1
|
Batoon L, Keshvari S, Irvine KM, Ho E, Caruso M, Patkar OL, Sehgal A, Millard SM, Hume DA, Pettit AR. Relative contributions of osteal macrophages and osteoclasts to postnatal bone development in CSF1R-deficient rats and phenotype rescue following wild-type bone marrow cell transfer. J Leukoc Biol 2024:qiae077. [PMID: 38526212 DOI: 10.1093/jleuko/qiae077] [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: 09/29/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Macrophage and osteoclast proliferation, differentiation and survival are regulated by colony-stimulating factor-1 receptor (CSF1R) signaling. Osteopetrosis associated with Csf1 and Csf1r mutations has been attributed to the loss of osteoclasts and deficiency in bone resorption. Here we demonstrate that homozygous Csf1r mutation in rat leads to delayed postnatal skeletal ossification associated with substantial loss of osteal macrophages (osteomacs) in addition to osteoclasts. Osteosclerosis and site-specific skeletal abnormalities were reversed by intraperitoneal transfer of wild-type bone marrow cells (BMT) at weaning. Following BMT, IBA1+ macrophages were detected before TRAP+ osteoclasts at sites of ossification restoration. These observations extend evidence that osteomacs independently contribute to bone anabolism and are required for normal postnatal bone growth and morphogenesis.
Collapse
Affiliation(s)
- Lena Batoon
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Sahar Keshvari
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Katharine M Irvine
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Eileen Ho
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Melanie Caruso
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Omkar L Patkar
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Anuj Sehgal
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Susan M Millard
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - David A Hume
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| | - Allison R Pettit
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia 4102
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Huang S, Carter-Cusack D, Maxwell E, Patkar OL, Irvine KM, Hume DA. Genetic and Immunohistochemistry Tools to Visualize Rat Macrophages In Situ. Methods Mol Biol 2024; 2713:99-115. [PMID: 37639117 DOI: 10.1007/978-1-0716-3437-0_6] [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] [Indexed: 08/29/2023]
Abstract
Macrophages contribute to many aspects of development and homeostasis, innate and acquired immunity, immunopathology, and tissue repair. Every tissue contains an abundant resident macrophage population. Inflammatory stimuli promote the recruitment of monocytes from the blood and their adaptation promotes the removal of the stimulus and subsequent restoration of normal tissue architecture. Dysregulation of this response leads to chronic inflammation and tissue injury. In many tissues, their differentiation and survival are dependent on the colony stimulating factor 1 receptor (CSF1R) signalling axis, which is highly conserved across all vertebrates. Complete loss of either CSF1R or its cognate ligands, colony stimulating factor 1 (CSF1), and interleukin 34 (IL-34), results in the loss of many tissue-resident macrophage populations. This provides a useful paradigm to study macrophages.There are many tools used to visualize tissue-resident macrophages and their precursors, monocytes, in mice and humans. Particularly in mice there are genetic tools available to delete, enhance and manipulate monocytes and macrophages and their gene products to gain insight into phenotype and function. The laboratory rat has many advantages as an experimental model for the understanding of human disease, but the analytical resources are currently more limited than in mice. Here, we describe available genetic models, antibodies, and immunohistochemistry (IHC) methods that may be used to visualize tissue-resident macrophages in rats.
Collapse
Affiliation(s)
- Stephen Huang
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Emma Maxwell
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Omkar L Patkar
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Katharine M Irvine
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia.
| | - David A Hume
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia.
| |
Collapse
|
5
|
Waddell LA, Wu Z, Sauter KA, Hope JC, Hume DA. A novel monoclonal antibody against porcine macrophage colony-stimulating factor (CSF1) detects expression on the cell surface of macrophages. Vet Immunol Immunopathol 2023; 266:110681. [PMID: 37992576 DOI: 10.1016/j.vetimm.2023.110681] [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: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
Macrophage colony-stimulating factor (CSF1) controls the proliferation and differentiation of cells of the mononuclear phagocyte system through binding to the receptor CSF1R. The expression and function of CSF1 has been well-studied in rodents and humans, but knowledge is lacking in other veterinary species. The development of a novel mouse anti-porcine CSF1 monoclonal antibody (mAb) facilitates the characterisation of this growth factor in pigs. Cell surface expression of CSF1 was confirmed on differentiated macrophage populations derived from blood and bone marrow monocytes, and on lung resident macrophages, the first species for this to be confirmed. However, monocytes isolated from blood and bone marrow lacked CSF1 expression. This species-specific mAb delivers the opportunity to further understanding of porcine myeloid cell biology. This is not only vital for the role of pigs as a model for human health, but also as a veterinary species of significant economic and agricultural importance.
