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O'Brien CL, Summers KM, Martin NM, Carter-Cusack D, Yang Y, Barua R, Dixit OVA, Hume DA, Pavli P. The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease. Hum Genet 2024; 143:233-261. [PMID: 38421405 PMCID: PMC11043138 DOI: 10.1007/s00439-024-02642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024]
Abstract
The differentiation of resident intestinal macrophages from blood monocytes depends upon signals from the macrophage colony-stimulating factor receptor (CSF1R). Analysis of genome-wide association studies (GWAS) indicates that dysregulation of macrophage differentiation and response to microorganisms contributes to susceptibility to chronic inflammatory bowel disease (IBD). Here, we analyzed transcriptomic variation in monocyte-derived macrophages (MDM) from affected and unaffected sib pairs/trios from 22 IBD families and 6 healthy controls. Transcriptional network analysis of the data revealed no overall or inter-sib distinction between affected and unaffected individuals in basal gene expression or the temporal response to lipopolysaccharide (LPS). However, the basal or LPS-inducible expression of individual genes varied independently by as much as 100-fold between subjects. Extreme independent variation in the expression of pairs of HLA-associated transcripts (HLA-B/C, HLA-A/F and HLA-DRB1/DRB5) in macrophages was associated with HLA genotype. Correlation analysis indicated the downstream impacts of variation in the immediate early response to LPS. For example, variation in early expression of IL1B was significantly associated with local SNV genotype and with subsequent peak expression of target genes including IL23A, CXCL1, CXCL3, CXCL8 and NLRP3. Similarly, variation in early IFNB1 expression was correlated with subsequent expression of IFN target genes. Our results support the view that gene-specific dysregulation in macrophage adaptation to the intestinal milieu is associated with genetic susceptibility to IBD.
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Affiliation(s)
- Claire L O'Brien
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Natalia M Martin
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Yuanhao Yang
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Rasel Barua
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Ojas V A Dixit
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
| | - Paul Pavli
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia.
- School of Medicine and Psychology, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
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Keshvari S, Masson JJR, Ferrari-Cestari M, Bodea LG, Nooru-Mohamed F, Tse BWC, Sokolowski KA, Batoon L, Patkar OL, Sullivan MA, Ebersbach H, Stutz C, Parton RG, Summers KM, Pettit AR, Hume DA, Irvine KM. Reversible expansion of tissue macrophages in response to macrophage colony-stimulating factor (CSF1) transforms systemic lipid and carbohydrate metabolism. Am J Physiol Endocrinol Metab 2024; 326:E149-E165. [PMID: 38117267 DOI: 10.1152/ajpendo.00347.2023] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/01/2023] [Accepted: 12/17/2023] [Indexed: 12/21/2023]
Abstract
Macrophages regulate metabolic homeostasis in health and disease. Macrophage colony-stimulating factor (CSF1)-dependent macrophages contribute to homeostatic control of the size of the liver. This study aimed to determine the systemic metabolic consequences of elevating circulating CSF1. Acute administration of a CSF1-Fc fusion protein to mice led to monocytosis, increased resident tissue macrophages in the liver and all major organs, and liver growth. These effects were associated with increased hepatic glucose uptake and extensive mobilization of body fat. The impacts of CSF1 on macrophage abundance, liver size, and body composition were rapidly reversed to restore homeostasis. The effects of CSF1 on metabolism were independent of several known endocrine regulators and did not impact the physiological fasting response. Analysis using implantable telemetry in metabolic cages revealed progressively reduced body temperature and physical activity with no change in diurnal food intake. These results demonstrate the existence of a dynamic equilibrium between CSF1, the mononuclear phagocyte system, and control of liver-to-body weight ratio, which in turn controls systemic metabolic homeostasis. This novel macrophage regulatory axis has the potential to promote fat mobilization, without changes in appetence, which may have novel implications for managing metabolic syndrome.NEW & NOTEWORTHY CSF1 administration expands tissue macrophages, which transforms systemic metabolism. CSF1 drives fat mobilization and glucose uptake to support liver growth. The effects of CSF1 are independent of normal hormonal metabolic regulation. The effects of CSF1 are rapidly reversible, restoring homeostatic body composition. CSF1-dependent macrophages and liver size are coupled in a dynamic equilibrium.
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Affiliation(s)
- Sahar Keshvari
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Jesse J R Masson
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Michelle Ferrari-Cestari
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing and Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Fathima Nooru-Mohamed
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Brian W C Tse
- Preclinical Imaging Facility, Translational Research Institute, Brisbane, Queensland, Australia
| | - Kamil A Sokolowski
- Preclinical Imaging Facility, Translational Research Institute, Brisbane, Queensland, Australia
| | - Lena Batoon
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Omkar L Patkar
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Mitchell A Sullivan
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Hilmar Ebersbach
- Novartis Institutes for Biomedical Research (NIBR), Basel, Switzerland
| | - Cian Stutz
- Novartis Institutes for Biomedical Research (NIBR), Basel, Switzerland
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Kim M Summers
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Allison R Pettit
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - David A Hume
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Katharine M Irvine
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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Summers KM. Genetic models of fibrillinopathies. Genetics 2024; 226:iyad189. [PMID: 37972149 PMCID: PMC11021029 DOI: 10.1093/genetics/iyad189] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023] Open
Abstract
The fibrillinopathies represent a group of diseases in which the 10-12 nm extracellular microfibrils are disrupted by genetic variants in one of the genes encoding fibrillin molecules, large glycoproteins of the extracellular matrix. The best-known fibrillinopathy is Marfan syndrome, an autosomal dominant condition affecting the cardiovascular, ocular, skeletal, and other systems, with a prevalence of around 1 in 3,000 across all ethnic groups. It is caused by variants of the FBN1 gene, encoding fibrillin-1, which interacts with elastin to provide strength and elasticity to connective tissues. A number of mouse models have been created in an attempt to replicate the human phenotype, although all have limitations. There are also natural bovine models and engineered models in pig and rabbit. Variants in FBN2 encoding fibrillin-2 cause congenital contractural arachnodactyly and mouse models for this condition have also been produced. In most animals, including birds, reptiles, and amphibians, there is a third fibrillin, fibrillin-3 (FBN3 gene) for which the creation of models has been difficult as the gene is degenerate and nonfunctional in mice and rats. Other eukaryotes such as the nematode C. elegans and zebrafish D. rerio have a gene with some homology to fibrillins and models have been used to discover more about the function of this family of proteins. This review looks at the phenotype, inheritance, and relevance of the various animal models for the different fibrillinopathies.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba QLD 4102, Australia
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Sehgal A, Carter-Cusack D, Keshvari S, Patkar O, Huang S, Summers KM, Hume DA, Irvine KM. Intraperitoneal transfer of wild-type bone marrow repopulates tissue macrophages in the Csf1r knockout rat without contributing to monocytopoiesis. Eur J Immunol 2023; 53:e2250312. [PMID: 37059596 DOI: 10.1002/eji.202250312] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/13/2023] [Accepted: 04/13/2023] [Indexed: 04/16/2023]
Abstract
Homozygous null mutation of the Csf1r gene (Csf1rko) in rats leads to the loss of most tissue macrophage populations and pleiotropic impacts on postnatal growth and organ maturation, leading to early mortality. The phenotype can be reversed by intraperitoneal transfer of WT BM cells (BMT) at weaning. Here, we used a Csf1r-mApple transgenic reporter to track the fate of donor-derived cells. Following BMT into Csf1rko recipients, mApple+ve cells restored IBA1+ tissue macrophage populations in every tissue. However, monocytes, neutrophils, and B cells in the BM, blood, and lymphoid tissues remained of recipient (mApple-ve ) origin. An mApple+ve cell population expanded in the peritoneal cavity and invaded locally in the mesentery, fat pads, omentum, and diaphragm. One week after BMT, distal organs contained foci of mApple+ve , IBA1-ve immature progenitors that appeared to proliferate, migrate, and differentiate locally. We conclude that rat BM contains progenitor cells that are able to restore, replace, and maintain all tissue macrophage populations in a Csf1rko rat directly without contributing to the BM progenitor or blood monocyte populations.
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Affiliation(s)
- Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Omkar Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Stephen Huang
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Australia
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Summers KM, Scherer A, Chasco EE, Ryan GL. Defining infertility: a qualitative interview study of patients and physicians. J Reprod Infant Psychol 2023:1-15. [PMID: 37288784 DOI: 10.1080/02646838.2023.2221277] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE To investigate if infertility patients and physicians apply a traditional biomedical model of disease in their conceptualisation of infertility, examine any contradictions and conflicts in conceptualisations, and examine areas of concordance and discordance between physicians and patients. METHODS Semi-structured interviews were conducted with 20 infertility patients and 18 infertility physicians between September 2010 and April 2012. Interviews were analysed qualitatively to determine physician and patient conceptualisations of infertility, reactions to the definition of infertility as a disease, and potential benefits and concerns related to application of a disease label to the condition. RESULTS Most physicians (n = 14/18) and a minority of patients (n = 6/20) were supportive of defining infertility as a disease. Many of the patients who agreed with classifying infertility as a disease expressed that they had not personally defined it as such previously. Physicians (n = 14) and patients (n = 13) described potential benefits of a disease label, including increases in research funding, insurance coverage, and social acceptability. Some patients (n = 10) described potential stigma as a negative consequence. When describing appraisals of infertility, both physicians (n = 7) and patients (n = 8) invoked religious/spiritual concepts. The potential for religious/spiritual appraisal to contribute to stigmatising or de-stigmatising infertility was discussed. CONCLUSION Our findings contradict the assumption that infertility physicians and patients are fully supportive of defining infertility as a disease. While potential benefits of the disease label were recognised by both groups, caution against potential for stigmatisation and unsolicited invocation of religion/spirituality suggest a more holistic model may be appropriate.
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Affiliation(s)
- K M Summers
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Iowa Hospital and Clinics, Iowa City, IA, USA
| | - A Scherer
- Department of Internal Medicine, University of Iowa Hospital and Clinics, Iowa City, IA, USA
| | - E E Chasco
- Institute for Clinical and Translational Science, University of Iowa, Iowa City, IA, USA
- Center for Access and Delivery Research and Evaluation (CADRE), Iowa City VA Health Care System, Iowa City, IA, USA
| | - G L Ryan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Washington Medical Center Montlake, Seattle, WA, USA
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Summers KM, Bush SJ, Davis MR, Hume DA, Keshvari S, West JA. Fibrillin-1 and asprosin, novel players in metabolic syndrome. Mol Genet Metab 2023; 138:106979. [PMID: 36630758 DOI: 10.1016/j.ymgme.2022.106979] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Fibrillin-1 is a major component of the extracellular microfibrils, where it interacts with other extracellular matrix proteins to provide elasticity to connective tissues, and regulates the bioavailability of TGFβ family members. A peptide consisting of the C-terminal 140 amino acids of fibrillin-1 has recently been identified as a glucogenic hormone, secreted from adipose tissue during fasting and targeting the liver to release glucose. This fragment, called asprosin, also signals in the hypothalamus to stimulate appetite. Asprosin levels are correlated with many of the pathologies indicative of metabolic syndrome, including insulin resistance and obesity. Previous studies and reviews have addressed the therapeutic potential of asprosin as a target in obesity, diabetes and related conditions without considering mechanisms underlying the relationship between generation of asprosin and expression of the much larger fibrillin-1 protein. Profibrillin-1 undergoes obligatory cleavage at the cell surface as part of its assembly into microfibrils, producing the asprosin peptide as well as mature fibrillin-1. Patterns of FBN1 mRNA expression are inconsistent with the necessity for regulated release of asprosin. The asprosin peptide may be protected from degradation in adipose tissue. We present evidence for an alternative possibility, that asprosin mRNA is generated independently from an internal promoter within the 3' end of the FBN1 gene, which would allow for regulation independent of fibrillin-synthesis and is more economical of cellular resources. The discovery of asprosin opened exciting possibilities for treatment of metabolic syndrome related conditions, but there is much to be understood before such therapies could be introduced into the clinic.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, United Kingdom.
| | - Margaret R Davis
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Jennifer A West
- Faculty of Medicine, The University of Queensland, Mayne Medical Building, 288 Herston Road, Herston, Queensland 4006, Australia.
