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Stöger R, Choi M, Begum K, Leeman G, Emes RD, Melamed P, Bentley GR. Childhood environment influences epigenetic age and methylation concordance of a CpG clock locus in British-Bangladeshi migrants. Epigenetics 2023; 18:2153511. [PMID: 36495138 PMCID: PMC9980690 DOI: 10.1080/15592294.2022.2153511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Migration from one location to another often comes with a change in environmental conditions. Here, we analysed features of DNA methylation in young, adult British-Bangladeshi women who experienced different environments during their childhoods: a) migrants, who grew up in Bangladesh with exposure to comparatively higher pathogen loads and poorer health care, and b) second-generation British-Bangladeshis, born to Bangladeshi parents, who grew up in the UK. We used buccal DNA to estimate DNA methylation-based age (DNAm age) from 14 migrants and 11 second-generation migrants, aged 18-35 years. 'AgeAccel,' a measure of DNAm age, independent of chronological age, showed that the group of women who spent their childhood in Bangladesh had higher AgeAccel (P = 0.028), compared to their UK peers. Since epigenetic clocks have been proposed to be associated with maintenance processes of epigenetic systems, we evaluated the preference for concordant DNA methylation at the luteinizing hormone/choriogonadotropin receptor (LHCGR/LHR) locus, which harbours one of the CpGs contributing to Horvath's epigenetic clock. Measurements on both strands of individual, double-stranded DNA molecules indicate higher stability of DNA methylation states at this LHCGR/LHR locus in samples of women who grew up in Bangladesh. Together, our two independent analytical approaches imply that childhood environments may induce subtle changes that are detectable long after exposure occurred, which might reflect altered activity of the epigenetic maintenance system or a difference in the proportion of cell types in buccal tissue. This exploratory work supports our earlier findings that adverse childhood environments lead to phenotypic life history trade-offs.
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Affiliation(s)
- Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Minseung Choi
- School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Gregory Leeman
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK.,Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gillian R Bentley
- Department of Anthropology, Durham University, Durham, UK.,Wolfson Research Institute for Health and Wellbeing, Durham University, Durham, UK
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Tutt DAR, Guven-Ates G, Kwong WY, Simmons R, Sang F, Silvestri G, Canedo-Ribeiro C, Handyside AH, Labrecque R, Sirard MA, Emes RD, Griffin DK, Sinclair KD. Developmental, cytogenetic and epigenetic consequences of removing complex proteins and adding melatonin during in vitro maturation of bovine oocytes. Front Endocrinol (Lausanne) 2023; 14:1280847. [PMID: 38027209 PMCID: PMC10647927 DOI: 10.3389/fendo.2023.1280847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Background In vitro maturation (IVM) of germinal vesicle intact oocytes prior to in vitro fertilization (IVF) is practiced widely in animals. In human assisted reproduction it is generally reserved for fertility preservation or where ovarian stimulation is contraindicated. Standard practice incorporates complex proteins (CP), in the form of serum and/or albumin, into IVM media to mimic the ovarian follicle environment. However, the undefined nature of CP, together with batch variation and ethical concerns regarding their origin, necessitate the development of more defined formulations. A known component of follicular fluid, melatonin, has multifaceted roles including that of a metabolic regulator and antioxidant. In certain circumstances it can enhance oocyte maturation. At this stage in development, the germinal-vesicle intact oocyte is prone to aneuploidy and epigenetic dysregulation. Objectives To determine the developmental, cytogenetic and epigenetic consequences of removing CP and including melatonin during bovine IVM. Materials and methods The study comprised a 2 x 2 factorial arrangement comparing (i) the inclusion or exclusion of CP, and (ii) the addition (100 nM) or omission of melatonin, during IVM. Cumulus-oocyte complexes (COCs) were retrieved from stimulated cycles. Following IVM and IVF, putative zygotes were cultured to Day 8 in standard media. RNAseq was performed on isolated cumulus cells, cytogenetic analyses (SNP-based algorithms) on isolated trophectoderm cells, and DNA methylation analysis (reduced representation bisulfite sequencing) on isolated cells of the inner-cell mass. Results Removal of CP during IVM led to modest reductions in blastocyst development, whilst added melatonin was beneficial in the presence but detrimental in the absence of CP. The composition of IVM media did not affect the nature or incidence of chromosomal abnormalities but cumulus-cell transcript expression indicated altered metabolism (primarily lipid) in COCs. These effects preceded the establishment of distinct metabolic and epigenetic signatures several days later in expanded and hatching blastocysts. Conclusions These findings highlight the importance of lipid, particularly sterol, metabolism by the COC during IVM. They lay the foundation for future studies that seek to develop chemically defined systems of IVM for the generation of transferrable embryos that are both cytogenetically and epigenetically normal.
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Affiliation(s)
- Desmond A. R. Tutt
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Gizem Guven-Ates
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Wing Yee Kwong
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Rob Simmons
- Paragon Veterinary Group, Carlisle, United Kingdom
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | | | - Alan H. Handyside
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | | | - Marc-André Sirard
- CRDSI, Département des Sciences Animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, QC, Canada
| | - Richard D. Emes
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Kevin D. Sinclair
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
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3
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Emes RD, Pirooznia M, Zou Q, Pellegrini M. Editorial: Insights in computational genomics: 2022. Front Genet 2023; 14:1256011. [PMID: 37554406 PMCID: PMC10406376 DOI: 10.3389/fgene.2023.1256011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
| | - Mehdi Pirooznia
- School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Pharmaceutical Data Sciences, R&D Johnson & Johnson, Boston, MA, United States
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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Lothion-Roy J, Haigh DB, Harris AE, Metzler VM, Alsaleem M, Toss MS, Kariri Y, Ntekim A, Robinson BD, Khani F, Gudas LJ, Allegrucci C, James VH, Madhusudan S, Mather M, Emes RD, Archer N, Fray RG, Rakha E, Jeyapalan JN, Rutland CS, Mongan NP, Woodcock CL. Clinical and molecular significance of the RNA m 6A methyltransferase complex in prostate cancer. Front Genet 2023; 13:1096071. [PMID: 36733939 PMCID: PMC9887525 DOI: 10.3389/fgene.2022.1096071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal mRNA modification and is dynamically regulated through distinct protein complexes that methylate, demethylate, and/or interpret the m6A modification. These proteins, and the m6A modification, are involved in the regulation of gene expression, RNA stability, splicing and translation. Given its role in these crucial processes, m6A has been implicated in many diseases, including in cancer development and progression. Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous cancer in men and recent studies support a role for m6A in PCa. Despite this, the literature currently lacks an integrated analysis of the expression of key components of the m6A RNA methyltransferase complex, both in PCa patients and in well-established cell line models. For this reason, this study used immunohistochemistry and functional studies to investigate the mechanistic and clinical significance of the METTL3, METTL14, WTAP and CBLL1 components of the m6A methyltransferase complex in PCa specimens and cell lines. Expression of METTL3 and CBLL1, but not METTL14 and WTAP, was associated with poorer PCa patient outcomes. Expression of METTL3, METTL14, WTAP and CBLL1 was higher in PCa cells compared with non-malignant prostate cells, with the highest expression seen in castrate-sensitive, androgen-responsive PCa cells. Moreover, in PCa cell lines, expression of METTL3 and WTAP was found to be androgen-regulated. To investigate the mechanistic role(s) of the m6A methyltransferase complex in PCa cells, short hairpin RNA (shRNA)-mediated knockdown coupled with next generation sequencing was used to determine the transcriptome-wide roles of METTL3, the catalytic subunit of the m6A methyltransferase complex. Functional depletion of METTL3 resulted in upregulation of the androgen receptor (AR), together with 134 AR-regulated genes. METTL3 knockdown also resulted in altered splicing, and enrichment of cell cycle, DNA repair and metabolic pathways. Collectively, this study identified the functional and clinical significance of four essential m6A complex components in PCa patient specimens and cell lines for the first time. Further studies are now warranted to determine the potential therapeutic relevance of METTL3 inhibitors in development to treat leukaemia to benefit patients with PCa.
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Affiliation(s)
- Jennifer Lothion-Roy
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Daisy B. Haigh
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Anna E. Harris
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Veronika M. Metzler
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Mansour Alsaleem
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom,Department of Applied Medical Science, Applied College, Qassim University, Qassim, Saudi Arabia
| | - Michael S. Toss
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Yousif Kariri
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom,Department of Clinical Laboratory Science, Faculty of Applied Medical Science, Shaqra University, Shaqra, Saudi Arabia
| | - Atara Ntekim
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom,Department of Radiation Oncology, University Hospital Ibadan, University of Ibadan, Ibadan, Nigeria
| | - Brian D. Robinson
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Francesca Khani
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
| | - Cinzia Allegrucci
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Victoria H. James
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Srinivasan Madhusudan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Melissa Mather
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Richard D. Emes
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nathan Archer
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Rupert G. Fray
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Emad Rakha
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Jennie N. Jeyapalan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Catrin S. Rutland
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Nigel P. Mongan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom,Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States,*Correspondence: Nigel P. Mongan, , ; Corinne L. Woodcock,
| | - Corinne L. Woodcock
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom,School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom,*Correspondence: Nigel P. Mongan, , ; Corinne L. Woodcock,
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5
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Maciel-Guerra A, Baker M, Hu Y, Wang W, Zhang X, Rong J, Zhang Y, Zhang J, Kaler J, Renney D, Loose M, Emes RD, Liu L, Chen J, Peng Z, Li F, Dottorini T. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. ISME J 2023; 17:21-35. [PMID: 36151458 PMCID: PMC9751072 DOI: 10.1038/s41396-022-01315-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.
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Affiliation(s)
- Alexandre Maciel-Guerra
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Michelle Baker
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Yue Hu
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Wei Wang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Xibin Zhang
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Jia Rong
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Yimin Zhang
- grid.440622.60000 0000 9482 4676College of Food Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018 People’s Republic of China
| | - Jing Zhang
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Jasmeet Kaler
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ UK
| | - Matthew Loose
- grid.4563.40000 0004 1936 8868DeepSeq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard D. Emes
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD UK
| | - Longhai Liu
- grid.508175.eNew Hope Liuhe Co., Ltd., Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture, Beijing 100102 and Weifang Heshengyuan Food Co. Ltd., Weifang, 262167 People’s Republic of China
| | - Junshi Chen
- grid.464207.30000 0004 4914 5614NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021 People’s Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, LE12 5RD, UK.
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6
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Baker M, Williams AD, Hooton SPT, Helliwell R, King E, Dodsworth T, María Baena-Nogueras R, Warry A, Ortori CA, Todman H, Gray-Hammerton CJ, Pritchard ACW, Iles E, Cook R, Emes RD, Jones MA, Kypraios T, West H, Barrett DA, Ramsden SJ, Gomes RL, Hudson C, Millard AD, Raman S, Morris C, Dodd CER, Kreft JU, Hobman JL, Stekel DJ. Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control. Environ Int 2022; 169:107516. [PMID: 36122459 DOI: 10.1016/j.envint.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.
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Affiliation(s)
- Michelle Baker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Alexander D Williams
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Steven P T Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Richard Helliwell
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Ruralis, University Centre Dragvoll, N-7491 Trondheim, Norway
| | - Elizabeth King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Thomas Dodsworth
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; ResChem Analytical Ltd, 8 Jubilee Parkway, Jubilee Business Park, Stores Road, Derby DE21 4BJ, UK
| | - Rosa María Baena-Nogueras
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Catherine A Ortori
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Henry Todman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Charlotte J Gray-Hammerton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Alexander C W Pritchard
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ethan Iles
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Helen West
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - David A Barrett
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Rachel L Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Chris Hudson
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Andrew D Millard
- (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sujatha Raman
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Centre for Public Awareness of Science, Australian National University, Linnaeus Way, Acton ACT 2601, Canberra, Australia
| | - Carol Morris
- School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Jan-Ulrich Kreft
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Auckland Park Kingsway Campus, Rossmore, Johannesburg, South Africa.
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7
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Tarlinton RE, Legione AR, Sarker N, Fabijan J, Meers J, McMichael L, Simmons G, Owen H, Seddon JM, Dick G, Ryder JS, Hemmatzedah F, Trott DJ, Speight N, Holmes N, Loose M, Emes RD. Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution. J Gen Virol 2022; 103. [PMID: 35762858 DOI: 10.1099/jgv.0.001749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals in the southern part of the natural range of koalas were previously thought to be either virus-free or to have only exogenous variants of KoRV with low rates of KoRV-induced disease. In contrast, animals in the northern part of their range universally have both endogenous and exogenous KoRV with very high rates of KoRV-induced disease such as lymphoma. In this study we use a combination of sequencing technologies, Illumina RNA sequencing of 'southern' (south Australian) and 'northern' (SE QLD) koalas and CRISPR enrichment and nanopore sequencing of DNA of 'southern' (South Australian and Victorian animals) to retrieve full-length loci and intregration sites of KoRV variants. We demonstrate that koalas that tested negative to the KoRV pol gene qPCR, used to detect replication-competent KoRV, are not in fact KoRV-free but harbour defective, presumably endogenous, 'RecKoRV' variants that are not fixed between animals. This indicates that these populations have historically been exposed to KoRV and raises questions as to whether these variants have arisen by chance or whether they provide a protective effect from the infectious forms of KoRV. This latter explanation would offer the intriguing prospect of being able to monitor and selectively breed for disease resistance to protect the wild koala population from KoRV-induced disease.