Collapse
Affiliation(s)
- Lindsey A Waddell
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Zhiguang Wu
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Kristin A Sauter
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Jayne C Hope
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - David A Hume
- Mater Research Institute-University of Queensland, 37 Kent St, Woolloongabba, Qld 4104, Australia
| |
Collapse
|
6
|
Hume DA, Teakle N, Keshvari S, Irvine KM. Macrophage deficiency in CSF1R-knockout rat embryos does not compromise placental or embryo development. J Leukoc Biol 2023; 114:421-433. [PMID: 37167456 DOI: 10.1093/jleuko/qiad052] [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: 09/01/2022] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023] Open
Abstract
Macrophages are an abundant cell population in the placenta and developing embryo and appear to be involved in processes of vascularization, morphogenesis, organogenesis, and hematopoiesis. The proliferation, differentiation, and survival are dependent on signals from the macrophage colony-stimulating factor receptor, CSF1R. Aside from the role in macrophages, Csf1r mRNA is highly expressed in placental trophoblasts. To explore the function of macrophages and Csf1r in placental and embryonic development, we analyzed the impact of homozygous Csf1r null mutation (Csf1rko) in the rat. In late gestation, IBA1+ macrophages were abundant in control embryos in all tissues, including the placenta, and greatly reduced in the Csf1rko. CSF1R was also detected in stellate macrophage-like cells and in neurons using anti-CSF1R antibody but was undetectable in trophoblasts. However, the neuronal signal was not abolished in the Csf1rko. CD163 was most abundant in cells forming the center of erythroblastic islands in the liver and was also CSF1R dependent. Despite the substantial reduction in macrophage numbers, we detected no effect of the Csf1rko on development of the placenta or any organs, the relative abundance of vascular elements (CD31 staining), or cell proliferation (Ki67 staining). The loss of CD163+ erythroblastic island macrophages in the liver was not associated with anemia or any reduction in the proliferative activity in the liver, but there was a premature expansion of CD206+ cells, presumptive precursors of liver sinusoidal endothelial cells. We suggest that many functions of macrophages in development of the placenta and embryo can be provided by other cell types in their absence.
Collapse
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woollongabba, Brisbane, Qld 4102, Australia
| | - Ngari Teakle
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woollongabba, Brisbane, Qld 4102, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woollongabba, Brisbane, Qld 4102, Australia
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woollongabba, Brisbane, Qld 4102, Australia
| |
Collapse
|
7
|
Hume DA, Millard SM, Pettit AR. Macrophage heterogeneity in the single-cell era: facts and artifacts. Blood 2023; 142:1339-1347. [PMID: 37595274 DOI: 10.1182/blood.2023020597] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
In this spotlight, we review technical issues that compromise single-cell analysis of tissue macrophages, including limited and unrepresentative yields, fragmentation and generation of remnants, and activation during tissue disaggregation. These issues may lead to a misleading definition of subpopulations of macrophages and the expression of macrophage-specific transcripts by unrelated cells. Recognition of the technical limitations of single-cell approaches is required in order to map the full spectrum of tissue-resident macrophage heterogeneity and assess its biological significance.
Collapse
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Susan M Millard
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Allison R Pettit
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| |
Collapse
|
8
|
Hume DA. Letter to the Editor: Questioning the existence of Aif1+ , Csf1r+ mesenchymal stem cells. Hepatology 2023; 78:E25. [PMID: 36166318 DOI: 10.1002/hep.32809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/08/2022]
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute , Brisbane , Queensland , Australia
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Chundru VK, Marioni RE, Prendergast JGD, Lin T, Beveridge AJ, Martin NG, Montgomery GW, Hume DA, Deary IJ, Visscher PM, Wray NR, McRae AF. Rare genetic variants underlie outlying levels of DNA methylation and gene-expression. Hum Mol Genet 2023; 32:1912-1921. [PMID: 36790133 PMCID: PMC10196672 DOI: 10.1093/hmg/ddad028] [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: 09/15/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Testing the effect of rare variants on phenotypic variation is difficult due to the need for extremely large cohorts to identify associated variants given expected effect sizes. An alternative approach is to investigate the effect of rare genetic variants on DNA methylation (DNAm) as effect sizes are expected to be larger for molecular traits compared with complex traits. Here, we investigate DNAm in healthy ageing populations-the Lothian Birth Cohorts of 1921 and 1936-and identify both transient and stable outlying DNAm levels across the genome. We find an enrichment of rare genetic single nucleotide polymorphisms (SNPs) within 1 kb of DNAm sites in individuals with stable outlying DNAm, implying genetic control of this extreme variation. Using a family-based cohort, the Brisbane Systems Genetics Study, we observed increased sharing of DNAm outliers among more closely related individuals, consistent with these outliers being driven by rare genetic variation. We demonstrated that outlying DNAm levels have a functional consequence on gene expression levels, with extreme levels of DNAm being associated with gene expression levels toward the tails of the population distribution. This study demonstrates the role of rare SNPs in the phenotypic variation of DNAm and the effect of extreme levels of DNAm on gene expression.