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7
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Stables J, Green EK, Sehgal A, Patkar OL, Keshvari S, Taylor I, Ashcroft ME, Grabert K, Wollscheid-Lengeling E, Szymkowiak S, McColl BW, Adamson A, Humphreys NE, Mueller W, Starobova H, Vetter I, Shabestari SK, Blurton-Jones MM, Summers KM, Irvine KM, Pridans C, Hume DA. A kinase-dead Csf1r mutation associated with adult-onset leukoencephalopathy has a dominant inhibitory impact on CSF1R signalling. Development 2022; 149:274819. [PMID: 35333324 PMCID: PMC9002114 DOI: 10.1242/dev.200237] [Citation(s) in RCA: 7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/04/2022] [Indexed: 12/21/2022]
Abstract
Amino acid substitutions in the kinase domain of the human CSF1R gene are associated with autosomal dominant adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP). To model the human disease, we created a disease-associated mutation (pGlu631Lys; E631K) in the mouse Csf1r locus. Homozygous mutation (Csf1rE631K/E631K) phenocopied the Csf1r knockout, with prenatal mortality or severe postnatal growth retardation and hydrocephalus. Heterozygous mutation delayed the postnatal expansion of tissue macrophage populations in most organs. Bone marrow cells from Csf1rE631K/+mice were resistant to CSF1 stimulation in vitro, and Csf1rE631K/+ mice were unresponsive to administration of a CSF1-Fc fusion protein, which expanded tissue macrophage populations in controls. In the brain, microglial cell numbers and dendritic arborisation were reduced in Csf1rE631K/+ mice, as in patients with ALSP. The microglial phenotype is the opposite of microgliosis observed in Csf1r+/- mice. However, we found no evidence of brain pathology or impacts on motor function in aged Csf1rE631K/+ mice. We conclude that heterozygous disease-associated CSF1R mutations compromise CSF1R signalling. We speculate that leukoencephalopathy associated with dominant human CSF1R mutations requires an environmental trigger and/or epistatic interaction with common neurodegenerative disease-associated alleles.
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Affiliation(s)
- Jennifer Stables
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Emma K Green
- Centre for Inflammation Research and Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Omkar L Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Isis Taylor
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Maisie E Ashcroft
- Centre for Inflammation Research and Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Kathleen Grabert
- Toxicology Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Evi Wollscheid-Lengeling
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Belvaux, L-4401, Luxembourg
| | - Stefan Szymkowiak
- UK Dementia Research Institute, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Barry W McColl
- UK Dementia Research Institute, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Antony Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Neil E Humphreys
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Werner Mueller
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Hana Starobova
- Institute for Molecular Biosciences & School of Pharmacy, University of Queensland, Brisbane, Qld 4072, Australia
| | - Irina Vetter
- Institute for Molecular Biosciences & School of Pharmacy, University of Queensland, Brisbane, Qld 4072, Australia
| | | | | | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Clare Pridans
- Centre for Inflammation Research and Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
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Summers KM, Bush SJ, Wu C, Hume DA. Generation and network analysis of an RNA-seq transcriptional atlas for the rat. NAR Genom Bioinform 2022; 4:lqac017. [PMID: 35265836 PMCID: PMC8900154 DOI: 10.1093/nargab/lqac017] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
The laboratory rat is an important model for biomedical research. To generate a comprehensive rat transcriptomic atlas, we curated and downloaded 7700 rat RNA-seq datasets from public repositories, downsampled them to a common depth and quantified expression. Data from 585 rat tissues and cells, averaged from each BioProject, can be visualized and queried at http://biogps.org/ratatlas. Gene co-expression network (GCN) analysis revealed clusters of transcripts that were tissue or cell type restricted and contained transcription factors implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes. Many of these clusters overlap with previous data from analysis of other species, while some (e.g. expressed specifically in immune cells, retina/pineal gland, pituitary and germ cells) are unique to these data. GCN analysis on large subsets of the data related specifically to liver, nervous system, kidney, musculoskeletal system and cardiovascular system enabled deconvolution of cell type-specific signatures. The approach is extensible and the dataset can be used as a point of reference from which to analyse the transcriptomes of cell types and tissues that have not yet been sampled. Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single-cell RNA-seq data.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David A Hume
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
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Millard SM, Heng O, Opperman KS, Sehgal A, Irvine KM, Kaur S, Sandrock CJ, Wu AC, Magor GW, Batoon L, Perkins AC, Noll JE, Zannettino ACW, Sester DP, Levesque JP, Hume DA, Raggatt LJ, Summers KM, Pettit AR. Fragmentation of tissue-resident macrophages during isolation confounds analysis of single-cell preparations from mouse hematopoietic tissues. Cell Rep 2021; 37:110058. [PMID: 34818538 DOI: 10.1016/j.celrep.2021.110058] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 04/21/2021] [Revised: 09/28/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022] Open
Abstract
Mouse hematopoietic tissues contain abundant tissue-resident macrophages that support immunity, hematopoiesis, and bone homeostasis. A systematic strategy to characterize macrophage subsets in mouse bone marrow (BM), spleen, and lymph node unexpectedly reveals that macrophage surface marker staining emanates from membrane-bound subcellular remnants associated with unrelated cells. Intact macrophages are not present within these cell preparations. The macrophage remnant binding profile reflects interactions between macrophages and other cell types in vivo. Depletion of CD169+ macrophages in vivo eliminates F4/80+ remnant attachment. Remnant-restricted macrophage-specific membrane markers, cytoplasmic fluorescent reporters, and mRNA are all detected in non-macrophage cells including isolated stem and progenitor cells. Analysis of RNA sequencing (RNA-seq) data, including publicly available datasets, indicates that macrophage fragmentation is a general phenomenon that confounds bulk and single-cell analysis of disaggregated hematopoietic tissues. Hematopoietic tissue macrophage fragmentation undermines the accuracy of macrophage ex vivo molecular profiling and creates opportunity for misattribution of macrophage-expressed genes to non-macrophage cells.
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Affiliation(s)
- Susan M Millard
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Ostyn Heng
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Khatora S Opperman
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, PO Box 11060, Adelaide, SA 5001, Australia
| | - Anuj Sehgal
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Katharine M Irvine
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Simranpreet Kaur
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia; The University of Queensland, UQ Diamantina Institute, Brisbane, QLD 4102, Australia
| | - Cheyenne J Sandrock
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Andy C Wu
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia; TRI Flow Cytometry Suite, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Graham W Magor
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia; Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Lena Batoon
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Andrew C Perkins
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia; Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Jacqueline E Noll
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, PO Box 11060, Adelaide, SA 5001, Australia
| | - Andrew C W Zannettino
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, PO Box 11060, Adelaide, SA 5001, Australia; Central Adelaide Local Health Network, Adelaide, SA 5001, Australia
| | - David P Sester
- TRI Flow Cytometry Suite, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Jean-Pierre Levesque
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - David A Hume
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Liza J Raggatt
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Kim M Summers
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Allison R Pettit
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia.
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10
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Lévesque JP, Summers KM, Bisht K, Millard SM, Winkler IG, Pettit AR. Macrophages form erythropoietic niches and regulate iron homeostasis to adapt erythropoiesis in response to infections and inflammation. Exp Hematol 2021; 103:1-14. [PMID: 34500024 DOI: 10.1016/j.exphem.2021.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022]
Abstract
It has recently emerged that tissue-resident macrophages are key regulators of several stem cell niches orchestrating tissue formation during development, as well as postnatally, when they also organize the repair and regeneration of many tissues including the hemopoietic tissue. The fact that macrophages are also master regulators and effectors of innate immunity and inflammation allows them to coordinate hematopoietic response to infections, injuries, and inflammation. After recently reviewing the roles of phagocytes and macrophages in regulating normal and pathologic hematopoietic stem cell niches, we now focus on the key roles of macrophages in regulating erythropoiesis and iron homeostasis. We review herein the recent advances in understanding how macrophages at the center of erythroblastic islands form an erythropoietic niche that controls the terminal differentiation and maturation of erythroblasts into reticulocytes; how red pulp macrophages in the spleen control iron recycling and homeostasis; how these macrophages coordinate emergency erythropoiesis in response to blood loss, infections, and inflammation; and how persistent infections or inflammation can lead to anemia of inflammation via macrophages. Finally, we discuss the technical challenges associated with the molecular characterization of erythroid island macrophages and red pulp macrophages.
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Affiliation(s)
- Jean-Pierre Lévesque
- Mater Research Institute - The University of Queensland, Woolloongabba, QLD, Australia.
| | - Kim M Summers
- Mater Research Institute - The University of Queensland, Woolloongabba, QLD, Australia
| | - Kavita Bisht
- Mater Research Institute - The University of Queensland, Woolloongabba, QLD, Australia
| | - Susan M Millard
- Mater Research Institute - The University of Queensland, Woolloongabba, QLD, Australia
| | - Ingrid G Winkler
- Mater Research Institute - The University of Queensland, Woolloongabba, QLD, Australia
| | - Allison R Pettit
- Mater Research Institute - The University of Queensland, Woolloongabba, QLD, Australia
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11
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Lévesque JP, Summers KM, Millard SM, Bisht K, Winkler IG, Pettit AR. Role of macrophages and phagocytes in orchestrating normal and pathologic hematopoietic niches. Exp Hematol 2021; 100:12-31.e1. [PMID: 34298116 DOI: 10.1016/j.exphem.2021.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
The bone marrow (BM) contains a mosaic of niches specialized in supporting different maturity stages of hematopoietic stem and progenitor cells such as hematopoietic stem cells and myeloid, lymphoid, and erythroid progenitors. Recent advances in BM imaging and conditional gene knockout mice have revealed that niches are a complex network of cells of mesenchymal, endothelial, neuronal, and hematopoietic origins, together with local physicochemical parameters. Within these complex structures, phagocytes, such as neutrophils, macrophages, and dendritic cells, all of which are of hematopoietic origin, have been found to be important in regulating several niches in the BM, including hematopoietic stem cell niches, erythropoietic niches, and niches involved in endosteal bone formation. There is also increasing evidence that these macrophages have an important role in adapting hematopoiesis, erythropoiesis, and bone formation in response to inflammatory stressors and play a key part in maintaining the integrity and function of these. Likewise, there is also accumulating evidence that subsets of monocytes, macrophages, and other phagocytes contribute to the progression and response to treatment of several lymphoid malignancies such as multiple myeloma, Hodgkin lymphoma, and non-Hodgkin lymphoma, as well as lymphoblastic leukemia, and may also play a role in myelodysplastic syndrome and myeloproliferative neoplasms associated with Noonan syndrome and aplastic anemia. In this review, the potential functions of macrophages and other phagocytes in normal and pathologic niches are discussed, as are the challenges in studying BM and other tissue-resident macrophages at the molecular level.
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Affiliation(s)
- Jean-Pierre Lévesque
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia.
| | - Kim M Summers
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Susan M Millard
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Kavita Bisht
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Ingrid G Winkler
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Allison R Pettit
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
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12
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Keshvari S, Caruso M, Teakle N, Batoon L, Sehgal A, Patkar OL, Ferrari-Cestari M, Snell CE, Chen C, Stevenson A, Davis FM, Bush SJ, Pridans C, Summers KM, Pettit AR, Irvine KM, Hume DA. CSF1R-dependent macrophages control postnatal somatic growth and organ maturation. PLoS Genet 2021; 17:e1009605. [PMID: 34081701 PMCID: PMC8205168 DOI: 10.1371/journal.pgen.1009605] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 04/08/2021] [Revised: 06/15/2021] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Homozygous mutation of the Csf1r locus (Csf1rko) in mice, rats and humans leads to multiple postnatal developmental abnormalities. To enable analysis of the mechanisms underlying the phenotypic impacts of Csf1r mutation, we bred a rat Csf1rko allele to the inbred dark agouti (DA) genetic background and to a Csf1r-mApple reporter transgene. The Csf1rko led to almost complete loss of embryonic macrophages and ablation of most adult tissue macrophage populations. We extended previous analysis of the Csf1rko phenotype to early postnatal development to reveal impacts on musculoskeletal development and proliferation and morphogenesis in multiple organs. Expression profiling of 3-week old wild-type (WT) and Csf1rko livers identified 2760 differentially expressed genes associated with the loss of macrophages, severe hypoplasia, delayed hepatocyte maturation, disrupted lipid metabolism and the IGF1/IGF binding protein system. Older Csf1rko rats developed severe hepatic steatosis. Consistent with the developmental delay in the liver Csf1rko rats had greatly-reduced circulating IGF1. Transfer of WT bone marrow (BM) cells at weaning without conditioning repopulated resident macrophages in all organs, including microglia in the brain, and reversed the mutant phenotypes enabling long term survival and fertility. WT BM transfer restored osteoclasts, eliminated osteopetrosis, restored bone marrow cellularity and architecture and reversed granulocytosis and B cell deficiency. Csf1rko rats had an elevated circulating CSF1 concentration which was rapidly reduced to WT levels following BM transfer. However, CD43hi non-classical monocytes, absent in the Csf1rko, were not rescued and bone marrow progenitors remained unresponsive to CSF1. The results demonstrate that the Csf1rko phenotype is autonomous to BM-derived cells and indicate that BM contains a progenitor of tissue macrophages distinct from hematopoietic stem cells. The model provides a unique system in which to define the pathways of development of resident tissue macrophages and their local and systemic roles in growth and organ maturation.