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Affiliation(s)
- R E Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - A R Legione
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Australia
| | - N Sarker
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - J Fabijan
- Longleat Safari Park, Durrel Wildlife Conservation Trust, UK
| | - J Meers
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - L McMichael
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - G Simmons
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - H Owen
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - J M Seddon
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - G Dick
- Longleat Safari Park, Durrel Wildlife Conservation Trust, UK
| | - J S Ryder
- Garston Veterinary Group, Somerset, UK
| | - F Hemmatzedah
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, Australia
| | - N Holmes
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - M Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
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8
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Appolinário CM, Daly JM, Emes RD, Marchi FA, Ribeiro BLD, Megid J. Gene Expression Profile Induced by Two Different Variants of Street Rabies Virus in Mice. Viruses 2022; 14:v14040692. [PMID: 35458422 PMCID: PMC9031335 DOI: 10.3390/v14040692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/30/2021] [Revised: 03/20/2022] [Accepted: 03/24/2022] [Indexed: 12/10/2022] Open
Abstract
Pathogenicity and pathology of rabies virus (RABV) varies according to the variant, but the mechanisms are not completely known. In this study, gene expression profile in brains of mice experimentally infected with RABV isolated from a human case of dog rabies (V2) or vampire bat-acquired rabies (V3) were analyzed. In total, 138 array probes associated with 120 genes were expressed differentially between mice inoculated with V2 and sham-inoculated control mice at day 10 post-inoculation. A single probe corresponding to an unannotated gene was identified in V3 versus control mice. Gene ontology (GO) analysis revealed that all of the genes upregulated in mice inoculated with V2 RABV were involved in the biological process of immune defense against pathogens. Although both variants are considered pathogenic, inoculation by the same conditions generated different gene expression results, which is likely due to differences in pathogenesis between the dog and bat RABV variants. This study demonstrated the global gene expression in experimental infection due to V3 wild-type RABV, from the vampire bat Desmodus rotundus, an important source of infection for humans, domestic animals and wildlife in Latin America.
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Affiliation(s)
- Camila M. Appolinário
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubião Júnior, s/n, CEP, Botucatu 18618-970, SP, Brazil;
- Correspondence: (C.M.A.); (J.M.)
| | - Janet M. Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (J.M.D.); (R.D.E.)
| | - Richard D. Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (J.M.D.); (R.D.E.)
| | | | - Bruna Leticia Devidé Ribeiro
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubião Júnior, s/n, CEP, Botucatu 18618-970, SP, Brazil;
| | - Jane Megid
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubião Júnior, s/n, CEP, Botucatu 18618-970, SP, Brazil;
- Correspondence: (C.M.A.); (J.M.)
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9
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Bar-Sadeh B, Amichai OE, Pnueli L, Begum K, Leeman G, Emes RD, Stöger R, Bentley GR, Melamed P. Epigenetic regulation of 5α reductase-1 underlies adaptive plasticity of reproductive function and pubertal timing. BMC Biol 2022; 20:11. [PMID: 34996447 PMCID: PMC8742331 DOI: 10.1186/s12915-021-01219-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/04/2021] [Accepted: 12/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Women facing increased energetic demands in childhood commonly have altered adult ovarian activity and shorter reproductive lifespan, possibly comprising a strategy to optimize reproductive success. Here, we sought to understand the mechanisms of early-life programming of reproductive function, by integrating analysis of reproductive tissues in an appropriate mouse model with methylation analysis of proxy tissue DNA in a well-characterized population of Bangladeshi migrants in the UK. Bangladeshi women whose childhood was in Bangladesh were found to have later pubertal onset and lower age-matched ovarian reserve than Bangladeshi women who grew-up in England. Subsequently, we aimed to explore the potential relevance to the altered reproductive phenotype of one of the genes that emerged from the screens. Results Of the genes associated with differential methylation in the Bangladeshi women whose childhood was in Bangladesh as compared to Bangladeshi women who grew up in the UK, 13 correlated with altered expression of the orthologous gene in the mouse model ovaries. These mice had delayed pubertal onset and a smaller ovarian reserve compared to controls. The most relevant of these genes for reproductive function appeared to be SRD5A1, which encodes the steroidogenic enzyme 5α reductase-1. SRD5A1 was more methylated at the same transcriptional enhancer in mice ovaries as in the women’s buccal DNA, and its expression was lower in the hypothalamus of the mice as well, suggesting a possible role in the central control of reproduction. The expression of Kiss1 and Gnrh was also lower in these mice compared to controls, and inhibition of 5α reductase-1 reduced Kiss1 and Gnrh mRNA levels and blocked GnRH release in GnRH neuronal cell cultures. Crucially, we show that inhibition of this enzyme in female mice in vivo delayed pubertal onset. Conclusions SRD5A1/5α reductase-1 responds epigenetically to the environment and its downregulation appears to alter the reproductive phenotype. These findings help to explain diversity in reproductive characteristics and how they are shaped by early-life environment and reveal novel pathways that might be targeted to mitigate health issues caused by life-history trade-offs. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01219-6.
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Affiliation(s)
- Ben Bar-Sadeh
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Or E Amichai
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Khurshida Begum
- Department of Anthropology, Durham University, Durham, DH1 3LE, UK
| | - Gregory Leeman
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Sciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | | | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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10
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Blythe MJ, Kocer A, Rubio-Roldan A, Giles T, Abakir A, Ialy-Radio C, Wheldon LM, Bereshchenko O, Bruscoli S, Kondrashov A, Drevet JR, Emes RD, Johnson AD, McCarrey JR, Gackowski D, Olinski R, Cocquet J, Garcia-Perez JL, Ruzov A. LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames. Commun Biol 2021; 4:691. [PMID: 34099857 PMCID: PMC8184969 DOI: 10.1038/s42003-021-02217-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/29/2019] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs. Although the rearrangement of DNA methylation patterns occurring in the zygote has been extensively characterized, little is known about the dynamics of DNA modifications during spermatid maturation. Here, we demonstrate that the dynamics of 5-carboxylcytosine (5caC) correlate with active transcription of LINE-1 retroelements during murine spermiogenesis. We show that the open reading frames of active and evolutionary young LINE-1s are 5caC-enriched in round spermatids and 5caC is eliminated from LINE-1s and spermiogenesis-specific genes during spermatid maturation, being simultaneously retained at promoters and introns of developmental genes. Our results reveal an association of 5caC with activity of LINE-1 retrotransposons suggesting a potential direct role for this DNA modification in fine regulation of their transcription.
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Affiliation(s)
- Martin J Blythe
- Deep Seq, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Ayhan Kocer
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
| | - Alejandro Rubio-Roldan
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Tom Giles
- Digital Research Service, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Abdulkadir Abakir
- School of Medicine, University of Nottingham, University Park, Nottingham, UK
| | - Côme Ialy-Radio
- INSERM U1016, Institut Cochin - CNRS UMR8104 - Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Lee M Wheldon
- Medical Molecular Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Oxana Bereshchenko
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - Stefano Bruscoli
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | | | - Joël R Drevet
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
| | - Richard D Emes
- Digital Research Service, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, UK. .,School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, UK.
| | - Andrew D Johnson
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | | | - Daniel Gackowski
- Department of Clinical Biochemistry, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Julie Cocquet
- INSERM U1016, Institut Cochin - CNRS UMR8104 - Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jose L Garcia-Perez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Alexey Ruzov
- School of Medicine, University of Nottingham, University Park, Nottingham, UK.
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11
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Cole J, Angyal A, Emes RD, Mitchell TJ, Dickman MJ, Dockrell DH. Pneumolysin Is Responsible for Differential Gene Expression and Modifications in the Epigenetic Landscape of Primary Monocyte Derived Macrophages. Front Immunol 2021; 12:573266. [PMID: 34046027 PMCID: PMC8145618 DOI: 10.3389/fimmu.2021.573266] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
Epigenetic modifications regulate gene expression in the host response to a diverse range of pathogens. The extent and consequences of epigenetic modification during macrophage responses to Streptococcus pneumoniae, and the role of pneumolysin, a key Streptococcus pneumoniae virulence factor, in influencing these responses, are currently unknown. To investigate this, we infected human monocyte derived macrophages (MDMs) with Streptococcus pneumoniae and addressed whether pneumolysin altered the epigenetic landscape and the associated acute macrophage transcriptional response using a combined transcriptomic and proteomic approach. Transcriptomic analysis identified 503 genes that were differentially expressed in a pneumolysin-dependent manner in these samples. Pathway analysis highlighted the involvement of transcriptional responses to core innate responses to pneumococci including modules associated with metabolic pathways activated in response to infection, oxidative stress responses and NFκB, NOD-like receptor and TNF signalling pathways. Quantitative proteomic analysis confirmed pneumolysin-regulated protein expression, early after bacterial challenge, in representative transcriptional modules associated with innate immune responses. In parallel, quantitative mass spectrometry identified global changes in the relative abundance of histone post translational modifications (PTMs) upon pneumococcal challenge. We identified an increase in the relative abundance of H3K4me1, H4K16ac and a decrease in H3K9me2 and H3K79me2 in a PLY-dependent fashion. We confirmed that pneumolysin blunted early transcriptional responses involving TNF-α and IL-6 expression. Vorinostat, a histone deacetylase inhibitor, similarly downregulated TNF-α production, reprising the pattern observed with pneumolysin. In conclusion, widespread changes in the macrophage transcriptional response are regulated by pneumolysin and are associated with global changes in histone PTMs. Modulating histone PTMs can reverse pneumolysin-associated transcriptional changes influencing innate immune responses, suggesting that epigenetic modification by pneumolysin plays a role in dampening the innate responses to pneumococci.
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Affiliation(s)
- Joby Cole
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield, Sheffield, United Kingdom
- Sheffield Teaching Hospitals NHS FT, Sheffield, United Kingdom
- The Florey Institute, University of Sheffield, Sheffield, United Kingdom
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Adrienn Angyal
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield, Sheffield, United Kingdom
| | - Richard D. Emes
- Advanced Data Analysis Centre, University of Nottingham, Nottingham, United Kingdom
- School of Veterinary Medicine and Science University of Nottingham, Nottingham, United Kingdom
| | - Tim John Mitchell
- Institute of Microbiology and Infection, University of Birmingham, Edinburgh, United Kingdom
| | - Mark J. Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - David H. Dockrell
- MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
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12
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Archer N, Egan SA, Coffey TJ, Emes RD, Addis MF, Ward PN, Blanchard AM, Leigh JA. A Paradox in Bacterial Pathogenesis: Activation of the Local Macrophage Inflammasome Is Required for Virulence of Streptococcus uberis. Pathogens 2020; 9:pathogens9120997. [PMID: 33260788 PMCID: PMC7768481 DOI: 10.3390/pathogens9120997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 10/09/2020] [Revised: 11/12/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the host–pathogen interactions during early colonisation are poorly understood. Intramammary challenge of dairy cows with S. uberis (strain 0140J) or isogenic mutants lacking the surface-anchored serine protease, SUB1154, demonstrated that virulence was dependent on the presence and correct location of this protein. Unlike the wild-type strain, the mutant lacking SUB1154 failed to elicit IL-1β from ex vivo CD14+ cells obtained from milk (bovine mammary macrophages, BMM), but this response was reinstated by complementation with recombinant SUB1154; the protein in isolation elicited no response. Production of IL-1β was ablated in the presence of various inhibitors, indicating dependency on internalisation and activation of NLRP3 and caspase-1, consistent with inflammasome activation. Similar transcriptomic changes were detected in ex vivo BMM in response to the wild-type or the SUB1154 deletion mutant, consistent with S. uberis priming BMM, enabling the SUB1154 protein to activate inflammasome maturation in a transcriptionally independent manner. These data can be reconciled in a novel model of pathogenesis in which, paradoxically, early colonisation is dependent on the innate response to the initial infection.