Collapse
Affiliation(s)
- V Kartik Chundru
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Allan J Beveridge
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, The University of Glasgow, Glasgow G61 1QH, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David A Hume
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
11
|
Hume DA. Fate-mapping studies in inbred mice: A model for understanding macrophage development and homeostasis? Eur J Immunol 2023:e2250242. [PMID: 37016273 DOI: 10.1002/eji.202250242] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/01/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2023]
Abstract
The mononuclear phagocyte system (MPS) was defined in the early 1970s as a family of cells including progenitors, monocytes in the circulation and resident tissue macrophages. They arise during development in three waves, in the yolk sac, fetal liver and bone marrow. Fate-mapping studies using conditional reporter genes and regulated expression of cre recombinase have led to the view that most resident tissue macrophage populations are established during embryonic development and maintained in the adult by self-renewal with minimal input from bone marrow progenitors or blood monocytes. The interpretation of fate-mapping studies depends upon multiple assumptions; (i) that expression of cre recombinase has no effect on monocyte-macrophage homeostasis, (ii) that tamoxifen is a neutral agonist, (iii) that life in an SPF animal facility reflects the normal life course of a mouse; (iv) that the C57Bl/6J inbred mouse is a generalizable model and the biology of the MPS is unaffected by mouse genetic background or species. This review summarizes evidence that questions each of these assumptions and concludes that fate-mapping studies may over-estimate the longevity and relative contribution of fetal-derived cells to resident tissue macrophage populations. In the opinion of the author, the original concept of the MPS does not require revision. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Brisbane, Qld, 4102, Australia
| |
Collapse
|
12
|
Grootveld AK, Kyaw W, Panova V, Lau AWY, Ashwin E, Seuzaret G, Dhenni R, Bhattacharyya ND, Khoo WH, Biro M, Mitra T, Meyer-Hermann M, Bertolino P, Tanaka M, Hume DA, Croucher PI, Brink R, Nguyen A, Bannard O, Phan TG. Apoptotic cell fragments locally activate tingible body macrophages in the germinal center. Cell 2023; 186:1144-1161.e18. [PMID: 36868219 PMCID: PMC7614509 DOI: 10.1016/j.cell.2023.02.004] [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: 09/23/2022] [Revised: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 03/05/2023]
Abstract
Germinal centers (GCs) that form within lymphoid follicles during antibody responses are sites of massive cell death. Tingible body macrophages (TBMs) are tasked with apoptotic cell clearance to prevent secondary necrosis and autoimmune activation by intracellular self antigens. We show by multiple redundant and complementary methods that TBMs derive from a lymph node-resident, CD169-lineage, CSF1R-blockade-resistant precursor that is prepositioned in the follicle. Non-migratory TBMs use cytoplasmic processes to chase and capture migrating dead cell fragments using a "lazy" search strategy. Follicular macrophages activated by the presence of nearby apoptotic cells can mature into TBMs in the absence of GCs. Single-cell transcriptomics identified a TBM cell cluster in immunized lymph nodes which upregulated genes involved in apoptotic cell clearance. Thus, apoptotic B cells in early GCs trigger activation and maturation of follicular macrophages into classical TBMs to clear apoptotic debris and prevent antibody-mediated autoimmune diseases.
Collapse
Affiliation(s)
- Abigail K Grootveld
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Wunna Kyaw
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Veera Panova
- MRC Human Immunology Unit, Nuffield Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angelica W Y Lau
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Emily Ashwin
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Seuzaret
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Département de Biologie, Université de Lyon, Lyon, France
| | - Rama Dhenni
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | | | - Weng Hua Khoo
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Tanmay Mitra
- Department of Systems Biology and Braunschweig Integrated Center for Systems Biology (BRICS), Helmholtz Center for Infection Research, Rebenring 56, D-38106 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Biology and Braunschweig Integrated Center for Systems Biology (BRICS), Helmholtz Center for Infection Research, Rebenring 56, D-38106 Braunschweig, Germany; Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Patrick Bertolino
- Centenary Institute and University of Sydney, AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Masato Tanaka
- Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - David A Hume
- Mater Research Institute, University of Queensland, Brisbane, QLD, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Robert Brink
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Akira Nguyen
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Oliver Bannard
- MRC Human Immunology Unit, Nuffield Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Tri Giang Phan
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Abstract
PURPOSE OF REVIEW The purpose of the review is to summarize the expression and function of CSF1R and its ligands in bone homeostasis and constraints on therapeutic targeting of this axis. RECENT FINDINGS Bone development and homeostasis depends upon interactions between mesenchymal cells and cells of the mononuclear phagocyte lineage (MPS), macrophages, and osteoclasts (OCL). The homeostatic interaction is mediated in part by the systemic and local production of growth factors, macrophage colony-stimulating factor (CSF1), and interleukin 34 (IL34) that interact with a receptor (CSF1R) expressed exclusively by MPS cells and their progenitors. Loss-of-function mutations in CSF1 or CSF1R lead to loss of OCL and macrophages and dysregulation of postnatal bone development. MPS cells continuously degrade CSF1R ligands via receptor-mediated endocytosis. As a consequence, any local or systemic increase or decrease in macrophage or OCL abundance is rapidly reversible. In principle, both CSF1R agonists and antagonists have potential in bone regenerative medicine but their evaluation in disease models and therapeutic application needs to carefully consider the intrinsic feedback control of MPS biology.