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Affiliation(s)
- Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Melanie Caruso
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Ngari Teakle
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Lena Batoon
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Omkar L. Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Michelle Ferrari-Cestari
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Cameron E. Snell
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Chen Chen
- School of Biomedical Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Alex Stevenson
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Felicity M. Davis
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Clare Pridans
- Centre for Inflammation Research and Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Allison R. Pettit
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
| | - Katharine M. Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
- * E-mail: (KMI); (DAH)
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, Australia
- * E-mail: (KMI); (DAH)
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13
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Gažová I, Lefevre L, Bush SJ, Rojo R, Hume DA, Lengeling A, Summers KM. CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1. Front Cell Dev Biol 2021; 9:679544. [PMID: 34136489 PMCID: PMC8203323 DOI: 10.3389/fcell.2021.679544] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
USP16 is a histone deubiquitinase which facilitates G2/M transition during the cell cycle, regulates DNA damage repair and contributes to inducible gene expression. We mutated the USP16 gene in a high differentiation clone of the acute monocytic leukemia cell line THP-1 using the CRISPR-Cas9 system and generated four homozygous knockout clones. All were able to proliferate and to differentiate in response to phorbol ester (PMA) treatment. One line was highly proliferative prior to PMA treatment and shut down proliferation upon differentiation, like wild type. Three clones showed sustained expression of the progenitor cell marker MYB, indicating that differentiation had not completely blocked proliferation in these clones. Network analysis of transcriptomic differences among wild type, heterozygotes and homozygotes showed clusters of genes that were up- or down-regulated after differentiation in all cell lines. Prior to PMA treatment, the homozygous clones had lower levels than wild type of genes relating to metabolism and mitochondria, including SRPRB, encoding an interaction partner of USP16. There was also apparent loss of interferon signaling. In contrast, a number of genes were up-regulated in the homozygous cells compared to wild type at baseline, including other deubiquitinases (USP12, BAP1, and MYSM1). However, three homozygotes failed to fully induce USP3 during differentiation. Other network clusters showed effects prior to or after differentiation in the homozygous clones. Thus the removal of USP16 affected the transcriptome of the cells, although all these lines were able to survive, which suggests that the functions attributed to USP16 may be redundant. Our analysis indicates that the leukemic line can adapt to the extreme selection pressure applied by the loss of USP16, and the harsh conditions of the gene editing and selection protocol, through different compensatory pathways. Similar selection pressures occur during the evolution of a cancer in vivo, and our results can be seen as a case study in leukemic cell adaptation. USP16 has been considered a target for cancer chemotherapy, but our results suggest that treatment would select for escape mutants that are resistant to USP16 inhibitors.
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Affiliation(s)
- Iveta Gažová
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Stephen J Bush
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Rocio Rojo
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - David A Hume
- Mater Research Institute - University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Andreas Lengeling
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Kim M Summers
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom.,Mater Research Institute - University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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14
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Hume DA, Caruso M, Keshvari S, Patkar OL, Sehgal A, Bush SJ, Summers KM, Pridans C, Irvine KM. The Mononuclear Phagocyte System of the Rat. J Immunol 2021; 206:2251-2263. [PMID: 33965905 DOI: 10.4049/jimmunol.2100136] [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] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
The laboratory rat continues to be the model of choice for many studies of physiology, behavior, and complex human diseases. Cells of the mononuclear phagocyte system (MPS; monocytes, macrophages, and dendritic cells) are abundant residents in every tissue in the body and regulate postnatal development, homeostasis, and innate and acquired immunity. Recruitment and proliferation of MPS cells is an essential component of both initiation and resolution of inflammation. The large majority of current knowledge of MPS biology is derived from studies of inbred mice, but advances in technology and resources have eliminated many of the advantages of the mouse as a model. In this article, we review the tools available and the current state of knowledge of development, homeostasis, regulation, and diversity within the MPS of the rat.
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Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Caruso
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Omkar L Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Clare Pridans
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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15
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Ewing AD, Cheetham SW, McGill JJ, Sharkey M, Walker R, West JA, West MJ, Summers KM. Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype. Am J Med Genet A 2021; 185:2070-2083. [PMID: 33960642 PMCID: PMC8251932 DOI: 10.1002/ajmg.a.62224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/23/2020] [Revised: 03/17/2021] [Accepted: 04/02/2021] [Indexed: 01/20/2023]
Abstract
Basal cell nevus syndrome (also known as Gorlin Syndrome; MIM109400) is an autosomal dominant disorder characterized by recurrent pathological features such as basal cell carcinomas and odontogenic keratocysts as well as skeletal abnormalities. Most affected individuals have point mutations or small insertions or deletions within the PTCH1 gene on human chromosome 9, but there are some cases with more extensive deletion of the region, usually including the neighboring FANCC and/or ERCC6L2 genes. We report a 16‐year‐old patient with a deletion of approximately 400,000 bases which removes only PTCH1 and some non‐coding RNA genes but leaves FANCC and ERCC6L2 intact. In spite of the small amount of DNA for which he is haploid, his phenotype is more extreme than many individuals with longer deletions in the region. This includes early presentation with a large number of basal cell nevi and other skin lesions, multiple jaw keratocysts, and macrosomia. We found that the deletion was in the paternal chromosome, in common with other macrosomia cases. Using public databases, we have examined possible interactions between sequences within and outside the deletion and speculate that a regulatory relationship exists with flanking genes, which is unbalanced by the deletion, resulting in abnormal activation or repression of the target genes and hence the severity of the phenotype.
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Affiliation(s)
- Adam D Ewing
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Seth W Cheetham
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - James J McGill
- Department of Chemical Pathology, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Michael Sharkey
- Paddington Dermatology Specialist Clinic, Paddington, Queensland, Australia
| | - Rick Walker
- QLD Youth Cancer Service, Queensland Children's Hospital, South Brisbane, Queensland, Australia.,School of Clinical Medicine, The University of Queensland, Herston, Queensland, Australia
| | - Jennifer A West
- Northside Clinical School, Prince Charles Hospital, The University of Queensland, Chermside, Queensland, Australia
| | - Malcolm J West
- Northside Clinical School, Prince Charles Hospital, The University of Queensland, Chermside, Queensland, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
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16
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Prieto Ramos J, Corda A, Swift S, Saderi L, De La Fuente Oliver G, Corcoran B, Summers KM, French AT. Clinical and Echocardiographic Findings in an Aged Population of Cavalier King Charles Spaniels. Animals (Basel) 2021; 11:ani11040949. [PMID: 33800666 PMCID: PMC8065390 DOI: 10.3390/ani11040949] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Myxomatous mitral valve disease (MMVD) is the most common cardiac disease in dogs. It varies from dogs without clinical signs to those developing left-sided congestive heart failure, leading to death. Cavalier King Charles Spaniels (CKCSs) are particularly susceptible to MMVD. We hypothesised that within the elderly CKCS population, there is a sub-cohort of MMVD-affected dogs that do not have cardiac remodelling. The objectives of the present study were (i) to determine the prevalence and the degree of cardiac remodelling associated with MMVD; and (ii) assess the effect of age, gender, and body weight on echocardiographic status in a population of aged CKCSs. A total of 126 CKCSs ≥ 8 years old were prospectively included. They all had a physical and echocardiographic examination. A systolic murmur was detected in 89% of dogs; the presence of clinical signs was reported in 19% of them; and echocardiographic evidence of MMVD was described in 100%. Despite the high prevalence, 44.4% of the dogs were clear of echocardiographic signs of cardiac remodelling. Age was significantly associated with the presence and severity of cardiac remodelling and mitral valve prolapse. Our results showed that a proportion of elderly CKCS with confirmed MMVD did not undergo advanced stages of this pathology.
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Affiliation(s)
| | - Andrea Corda
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-3494381468
| | - Simon Swift
- College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Laura Saderi
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy;
| | | | - Brendan Corcoran
- Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, University of Edinburgh, Midlothian EH25 9RG, UK;
| | - Kim M. Summers
- Translational Research Institute, Mater Research Institute-University of Queensland, 37 Kent St, Wooloongabba, QLD 4102, Australia;
| | - Anne T. French
- School of Veterinary Medicine, Ross University, Two mile hill st., Michael BB11093, Barbados;
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17
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Nguyen EB, Jacobs EA, Summers KM, Sparks AE, Van Voorhis BJ, Klenov VE, Duran EH. Embryo blastulation and quality between days 5 and 6 of extended embryo culture. J Assist Reprod Genet 2021; 38:2193-2198. [PMID: 33754252 DOI: 10.1007/s10815-021-02156-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/16/2021] [Indexed: 11/28/2022] Open
Abstract
PURPOSE This study aims to know what proportion of culture day 5 pre-blastocyst-stage embryos develop into blastocysts by culture day 6 and what patient and cycle characteristics are associated with delayed blastocyst formation. METHODS A retrospective observational cohort analysis was performed including a total of 9886 embryos from 1008 IVF cycles in 835 patients, who underwent treatment between January 1, 2016, and December 31, 2018. Autologous fresh in vitro fertilization (IVF) cycles at a single academic center were included in the analysis. Embryos were group-cultured using single-step culture media. Blastulation was defined as the presence of a new blastocyst. Usable blastulation was defined as the presence of a new good or excellent quality, expanded, hatching, or hatched blastocysts. RESULTS The mean blastulation rate between days 5 and 6 of extended embryo culture was 30.9%. The mean percentage of embryos developing into usable blastocyst-stage embryos was 19.8%. The factors associated with blastulation on day 6 included the total number of embryos and the number of pre-blastocysts on day 5, as well as the use of ICSI. Age, the number of total embryos, those remained in culture and pre-blastocysts, as well as the blastulation rate on day 5 were associated with usable blastulation. CONCLUSION It is important to know the usable blastocyst development rate between culture days 5 and 6 in order to adequately counsel patients debating whether to proceed with fresh ET on day 5 or forego ET with the expectation that embryos will be biopsied for PGT and/or cryopreserved on culture day 6. Our findings provide evidence to help guide patients in this difficult decision.
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Affiliation(s)
- E B Nguyen
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA.,Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - E A Jacobs
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - K M Summers
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - A E Sparks
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - B J Van Voorhis
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - V E Klenov
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - E H Duran
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA. .,Department of Obstetrics and Gynecology, 200 Hawkins Drive, 31322 PFP, Iowa City, IA, 52242, USA.
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18
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Patkar OL, Caruso M, Teakle N, Keshvari S, Bush SJ, Pridans C, Belmer A, Summers KM, Irvine KM, Hume DA. Analysis of homozygous and heterozygous Csf1r knockout in the rat as a model for understanding microglial function in brain development and the impacts of human CSF1R mutations. Neurobiol Dis 2021; 151:105268. [PMID: 33450391 PMCID: PMC7941205 DOI: 10.1016/j.nbd.2021.105268] [Citation(s) in RCA: 19] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Mutations in the human CSF1R gene have been associated with dominant and recessive forms of neurodegenerative disease. Here we describe the impacts of Csf1r mutation in the rat on development of the brain. Diffusion imaging indicated small reductions in major fiber tracts that may be associated in part with ventricular enlargement. RNA-seq profiling revealed a set of 105 microglial markers depleted in all brain regions of the Csf1rko rats. There was no evidence of region or sex-specific expression of microglia-associated transcripts. Other than the microglial signature, Csf1rko had no effect on any neuronal or region-specific transcript cluster. Expression of markers of oligodendrocytes, astrocytes, dopaminergic neurons and Purkinje cells was minimally affected. However, there were defects in dendritic arborization of doublecortin-positive neurogenic precursors and expression of poly-sialylated neural cell adhesion molecule (PS-NCAM) in the dentate gyrus of the hippocampus. Heterozygous Csf1rko rats had no detectable brain phenotype. We conclude that most brain developmental processes occur normally in the absence of microglia and that CSF1R haploinsufficiency is unlikely to cause leukoencephalopathy.
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Affiliation(s)
- Omkar L Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Caruso
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Ngari Teakle
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK and Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, UK
| | - Arnauld Belmer
- School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia.
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Summers KM, Bush SJ, Hume DA. Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system. PLoS Biol 2020; 18:e3000859. [PMID: 33031383 PMCID: PMC7575120 DOI: 10.1371/journal.pbio.3000859] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [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: 04/10/2020] [Revised: 10/20/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The mononuclear phagocyte system (MPS) is a family of cells including progenitors, circulating blood monocytes, resident tissue macrophages, and dendritic cells (DCs) present in every tissue in the body. To test the relationships between markers and transcriptomic diversity in the MPS, we collected from National Center for Biotechnology Information Gene Expression Omnibus (NCBI-GEO) a total of 466 quality RNA sequencing (RNA-seq) data sets generated from mouse MPS cells isolated from bone marrow, blood, and multiple tissues. The primary data were randomly downsized to a depth of 10 million reads and requantified. The resulting data set was clustered using the network analysis tool BioLayout. A sample-to-sample matrix revealed that MPS populations could be separated based upon tissue of origin. Cells identified as classical DC subsets, cDC1s and cDC2s, and lacking Fcgr1 (encoding the protein CD64) were contained within the MPS cluster, no more distinct than other MPS cells. A gene-to-gene correlation matrix identified large generic coexpression clusters associated with MPS maturation and innate immune function. Smaller coexpression gene clusters, including the transcription factors that drive them, showed higher expression within defined isolated cells, including monocytes, macrophages, and DCs isolated from specific tissues. They include a cluster containing Lyve1 that implies a function in endothelial cell (EC) homeostasis, a cluster of transcripts enriched in intestinal macrophages, and a generic lymphoid tissue cDC cluster associated with Ccr7. However, transcripts encoding Adgre1, Itgax, Itgam, Clec9a, Cd163, Mertk, Mrc1, Retnla, and H2-a/e (encoding class II major histocompatibility complex [MHC] proteins) and many other proposed macrophage subset and DC lineage markers each had idiosyncratic expression profiles. Coexpression of immediate early genes (for example, Egr1, Fos, Dusp1) and inflammatory cytokines and chemokines (tumour necrosis factor [Tnf], Il1b, Ccl3/4) indicated that all tissue disaggregation and separation protocols activate MPS cells. Tissue-specific expression clusters indicated that all cell isolation procedures also co-purify other unrelated cell types that may interact with MPS cells in vivo. Comparative analysis of RNA-seq and single-cell RNA-seq (scRNA-seq) data from the same lung cell populations indicated that MPS heterogeneity implied by global cluster analysis may be even greater at a single-cell level. This analysis highlights the power of large data sets to identify the diversity of MPS cellular phenotypes and the limited predictive value of surface markers to define lineages, functions, or subpopulations.