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Affiliation(s)
- Nathan Archer
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - Sharon A. Egan
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - Tracey J. Coffey
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - Richard D. Emes
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
| | - M. Filippa Addis
- Porto Conte Ricerche, 07041 Alghero, Italy;
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - Philip N. Ward
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK;
| | - Adam M. Blanchard
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - James A. Leigh
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
- Correspondence:
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13
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Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
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14
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Goulding LV, Yang J, Jiang Z, Zhang H, Lea D, Emes RD, Dottorini T, Pu J, Liu J, Chang KC. Thapsigargin at Non-Cytotoxic Levels Induces a Potent Host Antiviral Response that Blocks Influenza A Virus Replication. Viruses 2020; 12:v12101093. [PMID: 32992478 PMCID: PMC7600819 DOI: 10.3390/v12101093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 09/01/2020] [Revised: 09/21/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
Influenza A virus is a major global pathogen of humans, and there is an unmet need for effective antivirals. Current antivirals against influenza A virus directly target the virus and are vulnerable to mutational resistance. Harnessing an effective host antiviral response is an attractive alternative. We show that brief exposure to low, non-toxic doses of thapsigargin (TG), an inhibitor of the sarcoplasmic/endoplasmic reticulum (ER) Ca2+ ATPase pump, promptly elicits an extended antiviral state that dramatically blocks influenza A virus production. Crucially, oral administration of TG protected mice against lethal virus infection and reduced virus titres in the lungs of treated mice. TG-induced ER stress unfolded protein response appears as a key driver responsible for activating a spectrum of host antiviral defences that include an enhanced type I/III interferon response. Our findings suggest that TG is potentially a viable host-centric antiviral for the treatment of influenza A virus infection without the inherent problem of drug resistance.
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Affiliation(s)
- Leah V. Goulding
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK; (L.V.G.); (J.Y.); (R.D.E.); (T.D.)
| | - Jiayun Yang
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK; (L.V.G.); (J.Y.); (R.D.E.); (T.D.)
| | - Zhimin Jiang
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China; (Z.J.); (H.Z.); (J.P.); (J.L.)
| | - Hongyu Zhang
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China; (Z.J.); (H.Z.); (J.P.); (J.L.)
| | - Daniel Lea
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK;
| | - Richard D. Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK; (L.V.G.); (J.Y.); (R.D.E.); (T.D.)
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK;
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK; (L.V.G.); (J.Y.); (R.D.E.); (T.D.)
| | - Juan Pu
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China; (Z.J.); (H.Z.); (J.P.); (J.L.)
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, China; (Z.J.); (H.Z.); (J.P.); (J.L.)
| | - Kin-Chow Chang
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK; (L.V.G.); (J.Y.); (R.D.E.); (T.D.)
- Correspondence:
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15
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Fabijan J, Sarker N, Speight N, Owen H, Meers J, Simmons G, Seddon J, Emes RD, Tarlinton R, Hemmatzadeh F, Woolford L, Trott DJ. Pathological Findings in Koala Retrovirus-positive Koalas (Phascolarctos cinereus) from Northern and Southern Australia. J Comp Pathol 2020; 176:50-66. [PMID: 32359636 DOI: 10.1016/j.jcpa.2020.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 01/05/2023]
Abstract
Koala retrovirus (KoRV) infection shows differences in prevalence and load between northern and southern Australian koala populations; however, the effect of this on diseases such as lymphoma and chlamydial disease is unclear. This study compared clinicopathological findings, haematology and splenic lymphoid area of KoRV-positive koalas from northern (Queensland [Qld], n = 67) and southern (South Australia [SA], n = 92) populations in order to provide further insight into KoRV pathogenesis. Blood was collected for routine haematology and for measurement of KoRV proviral load by quantitative polymerase chain reaction (qPCR). Plasma samples were assessed for KoRV viral load by reverse transcriptase qPCR and conjunctival and cloacal swabs were collected for measurement of the load of Chlamydia pecorum (qPCR). During necropsy examination, spleen was collected for lymphoid area analysis. Lymphoma was morphologically similar between the populations and occurred in koalas with the highest KoRV proviral and viral loads. Severe ocular chlamydial disease was observed in both populations, but urinary tract disease was more severe in Qld, despite similar C. pecorum loads. No associations between KoRV and chlamydial disease severity or load were observed, except in SA where viral load correlated positively with chlamydial disease severity. In both populations, proviral and viral loads correlated positively with lymphocyte and metarubricyte counts and correlated negatively with erythrocyte and neutrophil counts. Splenic lymphoid area was correlated positively with viral load. This study has shown further evidence for KoRV-induced oncogenesis and highlighted that lymphocytes and splenic lymphoid tissue may be key sites for KoRV replication. However, KoRV infection appears to be highly complex and continued investigation is required to fully understand its pathogenesis.
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Affiliation(s)
- J Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia.
| | - N Sarker
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - H Owen
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - J Meers
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - G Simmons
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - J Seddon
- School of Veterinary Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - R Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - F Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
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16
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Abakir A, Giles TC, Cristini A, Foster JM, Dai N, Starczak M, Rubio-Roldan A, Li M, Eleftheriou M, Crutchley J, Flatt L, Young L, Gaffney DJ, Denning C, Dalhus B, Emes RD, Gackowski D, Corrêa IR, Garcia-Perez JL, Klungland A, Gromak N, Ruzov A. N 6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat Genet 2019; 52:48-55. [PMID: 31844323 PMCID: PMC6974403 DOI: 10.1038/s41588-019-0549-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [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: 01/23/2019] [Accepted: 11/13/2019] [Indexed: 11/21/2022]
Abstract
R-loops are nucleic acid structures formed by an RNA:DNA hybrid and unpaired single stranded DNA that represent a source of genomic instability in mammalian cells1–4. Here we show that N6-methyladenosine (m6A) modification, contributing to different aspects of mRNA metabolism5, 6, is detectable on the majority of RNA:DNA hybrids in human pluripotent stem cells (hPSCs). We demonstrate that m6A-containing R-loops accumulate during G2/M and are depleted at G0/G1 phases of the cell cycle and that the m6A reader promoting mRNA degradation, YTHDF27, interacts with R-loops-enriched loci in dividing cells. Consequently, YTHDF2 knockout leads to increased R-loop levels, cell growth retardation and accumulation of γH2AX, a marker for DNA double-strand breaks, in mammalian cells. Our results suggest that m6A regulates accumulation of R-loops, implying a role for this modification in safeguarding genomic stability.
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Affiliation(s)
- Abdulkadir Abakir
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK
| | - Tom C Giles
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington, UK.,Digital Research Service, University of Nottingham, Sutton Bonington, UK
| | - Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Nan Dai
- New England Biolabs, Inc., Ipswich, MA, USA
| | - Marta Starczak
- Department of Clinical Biochemistry, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Alejandro Rubio-Roldan
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Miaomiao Li
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Maria Eleftheriou
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK
| | - James Crutchley
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK
| | - Luke Flatt
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK
| | - Lorraine Young
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK
| | | | - Chris Denning
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK
| | - Bjørn Dalhus
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Medical Biochemistry, University of Oslo, Oslo, Norway
| | - Richard D Emes
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington, UK.,School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | | | - Jose L Garcia-Perez
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway. .,Department of Molecular Medicine, University of Oslo, Oslo, Norway.
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Alexey Ruzov
- Department of Stem Cell Biology, University of Nottingham, Nottingham, UK.
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17
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Geoghegan IA, Emes RD, Archer DB, Avery SV. Method for RNA extraction and transcriptomic analysis of single fungal spores. MethodsX 2019; 7:50-55. [PMID: 31908984 PMCID: PMC6938798 DOI: 10.1016/j.mex.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 09/26/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Transcriptomic analysis of single cells has been increasingly in demand in recent years, thanks to technological and methodological advances as well as growing recognition of the importance of individuals in biological systems. However, the majority of these studies have been performed in mammalian cells, due to their ease of lysis and high RNA content. No single cell transcriptomic analysis has yet been described in microbial spores, even though it is known that heterogeneity at the phenotype level exists among individual spores. Transcriptomic analysis of single spores is challenging, in part due to the physically robust nature of the spore wall. This precludes the use of methods commonly used for mammalian cells. Here, we describe a simple method for extraction and amplification of transcripts from single fungal conidia (asexual spores), and its application in single-cell transcriptomics studies. The method can also be used for studies of small numbers of fungal conidia, which may be necessary in the case of limited sample availability, low-abundance transcripts or interest in small subpopulations of conidia. •The method allows detection of transcripts from single conidia of Aspergillus niger•The method allows detection of genomic DNA from single conidia of Aspergillus niger.
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Affiliation(s)
- Ivey A. Geoghegan
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard D. Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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18
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Bewley MA, Budd RC, Ryan E, Cole J, Collini P, Marshall J, Kolsum U, Beech G, Emes RD, Tcherniaeva I, Berbers GAM, Walmsley SR, Donaldson G, Wedzicha JA, Kilty I, Rumsey W, Sanchez Y, Brightling CE, Donnelly LE, Barnes PJ, Singh D, Whyte MKB, Dockrell DH. Opsonic Phagocytosis in Chronic Obstructive Pulmonary Disease Is Enhanced by Nrf2 Agonists. Am J Respir Crit Care Med 2019; 198:739-750. [PMID: 29547002 DOI: 10.1164/rccm.201705-0903oc] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RATIONALE Previous studies have identified defects in bacterial phagocytosis by alveolar macrophages (AMs) in patients with chronic obstructive pulmonary disease (COPD), but the mechanisms and clinical consequences remain incompletely defined. OBJECTIVES To examine the effect of COPD on AM phagocytic responses and identify the mechanisms, clinical consequences, and potential for therapeutic manipulation of these defects. METHODS We isolated AMs and monocyte-derived macrophages (MDMs) from a cohort of patients with COPD and control subjects within the Medical Research Council COPDMAP consortium and measured phagocytosis of bacteria in relation to opsonic conditions and clinical features. MEASUREMENTS AND MAIN RESULTS COPD AMs and MDMs have impaired phagocytosis of Streptococcus pneumoniae. COPD AMs have a selective defect in uptake of opsonized bacteria, despite the presence of antipneumococcal antibodies in BAL, not observed in MDMs or healthy donor AMs. AM defects in phagocytosis in COPD are significantly associated with exacerbation frequency, isolation of pathogenic bacteria, and health-related quality-of-life scores. Bacterial binding and initial intracellular killing of opsonized bacteria in COPD AMs was not reduced. COPD AMs have reduced transcriptional responses to opsonized bacteria, such as cellular stress responses that include transcriptional modules involving antioxidant defenses and Nrf2 (nuclear factor erythroid 2-related factor 2)-regulated genes. Agonists of the cytoprotective transcription factor Nrf2 (sulforaphane and compound 7) reverse defects in phagocytosis of S. pneumoniae and nontypeable Haemophilus influenzae by COPD AMs. CONCLUSIONS Patients with COPD have clinically relevant defects in opsonic phagocytosis by AMs, associated with impaired transcriptional responses to cellular stress, which are reversed by therapeutic targeting with Nrf2 agonists.