Collapse
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
| | - Lena Batoon
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| |
Collapse
|
15
|
Ferrari-Cestari M, Okano S, Patel PJ, Horsfall LU, Keshvari S, Hume DA, Williams S, Russell A, Powell EE, Irvine KM. Serum CCL2 is associated with visceral adiposity but not fibrosis in patients with Non-alcoholic Fatty Liver Disease (NAFLD). Dig Dis 2022; 41:439-446. [PMID: 36327947 DOI: 10.1159/000527784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is caused by ectopic fat accumulation in the liver as a consequence of metabolic perturbations associated with obesity, type 2 diabetes, dyslipidemia and insulin resistance. People with NAFLD may develop metabolic and cardiovascular complications, and/or liver-related complications, especially fibrosis and hepatocellular carcinoma, associated with high morbidity and mortality. Due to the high and increasing prevalence of NAFLD there is an urgent need to identify people at risk of developing liver fibrosis and complications. CC-chemokine ligand 2 (CCL2) is chemokine that attracts inflammatory monocytes to stressed or injured tissues. Infiltrating inflammatory monocytes, and CCL2, are strongly implicated in the pathogenesis of liver disease in animal models, however evidence in patient cohorts is conflicting. METHODS We investigated associations between circulating CCL2 and clinical parameters, including fibrosis assessed by liver stiffness measurement, in a cohort of 250 NAFLD patients. We also measured Fatty Acid Binding Protein 2 (FABP2), a putative biomarker of intestinal permeability in patients with liver disease, since pro-inflammatory gut-derived microbial products may induce inflammatory chemokines such as CCL2. RESULTS Serum CCL2 levels were weakly associated with liver stiffness, but the association was no longer significant after accounting for age, diabetes and BMI in a multivariable model. Consistent with this, girth and BMI were the strongest predictors of elevated circulating CCL2. Serum FABP2 was weakly, but significantly, correlated with CCL2, and negatively correlated with estimated Glomerular Filtration Rate (eGFR). CONCLUSION Circulating CCL2 and FABP2 are associated with NAFLD co-morbidities, but not liver disease progression in patients with NAFLD.
Collapse
|
16
|
Paolicelli RC, Sierra A, Stevens B, Tremblay ME, Aguzzi A, Ajami B, Amit I, Audinat E, Bechmann I, Bennett M, Bennett F, Bessis A, Biber K, Bilbo S, Blurton-Jones M, Boddeke E, Brites D, Brône B, Brown GC, Butovsky O, Carson MJ, Castellano B, Colonna M, Cowley SA, Cunningham C, Davalos D, De Jager PL, de Strooper B, Denes A, Eggen BJL, Eyo U, Galea E, Garel S, Ginhoux F, Glass CK, Gokce O, Gomez-Nicola D, González B, Gordon S, Graeber MB, Greenhalgh AD, Gressens P, Greter M, Gutmann DH, Haass C, Heneka MT, Heppner FL, Hong S, Hume DA, Jung S, Kettenmann H, Kipnis J, Koyama R, Lemke G, Lynch M, Majewska A, Malcangio M, Malm T, Mancuso R, Masuda T, Matteoli M, McColl BW, Miron VE, Molofsky AV, Monje M, Mracsko E, Nadjar A, Neher JJ, Neniskyte U, Neumann H, Noda M, Peng B, Peri F, Perry VH, Popovich PG, Pridans C, Priller J, Prinz M, Ragozzino D, Ransohoff RM, Salter MW, Schaefer A, Schafer DP, Schwartz M, Simons M, Smith CJ, Streit WJ, Tay TL, Tsai LH, Verkhratsky A, von Bernhardi R, Wake H, Wittamer V, Wolf SA, Wu LJ, Wyss-Coray T. Microglia states and nomenclature: A field at its crossroads. Neuron 2022; 110:3458-3483. [PMID: 36327895 PMCID: PMC9999291 DOI: 10.1016/j.neuron.2022.10.020] [Citation(s) in RCA: 399] [Impact Index Per Article: 199.5] [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: 03/15/2022] [Revised: 08/06/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Microglial research has advanced considerably in recent decades yet has been constrained by a rolling series of dichotomies such as "resting versus activated" and "M1 versus M2." This dualistic classification of good or bad microglia is inconsistent with the wide repertoire of microglial states and functions in development, plasticity, aging, and diseases that were elucidated in recent years. New designations continuously arising in an attempt to describe the different microglial states, notably defined using transcriptomics and proteomics, may easily lead to a misleading, although unintentional, coupling of categories and functions. To address these issues, we assembled a group of multidisciplinary experts to discuss our current understanding of microglial states as a dynamic concept and the importance of addressing microglial function. Here, we provide a conceptual framework and recommendations on the use of microglial nomenclature for researchers, reviewers, and editors, which will serve as the foundations for a future white paper.