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Affiliation(s)
- Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
- * E-mail:
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20
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Markby GR, Macrae VE, Corcoran BM, Summers KM. Comparative transcriptomic profiling of myxomatous mitral valve disease in the cavalier King Charles spaniel. BMC Vet Res 2020; 16:350. [PMID: 32967675 PMCID: PMC7509937 DOI: 10.1186/s12917-020-02542-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Almost all elderly dogs develop myxomatous mitral valve disease by the end of their life, but the cavalier King Charles spaniel (CKCS) has a heightened susceptibility, frequently resulting in death at a young age and suggesting that there is a genetic component to the condition in this breed. Transcriptional profiling can reveal the impact of genetic variation through differences in gene expression levels. The aim of this study was to determine whether expression patterns were different in mitral valves showing myxomatous degeneration from CKCS dogs compared to valves from non-CKCS dogs. RESULTS Gene expression patterns in three groups of canine valves resulted in distinct separation of normal valves, diseased valves from CKCS and diseased valves from other breeds; the latter were more similar to the normal valves than were the valves from CKCS. Gene expression patterns in diseased valves from CKCS dogs were quite different from those in the valves from other dogs, both affected and normal. Patterns in all diseased valves (from CKCS and other breeds) were also somewhat different from normal non-diseased samples. Analysis of differentially expressed genes showed enrichment in GO terms relating to cardiac development and function and to calcium signalling canonical pathway in the genes down-regulated in the diseased valves from CKCS, compared to normal valves and to diseased valves from other breeds. F2 (prothrombin) (CKCS diseased valves compared to normal) and MEF2C pathway activation (CKCS diseased valves compared to non-CKCS diseased valves) had the strongest association with the gene changes. A large number of genes that were differentially expressed in the CKCS diseased valves compared with normal valves and diseased valves from other breeds were associated with cardiomyocytes including CASQ2, TNNI3 and RYR2. CONCLUSION Transcriptomic profiling identified gene expression changes in CKCS diseased valves that were not present in age and disease severity-matched non-CKCS valves. These genes are associated with cardiomyocytes, coagulation and extra-cellular matrix remodelling. Identification of genes that vary in the CKCS will allow exploration of genetic variation to understand the aetiology of the disease in this breed, and ultimately development of breeding strategies to eliminate this disease from the breed.
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Affiliation(s)
- G R Markby
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG
| | - V E Macrae
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG
| | - B M Corcoran
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG.
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG.
| | - K M Summers
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG
- Mater Research Institute-University of Queensland, 37 Kent St, Woolloongabba, QLD, 4102, Australia
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21
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Tsang HG, Clark EL, Markby GR, Bush SJ, Hume DA, Corcoran BM, MacRae VE, Summers KM. Expression of Calcification and Extracellular Matrix Genes in the Cardiovascular System of the Healthy Domestic Sheep ( Ovis aries). Front Genet 2020; 11:919. [PMID: 33101359 PMCID: PMC7506100 DOI: 10.3389/fgene.2020.00919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
The maintenance of a healthy cardiovascular system requires expression of genes that contribute to essential biological activities and repression of those that are associated with functions likely to be detrimental to cardiovascular homeostasis. Vascular calcification is a major disruption to cardiovascular homeostasis, where tissues of the cardiovascular system undergo ectopic calcification and consequent dysfunction, but little is known about the expression of calcification genes in the healthy cardiovascular system. Large animal models are of increasing importance in cardiovascular disease research as they demonstrate more similar cardiovascular features (in terms of anatomy, physiology and size) to humans than do rodent species. We used RNA sequencing results from the sheep, which has been utilized extensively to examine calcification of prosthetic cardiac valves, to explore the transcriptome of the heart and cardiac valves in this large animal, in particular looking at expression of calcification and extracellular matrix genes. We then examined genes implicated in the process of vascular calcification in a wide array of cardiovascular tissues and across multiple developmental stages, using RT-qPCR. Our results demonstrate that there is a balance between genes that promote and those that suppress mineralization during development and across cardiovascular tissues. We show extensive expression of genes encoding proteins involved in formation and maintenance of the extracellular matrix in cardiovascular tissues, and high expression of hematopoietic genes in the cardiac valves. Our analysis will support future research into the functions of implicated genes in the development of valve calcification, and increase the utility of the sheep as a large animal model for understanding ectopic calcification in cardiovascular disease. This study provides a foundation to explore the transcriptome of the developing cardiovascular system and is a valuable resource for the fields of mammalian genomics and cardiovascular research.
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Affiliation(s)
- Hiu-Gwen Tsang
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Emily L. Clark
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Greg R. Markby
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Brendan M. Corcoran
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Vicky E. MacRae
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Kim M. Summers
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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22
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Sheng YH, Ng GZ, Summers KM, Every AL, Price G, Hasnain SZ, Sutton P, McGuckin MA. Influence of the MUC1 Cell Surface Mucin on Gastric Mucosal Gene Expression Profiles in Response to Helicobacter pylori Infection in Mice. Front Cell Infect Microbiol 2020; 10:343. [PMID: 32793510 PMCID: PMC7393270 DOI: 10.3389/fcimb.2020.00343] [Citation(s) in RCA: 2] [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: 03/19/2020] [Accepted: 06/04/2020] [Indexed: 11/26/2022] Open
Abstract
The cell surface mucin MUC1 is an important host factor limiting Helicobacter pylori (H. pylori) pathogenesis in both humans and mice by providing a protective barrier and modulating mucosal epithelial and leukocyte responses. The aim of this study was to establish the time-course of molecular events in MUC1-modulated gene expression profiles in response to H. pylori infection in wild type (WT) and MUC1-deficient mice using microarray-determined mRNA expression, gene network analysis and Ingenuity Pathway Analysis (IPA). A time-course over the first 72 h of infection showed significantly higher mucosal loads of bacteria at 8 h of infection in Muc1−/− mice compared with WT, confirming its importance in the early stages of infection (P = 0.0003). Microarray analysis revealed 266 differentially expressed genes at one or more time-points over 72 h in the gastric mucosa of Muc1−/− mice compared with WT control using a threshold of 2-fold change. The SPINK1 pancreatic cancer canonical pathway was strongly inhibited in Muc1−/− mice compared with WT at sham and 8 h infection (P = 6.08E-14 and P = 2.25 E-19, respectively) but potently activated at 24 and 72 h post-infection (P = 1.38E-22 and P = 5.87E-13, respectively). The changes in this pathway are reflective of higher expression of genes mediating digestion and absorption of lipids, carbohydrates, and proteins at sham and 8 h infection in the absence of MUC1, but that this transcriptional signature is highly down regulated as infection progresses in the absence of MUC1. Uninfected Muc1−/− gastric tissue was highly enriched for expression of factors involved in lipid metabolism and 8 h infection further activated this network compared with WT. As infection progressed, a network of antimicrobial and anti-inflammatory response genes was more highly activated in Muc1−/− than WT mice. Key target genes identified by time-course microarrays were independently validated using RT-qPCR. These results highlight the dynamic interplay between the host and H. pylori, and the role of MUC1 in host defense, and provide a general picture of changes in cellular gene expression modulated by MUC1 in a time-dependent manner in response to H. pylori infection.
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Affiliation(s)
- Yong H Sheng
- Inflammatory Disease Biology and Therapeutics Group, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Garrett Z Ng
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kim M Summers
- Genetics, Genomics & Transcriptomics of Disease Group, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Alison L Every
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Gareth Price
- QCIF Facility for Advanced Bioinformatics, Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Sumaira Z Hasnain
- Inflammatory Disease Biology and Therapeutics Group, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Philip Sutton
- Mucosal Immunology, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Michael A McGuckin
- Inflammatory Disease Biology and Therapeutics Group, Mater Research Institute - The University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia.,Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, Australia
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23
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Bush SJ, McCulloch MEB, Lisowski ZM, Muriuki C, Clark EL, Young R, Pridans C, Prendergast JGD, Summers KM, Hume DA. Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages. Front Cell Dev Biol 2020; 8:661. [PMID: 32793601 PMCID: PMC7386301 DOI: 10.3389/fcell.2020.00661] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 02/02/2023] Open
Abstract
Mammalian macrophages differ in their basal gene expression profiles and response to the toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS). In human macrophages, LPS elicits a temporal cascade of transient gene expression including feed forward activators and feedback regulators that limit the response. Here we present a transcriptional network analysis of the response of sheep bone marrow-derived macrophages (BMDM) to LPS based upon RNA-seq at 0, 2, 4, 7, and 24 h post-stimulation. The analysis reveals a conserved transcription factor network with humans, and rapid induction of feedback regulators that constrain the response at every level. The gene expression profiles of sheep BMDM at 0 and 7 h post LPS addition were compared to similar data obtained from goat, cow, water buffalo, horse, pig, mouse and rat BMDM. This comparison was based upon identification of 8,200 genes annotated in all species and detected at >10TPM in at least one sample. Analysis of expression of transcription factors revealed a conserved transcriptional millieu associated with macrophage differentiation and LPS response. The largest co-expression clusters, including genes encoding cell surface receptors, endosome–lysosome components and secretory activity, were also expressed in all species and the combined dataset defines a macrophage functional transcriptome. All of the large animals differed from rodents in lacking inducible expression of genes involved in arginine metabolism and nitric oxide production. Instead, they expressed inducible transporters and enzymes of tryptophan and kynurenine metabolism. BMDM from all species expressed high levels of transcripts encoding transporters and enzymes involved in glutamine metabolism suggesting that glutamine is a major metabolic fuel. We identify and discuss transcripts that were uniquely expressed or regulated in rodents compared to large animals including ACOD1, CXC and CC chemokines, CD163, CLEC4E, CPM, CSF1, CSF2, CTSK, MARCO, MMP9, SLC2A3, SLC7A7, and SUCNR1. Conversely, the data confirm the conserved regulation of multiple transcripts for which there is limited functional data from mouse models and knockouts. The data provide a resource for functional annotation and interpretation of loci involved in susceptibility to infectious and inflammatory disease in humans and large animal species.
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Affiliation(s)
- Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mary E B McCulloch
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Zofia M Lisowski
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Charity Muriuki
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Emily L Clark
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rachel Young
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Clare Pridans
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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24
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Gažová I, Lefevre L, Bush SJ, Clohisey S, Arner E, de Hoon M, Severin J, van Duin L, Andersson R, Lengeling A, Hume DA, Summers KM. The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1. Front Cell Dev Biol 2020; 8:498. [PMID: 32719792 PMCID: PMC7347797 DOI: 10.3389/fcell.2020.00498] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
The response of the human acute myeloid leukemia cell line THP-1 to phorbol esters has been widely studied to test candidate leukemia therapies and as a model of cell cycle arrest and monocyte-macrophage differentiation. Here we have employed Cap Analysis of Gene Expression (CAGE) to analyze a dense time course of transcriptional regulation in THP-1 cells treated with phorbol myristate acetate (PMA) over 96 h. PMA treatment greatly reduced the numbers of cells entering S phase and also blocked cells exiting G2/M. The PMA-treated cells became adherent and expression of mature macrophage-specific genes increased progressively over the duration of the time course. Within 1–2 h PMA induced known targets of tumor protein p53 (TP53), notably CDKN1A, followed by gradual down-regulation of cell-cycle associated genes. Also within the first 2 h, PMA induced immediate early genes including transcription factor genes encoding proteins implicated in macrophage differentiation (EGR2, JUN, MAFB) and down-regulated genes for transcription factors involved in immature myeloid cell proliferation (MYB, IRF8, GFI1). The dense time course revealed that the response to PMA was not linear and progressive. Rather, network-based clustering of the time course data highlighted a sequential cascade of transient up- and down-regulated expression of genes encoding feedback regulators, as well as transcription factors associated with macrophage differentiation and their inferred target genes. CAGE also identified known and candidate novel enhancers expressed in THP-1 cells and many novel inducible genes that currently lack functional annotation and/or had no previously known function in macrophages. The time course is available on the ZENBU platform allowing comparison to FANTOM4 and FANTOM5 data.