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Affiliation(s)
- Martin A Bewley
- 1 Department of Infection, Immunity and Cardiovascular Disease and.,2 The Florey Institute for Host-Pathogen Interactions, University of Sheffield Medical School, Sheffield, United Kingdom
| | - Richard C Budd
- 1 Department of Infection, Immunity and Cardiovascular Disease and.,2 The Florey Institute for Host-Pathogen Interactions, University of Sheffield Medical School, Sheffield, United Kingdom.,3 Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Eilise Ryan
- 4 Department of Respiratory Medicine.,5 MRC Centre for Inflammation Research, and
| | - Joby Cole
- 1 Department of Infection, Immunity and Cardiovascular Disease and.,2 The Florey Institute for Host-Pathogen Interactions, University of Sheffield Medical School, Sheffield, United Kingdom.,3 Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Paul Collini
- 1 Department of Infection, Immunity and Cardiovascular Disease and.,2 The Florey Institute for Host-Pathogen Interactions, University of Sheffield Medical School, Sheffield, United Kingdom.,3 Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Jennifer Marshall
- 5 MRC Centre for Inflammation Research, and.,6 Department of Infection Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Umme Kolsum
- 7 Medicines Evaluation Unit, University of Manchester, Manchester, United Kingdom.,8 University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Gussie Beech
- 7 Medicines Evaluation Unit, University of Manchester, Manchester, United Kingdom.,8 University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Richard D Emes
- 9 School of Veterinary Medicine and Science and.,10 Advanced Data Analysis Centre, University of Nottingham, United Kingdom
| | - Irina Tcherniaeva
- 11 Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Utrecht, the Netherlands
| | - Guy A M Berbers
- 11 Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Utrecht, the Netherlands
| | - Sarah R Walmsley
- 4 Department of Respiratory Medicine.,5 MRC Centre for Inflammation Research, and
| | - Gavin Donaldson
- 12 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jadwiga A Wedzicha
- 12 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Iain Kilty
- 13 Pfizer Inc., Cambridge, Massachusetts
| | - William Rumsey
- 14 Stress and Repair Discovery Performance Unit, Respiratory Therapy Area, GSK, King of Prussia, Pennsylvania; and
| | - Yolanda Sanchez
- 14 Stress and Repair Discovery Performance Unit, Respiratory Therapy Area, GSK, King of Prussia, Pennsylvania; and
| | | | - Louise E Donnelly
- 12 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Peter J Barnes
- 12 National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Dave Singh
- 7 Medicines Evaluation Unit, University of Manchester, Manchester, United Kingdom.,8 University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Moira K B Whyte
- 4 Department of Respiratory Medicine.,5 MRC Centre for Inflammation Research, and
| | - David H Dockrell
- 5 MRC Centre for Inflammation Research, and.,6 Department of Infection Medicine, University of Edinburgh, Edinburgh, United Kingdom
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19
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Awuah D, Alobaid M, Latif A, Salazar F, Emes RD, Ghaemmaghami AM. The Cross-Talk between miR-511-3p and C-Type Lectin Receptors on Dendritic Cells Affects Dendritic Cell Function. J Immunol 2019; 203:148-157. [PMID: 31118225 DOI: 10.4049/jimmunol.1801108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 04/29/2019] [Indexed: 12/20/2022]
Abstract
MicroRNAs are small, noncoding RNAs that function as posttranscriptional modulators of gene expression by binding target mRNAs and inhibiting translation. They are therefore crucial regulators of several biological as well as immunological events. Recently, miR-511-3p has been implicated in the development and differentiation of APCs, such as dendritic cells (DCs), and regulating several human diseases. Interestingly, miR-511-3p is embedded within the human MRC1 gene that encodes the mannose receptor. In this study, we sought to examine the impact of miR-511-3p up- or downregulation on human DC surface phenotype, cytokine profile, immunogenicity (using IDO activity as a surrogate), and downstream T cell polarization. Using gene silencing and a selection of microRNA mimics, we could successfully suppress or induce the expression of miR-511-3p in DCs. Consequently, we show for the first time, to our knowledge, that inhibition and/or overexpression of miR-511-3p has opposing effects on the expression levels of two key C-type lectin receptors, namely the mannose receptor and DC-specific ICAM 3 nonintegrin at protein and mRNA levels, thereby affecting C-type lectin receptor-induced modulation of IDO activity in DCs. Furthermore, we show that downregulation of miR-511-3p drives an anti-inflammatory DC response characterized by IL-10 production. Interestingly, the miR-511-3plow DCs also promoted IL-4 secretion and suppressed IL-17 in cocultures with autologous T cells. Together, our data highlight the potential role of miR-511 in regulating DC function and downstream events leading to Th polarization and immune modulation.
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Affiliation(s)
- Dennis Awuah
- Division of Immunology, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Meshal Alobaid
- Division of Immunology, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Arsalan Latif
- Division of Immunology, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Fabián Salazar
- Division of Immunology, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire LE12 5NT, United Kingdom; and.,Advanced Data Analysis Centre, University of Nottingham, Leicestershire LE12 5NT, United Kingdom
| | - Amir M Ghaemmaghami
- Division of Immunology, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
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20
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Abstract
Our understanding of the expanded genetic alphabet has been growing rapidly over the last two decades, and many of these developments came more than 80 years after the original discovery of a modified guanine in tuberculosis DNA. These new understandings, leading to the field of epigenetics, have led to exciting new fundamental and applied knowledge and to the development of novel classes of drugs exploiting this new biology. The number of methyl modifications to RNA is about seven times greater than those found on DNA, and our ability to interrogate these enigmatic nucleobases has lagged significantly until recent years as an explosion in technologies and understanding has revealed the roles and regulation of RNA methylation in several fundamental and disease-associated biological processes. Here, we outline how the technology has evolved and which strategies are commonly used in the modern epitranscriptomics revolution and give a foundation in the understanding and application of the rich variety of these methods to novel biological questions.
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Affiliation(s)
- Nigel P. Mongan
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Department of Pharmacology, Weill Cornell Medical Center, New York, NY, USA
| | - Richard D. Emes
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Advanced Data Analysis Centre , University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Nathan Archer
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
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21
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Izquierdo A, Fahrenberger M, Persampieri T, Benedict MQ, Giles T, Catteruccia F, Emes RD, Dottorini T. Evolution of gene expression levels in the male reproductive organs of Anopheles mosquitoes. Life Sci Alliance 2019; 2:e201800191. [PMID: 30623175 PMCID: PMC6315087 DOI: 10.26508/lsa.201800191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/12/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Modifications in gene expression determine many of the phenotypic differentiations between closely related species. This is particularly evident in reproductive tissues, where evolution of genes is more rapid, facilitating the appearance of distinct reproductive characteristics which may lead to species isolation and phenotypic variation. Large-scale, comparative analyses of transcript expression levels have been limited until recently by lack of inter-species data mining solutions. Here, by combining expression normalisation across lineages, multivariate statistical analysis, evolutionary rate, and protein-protein interaction analysis, we investigate ortholog transcripts in the male accessory glands and testes across five closely related species in the Anopheles gambiae complex. We first demonstrate that the differentiation by transcript expression is consistent with the known Anopheles phylogeny. Then, through clustering, we discover groups of transcripts with tissue-dependent expression patterns conserved across lineages, or lineage-dependent patterns conserved across tissues. The strongest associations with reproductive function, transcriptional regulatory networks, protein-protein subnetworks, and evolutionary rate are found for the groups of transcripts featuring large expression differences in lineage or tissue-conserved patterns.
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Affiliation(s)
- Abril Izquierdo
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Martin Fahrenberger
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Tania Persampieri
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Mark Q Benedict
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Tom Giles
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Richard D Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK.,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
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22
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Cong W, Dottorini T, Khan F, Emes RD, Zhang FK, Zhou CX, He JJ, Zhang XX, Elsheikha HM, Zhu XQ. Acute Toxoplasma Gondii Infection in Cats Induced Tissue-Specific Transcriptional Response Dominated by Immune Signatures. Front Immunol 2018; 9:2403. [PMID: 30405608 PMCID: PMC6202952 DOI: 10.3389/fimmu.2018.02403] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 06/21/2018] [Accepted: 09/28/2018] [Indexed: 12/19/2022] Open
Abstract
RNA-sequencing was used to detect transcriptional changes in six tissues of cats, seven days after T. gondii infection. A total of 737 genes were differentially expressed (DEGs), of which 410 were up-regulated and 327 were down-regulated. The liver exhibited 151 DEGs, lung (149 DEGs), small intestine (130 DEGs), heart (123 DEGs), brain (104 DEGs), and spleen (80 DEGs)-suggesting tissue-specific transcriptional patterns. Gene ontology and KEGG analyses identified DEGs enriched in immune pathways, such as cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, NOD-like receptor signaling pathway, NF-kappa B signaling pathway, MAPK signaling pathway, T cell receptor signaling pathway, and the cytosolic DNA sensing pathway. C-X-C motif chemokine 10 (CXCL10) was involved in most of the immune-related pathways. PI3K/Akt expression was down-regulated in all tissues, except the spleen. The genes for phosphatase, indoleamine 2,3-dioxygenase, Hes Family BHLH Transcription Factor 1, and guanylate-binding protein 5, playing various roles in immune defense, were co-expressed across various feline tissues. Multivariate K-means clustering analysis produced seven gene clusters featuring similar gene expression patterns specific to individual tissues, with lung tissue cluster having the largest number of DEGs. These findings suggest the presence of a broad immune defense mechanism across various tissues in cats against acute T. gondii infection.
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Affiliation(s)
- Wei Cong
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Department of Marine Engineering, Marine College, Shandong University, Weihai, China
| | - Tania Dottorini
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham, Loughborough, United Kingdom
| | - Faraz Khan
- Advanced Data Analysis Centre, University of Nottingham, Loughborough, United Kingdom
| | - Richard D Emes
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham, Loughborough, United Kingdom
| | - Fu-Kai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chun-Xue Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiao-Xuan Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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23
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Blanchard AM, Jolley KA, Maiden MCJ, Coffey TJ, Maboni G, Staley CE, Bollard NJ, Warry A, Emes RD, Davies PL, Tötemeyer S. The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus. Front Microbiol 2018; 9:551. [PMID: 29628922 PMCID: PMC5876313 DOI: 10.3389/fmicb.2018.00551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 12/04/2017] [Accepted: 03/12/2018] [Indexed: 11/17/2022] Open
Abstract
Dichelobacter nodosus (D. nodosus) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques. Multilocus sequence typing (MLST) measures nucleotide variations within several loci with slow accumulation of variation to enable the designation of allele numbers to determine a sequence type. The usage of whole genome sequence data enables the application of MLST, but also core and whole genome MLST for higher levels of strain discrimination with a negligible increase in experimental cost. An MLST database was developed alongside a seven loci scheme using publically available whole genome data from the sequence read archive. Sequence type designation and strain discrimination was compared to previously published data to ensure reproducibility. Multiple D. nodosus isolates from U.K. farms were directly compared to populations from other countries. The U.K. isolates define new clades within the global population of D. nodosus and predominantly consist of serogroups A, B and H, however serogroups C, D, E, and I were also found. The scheme is publically available at https://pubmlst.org/dnodosus/.
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Tracey J Coffey
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Grazieli Maboni
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Ceri E Staley
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Nicola J Bollard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Andrew Warry
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham, Nottingham, United Kingdom
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham, Nottingham, United Kingdom
| | - Peers L Davies
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
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24
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Sarker N, Fabijan J, Emes RD, Hemmatzadeh F, Meers J, Moreton J, Owen H, Seddon JM, Simmons G, Speight N, Trott D, Woolford L, Tarlinton RE. Identification of stable reference genes for quantitative PCR in koalas. Sci Rep 2018; 8:3364. [PMID: 29463845 PMCID: PMC5820254 DOI: 10.1038/s41598-018-21723-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 11/17/2017] [Accepted: 02/09/2018] [Indexed: 11/17/2022] Open
Abstract
To better understand host and immune response to diseases, gene expression studies require identification of reference genes with stable expression for accurate normalisation. This study describes the identification and testing of reference genes with stable expression profiles in koala lymph node tissues across two genetically distinct koala populations. From the 25 most stable genes identified in transcriptome analysis, 11 genes were selected for verification using reverse transcription quantitative PCR, in addition to the commonly used ACTB and GAPDH genes. The expression data were analysed using stable genes statistical software - geNorm, BestKeeper, NormFinder, the comparative ΔCt method and RefFinder. All 13 genes showed relative stability in expression in koala lymph node tissues, however Tmem97 and Hmg20a were identified as the most stable genes across the two koala populations.
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Affiliation(s)
- N Sarker
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - J Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom.,Advanced Data Analysis Centre (ADAC), University of Nottingham, Sutton Bonington, United Kingdom
| | - F Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - J Meers
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - J Moreton
- Advanced Data Analysis Centre (ADAC), University of Nottingham, Sutton Bonington, United Kingdom
| | - H Owen
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - J M Seddon
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - G Simmons
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - D Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - L Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - R E Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom.
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25
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Wu P, Farrell WE, Haworth KE, Emes RD, Kitchen MO, Glossop JR, Hanna FW, Fryer AA. Maternal genome-wide DNA methylation profiling in gestational diabetes shows distinctive disease-associated changes relative to matched healthy pregnancies. Epigenetics 2018; 13:122-128. [PMID: 27019060 DOI: 10.1080/15592294.2016.1166321] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Several recent reports have described associations between gestational diabetes (GDM) and changes to the epigenomic landscape where the DNA samples were derived from either cord or placental sources. We employed genome-wide 450K array analysis to determine changes to the epigenome in a unique cohort of maternal blood DNA from 11 pregnant women prior to GDM development relative to matched controls. Hierarchical clustering segregated the samples into 2 distinct clusters comprising GDM and healthy pregnancies. Screening identified 100 CpGs with a mean β-value difference of ≥0.2 between cases and controls. Using stringent criteria, 5 CpGs (within COPS8, PIK3R5, HAAO, CCDC124, and C5orf34 genes) demonstrated potentials to be clinical biomarkers as revealed by differential methylation in 8 of 11 women who developed GDM relative to matched controls. We identified, for the first time, maternal methylation changes prior to the onset of GDM that may prove useful as biomarkers for early therapeutic intervention.