Collapse
Affiliation(s)
- Rosa C Paolicelli
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Amanda Sierra
- Achucarro Basque Center for Neuroscience, Glial Cell Biology Lab, Leioa, Spain; Department of Neuroscience, University of the Basque Country EHU/UPV, Leioa, Spain; Ikerbasque Foundation, Bilbao, Spain.
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, (HHMI), MD, USA; Boston Children's Hospital, Boston, MA, USA.
| | - Marie-Eve Tremblay
- Centre de recherche du CHU de Québec-Université Laval, Québec City, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC, Canada; Center for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Bahareh Ajami
- Department of Molecular Microbiology & Immunology, Department of Behavioral and Systems Neuroscience, Oregon Health & Science University School of Medicine, Portland, OR, USA
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Etienne Audinat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, Leipzig, Germany
| | - Mariko Bennett
- Children's Hospital of Philadelphia, Department of Psychiatry, Department of Pediatrics, Division of Child Neurology, Philadelphia, PA, USA
| | - Frederick Bennett
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Alain Bessis
- École Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Paris Sciences et Lettres Research University, Paris, France
| | - Knut Biber
- Neuroscience Discovery, AbbVie Deutschland GmbH, Ludwigshafen, Germany
| | - Staci Bilbo
- Departments of Psychology & Neuroscience, Neurobiology, and Cell Biology, Duke University, Durham, NC, USA
| | - Mathew Blurton-Jones
- Center for the Neurobiology of Learning and Memory, UCI MIND, University of California, Irvine, CA, USA
| | - Erik Boddeke
- Department Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center, Groningen, the Netherlands
| | - Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Bert Brône
- BIOMED Research Institute, University of Hasselt, Hasselt, Belgium
| | - Guy C Brown
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Oleg Butovsky
- Ann Romney Center for Neurologic Diseases, Department Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Monica J Carson
- Center for Glial-Neuronal Interactions, Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Bernardo Castellano
- Unidad de Histología Medica, Depto. Biología Celular, Fisiología e Inmunología, Barcelona, Spain; Instituto de Neurociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Colm Cunningham
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Republic of Ireland; Trinity College Institute of Neuroscience, Trinity College, Dublin, Republic of Ireland
| | - Dimitrios Davalos
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Bart de Strooper
- UK Dementia Research Institute at University College London, London, UK; Vlaams Instituut voor Biotechnologie at Katholieke Universiteit Leuven, Leuven, Belgium
| | - Adam Denes
- "Momentum" Laboratory of Neuroimmunology, Institute of Experimental Medicine, Budapest, Hungary
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, section Molecular Neurobiology, University of Groningen, Groningen, the Netherlands; University Medical Center Groningen, Groningen, the Netherlands
| | - Ukpong Eyo
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Elena Galea
- Institut de Neurociències and Departament de Bioquímica, Unitat de Bioquímica, Universitat Autònoma de Barcelona, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Sonia Garel
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Paris, France; College de France, Paris, France
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Ozgun Gokce
- Institute for Stroke and Dementia Research, Ludwig Maximillian's University of Munich, Munich, Germany
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Berta González
- Unidad de Histología Medica, Depto. Biología Celular, Fisiología e Inmunología and Instituto de Neurociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Siamon Gordon
- Chang Gung University, Taoyuan City, Taiwan (ROC); Sir William Dunn School of Pathology, Oxford, UK
| | - Manuel B Graeber
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Andrew D Greenhalgh
- Lydia Becker Institute of Immunology and Inflammation, Geoffrey Jefferson Brain Research Centre, Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Pierre Gressens
- Université Paris Cité, Inserm, NeuroDiderot, 75019 Paris, France
| | - Melanie Greter
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Christian Haass
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center (BMC), Ludwig-Maximilians-Universität Munchen, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy); Munich, Germany
| | - Michael T Heneka
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Soyon Hong
- UK Dementia Research Institute at University College London, London, UK
| | - David A Hume
- Mater Research Institute-University of Queensland, Brisbane, QLD, Australia
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Helmut Kettenmann
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany; Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan Kipnis
- Center for Brain Immunology and Glia (BIG), Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryuta Koyama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Greg Lemke
- MNL-L, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marina Lynch
- Trinity College Institute of Neuroscience, Trinity College, Dublin, Republic of Ireland
| | - Ania Majewska
- Department of Neuroscience, University of Rochester, Rochester, NY, USA
