Hospital, Taunton
| | | | - Athimalaipet V Ramanan
- University Hospitals Bristol NHS Foundation Trust & Bristol Medical School, University of Bristol, Bristol
| | - Satyapal Rangaraj
- Department of Paediatric Rheumatology, Nottingham University Hospitals, Nottingham
| | - Phil Riley
- Department of Paediatric Rheumatology, Royal Manchester Children’s Hospital, Manchester
| | - Arani Sridhar
- Department of Paediatrics, Leicester Royal Infirmary, Leicester, UK
| | - Michael W Beresford
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences
- Centre for Genomic Research, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool
| | - Christian M Hedrich
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences
- Centre for Genomic Research, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool
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Gardiner LJ, Joynson R, Omony J, Rusholme-Pilcher R, Olohan L, Lang D, Bai C, Hawkesford M, Salt D, Spannagl M, Mayer KFX, Kenny J, Bevan M, Hall N, Hall A. Hidden variation in polyploid wheat drives local adaptation. Genome Res 2018; 28:1319-1332. [PMID: 30093548 PMCID: PMC6120627 DOI: 10.1101/gr.233551.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Wheat has been domesticated into a large number of agricultural environments and has the ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content, and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat genome and that ancestral methylation states become preferentially "hard coded" as single nucleotide polymorphisms (SNPs) via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside SNP-based markers for breeding.
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Affiliation(s)
| | - Ryan Joynson
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | - Jimmy Omony
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | | | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Daniel Lang
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | - Caihong Bai
- Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
| | | | - David Salt
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, United Kingdom
| | - Manuel Spannagl
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | - Klaus F X Mayer
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany.,Wissenschaftszentrum Weihenstephan (WZW), Technical University Munich, Freising, 85354, Germany
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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Olohan L, Gardiner LJ, Lucaci A, Steuernagel B, Wulff B, Kenny J, Hall N, Hall A. A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample. BMC Genomics 2018; 19:250. [PMID: 29653520 PMCID: PMC5899405 DOI: 10.1186/s12864-018-4640-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 04/03/2018] [Indexed: 01/01/2023] Open
Abstract
Background Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. Electronic supplementary material The online version of this article (10.1186/s12864-018-4640-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Anita Lucaci
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Brande Wulff
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich research Park, Norwich, UK.,University of East Anglia, Norwich, UK
| | - Anthony Hall
- Earlham Institute, Norwich research Park, Norwich, UK. .,University of East Anglia, Norwich, UK.
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Gardiner LJ, Bansept-Basler P, Olohan L, Joynson R, Brenchley R, Hall N, O'Sullivan DM, Hall A. Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat. Plant J 2016; 87:403-19. [PMID: 27144898 PMCID: PMC5026171 DOI: 10.1111/tpj.13204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 01/09/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 05/20/2023]
Abstract
Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Ryan Joynson
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Rachel Brenchley
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, PO Box 237, Whiteknights, Reading, RG6 6AR, UK
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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Haywood S, Boursnell M, Loughran MJ, Trafford J, Isherwood D, Liu X, Olohan L, Carter SD. Copper toxicosis in non-COMMD1 Bedlington terriers is associated with metal transport gene ABCA12. J Trace Elem Med Biol 2016; 35:83-9. [PMID: 27049130 DOI: 10.1016/j.jtemb.2016.01.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 11/20/2022]
Abstract
Wilson's disease, caused by a mutation in the ATP-ase 7B gene, is the only genetically characterised human disease with inhibition of biliary copper excretion and toxic copper accumulation in liver and occasionally brain. A similar copper toxicosis occurs in Bedlington terriers (CT) with liver damage only. Although CT has been associated with a defect in the COMMD1 gene (COMMD1 (del/del)), Bedlington terriers with CT and lacking this mutation are also recognised (non-COMMD1 (del/del)). A study was designed to identify any other gene polymorphisms associated with copper toxicity in Bedlington terriers employing genome wide association studies (GWAS) followed by deep sequencing of the candidate region. Blood for DNA analysis and liver for confirmation of the diagnosis was obtained from 30 non-COMMD1 (del/del) Bedlington terriers comprising equal numbers of CT-affected dogs and controls. DNA was initially subjected to GWAS screening and then further sequencing to target the putative mutant gene. The study has identified a significant disease association with a region on chromosome 37 containing identified SNP's which are highly significantly associated with non-COMMD1 (del/del) Bedlington terrier CT. This region contains the ABCA12 gene which bears a close functional relationship to ATP-ase 7B responsible for Wilson's disease in man.