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Affiliation(s)
- Pensee Wu
- a Institute for Science and Technology in Medicine , Keele University, Guy Hilton Research Center , Staffordshire , UK.,b Academic Unit of Obstetrics and Gynecology, University Hospital of North Midlands NHS Trust , Stoke-on-Trent, Staffordshire , UK
| | - William E Farrell
- a Institute for Science and Technology in Medicine , Keele University, Guy Hilton Research Center , Staffordshire , UK
| | - Kim E Haworth
- a Institute for Science and Technology in Medicine , Keele University, Guy Hilton Research Center , Staffordshire , UK
| | - Richard D Emes
- c School of Veterinary Medicine and Science, University of Nottingham , Leicestershire , UK.,d Advanced Data Analysis Center , University of Nottingham , Leicestershire , UK
| | - Mark O Kitchen
- a Institute for Science and Technology in Medicine , Keele University, Guy Hilton Research Center , Staffordshire , UK
| | - John R Glossop
- a Institute for Science and Technology in Medicine , Keele University, Guy Hilton Research Center , Staffordshire , UK.,e Haywood Rheumatology Center, Haywood Hospital , Staffordshire , UK
| | - Fahmy W Hanna
- f Department of Diabetes and Endocrinology , University Hospital of North Midlands NHS Trust , Stoke-on-Trent, Staffordshire , UK
| | - Anthony A Fryer
- a Institute for Science and Technology in Medicine , Keele University, Guy Hilton Research Center , Staffordshire , UK
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26
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Kitchen MO, Bryan RT, Emes RD, Luscombe CJ, Cheng KK, Zeegers MP, James ND, Gommersall LM, Fryer AA. HumanMethylation450K Array-Identified Biomarkers Predict Tumour Recurrence/Progression at Initial Diagnosis of High-risk Non-muscle Invasive Bladder Cancer. Biomark Cancer 2018; 10:1179299X17751920. [PMID: 29343995 PMCID: PMC5764140 DOI: 10.1177/1179299x17751920] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 11/15/2017] [Indexed: 01/03/2023]
Abstract
Background: High-risk non-muscle invasive bladder cancer (HR-NMIBC) is a clinically unpredictable disease. Despite clinical risk estimation tools, many patients are undertreated with intra-vesical therapies alone, whereas others may be over-treated with early radical surgery. Molecular biomarkers, particularly DNA methylation, have been reported as predictive of tumour/patient outcomes in numerous solid organ and haematologic malignancies; however, there are few reports in HR-NMIBC and none using genome-wide array assessment. We therefore sought to identify novel DNA methylation markers of HR-NMIBC clinical outcomes that might predict tumour behaviour at initial diagnosis and help guide patient management. Patients and methods: A total of 21 primary initial diagnosis HR-NMIBC tumours were analysed by Illumina HumanMethylation450 BeadChip arrays and subsequently bisulphite Pyrosequencing. In all, 7 had not recurred at 1 year after resection and 14 had recurred and/or progressed despite intra-vesical BCG. A further independent cohort of 32 HR-NMIBC tumours (17 no recurrence and 15 recurrence and/or progression despite BCG) were also assessed by bisulphite Pyrosequencing. Results: Array analyses identified 206 CpG loci that segregated non-recurrent HR-NMIBC tumours from clinically more aggressive recurrence/progression tumours. Hypermethylation of CpG cg11850659 and hypomethylation of CpG cg01149192 in combination predicted HR-NMIBC recurrence and/or progression within 1 year of diagnosis with 83% sensitivity, 79% specificity, and 83% positive and 79% negative predictive values. Conclusions: This is the first genome-wide DNA methylation analysis of a unique HR-NMIBC tumour cohort encompassing known 1-year clinical outcomes. Our analyses identified potential novel epigenetic markers that could help guide individual patient management in this clinically unpredictable disease.
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Affiliation(s)
- Mark O Kitchen
- Institute for Science and Technology in Medicine, Keele University, London, UK.,Urology Department, University Hospitals of North Midlands NHS Trust, Stafford, UK
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard D Emes
- Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK
| | | | - K K Cheng
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Maurice P Zeegers
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.,Department of Complex Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.,NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands.,CAPHRI School for Public Health and Primary Care, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | - Lyndon M Gommersall
- Urology Department, University Hospitals of North Midlands NHS Trust, Stafford, UK
| | - Anthony A Fryer
- Institute for Science and Technology in Medicine, Keele University, London, UK
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27
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Al-Mayyahi RS, Sterio LD, Connolly JB, Adams CF, Al-Tumah WA, Sen J, Emes RD, Hart SR, Chari DM. A proteomic investigation into mechanisms underpinning corticosteroid effects on neural stem cells. Mol Cell Neurosci 2018; 86:30-40. [DOI: 10.1016/j.mcn.2017.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 12/13/2022] Open
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28
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Singh S, Awuah D, Rostam HM, Emes RD, Kandola NK, Onion D, Htwe SS, Rajchagool B, Cha BH, Kim D, Tighe PJ, Vrana NE, Khademhosseini A, Ghaemmaghami A. Unbiased Analysis of the Impact of Micropatterned Biomaterials on Macrophage Behavior Provides Insights beyond Predefined Polarization States. ACS Biomater Sci Eng 2017; 3:969-978. [PMID: 33429569 DOI: 10.1021/acsbiomaterials.7b00104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Macrophages are master regulators of immune responses toward implanted biomaterials. The activation state adopted by macrophages in response to biomaterials determines their own phenotype and function as well as those of other resident and infiltrating immune and nonimmune cells in the area. A wide spectrum of macrophage activation states exists, with M1 (pro-inflammatory) and M2 (anti-inflammatory) representing either ends of the spectrum. In biomaterials research, cell-instructive surfaces that favor or induce M2 macrophages have been considered as beneficial due to the anti-inflammatory and pro-regenerative properties of these cells. In this study, we used a gelatin methacryloyl (GelMA) hydrogel platform to determine whether micropatterned surfaces can modulate the phenotype and function of human macrophages. The effect of microgrooves/ridges and micropillars on macrophage phenotype, function, and gene expression profile were assessed using conventional methods (morphology, cytokine profile, surface marker expression, phagocytosis) and gene microarrays. Our results demonstrated that micropatterns did induce distinct gene expression profiles in human macrophages cultured on microgrooves/ridges and micropillars. Significant changes were observed in genes related to primary metabolic processes such as transcription, translation, protein trafficking, DNA repair, and cell survival. However, interestingly conventional phenotyping methods, relying on surface marker expression and cytokine profile, were not able to distinguish between the different conditions, and indicated no clear shift in cell activation towards M1 or M2 phenotypes. This highlights the limitations of studying the effect of different physicochemical conditions on macrophages by solely relying on conventional markers that are primarily developed to differentiate between cytokine polarized M1 and M2 macrophages. We therefore propose the adoption of unbiased screening methods in determining macrophage responses to biomaterials. Our data clearly show that the exclusive use of conventional markers and methods for determining macrophage activation status could lead to missed opportunities for understanding and exploiting macrophage responses to biomaterials.
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Affiliation(s)
- Sonali Singh
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Dennis Awuah
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Hassan M Rostam
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | | | - Navrohit K Kandola
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - David Onion
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Su Su Htwe
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Buddharaksa Rajchagool
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Byung-Hyun Cha
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Duckjin Kim
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick J Tighe
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Nihal E Vrana
- INSERM UMR 1121, 11 rue Humann, 67085 Strasbourg, France.,Protip Medical, 8 Place de l'Hôpital, 67000 Strasbourg, France
| | - Ali Khademhosseini
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Amir Ghaemmaghami
- Division of Immunology, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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29
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Olcese C, Patel MP, Shoemark A, Kiviluoto S, Legendre M, Williams HJ, Vaughan CK, Hayward J, Goldenberg A, Emes RD, Munye MM, Dyer L, Cahill T, Bevillard J, Gehrig C, Guipponi M, Chantot S, Duquesnoy P, Thomas L, Jeanson L, Copin B, Tamalet A, Thauvin-Robinet C, Papon JF, Garin A, Pin I, Vera G, Aurora P, Fassad MR, Jenkins L, Boustred C, Cullup T, Dixon M, Onoufriadis A, Bush A, Chung EMK, Antonarakis SE, Loebinger MR, Wilson R, Armengot M, Escudier E, Hogg C, Amselem S, Sun Z, Bartoloni L, Blouin JL, Mitchison HM. X-linked primary ciliary dyskinesia due to mutations in the cytoplasmic axonemal dynein assembly factor PIH1D3. Nat Commun 2017; 8:14279. [PMID: 28176794 PMCID: PMC5309803 DOI: 10.1038/ncomms14279] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/15/2016] [Indexed: 01/06/2023] Open
Abstract
By moving essential body fluids and molecules, motile cilia and flagella govern respiratory mucociliary clearance, laterality determination and the transport of gametes and cerebrospinal fluid. Primary ciliary dyskinesia (PCD) is an autosomal recessive disorder frequently caused by non-assembly of dynein arm motors into cilia and flagella axonemes. Before their import into cilia and flagella, multi-subunit axonemal dynein arms are thought to be stabilized and pre-assembled in the cytoplasm through a DNAAF2–DNAAF4–HSP90 complex akin to the HSP90 co-chaperone R2TP complex. Here, we demonstrate that large genomic deletions as well as point mutations involving PIH1D3 are responsible for an X-linked form of PCD causing disruption of early axonemal dynein assembly. We propose that PIH1D3, a protein that emerges as a new player of the cytoplasmic pre-assembly pathway, is part of a complementary conserved R2TP-like HSP90 co-chaperone complex, the loss of which affects assembly of a subset of inner arm dyneins. Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disease resulting in reduced mucus clearance and impaired lung function. Here, the authors show that mutations in PIH1D3 are responsible for an X-linked form of PCD, affecting assembly of a subset of inner arm dyneins.
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Affiliation(s)
- Chiara Olcese
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Life Sciences and Biotechnologies, University of Ferrara, 46-44121 Ferrara, Italy
| | - Mitali P Patel
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Amelia Shoemark
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | - Santeri Kiviluoto
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Marie Legendre
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Hywel J Williams
- GOSgene, Genetics and Genomic Medicine Programme, University College London (UCL) Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Cara K Vaughan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Biological Sciences, Malet Street, London, WC1E 7HX, UK
| | - Jane Hayward
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Alice Goldenberg
- Service de Génétique, CHU de Rouen, INSERM U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Mustafa M Munye
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Laura Dyer
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Thomas Cahill
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | - Jeremy Bevillard
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, CH-1211 Geneva, Switzerland
| | - Sandra Chantot
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Philippe Duquesnoy
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Lucie Thomas
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Ludovic Jeanson
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Bruno Copin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Aline Tamalet
- Service de Pneumologie Pédiatrique, Centre National de Référence des Maladies Respiratoires Rares, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Christel Thauvin-Robinet
- Centre de génétique, CHU Dijon Bourgogne, Équipe EA4271 GAD, Université de Bourgogne, Hôpital François Mitterrand, 21000 Dijon, France
| | - Jean-François Papon
- Service d'Oto-Rhino-Laryngologie et de Chirurgie Cervico-Maxillo-Faciale, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre 94275, France
| | - Antoine Garin
- Service d'Oto-Rhino-Laryngologie et de Chirurgie Cervico-Maxillo-Faciale, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre 94275, France
| | - Isabelle Pin
- Pédiatrie, CHU Grenoble Alpes, INSERM U 1209, Institut for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Gabriella Vera
- Service de Génétique, CHU de Rouen, INSERM U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Paul Aurora
- Department of Paediatric Respiratory Medicine, Great Ormond Street Hospital for Children, London WC1N 3JH, UK.,Department of Respiratory, Critical Care and Anaesthesia Unit, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK.,Human Genetics Department, Medical Research Institute, Alexandria University, El-Hadra Alexandria 21561, Egypt
| | - Lucy Jenkins
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, Queen Square, London WC1N 3BH, UK
| | - Christopher Boustred
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, Queen Square, London WC1N 3BH, UK
| | - Thomas Cullup
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, Queen Square, London WC1N 3BH, UK
| | - Mellisa Dixon
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | - Alexandros Onoufriadis
- Department of Medical and Molecular Genetics, Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Andrew Bush
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK.,Department of Paediatric Respiratory Medicine, National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Eddie M K Chung
- Population, Policy and Practice, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, CH-1211 Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, iGE3, CH-1211 Geneva, Switzerland
| | - Michael R Loebinger
- Host Defence Unit, Respiratory Medicine, Royal Brompton Hospital, London SW3 6NP, UK
| | - Robert Wilson
- Host Defence Unit, Respiratory Medicine, Royal Brompton Hospital, London SW3 6NP, UK
| | - Miguel Armengot
- Rhinology and Primary Ciliary Dyskinesia Unit, General and University Hospital, Medical School, Valencia University, Valencia E-46014, Spain
| | - Estelle Escudier
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Claire Hogg
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | | | - Serge Amselem
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Zhaoxia Sun
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Lucia Bartoloni
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,UOSD Laboratorio Analisi Venezia, ULSS12 Veneziana, 30121 Venezia, Italy
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, CH-1211 Geneva, Switzerland
| | - Hannah M Mitchison
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
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Abstract
Recent technological advances in sequencing and high-throughput DNA cloning have resulted in the generation of vast quantities of biological sequence data. Ideally the functions of individual genes and proteins predicted by these methods should be assessed experimentally within the context of a defined hypothesis. However, if no hypothesis is known a priori, or the number of sequences to be assessed is large, bioinformatics techniques may be useful in predicting function.This chapter proposes a pipeline of freely available Web-based tools to analyze protein-coding DNA and peptide sequences of unknown function. Accumulated information obtained during each step of the pipeline is used to build a testable hypothesis of function.The following methods are described in detail: 1. Annotation of gene function through Protein domain detection (SMART and Pfam). 2. Sequence similarity methods for homolog detection (BLAST and DELTA-BLAST). 3. Comparing sequences to whole genome data.