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Affiliation(s)
- Iveta Gažová
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J Bush
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sara Clohisey
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama, Japan
| | - Lucas van Duin
- Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Robin Andersson
- Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - David A Hume
- Mater Research Institute - University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Kim M Summers
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom.,Mater Research Institute - University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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25
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Markby GR, Macrae VE, Summers KM, Corcoran BM. Disease Severity-Associated Gene Expression in Canine Myxomatous Mitral Valve Disease Is Dominated by TGFβ Signaling. Front Genet 2020; 11:372. [PMID: 32395121 PMCID: PMC7197751 DOI: 10.3389/fgene.2020.00372] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/17/2019] [Accepted: 03/26/2020] [Indexed: 12/21/2022] Open
Abstract
Myxomatous mitral valve disease (MMVD) is the most common acquired canine cardiovascular disease and shares many similarities with human mitral valvulopathies. While transcriptomic datasets are available for the end-stage disease in both species, there is no information on how gene expression changes as the disease progresses, such that it cannot be stated with certainty if the changes seen in end-stage disease are casual or consequential. In contrast to humans, the disease in dogs can be more readily examined as it progresses, and this allows an opportunity for insight into disease pathogenesis relevant to both species. The aim of this study was to identify changes in valve gene expression as canine MMVD advances over an entire life-time, from normal (grade 0) to severely affected (grade 4), and differences in gene expression comparing normal and disease areas of the same valve. Transcriptomic profiling identified 1002 differentially expressed genes (DEGs) across all four disease grades when compared with normal valves with the greatest number of DEGs in grade 3 (673) and grade 4 (507). DEGs were associated with a large number of gene families, including genes encoding cytoskeletal filaments, peptidases, extra-cellular matrix (ECM) proteins, chemokines and integrins. Gene enrichment analysis identified significant grade-dependent changes in gene clustering, with clusters trending both up and down as disease progressed. Significant grade-dependent changes in hallmark disease gene expression intensity were identified, including ACTA2, HTR2B, MMP12, and CDKN2A. Gene Ontology terms were dominated by terms for ECM and inflammation with TGFβ1, TNF, IFGN identified as the top up-stream regulators in both whole and dissected diseased valve samples. These data show that while disease progression in MMVD is associated with increasing numbers of DEGs, TGFβ appears to be the dominant signaling pathway controlling pathogenesis irrespective of disease severity.
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Affiliation(s)
- Greg R Markby
- The Roslin Institute, University of Edinburgh, Scotland, United Kingdom
| | - Vicky E Macrae
- The Roslin Institute, University of Edinburgh, Scotland, United Kingdom
| | - Kim M Summers
- The Roslin Institute, University of Edinburgh, Scotland, United Kingdom
| | - Brendan M Corcoran
- The Roslin Institute, University of Edinburgh, Scotland, United Kingdom.,Royal Dick, School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom
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26
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Summers KM, Bush SJ, Wu C, Su AI, Muriuki C, Clark EL, Finlayson HA, Eory L, Waddell LA, Talbot R, Archibald AL, Hume DA. Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas. Front Genet 2020; 10:1355. [PMID: 32117413 PMCID: PMC7034361 DOI: 10.3389/fgene.2019.01355] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
The domestic pig (Sus scrofa) is both an economically important livestock species and a model for biomedical research. Two highly contiguous pig reference genomes have recently been released. To support functional annotation of the pig genomes and comparative analysis with large human transcriptomic data sets, we aimed to create a pig gene expression atlas. To achieve this objective, we extended a previous approach developed for the chicken. We downloaded RNAseq data sets from public repositories, down-sampled to a common depth, and quantified expression against a reference transcriptome using the mRNA quantitation tool, Kallisto. We then used the network analysis tool Graphia to identify clusters of transcripts that were coexpressed across the merged data set. Consistent with the principle of guilt-by-association, we identified coexpression clusters that were highly tissue or cell-type restricted and contained transcription factors that have previously been implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes, such as the cell cycle and oxidative phosphorylation. The same approach was used to identify coexpression clusters within RNAseq data from multiple individual liver and brain samples, highlighting cell type, process, and region-specific gene expression. Evidence of conserved expression can add confidence to assignment of orthology between pig and human genes. Many transcripts currently identified as novel genes with ENSSSCG or LOC IDs were found to be coexpressed with annotated neighbouring transcripts in the same orientation, indicating they may be products of the same transcriptional unit. The meta-analytic approach to utilising public RNAseq data is extendable to include new data sets and new species and provides a framework to support the Functional Annotation of Animals Genomes (FAANG) initiative.
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Affiliation(s)
- Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andrew I. Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Charity Muriuki
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Emily L. Clark
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | | | - Lel Eory
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Lindsey A. Waddell
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Richard Talbot
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Alan L. Archibald
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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27
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McInerney-Leo AM, West J, Wheeler L, Leo PJ, Summers KM, Anderson L, Brown MA, West M, Duncan EL. Compound heterozygous mutations in FBN1 in a large family with Marfan syndrome. Mol Genet Genomic Med 2020; 8:e1116. [PMID: 31950671 PMCID: PMC7057098 DOI: 10.1002/mgg3.1116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/15/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022] Open
Abstract
Background Marfan syndrome (MFS) is a dominant monogenic disorder caused by mutations in fibrillin 1 (FBN1). Rarely, compound heterozygosity for FBN1 mutations has been described. Methods A large kindred with MFS was assessed clinically over decades, and genetically using exome and/or Sanger sequencing. Results A previously identified FBN1 missense variant (p.Tyr754Cys) was confirmed in all subjects with MFS. An additional variant (p.Met2273Thr), previously associated with incomplete MFS, was identified in three siblings. These three compound heterozygous individuals had aortic dilatation at early age (all <30 years): one also had cerebral and ocular aneurysms; and one, who had undergone surgical repair aged 18 years, died from aortic dissection at 31 years. In contrast, their heterozygous father (p.Tyr754Cys) with MFS died at 57 years (myocardial infarction) without requiring surgical intervention and one heterozygous (p.Tyr754Cys) sibling has aortic dilatation presenting >40 years but not requiring surgical intervention. Another heterozygous (p.Tyr754Cys) sibling did require aortic root repair (28 years). The heterozygous (p.Met2273Thr) mother had aortic dilatation diagnosed at age 68 years but has not required surgical repair. Conclusion Although compound heterozygosity or homozygosity is rare in MFS, it should be considered when there is an unusually severe phenotype in a subset of family members.
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Affiliation(s)
- Aideen M McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia.,Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD, Australia
| | - Jennifer West
- School of Clinical Medicine, Prince Charles Hospital Clinical Unit, The University of Queensland, Brisbane, QLD, Australia
| | - Lawrie Wheeler
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD, Australia
| | - Paul J Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Lisa Anderson
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD, Australia
| | - Matthew A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD, Australia
| | - Malcolm West
- School of Clinical Medicine, Prince Charles Hospital Clinical Unit, The University of Queensland, Brisbane, QLD, Australia
| | - Emma L Duncan
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD, Australia.,Department of Endocrinology, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
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Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC. Visualization and analysis of RNA-Seq assembly graphs. Nucleic Acids Res 2019; 47:7262-7275. [PMID: 31305886 PMCID: PMC6698738 DOI: 10.1093/nar/gkz599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/19/2018] [Revised: 05/31/2019] [Accepted: 07/10/2019] [Indexed: 01/20/2023] Open
Abstract
RNA-Seq is a powerful transcriptome profiling technology enabling transcript discovery and quantification. Whilst most commonly used for gene-level quantification, the data can be used for the analysis of transcript isoforms. However, when the underlying transcript assemblies are complex, current visualization approaches can be limiting, with splicing events a challenge to interpret. Here, we report on the development of a graph-based visualization method as a complementary approach to understanding transcript diversity from short-read RNA-Seq data. Following the mapping of reads to a reference genome, a read-to-read comparison is performed on all reads mapping to a given gene, producing a weighted similarity matrix between reads. This is used to produce an RNA assembly graph, where nodes represent reads and edges similarity scores between them. The resulting graphs are visualized in 3D space to better appreciate their sometimes large and complex topology, with other information being overlaid on to nodes, e.g. transcript models. Here we demonstrate the utility of this approach, including the unusual structure of these graphs and how they can be used to identify issues in assembly, repetitive sequences within transcripts and splice variants. We believe this approach has the potential to significantly improve our understanding of transcript complexity.
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Affiliation(s)
- Fahmi W Nazarie
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Barbara Shih
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tim Angus
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Mark W Barnett
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sz-Hau Chen
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Kim M Summers
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK.,Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia
| | - Karsten Klein
- Life Science Informatics Group, Department of Computer Science, Konstanz University, 78457 Konstanz, Germany
| | - Geoffrey J Faulkner
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia
| | - Harpreet K Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, UK
| | - Mick Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Stijn van Dongen
- Cellular Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Anton J Enright
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Tom C Freeman
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
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Freem L, Summers KM, Gheyas AA, Psifidi A, Boulton K, MacCallum A, Harne R, O’Dell J, Bush SJ, Hume DA. Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens. Front Genet 2019; 10:1032. [PMID: 31803225 PMCID: PMC6870463 DOI: 10.3389/fgene.2019.01032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/25/2019] [Indexed: 01/05/2023] Open
Abstract
There is increasing recognition that the underlying genetic variation contributing to complex traits influences transcriptional regulation and can be detected at a population level as expression quantitative trait loci. At the level of an individual, allelic variation in transcriptional regulation of individual genes can be detected by measuring allele-specific expression in RNAseq data. We reasoned that extreme variants in gene expression could be identified by analysis of inbred progeny with shared grandparents. Commercial chickens have been intensively selected for production traits. Selection is associated with large blocks of linkage disequilibrium with considerable potential for co-selection of closely linked "hitch-hiker alleles" affecting traits unrelated to the feature being selected, such as immune function, with potential impact on the productivity and welfare of the animals. To test this hypothesis that there is extreme allelic variation in immune-associated genes we sequenced a founder population of commercial broiler and layer birds. These birds clearly segregated genetically based upon breed type. Each genome contained numerous candidate null mutations, protein-coding variants predicted to be deleterious and extensive non-coding polymorphism. We mated selected broiler-layer pairs then generated cohorts of F2 birds by sibling mating of the F1 generation. Despite the predicted prevalence of deleterious coding variation in the genomic sequence of the founders, clear detrimental impacts of inbreeding on survival and post-hatch development were detected in only one F2 sibship of 15. There was no effect on circulating leukocyte populations in hatchlings. In selected F2 sibships we performed RNAseq analysis of the spleen and isolated bone marrow-derived macrophages (with and without lipopolysaccharide stimulation). The results confirm the predicted emergence of very large differences in expression of individual genes and sets of genes. Network analysis of the results identified clusters of co-expressed genes that vary between individuals and suggested the existence of trans-acting variation in the expression in macrophages of the interferon response factor family that distinguishes the parental broiler and layer birds and influences the global response to lipopolysaccharide. This study shows that the impact of inbreeding on immune cell gene expression can be substantial at the transcriptional level, and potentially opens a route to accelerate selection using specific alleles known to be associated with desirable expression levels.
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Affiliation(s)
- Lucy Freem
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Almas A. Gheyas
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Androniki Psifidi
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, London, United Kingdom
| | - Kay Boulton
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Amanda MacCallum
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Rakhi Harne
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jenny O’Dell
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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30
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Young R, Lefevre L, Bush SJ, Joshi A, Singh SH, Jadhav SK, Dhanikachalam V, Lisowski ZM, Iamartino D, Summers KM, Williams JL, Archibald AL, Gokhale S, Kumar S, Hume DA. A Gene Expression Atlas of the Domestic Water Buffalo ( Bubalus bubalis). Front Genet 2019; 10:668. [PMID: 31428126 PMCID: PMC6689995 DOI: 10.3389/fgene.2019.00668] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/19/2022] Open
Abstract
The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides, and draught power. The global water buffalo population is predominantly found in Asia, and per head of population more people depend upon the buffalo than on any other livestock species. Despite its agricultural importance, there are comparatively fewer genomic and transcriptomic resources available for buffalo than for other livestock species. We have generated a large-scale gene expression atlas covering multiple tissue and cell types from all major organ systems collected from three breeds of riverine water buffalo (Mediterranean, Pandharpuri and Bhadawari) and used the network analysis tool Graphia Professional to identify clusters of genes with similar expression profiles. Alongside similar data, we and others have generated for ruminants as part of the Functional Annotation of Animal Genomes Consortium; this comprehensive transcriptome supports functional annotation and comparative analysis of the water buffalo genome.