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Affiliation(s)
- Susan Haywood
- Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, ic2 Science Park, Brownlow Hill, Liverpool L3 5RF, United Kingdom.
| | - Mike Boursnell
- Canine Genetics, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, United Kingdom
| | - Michael J Loughran
- Clinical Engineering, Institute of Ageing and Chronic Disease, Faculty of Health & Life Science, University of Liverpool, Liverpool L69 3G, United Kingdom
| | - James Trafford
- Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, ic2 Science Park, Brownlow Hill, Liverpool L3 5RF, United Kingdom
| | - Diana Isherwood
- Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, ic2 Science Park, Brownlow Hill, Liverpool L3 5RF, United Kingdom
| | - Xuan Liu
- Centre for Genomics Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Lisa Olohan
- Centre for Genomics Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Stuart D Carter
- Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, ic2 Science Park, Brownlow Hill, Liverpool L3 5RF, United Kingdom
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Gardiner LJ, Quinton-Tulloch M, Olohan L, Price J, Hall N, Hall A. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol 2015; 16:273. [PMID: 26653535 PMCID: PMC4674939 DOI: 10.1186/s13059-015-0838-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [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] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/17/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. RESULTS While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. CONCLUSIONS We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Mark Quinton-Tulloch
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Jonathan Price
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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Gardiner LJ, Gawroński P, Olohan L, Schnurbusch T, Hall N, Hall A. Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species. Plant J 2014; 80:895-904. [PMID: 25205592 DOI: 10.1111/tpj.12660] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 05/02/2014] [Revised: 08/29/2014] [Accepted: 09/02/2014] [Indexed: 05/23/2023]
Abstract
Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
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Stensløkken KO, Ellefsen S, Vasieva O, Fang Y, Farrell AP, Olohan L, Vaage J, Nilsson GE, Cossins AR. Life without oxygen: gene regulatory responses of the crucian carp (Carassius carassius) heart subjected to chronic anoxia. PLoS One 2014; 9:e109978. [PMID: 25372666 PMCID: PMC4220927 DOI: 10.1371/journal.pone.0109978] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/09/2014] [Indexed: 11/19/2022] Open
Abstract
Crucian carp are unusual among vertebrates in surviving extended periods in the complete absence of molecular oxygen. During this time cardiac output is maintained though these mechanisms are not well understood. Using a high-density cDNA microarray, we have defined the genome-wide gene expression responses of cardiac tissue after exposing the fish at two temperatures (8 and 13°C) to one and seven days of anoxia, followed by seven days after restoration to normoxia. At 8°C, using a false discovery rate of 5%, neither anoxia nor re-oxygenation elicited appreciable changes in gene expression. By contrast, at 13°C, 777 unique genes responded strongly. Up-regulated genes included those involved in protein turnover, the pentose phosphate pathway and cell morphogenesis while down-regulated gene categories included RNA splicing and transcription. Most genes were affected between one and seven days of anoxia, indicating gene regulation over the medium term but with few early response genes. Re-oxygenation for 7 days was sufficient to completely reverse these responses. Glycolysis displayed more complex responses with anoxia up-regulated transcripts for the key regulatory enzymes, hexokinase and phosphofructokinase, but with down-regulation of most of the non-regulatory genes. This complex pattern of responses in genomic transcription patterns indicates divergent cardiac responses to anoxia, with the transcriptionally driven reprogramming of cardiac function seen at 13°C being largely completed at 8°C.
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Affiliation(s)
- Kåre-Olav Stensløkken
- Section for Physiology and Cell biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- * E-mail:
| | - Stian Ellefsen
- Section for Sports Science, Department for Social Sciences, Lillehammer University College, Lillehammer, Norway
| | - Olga Vasieva
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Anthony P. Farrell
- Department of Zoology, Faculty of Land and Food Systems, University of British Colombia, Vancouver, Canada
| | - Lisa Olohan
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jarle Vaage
- Department of Emergency Medicine and Intensive Care, Institute of Clinical Medicine, Oslo University Hospital Ullevål, Oslo, Norway
| | - Göran E. Nilsson
- Section for Physiology and Cell biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Andrew R. Cossins
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Pascoal S, Carvalho G, Vasieva O, Hughes R, Cossins A, Fang Y, Ashelford K, Olohan L, Barroso C, Mendo S, Creer S. Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus. Mol Ecol 2012. [PMID: 23205577 DOI: 10.1111/mec.12137] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this 'nonmodel' species, we combined Roche 454 pyrosequencing with custom oligoarray fabrication inexpensively to both generate gene models and identify those responding to chronic tributyltin (TBT) treatment. The results supported the involvement of steroid, neuroendocrine peptide hormone dysfunction and retinoid mechanisms, but suggested additionally the involvement of putative peroxisome proliferator-activated receptor (PPAR) pathways. Application of rosiglitazone, a well-known vertebrate PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus, while TBT-induced imposex is linked to the induction of many genes and has a complex phenotype, it is likely also to be driven by PPAR-responsive pathways, hitherto not described in invertebrates. Our findings provide further evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption.
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Affiliation(s)
- Sonia Pascoal
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK
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