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Affiliation(s)
- Tom C Giles
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
- Advanced Data Analysis Centre, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK.
- Advanced Data Analysis Centre, University of Nottingham, Leicestershire, LE12 5RD, UK.
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31
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Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, Emes RD, Lynch VJ. Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. eLife 2016; 5. [PMID: 27997337 PMCID: PMC5173317 DOI: 10.7554/elife.24307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 11/15/2022] Open
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32
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Glossop JR, Nixon NB, Emes RD, Sim J, Packham JC, Mattey DL, Farrell WE, Fryer AA. DNA methylation at diagnosis is associated with response to disease-modifying drugs in early rheumatoid arthritis. Epigenomics 2016; 9:419-428. [PMID: 27885849 DOI: 10.2217/epi-2016-0042] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM A proof-of-concept study to explore whether DNA methylation at first diagnosis is associated with response to disease-modifying antirheumatic drugs (DMARDs) in patients with early rheumatoid arthritis (RA). PATIENTS & METHODS DNA methylation was quantified in T-lymphocytes from 46 treatment-naive patients using HumanMethylation450 BeadChips. Treatment response was determined in 6 months using the European League Against Rheumatism (EULAR) response criteria. RESULTS Initial filtering identified 21 cytosine-phosphate-guanines (CpGs) that were differentially methylated between responders and nonresponders. After conservative adjustment for multiple testing, six sites remained statistically significant, of which four showed high sensitivity and/or specificity (≥75%) for response to treatment. Moreover, methylation at two sites in combination was the strongest factor associated with response (80.0% sensitivity, 90.9% specificity, AUC 0.85). CONCLUSION DNA methylation at diagnosis is associated with disease-modifying antirheumatic drug treatment response in early RA.
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Affiliation(s)
- John R Glossop
- Guy Hilton Research Centre, Institute for Applied Clinical Sciences, Keele University, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Nicola B Nixon
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Richard D Emes
- School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Julius Sim
- School of Health & Rehabilitation, Keele University, Staffordshire, ST5 5BG, UK
| | - Jon C Packham
- Guy Hilton Research Centre, Institute for Applied Clinical Sciences, Keele University, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Derek L Mattey
- Guy Hilton Research Centre, Institute for Applied Clinical Sciences, Keele University, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - William E Farrell
- Guy Hilton Research Centre, Institute for Applied Clinical Sciences, Keele University, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Anthony A Fryer
- Guy Hilton Research Centre, Institute for Applied Clinical Sciences, Keele University, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
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Sulaiman AA, Zolnierczyk K, Japa O, Owen JP, Maddison BC, Emes RD, Hodgkinson JE, Gough KC, Flynn RJ. A Trematode Parasite Derived Growth Factor Binds and Exerts Influences on Host Immune Functions via Host Cytokine Receptor Complexes. PLoS Pathog 2016; 12:e1005991. [PMID: 27806135 PMCID: PMC5091765 DOI: 10.1371/journal.ppat.1005991] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [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: 08/09/2016] [Accepted: 10/11/2016] [Indexed: 12/03/2022] Open
Abstract
The trematode Fasciola hepatica is responsible for chronic zoonotic infection globally. Despite causing a potent T-helper 2 response, it is believed that potent immunomodulation is responsible for rendering this host reactive non-protective host response thereby allowing the parasite to remain long-lived. We have previously identified a growth factor, FhTLM, belonging to the TGF superfamily can have developmental effects on the parasite. Herein we demonstrate that FhTLM can exert influence over host immune functions in a host receptor specific fashion. FhTLM can bind to receptor members of the Transforming Growth Factor (TGF) superfamily, with a greater affinity for TGF-β RII. Upon ligation FhTLM initiates the Smad2/3 pathway resulting in phenotypic changes in both fibroblasts and macrophages. The formation of fibroblast CFUs is reduced when cells are cultured with FhTLM, as a result of TGF-β RI kinase activity. In parallel the wound closure response of fibroblasts is also delayed in the presence of FhTLM. When stimulated with FhTLM blood monocyte derived macrophages adopt an alternative or regulatory phenotype. They express high levels interleukin (IL)-10 and arginase-1 while displaying low levels of IL-12 and nitric oxide. Moreover they also undergo significant upregulation of the inhibitory receptor PD-L1 and the mannose receptor. Use of RNAi demonstrates that this effect is dependent on TGF-β RII and mRNA knock-down leads to a loss of IL-10 and PD-L1. Finally, we demonstrate that FhTLM aids newly excysted juveniles (NEJs) in their evasion of antibody-dependent cell cytotoxicity (ADCC) by reducing the NO response of macrophages—again dependent on TGF-β RI kinase. FhTLM displays restricted expression to the F. hepatica gut resident NEJ stages. The altered fibroblast responses would suggest a role for dampened tissue repair responses in facilitating parasite migration. Furthermore, the adoption of a regulatory macrophage phenotype would allow for a reduced effector response targeting juvenile parasites which we demonstrate extends to an abrogation of the ADCC response. Thus suggesting that FhTLM is a stage specific evasion molecule that utilises host cytokine receptors. These findings are the first to clearly demonstrate the interaction of a helminth cytokine with a host receptor complex resulting in immune modifications that facilitate the non-protective chronic immune response which is characteristic of F. hepatica infection. Parasitic worms, helminths, can cause long-lived chronic infection in many hosts that they infection. The liver fluke, Fasciola hepatica, is one such parasite causing global infection of both humans and animals. F. hepatica exerts an influence over the immune system such that it avoids effector mechanisms and prevents the development of effective immunity. Here we characterise a molecule—FhTLM—derived from juvenile parasites that is similar to the regulatory cytokine TGF-β. We show that FhTLM will bind to host TGF-β receptors with a reduced affinity when compared with mammalian TGF-β. Despite this FhTLM can induce Smad2/3 signalling in host leukocytes, which is key to initiating gene transcription. Phenotypically FhTLM causes fibroblasts to slow their growth and replication response resulting in slower wound healing. Importantly FhTLM induces a macrophage phenotype that resembles a regulatory macrophage phenotype identified in other species undergoing helminth infection. Finally we Our work highlights the potential of FhTLM to play important roles in controlling host immunity when initially infected with juvenile parasites, thereby preventing the development of effective immunity.
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Affiliation(s)
- Azad A. Sulaiman
- School of Veterinary Medicine and Science, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Katarzyna Zolnierczyk
- School of Veterinary Medicine and Science, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Ornampai Japa
- School of Veterinary Medicine and Science, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
- School of Medicine, University of Phayao, Phayao, Thailand
| | - Jonathan P. Owen
- ADAS UK, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Ben C. Maddison
- ADAS UK, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Richard D. Emes
- School of Veterinary Medicine and Science, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Jane E. Hodgkinson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Kevin C. Gough
- School of Veterinary Medicine and Science, the University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Robin J. Flynn
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Blanchard AM, Egan SA, Emes RD, Warry A, Leigh JA. PIMMS (Pragmatic Insertional Mutation Mapping System) Laboratory Methodology a Readily Accessible Tool for Identification of Essential Genes in Streptococcus. Front Microbiol 2016; 7:1645. [PMID: 27826289 PMCID: PMC5078762 DOI: 10.3389/fmicb.2016.01645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 07/01/2016] [Accepted: 10/03/2016] [Indexed: 12/27/2022] Open
Abstract
The Pragmatic Insertional Mutation Mapping (PIMMS) laboratory protocol was developed alongside various bioinformatics packages (Blanchard et al., 2015) to enable detection of essential and conditionally essential genes in Streptococcus and related bacteria. This extended the methodology commonly used to locate insertional mutations in individual mutants to the analysis of mutations in populations of bacteria. In Streptococcus uberis, a pyogenic Streptococcus associated with intramammary infection and mastitis in ruminants, the mutagen pGhost9:ISS1 was shown to integrate across the entire genome. Analysis of >80,000 mutations revealed 196 coding sequences, which were not be mutated and a further 67 where mutation only occurred beyond the 90th percentile of the coding sequence. These sequences showed good concordance with sequences within the database of essential genes and typically matched sequences known to be associated with basic cellular functions. Due to the broad utility of this mutagen and the simplicity of the methodology it is anticipated that PIMMS will be of value to a wide range of laboratories in functional genomic analysis of a wide range of Gram positive bacteria (Streptococcus, Enterococcus, and Lactococcus) of medical, veterinary, and industrial significance.
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
| | - Sharon A Egan
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of NottinghamSutton Bonington, UK; Advanced Data Analysis Centre, University of NottinghamSutton Bonington, UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham Sutton Bonington, UK
| | - James A Leigh
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
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Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, Emes RD, Lynch VJ. TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. eLife 2016; 5. [PMID: 27642012 PMCID: PMC5061548 DOI: 10.7554/elife.11994] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 09/17/2016] [Indexed: 12/21/2022] Open
Abstract
A major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. There is no correlation, however, between body size and cancer risk. This lack of correlation is often referred to as 'Peto's Paradox'. Here, we show that the elephant genome encodes 20 copies of the tumor suppressor gene TP53 and that the increase in TP53 copy number occurred coincident with the evolution of large body sizes, the evolution of extreme sensitivity to genotoxic stress, and a hyperactive TP53 signaling pathway in the elephant (Proboscidean) lineage. Furthermore, we show that several of the TP53 retrogenes (TP53RTGs) are transcribed and likely translated. While TP53RTGs do not appear to directly function as transcription factors, they do contribute to the enhanced sensitivity of elephant cells to DNA damage and the induction of apoptosis by regulating activity of the TP53 signaling pathway. These results suggest that an increase in the copy number of TP53 may have played a direct role in the evolution of very large body sizes and the resolution of Peto's paradox in Proboscideans. DOI:http://dx.doi.org/10.7554/eLife.11994.001 As time passes, healthy cells are more likely to become cancerous because more and more damaging mutations accumulate in the cell’s DNA. Assuming that all cells have a similar risk of acquiring mutations, larger and longer-lived animals – like elephants – should have a higher risk of cancer than smaller, shorter-lived animals – like mice. However, there does not appear to be any link between the size of an animal and its risk of developing cancer. Consequently, a key question in cancer biology is how very large animals protect themselves against these diseases. One gene that is often damaged during an animal’s lifetime is called TP53. This gene normally produces a tumor suppressor protein that senses when DNA is damaged or a cell is under stress and either briefly slows the cell’s growth while the damage is repaired or triggers cell death if the stress is overwhelming. One way that large animals could reduce their risk of cancer is to have extra copies of TP53 or other genes that encode tumor suppressor proteins. Here Sulak et al. used an evolutionary genomics approach to study TP53 in 61 animals of various sizes, including several large animals such as African elephants and Minke whales. All of the animals studied had at least one copy of TP53, and several had a few extra copies, known as TP53 retrogenes. African elephants – the largest living land mammal – had more retrogenes than any of the others with 19 in total. To investigate why African elephants have so many TP53 retrogenes, Sulak et al. also analyzed DNA from Asian elephants and several other closely related, but now extinct species, including the woolly mammoth. As expected, as species evolved larger body sizes they also evolved more TP53 retrogenes. Further experiments indicate that several of the TP53 retrogenes in African elephants are likely to be able to produce the tumor suppressor protein and that they contribute to elephant cells being better equipped to deal with DNA damage. The next step following on from this work will be to find out exactly how TP53 retrogenes help to protect animals from cancer. DOI:http://dx.doi.org/10.7554/eLife.11994.002
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Affiliation(s)
- Michael Sulak
- Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Lindsey Fong
- Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Katelyn Mika
- Department of Human Genetics, The University of Chicago, Chicago, United States
| | | | - Lisa Yon
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom.,Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, United Kingdom
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom.,Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, United Kingdom.,Department of Pharmacology, Weill Cornell Medical College, New York, United States
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom.,Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham UK, Nottingham, United Kingdom
| | - Vincent J Lynch
- Department of Human Genetics, The University of Chicago, Chicago, United States
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Tarlinton RE, Alder L, Moreton J, Maboni G, Emes RD, Tötemeyer S. RNA expression of TLR10 in normal equine tissues. BMC Res Notes 2016; 9:353. [PMID: 27435589 PMCID: PMC4952062 DOI: 10.1186/s13104-016-2161-9] [Citation(s) in RCA: 6] [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: 03/17/2016] [Accepted: 07/13/2016] [Indexed: 11/14/2022] Open
Abstract
Background Toll like receptors are one of the major innate immune system pathogen recognition systems. There is little data on the expression of the TLR10 member of this family in the horse. Results This paper describes the genetic structure of the Equine TLR10 gene and its RNA expression in a range of horse tissues. It describes the phylogenetic analysis of the Equine TLR1,6,10,2 annotations in the horse genome, firmly identifying them in their corresponding gene clades compared to other species and firmly placing the horse gene with other TLR10 genes from odd-toed ungulates. Additional 3’ transcript extensions to that annotated for TLR10 in the horse genome have been identified by analysis of RNAseq data. RNA expression of the equine TLR10 gene was highest in peripheral blood mononucleocytes and lymphoid tissue (lymph nodes and spleen), however some expression was detected in all tissues tested (jejunum, caudal mesenteric lymph nodes, bronchial lymph node, spleen, lung, colon, kidney and liver). Additional data on RNAseq expression of all equine TLR genes (1–4 and 6–10) demonstrate higher expression of TLR4 than other equine TLRs in all tissues. Conclusion The equine TLR10 gene displays significant homology to other mammalian TLR10 genes and could be reasonably assumed to have similar fuctions. Its RNA level expression is higher in resting state PBMCs in horses than in other tissues. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2161-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachael E Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
| | - Lauren Alder
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Joanna Moreton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Grazieli Maboni
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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Brown DM, Williams H, Ryan KJP, Wilson TL, Daniel ZCTR, Mareko MHD, Emes RD, Harris DW, Jones S, Wattis JAD, Dryden IL, Hodgman TC, Brameld JM, Parr T. Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) and serine biosynthetic pathway genes are co-ordinately increased during anabolic agent-induced skeletal muscle growth. Sci Rep 2016; 6:28693. [PMID: 27350173 PMCID: PMC4923900 DOI: 10.1038/srep28693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 03/15/2016] [Accepted: 06/08/2016] [Indexed: 02/04/2023] Open
Abstract
We aimed to identify novel molecular mechanisms for muscle growth during administration of anabolic agents. Growing pigs (Duroc/(Landrace/Large-White)) were administered Ractopamine (a beta-adrenergic agonist; BA; 20 ppm in feed) or Reporcin (recombinant growth hormone; GH; 10 mg/48 hours injected) and compared to a control cohort (feed only; no injections) over a 27-day time course (1, 3, 7, 13 or 27-days). Longissimus Dorsi muscle gene expression was analyzed using Agilent porcine transcriptome microarrays and clusters of genes displaying similar expression profiles were identified using a modified maSigPro clustering algorithm. Anabolic agents increased carcass (p = 0.002) and muscle weights (Vastus Lateralis: p < 0.001; Semitendinosus: p = 0.075). Skeletal muscle mRNA expression of serine/one-carbon/glycine biosynthesis pathway genes (Phgdh, Psat1 and Psph) and the gluconeogenic enzyme, phosphoenolpyruvate carboxykinase-M (Pck2/PEPCK-M), increased during treatment with BA, and to a lesser extent GH (p < 0.001, treatment x time interaction). Treatment with BA, but not GH, caused a 2-fold increase in phosphoglycerate dehydrogenase (PHGDH) protein expression at days 3 (p < 0.05) and 7 (p < 0.01), and a 2-fold increase in PEPCK-M protein expression at day 7 (p < 0.01). BA treated pigs exhibit a profound increase in expression of PHGDH and PEPCK-M in skeletal muscle, implicating a role for biosynthetic metabolic pathways in muscle growth.