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Affiliation(s)
- Rachel Young
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Akshay Joshi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Velu Dhanikachalam
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Zofia M. Lisowski
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Suresh Gokhale
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Satish Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Life Science, Central University of Haryana, Mahendergargh, India
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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31
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Hume DA, Caruso M, Ferrari-Cestari M, Summers KM, Pridans C, Irvine KM. Phenotypic impacts of CSF1R deficiencies in humans and model organisms. J Leukoc Biol 2019; 107:205-219. [PMID: 31330095 DOI: 10.1002/jlb.mr0519-143r] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
Mϕ proliferation, differentiation, and survival are controlled by signals from the Mϕ CSF receptor (CSF1R). Mono-allelic gain-of-function mutations in CSF1R in humans are associated with an autosomal-dominant leukodystrophy and bi-allelic loss-of-function mutations with recessive skeletal dysplasia, brain disorders, and developmental anomalies. Most of the phenotypes observed in these human disease states are also observed in mice and rats with loss-of-function mutations in Csf1r or in Csf1 encoding one of its two ligands. Studies in rodent models also highlight the importance of genetic background and likely epistatic interactions between Csf1r and other loci. The impacts of Csf1r mutations on the brain are usually attributed solely to direct impacts on microglial number and function. However, analysis of hypomorphic Csf1r mutants in mice and several other lines of evidence suggest that primary hydrocephalus and loss of the physiological functions of Mϕs in the periphery contribute to the development of brain pathology. In this review, we outline the evidence that CSF1R is expressed exclusively in mononuclear phagocytes and explore the mechanisms linking CSF1R mutations to pleiotropic impacts on postnatal growth and development.
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Affiliation(s)
- David A Hume
- Mater Research Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Melanie Caruso
- Mater Research Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | | | - Kim M Summers
- Mater Research Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Clare Pridans
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M Irvine
- Mater Research Institute, University of Queensland, Woolloongabba, Queensland, Australia
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32
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Rojo R, Raper A, Ozdemir DD, Lefevre L, Grabert K, Wollscheid-Lengeling E, Bradford B, Caruso M, Gazova I, Sánchez A, Lisowski ZM, Alves J, Molina-Gonzalez I, Davtyan H, Lodge RJ, Glover JD, Wallace R, Munro DAD, David E, Amit I, Miron VE, Priller J, Jenkins SJ, Hardingham GE, Blurton-Jones M, Mabbott NA, Summers KM, Hohenstein P, Hume DA, Pridans C. Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations. Nat Commun 2019; 10:3215. [PMID: 31324781 PMCID: PMC6642117 DOI: 10.1038/s41467-019-11053-8] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [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: 01/29/2019] [Accepted: 06/15/2019] [Indexed: 02/06/2023] Open
Abstract
The proliferation, differentiation and survival of mononuclear phagocytes depend on signals from the receptor for macrophage colony-stimulating factor, CSF1R. The mammalian Csf1r locus contains a highly conserved super-enhancer, the fms-intronic regulatory element (FIRE). Here we show that genomic deletion of FIRE in mice selectively impacts CSF1R expression and tissue macrophage development in specific tissues. Deletion of FIRE ablates macrophage development from murine embryonic stem cells. Csf1rΔFIRE/ΔFIRE mice lack macrophages in the embryo, brain microglia and resident macrophages in the skin, kidney, heart and peritoneum. The homeostasis of other macrophage populations and monocytes is unaffected, but monocytes and their progenitors in bone marrow lack surface CSF1R. Finally, Csf1rΔFIRE/ΔFIRE mice are healthy and fertile without the growth, neurological or developmental abnormalities reported in Csf1r-/- rodents. Csf1rΔFIRE/ΔFIRE mice thus provide a model to explore the homeostatic, physiological and immunological functions of tissue-specific macrophage populations in adult animals.
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Affiliation(s)
- Rocío Rojo
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. Ignacio Morones Prieto 3000 Pte, Col. Los Doctores, C.P. 64710, Monterrey, N.L., Mexico
| | - Anna Raper
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Derya D Ozdemir
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Lucas Lefevre
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Kathleen Grabert
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Department of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Box 210, SE-171 77, Stockholm, Sweden
| | - Evi Wollscheid-Lengeling
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Barry Bradford
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Melanie Caruso
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Iveta Gazova
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Alejandra Sánchez
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zofia M Lisowski
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Joana Alves
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Irene Molina-Gonzalez
- The MRC University of Edinburgh Centre for Reproductive Health, The Queen's Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Hayk Davtyan
- Department of Neurobiology and Behavior, University of California Irvine, 3014 Gross Hall 845 Health Sciences Rd, Irvine, CA, 92697-1705, USA
| | - Rebecca J Lodge
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - James D Glover
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Robert Wallace
- The Department of Orthopedic Surgery, University of Edinburgh, Chancellor's Building, Edinburgh BioQuarter, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - David A D Munro
- UK Dementia Research Institute, The University of Edinburgh, Chancellor's Building, Edinburgh BioQuarter, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, 234 Herzl St., Rehovot, 7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, 234 Herzl St., Rehovot, 7610001, Israel
| | - Véronique E Miron
- The MRC University of Edinburgh Centre for Reproductive Health, The Queen's Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Josef Priller
- UK Dementia Research Institute, The University of Edinburgh, Chancellor's Building, Edinburgh BioQuarter, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Stephen J Jenkins
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Giles E Hardingham
- UK Dementia Research Institute, The University of Edinburgh, Chancellor's Building, Edinburgh BioQuarter, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California Irvine, 3014 Gross Hall 845 Health Sciences Rd, Irvine, CA, 92697-1705, USA
| | - Neil A Mabbott
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Peter Hohenstein
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK.
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Gažová I, Lengeling A, Summers KM. Lysine demethylases KDM6A and UTY: The X and Y of histone demethylation. Mol Genet Metab 2019; 127:31-44. [PMID: 31097364 DOI: 10.1016/j.ymgme.2019.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Histone demethylases remove transcriptional repressive marks from histones in the nucleus. KDM6A (also known as UTX) is a lysine demethylase which acts on the trimethylated lysine at position 27 in histone 3. The KDM6A gene is located on the X chromosome but escapes X inactivation even though it is not located in the pseudoautosomal region. There is a homologue of KDM6A on the Y chromosome, known as UTY. UTY was thought to have lost its demethylase activity and to represent a non-functional remnant of the ancestral KDM6A gene. However, results with knockout mice suggest that the gene is expressed and the protein performs some function within the cell. Female mice with homozygous deletion of Kdm6a do not survive, but hemizygous males are viable, attributed to the presence of the Uty gene. KDM6A is mutated in the human condition Kabuki syndrome type 2 (OMIM 300867) and in many cases of cancer. The amino acid sequence of KDM6A has been conserved across animal phyla, although it is only found on the X chromosome in eutherian mammals. In this review, we reanalyse existing data from various sources (protein sequence comparison, evolutionary genetics, transcription factor binding and gene expression analysis) to determine the function, expression and evolution of KDM6A and UTY and show that UTY has a functional role similar to KDM6A in metabolism and development.
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Affiliation(s)
- Iveta Gažová
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Andreas Lengeling
- Max Planck Society, Administrative Headquarters, Hofgartenstrasse 8, 80539 Munich, Germany
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia.
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34
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Pridans C, Raper A, Davis GM, Alves J, Sauter KA, Lefevre L, Regan T, Meek S, Sutherland L, Thomson AJ, Clohisey S, Bush SJ, Rojo R, Lisowski ZM, Wallace R, Grabert K, Upton KR, Tsai YT, Brown D, Smith LB, Summers KM, Mabbott NA, Piccardo P, Cheeseman MT, Burdon T, Hume DA. Correction: Pleiotropic Impacts of Macrophage and Microglial Deficiency on Development in Rats with Targeted Mutation of the Csf1r Locus. J Immunol 2019; 202:3334-3335. [PMID: 31028122 PMCID: PMC6526391 DOI: 10.4049/jimmunol.1900420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Pugh CA, Farrell LL, Carlisle AJ, Bush SJ, Ewing A, Trejo-Reveles V, Matika O, de Kloet A, Walsh C, Bishop SC, Prendergast JGD, Rainger J, Schoenebeck JJ, Summers KM. Arginine to Glutamine Variant in Olfactomedin Like 3 ( OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed. G3 (Bethesda) 2019; 9:943-954. [PMID: 30696701 PMCID: PMC6404605 DOI: 10.1534/g3.118.200944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/19/2019] [Indexed: 12/23/2022]
Abstract
Goniodysgenesis is a developmental abnormality of the anterior chamber of the eye. It is generally considered to be congenital in dogs (Canis lupus familiaris), and has been associated with glaucoma and blindness. Goniodysgenesis and early-onset glaucoma initially emerged in Border Collies in Australia in the late 1990s and have subsequently been found in this breed in Europe and the USA. The objective of the present study was to determine the genetic basis of goniodysgenesis in Border Collies. Clinical diagnosis was based on results of examinations by veterinary ophthalmologists of affected and unaffected dogs from eleven different countries. Genotyping using the Illumina high density canine single nucleotide variant genotyping chip was used to identify a candidate genetic region. There was a highly significant peak of association over chromosome 17, with a p-value of 2 × 10-13 Expression profiles and evolutionary conservation of candidate genes were assessed using public databases. Whole genome sequences of three dogs with glaucoma, three severely affected by goniodysgenesis and three unaffected dogs identified a missense variant in the olfactomedin like 3 (OLFML3) gene in all six affected animals. This was homozygous for the risk allele in all nine cases with glaucoma and 12 of 14 other severely affected animals. Of 67 reportedly unaffected animals, only one was homozygous for this variant (offspring of parents both with goniodysgenesis who were also homozygous for the variant). Analysis of pedigree information was consistent with an autosomal recessive mode of inheritance for severe goniodysgenesis (potentially leading to glaucoma) in this breed. The identification of a candidate genetic region and putative causative variant will aid breeders to reduce the frequency of goniodysgenesis and the risk of glaucoma in the Border Collie population.
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Affiliation(s)
- Carys A Pugh
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Lindsay L Farrell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Ailsa J Carlisle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Stephen J Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - Adam Ewing
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
| | - Violeta Trejo-Reveles
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Oswald Matika
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Arne de Kloet
- Animal Genetics, 1336 Timberlane Rd, Tallahassee, FL 32312
| | - Caitlin Walsh
- Animal Genetics, 1336 Timberlane Rd, Tallahassee, FL 32312
| | - Stephen C Bishop
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Joe Rainger
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Jeffrey J Schoenebeck
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
| | - Kim M Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, EH25 9RG, United Kingdom
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Qld 4102, Australia
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Karagianni AE, Summers KM, Couroucé A, Depecker M, McGorum BC, Hume DA, Pirie RS. The Effect of Race Training on the Basal Gene Expression of Alveolar Macrophages Derived From Standardbred Racehorses. J Equine Vet Sci 2019; 75:48-54. [PMID: 31002092 DOI: 10.1016/j.jevs.2019.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 01/12/2023]
Abstract
Mild-to-moderate equine asthma is prevalent in young racehorses, particularly early in their training period. Although the precise etiopathogenesis remains undetermined, it is possible that the susceptibility of this population might partly reflect an exercise-associated immune derangement at the level of the airway. We performed a genome-wide basal gene expression scan on alveolar macrophages (AMs) isolated from Standardbred racehorses before and after commencement of competition race training with a view to identifying any exercise-associated gene expression modulation consistent with functional alterations, which might reflect training-associated immunological derangement. Microarray technology was used to analyze the basal gene expression profiles of bronchoalveolar fluid-derived AMs, harvested from six systemically healthy Standardbred racehorses before (T0) and after (T1) entry into training. In addition, AM lipopolysaccharide (LPS)-induced TNF-α and IL-10 release at T0 and T1 was assessed. Although the data revealed significant interhorse heterogeneity in relation to the magnitude of individual gene expression at each timepoint, within each horse, several inflammatory-related genes [e.g., chemokine ligands, interferons, and nuclear factor kappa-light-chain-enhancer of activated B cells (NFKB)] declined in expression from T0 to T1. Entry into training did not significantly alter AM LPS-induced TNF-α or IL-10 release. The data support a direct effect of training on AM basal gene expression, particularly with respect to immune-related genes. The pattern of training-associated differential gene expression may indicate relative downregulation of inflammatory-related genes, consistent with an immunosuppressive effect of training and an increased susceptibility to opportunistic pathogens.