| | - Marzia Malcangio
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Tarja Malm
- University of Eastern Finland, Kuopio, Finland
| | - Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Takahiro Masuda
- Department of Molecular and System Pharmacology, Graduate School of Pharmaceutical Sciences, Kyushu University, Japan
| | - Michela Matteoli
- Humanitas University, Department of Biomedical Sciences, Milan, Italy
| | - Barry W McColl
- UK Dementia Research Institute, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, UK; UK Dementia Research Institute at the University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | | | - Michelle Monje
- Howard Hughes Medical Institute, (HHMI), MD, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Agnes Nadjar
- Neurocentre Magendie, University of Bordeaux, Bordeaux, France; Institut Universitaire de France (IUF), Paris, France
| | - Jonas J Neher
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Urte Neniskyte
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania; Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Harald Neumann
- Institute of Reconstructive Neurobiology, Medical Faculty and University Hospital of Bonn, University of Bonn, Bonn, Germany
| | - Mami Noda
- Laboratory of Pathophysiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan; Institute of Mitochondrial Biology and Medicine of Xi'an Jiaotong University School of Life Science and Technology, Xi'an, China
| | - Bo Peng
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Francesca Peri
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - V Hugh Perry
- UK Dementia Research Institute, University College London, London, UK; School of Biological Sciences, University of Southampton, Southampton, UK
| | - Phillip G Popovich
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Clare Pridans
- University of Edinburgh, Centre for Inflammation Research, Edinburgh, UK
| | - Josef Priller
- Department of Psychiatry & Psychotherapy, School of Medicine, Technical University of Munich, Munich, Germany; Charité - Universitätsmedizin Berlin and DZNE, Berlin, Germany; University of Edinburgh and UK DRI, Edinburgh, UK
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Davide Ragozzino
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy; Santa Lucia Foundation (IRCCS Fondazione Santa Lucia), Rome, Italy
| | | | - Michael W Salter
- Hospital for Sick Children, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Anne Schaefer
- Nash Family Department of Neuroscience, Center for Glial Biology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Max Planck Institute for Biology of Ageing, Koeln, Germany
| | - Dorothy P Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michal Schwartz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Cody J Smith
- Galvin Life Science Center, University of Notre Dame, Indianapolis, IN, USA
| | - Wolfgang J Streit
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Tuan Leng Tay
- Faculty of Biology, University of Freiburg, Freiburg, Germany; BrainLinks-BrainTools Centre, University of Freiburg, Freiburg, Germany; Freiburg Institute of Advanced Studies, University of Freiburg, Freiburg, Germany; Department of Biology, Boston University, Boston, MA, USA; Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Li-Huei Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexei Verkhratsky
- Achucarro Basque Center for Neuroscience, Glial Cell Biology Lab, Leioa, Spain; Department of Neuroscience, University of the Basque Country EHU/UPV, Leioa, Spain; Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Hiroaki Wake
- Department of Anatomy and Molecular Cell Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Valérie Wittamer
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium; ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Susanne A Wolf
- Charité Universitätsmedizin, Experimental Ophthalmology and Neuroimmunology, Berlin, Germany
| | - Long-Jun Wu
- Department of Neurology and Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
17
|
Bradford BM, McGuire LI, Hume DA, Pridans C, Mabbott NA. Microglia deficiency accelerates prion disease but does not enhance prion accumulation in the brain. Glia 2022; 70:2169-2187. [PMID: 35852018 PMCID: PMC9544114 DOI: 10.1002/glia.24244] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 01/08/2023]
Abstract
Prion diseases are transmissible, neurodegenerative disorders associated with misfolding of the prion protein. Previous studies show that reduction of microglia accelerates central nervous system (CNS) prion disease and increases the accumulation of prions in the brain, suggesting that microglia provide neuroprotection by phagocytosing and destroying prions. In Csf1rΔFIRE mice, the deletion of an enhancer within Csf1r specifically blocks microglia development, however, their brains develop normally and show none of the deficits reported in other microglia-deficient models. Csf1rΔFIRE mice were used as a refined model in which to study the impact of microglia-deficiency on CNS prion disease. Although Csf1rΔFIRE mice succumbed to CNS prion disease much earlier than wild-type mice, the accumulation of prions in their brains was reduced. Instead, astrocytes displayed earlier, non-polarized reactive activation with enhanced phagocytosis of neuronal contents and unfolded protein responses. Our data suggest that rather than simply phagocytosing and destroying prions, the microglia instead provide host-protection during CNS prion disease and restrict the harmful activities of reactive astrocytes.