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Affiliation(s)
- D M Brown
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - H Williams
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - K J P Ryan
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - T L Wilson
- VMRD Global Therapeutics Research, Zoetis, Kalamazoo, MI, 49007, USA
| | - Z C T R Daniel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - M H D Mareko
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - D W Harris
- VMRD Global Therapeutics Research, Zoetis, Kalamazoo, MI, 49007, USA
| | - S Jones
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - J A D Wattis
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - I L Dryden
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - T C Hodgman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - J M Brameld
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - T Parr
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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Kitchen MO, Bryan RT, Emes RD, Glossop JR, Luscombe C, Cheng KK, Zeegers MP, James ND, Devall AJ, Mein CA, Gommersall L, Fryer AA, Farrell WE. Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer. Epigenetics 2016; 11:237-46. [PMID: 26929985 DOI: 10.1080/15592294.2016.1154246] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
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Affiliation(s)
- Mark O Kitchen
- a Institute for Science and Technology in Medicine, Keele University , UK.,b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Richard T Bryan
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Richard D Emes
- d Advanced Data Analysis Center, University of Nottingham , UK
| | - John R Glossop
- a Institute for Science and Technology in Medicine, Keele University , UK
| | | | - K K Cheng
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Maurice P Zeegers
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK.,e Department of Complex Genetics , Maastricht University Medical Center , The Netherlands.,f NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center , The Netherlands.,g CAPHRI School for Public Health and Primary Care, Maastricht University Medical Center , The Netherlands
| | | | - Adam J Devall
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Charles A Mein
- i The Genome Center, Barts and the London School of Medicine and Dentistry , London , UK
| | - Lyndon Gommersall
- b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Anthony A Fryer
- a Institute for Science and Technology in Medicine, Keele University , UK
| | - William E Farrell
- a Institute for Science and Technology in Medicine, Keele University , UK
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Moreton J, Izquierdo A, Emes RD. Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. Front Genet 2016; 6:361. [PMID: 26793234 PMCID: PMC4707302 DOI: 10.3389/fgene.2015.00361] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 09/20/2015] [Accepted: 12/19/2015] [Indexed: 11/13/2022] Open
Abstract
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems?
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Affiliation(s)
- Joanna Moreton
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
| | - Abril Izquierdo
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
| | - Richard D. Emes
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
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40
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Mellanby RJ, Price J, Wooldridge L, Jonsson NN, Clegg PD, Emes RD, England G, Corr SA, Piercy RJ, Mulcahy G, Wood JL, Walker BR, Argyle DJ. Clinical research: developing an appropriate career structure. Vet Rec 2015; 177:544-7. [PMID: 26612910 DOI: 10.1136/vr.h6169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- R J Mellanby
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Roslin, Midlothian EH25 9RG,
| | - J Price
- School of Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol BS40 5DU
| | - L Wooldridge
- School of Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol BS40 5DU
| | - N N Jonsson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH
| | - P D Clegg
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Cheshire CH64 7TE
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD
| | - G England
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD
| | - S A Corr
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington Campus, Leicestershire LE12 5RD
| | - R J Piercy
- Department of Clinical Sciences and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire AL9 7TA
| | - G Mulcahy
- UCD School of Veterinary Medicine, Veterinary Sciences Centre, Belfield, Dublin 4, Ireland
| | - J L Wood
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES
| | - B R Walker
- Edinburgh Clinical Academic Track Programme, College of Medicine and Veterinary Medicine, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ
| | - D J Argyle
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Roslin, Midlothian EH25 9RG,
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41
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Glossop JR, Emes RD, Nixon NB, Packham JC, Fryer AA, Mattey DL, Farrell WE. Genome-wide profiling in treatment-naive early rheumatoid arthritis reveals DNA methylome changes in T and B lymphocytes. Epigenomics 2015; 8:209-24. [PMID: 26556652 DOI: 10.2217/epi.15.103] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AIM Although aberrant DNA methylation has been described in rheumatoid arthritis (RA), no studies have interrogated this epigenetic modification in early disease. Following recent investigations of T and B lymphocytes in established disease, we now characterize in these cell populations genome-wide DNA methylation in treatment-naive patients with early RA. PATIENTS & METHODS HumanMethylation450 BeadChips were used to examine genome-wide DNA methylation in lymphocyte populations from 23 early RA patients and 11 healthy individuals. RESULTS Approximately 2000 CpGs in each cell type were differentially methylated in early RA. Clustering analysis identified a novel methylation signature in each cell type (150 sites in T lymphocytes, 113 sites in B lymphocytes) that clustered all patients separately from controls. A subset of sites differentially methylated in early RA displayed similar changes in established disease. CONCLUSION Treatment-naive early RA patients display novel disease-specific DNA methylation aberrations, supporting a potential role for these changes in the development of RA.
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Affiliation(s)
- John R Glossop
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Richard D Emes
- School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Nicola B Nixon
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Jon C Packham
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Anthony A Fryer
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Derek L Mattey
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK.,Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - William E Farrell
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
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Abstract
INTRODUCTION Transgenic mice overexpressing the high mobility group A (HMGA) genes, Hmga1 or Hmga2 develop pituitary tumours and their overexpression is also a frequent finding in human pituitary adenomas. In some cases, increased expression of HMGA2 but not that of HMGA1 is consequent to genetic perturbations. However, recent studies show that down-regulation of microRNA (miRNA), that contemporaneously target the HMGA1 and HMGA2 transcripts, are associated with their overexpression. RESULTS In a cohort of primary pituitary adenoma we determine the impact of epigenetic modifications on the expression of HMGA-targeting miRNA. For these miRNAs, chromatin immunoprecipitations showed that transcript down-regulation is correlated with histone tail modifications associated with condensed silenced genes. The functional impact of epigenetic modification on miRNA expression was determined in the rodent pituitary cell line, GH3. In these cells, histone tail, miRNA-associated, modifications were similar to those apparent in human adenoma and likely account for their repression. Indeed, challenge of GH3 cells with the epidrugs, zebularine and TSA, led to enrichment of the histone modification, H3K9Ac, associated with active genes, and depletion of the modification, H3K27me3, associated with silent genes and re-expression of HMGA-targeting miRNA. Moreover, epidrugs challenges were also associated with a concomitant decrease in hmga1 transcript and protein levels and concurrent increase in bmp-4 expression. CONCLUSIONS These findings show that the inverse relationship between HMGA expression and targeting miRNA is reversible through epidrug interventions. In addition to showing a mechanistic link between epigenetic modifications and miRNA expression these findings underscore their potential as therapeutic targets in this and other diseases.
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Affiliation(s)
- Mark O Kitchen
- Human Disease and Genomics Group, Institute of Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
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Kitchen MO, Bryan RT, Haworth KE, Emes RD, Luscombe C, Gommersall L, Cheng KK, Zeegers MP, James ND, Devall AJ, Fryer AA, Farrell WE. Methylation of HOXA9 and ISL1 Predicts Patient Outcome in High-Grade Non-Invasive Bladder Cancer. PLoS One 2015; 10:e0137003. [PMID: 26332997 PMCID: PMC4558003 DOI: 10.1371/journal.pone.0137003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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: 05/14/2015] [Accepted: 08/11/2015] [Indexed: 12/28/2022] Open
Abstract
Introduction Inappropriate DNA methylation is frequently associated with human tumour development, and in specific cases, is associated with clinical outcomes. Previous reports of DNA methylation in low/intermediate grade non-muscle invasive bladder cancer (NMIBC) have suggested that specific patterns of DNA methylation may have a role as diagnostic or prognostic biomarkers. In view of the aggressive and clinically unpredictable nature of high-grade (HG) NMIBC, and the current shortage of the preferred treatment option (Bacillus:Calmette-Guerin), novel methylation analyses may similarly reveal biomarkers of disease outcome that could risk-stratify patients and guide clinical management at initial diagnosis. Methods Promoter-associated CpG island methylation was determined in primary tumour tissue of 36 initial presentation high-grade NMIBCs, 12 low/intermediate-grade NMIBCs and 3 normal bladder controls. The genes HOXA9, ISL1, NKX6-2, SPAG6, ZIC1 and ZNF154 were selected for investigation on the basis of previous reports and/or prognostic utility in low/intermediate-grade NMIBC. Methylation was determined by Pyrosequencing of sodium-bisulphite converted DNA, and then correlated with gene expression using RT-qPCR. Methylation was additionally correlated with tumour behaviour, including tumour recurrence and progression to muscle invasive bladder cancer or metastases. Results The ISL1 genes’ promoter-associated island was more frequently methylated in recurrent and progressive high-grade tumours than their non-recurrent counterparts (60.0% vs. 18.2%, p = 0.008). ISL1 and HOXA9 showed significantly higher mean methylation in recurrent and progressive tumours compared to non-recurrent tumours (43.3% vs. 20.9%, p = 0.016 and 34.5% vs 17.6%, p = 0.017, respectively). Concurrent ISL1/HOXA9 methylation in HG-NMIBC reliably predicted tumour recurrence and progression within one year (Positive Predictive Value 91.7%), and was associated with disease-specific mortality (DSM). Conclusions In this study we report methylation differences and similarities between clinical sub-types of high-grade NMIBC. We report the potential ability of methylation biomarkers, at initial diagnosis, to predict tumour recurrence and progression within one year of diagnosis. We found that specific biomarkers reliably predict disease outcome and therefore may help guide patient treatment despite the unpredictable clinical course and heterogeneity of high-grade NMIBC. Further investigation is required, including validation in a larger patient cohort, to confirm the clinical utility of methylation biomarkers in high-grade NMIBC.