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Affiliation(s)
- Anna E Karagianni
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.
| | - Kim M Summers
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Anne Couroucé
- LUNAM Université, ONIRIS, Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation de Nantes-Atlantique, UPSP 5304 Laboratoire de Physiopathologie animale et de Pharmacologie fonctionnelle, Nantes, France
| | - Marianne Depecker
- LUNAM Université, ONIRIS, Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation de Nantes-Atlantique, UPSP 5304 Laboratoire de Physiopathologie animale et de Pharmacologie fonctionnelle, Nantes, France
| | - Bruce C McGorum
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - David A Hume
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, QLD, Australia
| | - R Scott Pirie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
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Hu T, Wu Z, Bush SJ, Freem L, Vervelde L, Summers KM, Hume DA, Balic A, Kaiser P. Characterization of Subpopulations of Chicken Mononuclear Phagocytes That Express TIM4 and CSF1R. J Immunol 2019; 202:1186-1199. [PMID: 30626692 DOI: 10.4049/jimmunol.1800504] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/03/2018] [Indexed: 01/08/2023]
Abstract
The phosphatidylserine receptor TIM4, encoded by TIMD4, mediates the phagocytic uptake of apoptotic cells. We applied anti-chicken TIM4 mAbs in combination with CSF1R reporter transgenes to dissect the function of TIM4 in the chick (Gallus gallus). During development in ovo, TIM4 was present on the large majority of macrophages, but expression became more heterogeneous posthatch. Blood monocytes expressed KUL01, class II MHC, and CSF1R-mApple uniformly. Around 50% of monocytes were positive for surface TIM4. They also expressed many other monocyte-specific transcripts at a higher level than TIM4- monocytes. In liver, highly phagocytic TIM4hi cells shared many transcripts with mammalian Kupffer cells and were associated with uptake of apoptotic cells. Although they expressed CSF1R mRNA, Kupffer cells did not express the CSF1R-mApple transgene, suggesting that additional CSF1R transcriptional regulatory elements are required by these cells. By contrast, CSF1R-mApple was detected in liver TIM4lo and TIM4- cells, which were not phagocytic and were more abundant than Kupffer cells. These cells expressed CSF1R alongside high levels of FLT3, MHCII, XCR1, and other markers associated with conventional dendritic cells in mice. In bursa, TIM4 was present on the cell surface of two populations. Like Kupffer cells, bursal TIM4hi phagocytes coexpressed many receptors involved in apoptotic cell recognition. TIM4lo cells appear to be a subpopulation of bursal B cells. In overview, TIM4 is associated with phagocytes that eliminate apoptotic cells in the chick. In the liver, TIM4 and CSF1R reporters distinguished Kupffer cells from an abundant population of dendritic cell-like cells.
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Affiliation(s)
- Tuanjun Hu
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Zhiguang Wu
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Stephen J Bush
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Lucy Freem
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Lonneke Vervelde
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Kim M Summers
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom.,Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - David A Hume
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom; .,Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Adam Balic
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom;
| | - Pete Kaiser
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
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Pridans C, Raper A, Davis GM, Alves J, Sauter KA, Lefevre L, Regan T, Meek S, Sutherland L, Thomson AJ, Clohisey S, Bush SJ, Rojo R, Lisowski ZM, Wallace R, Grabert K, Upton KR, Tsai YT, Brown D, Smith LB, Summers KM, Mabbott NA, Piccardo P, Cheeseman MT, Burdon T, Hume DA. Pleiotropic Impacts of Macrophage and Microglial Deficiency on Development in Rats with Targeted Mutation of the Csf1r Locus. J Immunol 2018; 201:2683-2699. [PMID: 30249809 PMCID: PMC6196293 DOI: 10.4049/jimmunol.1701783] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Abstract
We have produced Csf1r-deficient rats by homologous recombination in embryonic stem cells. Consistent with the role of Csf1r in macrophage differentiation, there was a loss of peripheral blood monocytes, microglia in the brain, epidermal Langerhans cells, splenic marginal zone macrophages, bone-associated macrophages and osteoclasts, and peritoneal macrophages. Macrophages of splenic red pulp, liver, lung, and gut were less affected. The pleiotropic impacts of the loss of macrophages on development of multiple organ systems in rats were distinct from those reported in mice. Csf1r-/- rats survived well into adulthood with postnatal growth retardation, distinct skeletal and bone marrow abnormalities, infertility, and loss of visceral adipose tissue. Gene expression analysis in spleen revealed selective loss of transcripts associated with the marginal zone and, in brain regions, the loss of known and candidate novel microglia-associated transcripts. Despite the complete absence of microglia, there was little overt phenotype in brain, aside from reduced myelination and increased expression of dopamine receptor-associated transcripts in striatum. The results highlight the redundant and nonredundant functions of CSF1R signaling and of macrophages in development, organogenesis, and homeostasis.
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Affiliation(s)
- Clare Pridans
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom; .,The University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Anna Raper
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Gemma M Davis
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Joana Alves
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Kristin A Sauter
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Tim Regan
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Stephen Meek
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Linda Sutherland
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Alison J Thomson
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom.,New World Laboratories, Laval, Quebec H7V 5B7, Canada
| | - Sara Clohisey
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Stephen J Bush
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom.,Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom
| | - Rocío Rojo
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Zofia M Lisowski
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Robert Wallace
- Department of Orthopaedic Surgery, The University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Kathleen Grabert
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Kyle R Upton
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yi Ting Tsai
- Medical Research Council Centre for Reproductive Health, The University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Deborah Brown
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Lee B Smith
- Medical Research Council Centre for Reproductive Health, The University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom.,Faculty of Science, University of Newcastle, Callaghan, New South Wales 2309, Australia; and
| | - Kim M Summers
- Mater Research-University of Queensland, Brisbane, Queensland 4101, Australia
| | - Neil A Mabbott
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Pedro Piccardo
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Michael T Cheeseman
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - Tom Burdon
- The Roslin Institute, The University of Edinburgh, Easter Bush EH25 9RG, United Kingdom
| | - David A Hume
- The University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom; .,Mater Research-University of Queensland, Brisbane, Queensland 4101, Australia
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Brown SM, Bush SJ, Summers KM, Hume DA, Lawrence AB. Environmentally enriched pigs have transcriptional profiles consistent with neuroprotective effects and reduced microglial activity. Behav Brain Res 2018; 350:6-15. [PMID: 29778628 PMCID: PMC6002610 DOI: 10.1016/j.bbr.2018.05.015] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/27/2018] [Accepted: 05/15/2018] [Indexed: 01/03/2023]
Abstract
Environmental enrichment (EE) is widely used to study the effects of external factors on brain development, function and health in rodent models, but very little is known of the effects of EE on the brain in a large animal model such as the pig. Twenty-four young pigs (aged 5 weeks at start of study, 1:1 male: female ratio) were housed in environmentally enriched (EE) pens and provided with additional enrichment stimulation (a bag filled with straw) once daily. Litter, weight and sex matched controls n= (24) were housed in barren (B) conditions. Behaviour was recorded on alternate days from study day 10. After 21 days, RNA-sequencing of the frontal cortex of male piglets culled one hour after the enrichment stimulation, but not those at 4 h after stimulation, showed upregulation of genes involved in neuronal activity and synaptic plasticity in the EE compared to the B condition. This result is mirrored in the behavioural response to the stimulation which showed a peak in activity around the 1 h time-point. By contrast, EE piglets displayed a signature consistent with a relative decrease in microglial activity compared to those in the B condition. These results confirm those from rodents, suggesting that EE may also confer neuronal health benefits in large mammal models, through a potential relative reduction in neuroinflammatory process and increase in neuroprotection driven by an enrichment-induced increase in behavioural activity.
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Affiliation(s)
- S M Brown
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK.
| | - S J Bush
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - K M Summers
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK; Mater Research Institute-UQ, Translational Research Institute, 37 Kent St, Woolloongabba, QLd, 4102, Australia
| | - D A Hume
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK; Mater Research Institute-UQ, Translational Research Institute, 37 Kent St, Woolloongabba, QLd, 4102, Australia
| | - A B Lawrence
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK; SRUC, West Mains Road, Edinburgh, EH9 3JG, UK
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Tsang HG, Cui L, Farquharson C, Corcoran BM, Summers KM, Macrae VE. Exploiting novel valve interstitial cell lines to study calcific aortic valve disease. Mol Med Rep 2018; 17:2100-2106. [PMID: 29207136 PMCID: PMC5783449 DOI: 10.3892/mmr.2017.8163] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/14/2017] [Indexed: 01/07/2023] Open
Abstract
Calcific aortic valve disease (CAVD) involves progressive valve leaflet thickening and severe calcification, impairing leaflet motion. The in vitro calcification of primary rat, human, porcine and bovine aortic valve interstitial cells (VICs) is commonly employed to investigate CAVD mechanisms. However, to date, no published studies have utilised cell lines to investigate this process. The present study has therefore generated and evaluated the calcification potential of immortalized cell lines derived from sheep and rat VICs. Immortalised sheep (SAVIC) and rat (RAVIC) cell lines were produced by transduction with a recombinant lentivirus encoding the Simian virus (SV40) large and small T antigens (sheep), or large T antigen only (rat), which expressed markers of VICs (vimentin and α‑smooth muscle actin). Calcification was induced in the presence of calcium (Ca; 2.7 mM) in SAVICs (1.9 fold; P<0.001) and RAVICs (4.6 fold; P<0.01). Furthermore, a synergistic effect of calcium and phosphate was observed (2.7 mM Ca/2.0 mM Pi) on VIC calcification in the two cell lines (P<0.001). Analysis of SAVICs revealed significant increases in the mRNA expression of two key genes associated with vascular calcification in cells cultured under calcifying conditions, runt related transcription factor‑2 (RUNX2;1.3 fold; P<0.05 in 4.5 mM Ca) and sodium‑dependent phosphate transporter‑1 (PiT1; 1.2 fold; P<0.05 in 5.4 mM Ca). A concomitant decrease in the expression of the calcification inhibitor matrix Gla protein (MGP) was noted at 3.6 mM Ca (1.3 fold; P<0.01). Assessment of RAVICs revealed alterations in Runx2, Pit1 and Mgp mRNA expression levels (P<0.01). Furthermore, a significant reduction in calcification was observed in SAVICs following treatment with established calcification inhibitors, pyrophosphate (1.8 fold; P<0.01) and etidronate (3.2 fold; P<0.01). Overall, the present study demonstrated that the use of immortalised sheep and rat VIC cell lines is a convenient and cost effective system to investigate CAVD in vitro, and will make a useful contribution to increasing current understanding of the pathophysiological process.
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Affiliation(s)
- Hiu-Gwen Tsang
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Lin Cui
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Colin Farquharson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Brendan M. Corcoran
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Kim M. Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Vicky E. Macrae
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PLoS Genet 2017; 13:e1006997. [PMID: 28915238 PMCID: PMC5626511 DOI: 10.1371/journal.pgen.1006997] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/03/2017] [Accepted: 08/24/2017] [Indexed: 02/08/2023] Open
Abstract
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of 'guilt by association' was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.
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Affiliation(s)
- Emily L. Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Mary E. B. McCulloch
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Iseabail L. Farquhar
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rachel Young
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Clare Pridans
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Hiu G. Tsang
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Cyrus Afrasiabi
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - C. Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Tom C. Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Kim M. Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Mater Research Institute and University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - David A. Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Mater Research Institute and University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
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Summers KM, Hume DA. Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data. J Leukoc Biol 2017; 102:1081-1092. [DOI: 10.1189/jlb.1a0417-150rr] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 11/24/2022] Open
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43
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Markby GR, Summers KM, MacRae VE, Corcoran BM. Comparative Transcriptomic Profiling and Gene Expression for Myxomatous Mitral Valve Disease in the Dog and Human. Vet Sci 2017; 4:vetsci4030034. [PMID: 29056693 PMCID: PMC5644653 DOI: 10.3390/vetsci4030034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 03/01/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 12/28/2022] Open
Abstract
Myxomatous mitral valve disease is the single most important mitral valve disease in both dogs and humans. In the case of the dog it is ubiquitous, such that all aged dogs will have some evidence of the disease, and for humans it is known as Barlow's disease and affects up to 3% of the population, with an expected increase in prevalence as the population ages. Disease in the two species show many similarities and while both have the classic myxomatous degeneration only in humans is there extensive fibrosis. This dual pathology of the human disease markedly affects the valve transcriptome and the difference between the dog and human is dominated by changes in genes associated with fibrosis. This review will briefly examine the comparative valve pathology and then, in more detail, the transcriptomic profiling and gene expression reported so far for both species.
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Affiliation(s)
- Greg R Markby
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
| | - Kim M Summers
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
| | - Vicky E MacRae
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
| | - Brendan M Corcoran
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
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Bush SJ, McCulloch MEB, Summers KM, Hume DA, Clark EL. Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. BMC Bioinformatics 2017; 18:301. [PMID: 28610557 PMCID: PMC5470212 DOI: 10.1186/s12859-017-1714-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 01/24/2017] [Accepted: 06/05/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in such integration include sequencing depth and methods of RNA extraction and selection. Different selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs, resulting in different fractions of the transcriptome being sequenced. In particular, rRNA-depleted libraries sample a broader fraction of the transcriptome than polyA-selected libraries. This study aimed to develop a systematic means of accounting for library type that allows data from these two methods to be compared. RESULTS The method was developed by comparing two RNA-seq datasets from ovine macrophages, identical except for RNA selection method. Gene-level expression estimates were obtained using a two-part process centred on the high-speed transcript quantification tool Kallisto. Firstly, a set of reference transcripts was defined that constitute a standardised RNA space, with expression from both datasets quantified against it. Secondly, a simple ratio-based correction was applied to the rRNA-depleted estimates. The outcome is an almost perfect correlation between gene expression estimates, independent of library type and across the full range of levels of expression. CONCLUSION A combination of reference transcriptome filtering and a ratio-based correction can create equivalent expression profiles from both polyA-selected and rRNA-depleted libraries. This approach will allow meta-analysis and integration of existing RNA-seq data into transcriptional atlas projects.