Collapse
Affiliation(s)
- Barry M. Bradford
- The Roslin Institute and R(D)SVSUniversity of Edinburgh, Easter Bush CampusMidlothianUK
| | - Lynne I. McGuire
- The Roslin Institute and R(D)SVSUniversity of Edinburgh, Easter Bush CampusMidlothianUK
| | - David A. Hume
- Mater Research Institute‐University of Queensland, Translational Research InstituteWoolloongabbaQueenslandAustralia
| | - Clare Pridans
- Simons Initiative for the Developing Brain, Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson BuildingEdinburghUK
- Centre for Inflammation ResearchThe Queen's Medical Research Institute, Edinburgh BioQuarterEdinburghUK
| | - Neil A. Mabbott
- The Roslin Institute and R(D)SVSUniversity of Edinburgh, Easter Bush CampusMidlothianUK
| |
Collapse
|
18
|
Hume DA, Offermanns S, Bonnavion R. Contamination of isolated mouse Kupffer cells with liver sinusoidal endothelial cells. Immunity 2022; 55:1139-1140. [PMID: 35830818 DOI: 10.1016/j.immuni.2022.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/22/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Brisbane, Qld, Australia.
| | - Stefan Offermanns
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Remy Bonnavion
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| |
Collapse
|
19
|
Freeman TC, Horsewell S, Patir A, Harling-Lee J, Regan T, Shih BB, Prendergast J, Hume DA, Angus T. Graphia: A platform for the graph-based visualisation and analysis of high dimensional data. PLoS Comput Biol 2022; 18:e1010310. [PMID: 35877685 PMCID: PMC9352203 DOI: 10.1371/journal.pcbi.1010310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/16/2021] [Revised: 08/04/2022] [Accepted: 06/16/2022] [Indexed: 01/04/2023] Open
Abstract
Graphia is an open-source platform created for the graph-based analysis of the huge amounts of quantitative and qualitative data currently being generated from the study of genomes, genes, proteins metabolites and cells. Core to Graphia’s functionality is support for the calculation of correlation matrices from any tabular matrix of continuous or discrete values, whereupon the software is designed to rapidly visualise the often very large graphs that result in 2D or 3D space. Following graph construction, an extensive range of measurement algorithms, routines for graph transformation, and options for the visualisation of node and edge attributes are available, for graph exploration and analysis. Combined, these provide a powerful solution for the interpretation of high-dimensional data from many sources, or data already in the form of a network or equivalent adjacency matrix. Several use cases of Graphia are described, to showcase its wide range of applications in the analysis biological data. Graphia runs on all major desktop operating systems, is extensible through the deployment of plugins and is freely available to download from https://graphia.app/. Graphia is a new visual analytics platform specifically created for the network-based analysis of large and complex data, such as that generated in huge amounts by modern biological analyses. It works in a data agnostic, hypothesis-free manner to generate correlation networks from any table of numerical or discrete values, thereafter providing a means to rapidly visualise the often very large networks that result, in either 2D or 3D space. Following network construction, the tool offers an extensive range of analysis algorithms, routines for network transformation, and options for the visualisation of metadata. This provides a powerful analysis solution for the exploration and interpretation of high-dimensional data from any source, as well as any data already defined as a network. Several use cases of Graphia are described to showcase its wide range of applications in the analysis biological data. Graphia is open source and free to all.
Collapse
Affiliation(s)
- Tom C. Freeman
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
- Kajeka Limited, Roslin Innovation Centre, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Sebastian Horsewell
- Kajeka Limited, Roslin Innovation Centre, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anirudh Patir
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Josh Harling-Lee
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Regan
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Barbara B. Shih
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - James Prendergast
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Tim Angus
- Kajeka Limited, Roslin Innovation Centre, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
20
|
Kiani Shabestari S, Morabito S, Danhash EP, McQuade A, Sanchez JR, Miyoshi E, Chadarevian JP, Claes C, Coburn MA, Hasselmann J, Hidalgo J, Tran KN, Martini AC, Chang Rothermich W, Pascual J, Head E, Hume DA, Pridans C, Davtyan H, Swarup V, Blurton-Jones M. Absence of microglia promotes diverse pathologies and early lethality in Alzheimer's disease mice. Cell Rep 2022; 39:110961. [PMID: 35705056 PMCID: PMC9285116 DOI: 10.1016/j.celrep.2022.110961] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [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: 11/02/2021] [Revised: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 11/03/2022] Open
Abstract
Microglia are strongly implicated in the development and progression of Alzheimer's disease (AD), yet their impact on pathology and lifespan remains unclear. Here we utilize a CSF1R hypomorphic mouse to generate a model of AD that genetically lacks microglia. The resulting microglial-deficient mice exhibit a profound shift from parenchymal amyloid plaques to cerebral amyloid angiopathy (CAA), which is accompanied by numerous transcriptional changes, greatly increased brain calcification and hemorrhages, and premature lethality. Remarkably, a single injection of wild-type microglia into adult mice repopulates the microglial niche and prevents each of these pathological changes. Taken together, these results indicate the protective functions of microglia in reducing CAA, blood-brain barrier dysfunction, and brain calcification. To further understand the clinical implications of these findings, human AD tissue and iPSC-microglia were examined, providing evidence that microglia phagocytose calcium crystals, and this process is impaired by loss of the AD risk gene, TREM2.