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Affiliation(s)
- Mark O Kitchen
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, United Kingdom; Urology Department, University Hospitals of North Midlands NHS Trust, Stoke-on-Trent, United Kingdom
| | - Richard T Bryan
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kim E Haworth
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, United Kingdom
| | - Richard D Emes
- Advanced Data Analysis Centre, University of Nottingham, Nottingham, United Kingdom
| | - Christopher Luscombe
- Urology Department, University Hospitals of North Midlands NHS Trust, Stoke-on-Trent, United Kingdom
| | - Lyndon Gommersall
- Urology Department, University Hospitals of North Midlands NHS Trust, Stoke-on-Trent, United Kingdom
| | - K K Cheng
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Maurice P Zeegers
- Department of Complex Genetics, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Nicholas D James
- Cancer Research Unit, University of Warwick, Coventry, United Kingdom
| | - Adam J Devall
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Anthony A Fryer
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, United Kingdom
| | - William E Farrell
- Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, United Kingdom
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Haworth KE, Farrell WE, Emes RD, Ismail KMK, Carroll WD, Hubball E, Rooney A, Yates AM, Mein C, Fryer AA. Methylation of the FGFR2 gene is associated with high birth weight centile in humans. Epigenomics 2015; 6:477-91. [PMID: 25431941 DOI: 10.2217/epi.14.40] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIMS This study examined links between DNA methylation and birth weight centile (BWC), and explored the impact of genetic variation. MATERIALS & METHODS Using HumanMethylation450 arrays, we examined candidate gene-associated CpGs in cord blood from newborns with low (<15th centile), medium (40-60th centile) and high (>85th centile) BWC (n = 12). Candidates were examined in an investigation cohort (n = 110) using pyrosequencing and genotyping for putative methylation-associated polymorphisms performed using standard PCR. RESULTS Array analysis identified 314 candidate genes associated with BWC extremes, four of which showed ≥ 4 BWC-linked CpGs. Of these, PM20D1 and MI886 suggested genetically determined methylation levels. However, methylation at three CpGs in FGFR2 remained significantly associated with high BWC (p = 0.004-0.027). CONCLUSION We identified a novel biologically plausible candidate (FGFR2) for with BWC that merits further study.
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Affiliation(s)
- Kim E Haworth
- Institute of Science & Technology in Medicine, Keele University School of Medicine, University Hospital of North Staffordshire, Stoke-on-Trent, Staffordshire, UK
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Glossop JR, Haworth KE, Emes RD, Nixon NB, Packham JC, Dawes PT, Fryer AA, Mattey DL, Farrell WE. DNA methylation profiling of synovial fluid FLS in rheumatoid arthritis reveals changes common with tissue-derived FLS. Epigenomics 2015; 7:539-51. [DOI: 10.2217/epi.15.15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: Alterations in DNA methylation contribute to the abnormal phenotype of fibroblast-like synoviocytes (FLS) from patients with rheumatoid arthritis (RA). We profiled genome-wide DNA methylation in these cells from synovial fluid, a more readily accessible source of disease-associated cells. Patients & methods: Genome-wide DNA methylation was interrogated in fluid-derived FLS from five RA and six osteoarthritis patients using Human Methylation 450 Bead Chip and bisulfite pyrosequencing. Results: Array analysis identified 328 CpGs, representing 195 genes, that were differentially methylated between RA and osteoarthritis fluid-derived FLS. Comparison with the genes identified in two independent studies of tissue-derived FLS revealed 73 genes in common (˜40%), of which 22 shared identity with both studies. Pyrosequencing confirmed altered methylation of these genes. Conclusion: Synovial fluid-derived RA FLS show methylation changes common with tissue-derived FLS, supporting the use of fluid-derived FLS for future investigations.
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Affiliation(s)
- John R Glossop
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Kim E Haworth
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Richard D Emes
- School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Nicola B Nixon
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Jon C Packham
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Peter T Dawes
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - Anthony A Fryer
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
| | - Derek L Mattey
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
- Haywood Rheumatology Centre, Haywood Hospital, High Lane, Burslem, Stoke-on-Trent, Staffordshire, ST6 7AG, UK
| | - William E Farrell
- Institute for Science & Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, UK
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Hossain M, Egan SA, Coffey T, Ward PN, Wilson R, Leigh JA, Emes RD. Virulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence. BMC Genomics 2015; 16:334. [PMID: 25898893 PMCID: PMC4427978 DOI: 10.1186/s12864-015-1512-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 10/23/2014] [Accepted: 04/08/2015] [Indexed: 12/17/2022] Open
Abstract
Background Streptococcus uberis, a Gram-positive, catalase-negative member of the family Streptococcaceae is an important environmental pathogen responsible for a significant proportion of subclinical and clinical bovine intramammary infections. Currently, the genome of only a single reference strain (0140J) has been described. Here we present a comparative analysis of complete draft genome sequences of an additional twelve S. uberis strains. Results Pan and core genome analysis revealed the core genome common to all strains to be 1,550 genes in 1,509 orthologous clusters, complemented by 115-246 accessory genes present in one or more S. uberis strains but absent in the reference strain 0140J. Most of the previously predicted virulent genes were present in the core genome of all 13 strains but gene gain/loss was observed between the isolates in CDS associated with clustered regularly interspaced short palindromic repeats (CRISPRs), prophage and bacteriocin production. Experimental challenge experiments confirmed strain EF20 as non-virulent; only able to infect in a transient manner that did not result in clinical mastitis. Comparison of the genome sequence of EF20 with the validated virulent strain 0140J identified genes associated with virulence, however these did not relate clearly with clinical/non-clinical status of infection. Conclusion The gain/loss of mobile genetic elements such as CRISPRs and prophage are a potential driving force for evolutionary change. This first “whole-genome” comparison of strains isolated from clinical vs non-clinical intramammary infections including the type virulent vs non-virulent strains did not identify simple gene gain/loss rules that readily explain, or be confidently associated with, differences in virulence. This suggests that a more complex dynamic determines infection potential and clinical outcome not simply gene content. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1512-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, Sutton Bonington, UK.
| | - Sharon A Egan
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, Sutton Bonington, UK.
| | - Tracey Coffey
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, Sutton Bonington, UK.
| | - Philip N Ward
- Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK.
| | - Ray Wilson
- DeepSeq, School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK.
| | - James A Leigh
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, Sutton Bonington, UK.
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, Sutton Bonington, UK. .,Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK.
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Winter AD, Gillan V, Maitland K, Emes RD, Roberts B, McCormack G, Weir W, Protasio AV, Holroyd N, Berriman M, Britton C, Devaney E. A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites. BMC Genomics 2015; 16:331. [PMID: 25896062 PMCID: PMC4428239 DOI: 10.1186/s12864-015-1536-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/13/2015] [Indexed: 12/18/2022] Open
Abstract
Background Filarial nematodes are important pathogens in the tropics transmitted to humans via the bite of blood sucking arthropod vectors. The molecular mechanisms underpinning survival and differentiation of these parasites following transmission are poorly understood. microRNAs are small non-coding RNA molecules that regulate target mRNAs and we set out to investigate whether they play a role in the infection event. Results microRNAs differentially expressed during the early post-infective stages of Brugia pahangi L3 were identified by microarray analysis. One of these, bpa-miR-5364, was selected for further study as it is upregulated ~12-fold at 24 hours post-infection, is specific to clade III nematodes, and is a novel member of the let-7 family, which are known to have key developmental functions in the free-living nematode Caenorhabditis elegans. Predicted mRNA targets of bpa-miR-5364 were identified using bioinformatics and comparative genomics approaches that relied on the conservation of miR-5364 binding sites in the orthologous mRNAs of other filarial nematodes. Finally, we confirmed the interaction between bpa-miR-5364 and three of its predicted targets using a dual luciferase assay. Conclusions These data provide new insight into the molecular mechanisms underpinning the transmission of third stage larvae of filarial nematodes from vector to mammal. This study is the first to identify parasitic nematode mRNAs that are verified targets of specific microRNAs and demonstrates that post-transcriptional control of gene expression via stage-specific expression of microRNAs may be important in the success of filarial infection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1536-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alan D Winter
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Victoria Gillan
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Kirsty Maitland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK. .,Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK.
| | - Brett Roberts
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Gillian McCormack
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - William Weir
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Anna V Protasio
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Collette Britton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
| | - Eileen Devaney
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.
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Blanchard AM, Leigh JA, Egan SA, Emes RD. Transposon insertion mapping with PIMMS - Pragmatic Insertional Mutation Mapping System. Front Genet 2015; 6:139. [PMID: 25914720 PMCID: PMC4391243 DOI: 10.3389/fgene.2015.00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 03/01/2015] [Accepted: 03/23/2015] [Indexed: 01/24/2023] Open
Abstract
The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation. Availability: The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
| | - James A Leigh
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
| | - Sharon A Egan
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
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Simpson S, Edwards J, Emes RD, Cobb MA, Mongan NP, Rutland CS. A predictive model for canine dilated cardiomyopathy-a meta-analysis of Doberman Pinscher data. PeerJ 2015; 3:e842. [PMID: 25834770 PMCID: PMC4380154 DOI: 10.7717/peerj.842] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 11/14/2014] [Accepted: 02/27/2015] [Indexed: 11/20/2022] Open
Abstract
Dilated cardiomyopathy is a prevalent and often fatal disease in humans and dogs. Indeed dilated cardiomyopathy is the third most common form of cardiac disease in humans, reported to affect approximately 36 individuals per 100,000 individuals. In dogs, dilated cardiomyopathy is the second most common cardiac disease and is most prevalent in the Irish Wolfhound, Doberman Pinscher and Newfoundland breeds. Dilated cardiomyopathy is characterised by ventricular chamber enlargement and systolic dysfunction which often leads to congestive heart failure. Although multiple human loci have been implicated in the pathogenesis of dilated cardiomyopathy, the identified variants are typically associated with rare monogenic forms of dilated cardiomyopathy. The potential for multigenic interactions contributing to human dilated cardiomyopathy remains poorly understood. Consistent with this, several known human dilated cardiomyopathy loci have been excluded as common causes of canine dilated cardiomyopathy, although canine dilated cardiomyopathy resembles the human disease functionally. This suggests additional genetic factors contribute to the dilated cardiomyopathy phenotype.This study represents a meta-analysis of available canine dilated cardiomyopathy genetic datasets with the goal of determining potential multigenic interactions relating the sex chromosome genotype (XX vs. XY) with known dilated cardiomyopathy associated loci on chromosome 5 and the PDK4 gene in the incidence and progression of dilated cardiomyopathy. The results show an interaction between known canine dilated cardiomyopathy loci and an unknown X-linked locus. Our study is the first to test a multigenic contribution to dilated cardiomyopathy and suggest a genetic basis for the known sex-disparity in dilated cardiomyopathy outcomes.
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Affiliation(s)
- Siobhan Simpson
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Jennifer Edwards
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK ; Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Malcolm A Cobb
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK ; Department of Pharmacology, Weill Cornell Medical College , New York, NY , USA
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham , Leicestershire , UK
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Japa O, Hodgkinson JE, Emes RD, Flynn RJ. TGF-β superfamily members from the helminth Fasciola hepatica show intrinsic effects on viability and development. Vet Res 2015; 46:29. [PMID: 25879787 PMCID: PMC4354977 DOI: 10.1186/s13567-015-0167-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 12/02/2014] [Accepted: 02/25/2015] [Indexed: 12/31/2022] Open
Abstract
The helminth Fasciola hepatica causes fasciolosis throughout the world, a major disease of livestock and an emerging zoonotic disease in humans. Sustainable control mechanisms such as vaccination are urgently required. To discover potential vaccine targets we undertook a genome screen to identify members of the transforming growth factor (TGF) family of proteins. Herein we describe the discovery of three ligands belonging to this superfamily and the cloning and characterisation of an activin/TGF like molecule we term FhTLM. FhTLM has a limited expression pattern both temporally across the parasite stages but also spatially within the worm. Furthermore, a recombinant form of this protein is able to enhance the rate (or magnitude) of multiple developmental processes of the parasite indicating a conserved role for this protein superfamily in the developmental biology of a major trematode parasite. Our study demonstrates for the first time the existence of this protein superfamily within F. hepatica and assigns a function to one of the three identified ligands. Moreover further exploration of this superfamily may yield future targets for diagnostic or vaccination purposes due to its stage restricted expression and functional role.
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Affiliation(s)
- Ornampai Japa
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK.
| | - Jane E Hodgkinson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L3 5RF, UK.
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK.
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK.
| | - Robin J Flynn
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK.
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