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Affiliation(s)
- Stephen J. Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Mary E. B. McCulloch
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Kim M. Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - David A. Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Emily L. Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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Pugh CA, Bronsvoort BMDC, Handel IG, Querry D, Rose E, Summers KM, Clements DN. Incidence rates and risk factor analyses for owner reported vomiting and diarrhoea in Labrador Retrievers - findings from the Dogslife Cohort. Prev Vet Med 2017; 140:19-29. [PMID: 28460746 PMCID: PMC5424887 DOI: 10.1016/j.prevetmed.2017.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 11/30/2022]
Abstract
Dogslife collects data directly from owners of Labrador Retrievers across the UK including information regarding signs of illness irrespective of whether the signs precipitated a veterinary visit. In December 2015, the cohort comprised 6084 dogs aged up to six years and their owners had made 2687 and 2601 reports of diarrhoea and vomiting respectively. The co-occurrence of vomiting and diarrhoea with other signs was described and the frequencies and durations of the two signs were examined with reference to veterinary visitation. Age-specific illness rates were described and Cox Proportional Hazards models were used to estimate risk factors. Just 37% of diarrhoea reports were associated with a veterinary visit and the proportion was even lower for vomiting at 28%; indicating that studies of veterinary practice data miss the majority of signs of gastrointestinal upset. In terms of frequency and duration, diarrhoea typically needed to last two days before the dog would be taken to the vet but if the dog vomited at least every six hours, the owner would be more likely to take the dog to the vet after one day. The illness rates of both signs peaked when the dogs were aged between three and six months. There was also a seasonal pattern to the incidents with the lowest hazards for both in May. Diarrhoea incidents peaked in August-September each year but, while vomiting appeared to be higher in September, it peaked in February. Having another dog in the household was associated with a lower hazard for both vomiting and diarrhoea but having a cat was only associated with a reduced hazard of vomiting. In addition to the distinct seasonal patterns of reporting, there were clear differences in the geographic risks for the two signs. The hazard of diarrhoea was positively associated with human population density within Great Britain (according to home post code) whereas no significant geographical association was found with vomiting. This study is particularly relevant for dog owners because it highlights the wealth of gastrointestinal illnesses in dogs that are dealt with by owners but never seen by veterinarians. The risk factor analyses make use of owner-reported demographic information, highlighting the differences between vomiting and diarrhoea. The analyses give rise to the possibility that the presence of other pets in households may affect rates of illness and indicate new avenues for investigations of these distinct, and oft-suffered conditions.
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Affiliation(s)
- Carys A Pugh
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
| | - B Mark de C Bronsvoort
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
| | - Ian G Handel
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
| | - Damon Querry
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
| | - Erica Rose
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
| | - Kim M Summers
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, United Kingdom.
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Sauter KA, Waddell LA, Lisowski ZM, Young R, Lefevre L, Davis GM, Clohisey SM, McCulloch M, Magowan E, Mabbott NA, Summers KM, Hume DA. Macrophage colony-stimulating factor (CSF1) controls monocyte production and maturation and the steady-state size of the liver in pigs. Am J Physiol Gastrointest Liver Physiol 2016; 311:G533-47. [PMID: 27445344 PMCID: PMC5076001 DOI: 10.1152/ajpgi.00116.2016] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/17/2016] [Indexed: 01/31/2023]
Abstract
Macrophage colony-stimulating factor (CSF1) is an essential growth and differentiation factor for cells of the macrophage lineage. To explore the role of CSF1 in steady-state control of monocyte production and differentiation and tissue repair, we previously developed a bioactive protein with a longer half-life in circulation by fusing pig CSF1 with the Fc region of pig IgG1a. CSF1-Fc administration to pigs expanded progenitor pools in the marrow and selectively increased monocyte numbers and their expression of the maturation marker CD163. There was a rapid increase in the size of the liver, and extensive proliferation of hepatocytes associated with increased macrophage infiltration. Despite the large influx of macrophages, there was no evidence of liver injury and no increase in circulating liver enzymes. Microarray expression profiling of livers identified increased expression of macrophage markers, i.e., cytokines such as TNF, IL1, and IL6 known to influence hepatocyte proliferation, alongside cell cycle genes. The analysis also revealed selective enrichment of genes associated with portal, as opposed to centrilobular regions, as seen in hepatic regeneration. Combined with earlier data from the mouse, this study supports the existence of a CSF1-dependent feedback loop, linking macrophages of the liver with bone marrow and blood monocytes, to mediate homeostatic control of the size of the liver. The results also provide evidence of safety and efficacy for possible clinical applications of CSF1-Fc.
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Affiliation(s)
- Kristin A. Sauter
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Lindsey A. Waddell
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Zofia M. Lisowski
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Rachel Young
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Lucas Lefevre
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Gemma M. Davis
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Sara M. Clohisey
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Mary McCulloch
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Elizabeth Magowan
- 2Agri-Food and Biosciences Institute, Large Park, Hillsborough, Northern Ireland, United Kingdom
| | - Neil A. Mabbott
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - Kim M. Summers
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
| | - David A. Hume
- 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom; and
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Davis MR, Arner E, Duffy CRE, De Sousa PA, Dahlman I, Arner P, Summers KM. Expression of FBN1 during adipogenesis: Relevance to the lipodystrophy phenotype in Marfan syndrome and related conditions. Mol Genet Metab 2016; 119:174-85. [PMID: 27386756 PMCID: PMC5044862 DOI: 10.1016/j.ymgme.2016.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/18/2016] [Accepted: 06/18/2016] [Indexed: 01/27/2023]
Abstract
Fibrillin-1 is a large glycoprotein encoded by the FBN1 gene in humans. It provides strength and elasticity to connective tissues and is involved in regulating the bioavailability of the growth factor TGFβ. Mutations in FBN1 may be associated with depleted or abnormal adipose tissue, seen in some patients with Marfan syndrome and lipodystrophies. As this lack of adipose tissue does not result in high morbidity or mortality, it is generally under-appreciated, but is a cause of psychosocial problems particularly to young patients. We examined the role of fibrillin-1 in adipogenesis. In inbred mouse strains we found significant variation in the level of expression in the Fbn1 gene that correlated with variation in several measures of body fat, suggesting that mouse fibrillin-1 is associated with the level of fat tissue. Furthermore, we found that FBN1 mRNA was up-regulated in the adipose tissue of obese women compared to non-obese, and associated with an increase in adipocyte size. We used human mesenchymal stem cells differentiated in culture to adipocytes to show that fibrillin-1 declines after the initiation of differentiation. Gene expression results from a similar experiment (available through the FANTOM5 project) revealed that the decline in fibrillin-1 protein was paralleled by a decline in FBN1 mRNA. Examination of the FBN1 gene showed that the region commonly affected in FBN1-associated lipodystrophy is highly conserved both across the three human fibrillin genes and across genes encoding fibrillin-1 in vertebrates. These results suggest that fibrillin-1 is involved as the undifferentiated mesenchymal stem cells transition to adipogenesis but then declines as the developing adipocytes take on their final phenotype. Since the C-terminal peptide of fibrillin-1 is a glucogenic hormone, individuals with low fibrillin-1 (for example with FBN1 mutations associated with lipodystrophy) may fail to differentiate adipocytes and/or to accumulate adipocyte lipids, although this still needs to be shown experimentally.
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Affiliation(s)
- Margaret R Davis
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.
| | - Erik Arner
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST (DGT)), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Cairnan R E Duffy
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellors Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
| | - Paul A De Sousa
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellors Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
| | - Ingrid Dahlman
- Department of Medicine, Huddinge (Med H), Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden.
| | - Peter Arner
- Department of Medicine, Huddinge (Med H), Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden.
| | - Kim M Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.
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Davis MR, Arner E, Duffy CRE, De Sousa PA, Dahlman I, Arner P, Summers KM. Datasets of genes coexpressed with FBN1 in mouse adipose tissue and during human adipogenesis. Data Brief 2016; 8:851-7. [PMID: 27508231 PMCID: PMC4959917 DOI: 10.1016/j.dib.2016.06.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/22/2022] Open
Abstract
This article contains data related to the research article entitled “Expression of FBN1 during adipogenesis: relevance to the lipodystrophy phenotype in Marfan syndrome and related conditions” [1]. The article concerns the expression of FBN1, the gene encoding the extracellular matrix protein fibrillin-1, during adipogenesis in vitro and in relation to adipose tissue in vivo. The encoded protein has recently been shown to produce a short glucogenic peptide hormone, (Romere et al., 2016) [2], and this gene is therefore a key gene for regulating blood glucose levels. FBN1 and coexpressed genes were examined in mouse strains and in human cells undergoing adipogenesis. The data show the genes that were coexpressed with FBN1, including genes coding for other connective tissue proteins and the proteases that modify them and for the transcription factors that control their expression. Data analysed were derived from datasets available in the public domain and the analysis highlights the utility of such datasets for ongoing analysis and hence reduction in the use of experimental animals.
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Affiliation(s)
- Margaret R Davis
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Erik Arner
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST (DGT)), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Cairnan R E Duffy
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellors Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Paul A De Sousa
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellors Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Ingrid Dahlman
- Department of Medicine, Huddinge (Med H), Karolinska Universitetssjukhuset Huddinge, 141 86 Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Huddinge (Med H), Karolinska Universitetssjukhuset Huddinge, 141 86 Stockholm, Sweden
| | - Kim M Summers
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
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49
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Raffan E, Dennis RJ, O'Donovan CJ, Becker JM, Scott RA, Smith SP, Withers DJ, Wood CJ, Conci E, Clements DN, Summers KM, German AJ, Mellersh CS, Arendt ML, Iyemere VP, Withers E, Söder J, Wernersson S, Andersson G, Lindblad-Toh K, Yeo GSH, O'Rahilly S. A Deletion in the Canine POMC Gene Is Associated with Weight and Appetite in Obesity-Prone Labrador Retriever Dogs. Cell Metab 2016; 23:893-900. [PMID: 27157046 PMCID: PMC4873617 DOI: 10.1016/j.cmet.2016.04.012] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/16/2016] [Accepted: 04/13/2016] [Indexed: 11/29/2022]
Abstract
Sequencing of candidate genes for obesity in Labrador retriever dogs identified a 14 bp deletion in pro-opiomelanocortin (POMC) with an allele frequency of 12%. The deletion disrupts the β-MSH and β-endorphin coding sequences and is associated with body weight (per allele effect of 0.33 SD), adiposity, and greater food motivation. Among other dog breeds, the deletion was only found in the closely related flat-coat retriever (FCR), where it is similarly associated with body weight and food motivation. The mutation is significantly more common in Labrador retrievers selected to become assistance dogs than pets. In conclusion, the deletion in POMC is a significant modifier of weight and appetite in Labrador retrievers and FCRs and may influence other behavioral traits.
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Affiliation(s)
- Eleanor Raffan
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Rowena J Dennis
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Conor J O'Donovan
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Julia M Becker
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Robert A Scott
- MRC Epidemiology Unit, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stephen P Smith
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
| | - David J Withers
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Claire J Wood
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Elena Conci
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Dylan N Clements
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Kim M Summers
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Alexander J German
- Institute of Ageing and Chronic Disease, University of Liverpool, Neston, Cheshire CH64 7TE, UK
| | - Cathryn S Mellersh
- Department of Canine Genetics, Animal Health Trust, Newmarket, Suffolk CB8 7UU, UK
| | | | - Valentine P Iyemere
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Elaine Withers
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Josefin Söder
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Sara Wernersson
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Kerstin Lindblad-Toh
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Science for Life Laboratory, Uppsala 75123, Sweden
| | - Giles S H Yeo
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stephen O'Rahilly
- University of Cambridge Metabolic Research Laboratories, WT-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
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50
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Tsang HG, Rashdan NA, Whitelaw CBA, Corcoran BM, Summers KM, MacRae VE. Large animal models of cardiovascular disease. Cell Biochem Funct 2016; 34:113-32. [PMID: 26914991 PMCID: PMC4834612 DOI: 10.1002/cbf.3173] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [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: 09/09/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 12/12/2022]
Abstract
The human cardiovascular system is a complex arrangement of specialized structures with distinct functions. The molecular landscape, including the genome, transcriptome and proteome, is pivotal to the biological complexity of both normal and abnormal mammalian processes. Despite our advancing knowledge and understanding of cardiovascular disease (CVD) through the principal use of rodent models, this continues to be an increasing issue in today's world. For instance, as the ageing population increases, so does the incidence of heart valve dysfunction. This may be because of changes in molecular composition and structure of the extracellular matrix, or from the pathological process of vascular calcification in which bone-formation related factors cause ectopic mineralization. However, significant differences between mice and men exist in terms of cardiovascular anatomy, physiology and pathology. In contrast, large animal models can show considerably greater similarity to humans. Furthermore, precise and efficient genome editing techniques enable the generation of tailored models for translational research. These novel systems provide a huge potential for large animal models to investigate the regulatory factors and molecular pathways that contribute to CVD in vivo. In turn, this will help bridge the gap between basic science and clinical applications by facilitating the refinement of therapies for cardiovascular disease.
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Affiliation(s)
- H G Tsang
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, SCT, UK
| | - N A Rashdan
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, SCT, UK
| | - C B A Whitelaw
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, SCT, UK
| | - B M Corcoran
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, SCT, UK
| | - K M Summers
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, SCT, UK
| | - V E MacRae
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, SCT, UK
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