Collapse
Affiliation(s)
- Sepideh Kiani Shabestari
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Samuel Morabito
- Mathematical, Computational and System Biology (MCSB) Program, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Emma Pascal Danhash
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Amanda McQuade
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Jessica Ramirez Sanchez
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Emily Miyoshi
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA
| | - Jean Paul Chadarevian
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Christel Claes
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Morgan Alexandra Coburn
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Jonathan Hasselmann
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Jorge Hidalgo
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Kayla Nhi Tran
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Alessandra C Martini
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, UC Irvine, Irvine, CA 92697, USA
| | | | - Jesse Pascual
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, UC Irvine, Irvine, CA 92697, USA
| | - Elizabeth Head
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, UC Irvine, Irvine, CA 92697, USA
| | - David A Hume
- Mater Research Institute-University of Queensland, Brisbane, Australia
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK; Simons Initiative for the Developing Brain Centre, University of Edinburgh, Edinburgh, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK
| | - Hayk Davtyan
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
21
|
Laviron M, Petit M, Weber-Delacroix E, Combes AJ, Arkal AR, Barthélémy S, Courau T, Hume DA, Combadière C, Krummel MF, Boissonnas A. Tumor-associated macrophage heterogeneity is driven by tissue territories in breast cancer. Cell Rep 2022; 39:110865. [PMID: 35613577 DOI: 10.1016/j.celrep.2022.110865] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 09/10/2021] [Revised: 04/04/2022] [Accepted: 05/03/2022] [Indexed: 02/08/2023] Open
Abstract
Tissue-resident macrophages adapt to local signals within tissues to acquire specific functions. Neoplasia transforms the tissue, raising the question as to how the environmental perturbations contribute to tumor-associated macrophage (TAM) identity and functions. Combining single-cell RNA sequencing (scRNA-seq) with spatial localization of distinct TAM subsets by imaging, we discover that TAM transcriptomic programs follow two main differentiation paths according to their localization in the stroma or in the neoplastic epithelium of the mammary duct. Furthermore, this diversity is exclusively detected in a spontaneous tumor model and tracks the different tissue territories as well as the type of tumor lesion. These TAM subsets harbor distinct capacity to activate CD8+ T cells and phagocyte tumor cells, supporting that specific tumor regions, rather than defined activation states, are the major drivers of TAM plasticity and heterogeneity. The distinctions created here provide a framework to design cancer treatment targeting specific TAM niches.
Collapse
Affiliation(s)
- Marie Laviron
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, 75013 Paris, France
| | - Maxime Petit
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, 75013 Paris, France
| | - Eléonore Weber-Delacroix
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, 75013 Paris, France
| | - Alexis J Combes
- Department of Pathology, ImmunoX Initiative, UCSF Immunoprofiler Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arjun Rao Arkal
- Department of Pathology, ImmunoX Initiative, UCSF Immunoprofiler Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sandrine Barthélémy
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, 75013 Paris, France
| | - Tristan Courau
- Department of Pathology, ImmunoX Initiative, UCSF Immunoprofiler Initiative, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD 4101, Australia
| | - Christophe Combadière
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, 75013 Paris, France
| | - Matthew F Krummel
- Department of Pathology, ImmunoX Initiative, UCSF Immunoprofiler Initiative, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexandre Boissonnas
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, 75013 Paris, France.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Keshvari S, Genz B, Teakle N, Caruso M, Cestari MF, Patkar OL, Tse BWC, Sokolowski KA, Ebersbach H, Jascur J, MacDonald KPA, Miller G, Ramm GA, Pettit AR, Clouston AD, Powell EE, Hume DA, Irvine KM. Therapeutic potential of macrophage colony-stimulating factor (CSF1) in chronic liver disease. Dis Model Mech 2022; 15:274391. [PMID: 35169835 PMCID: PMC9044210 DOI: 10.1242/dmm.049387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/08/2022] [Indexed: 11/20/2022] Open
Abstract
Resident and recruited macrophages control the development and proliferation of the liver. We showed previously in multiple species that treatment with a macrophage colony stimulating factor (CSF1)-Fc fusion protein initiated hepatocyte proliferation and promoted repair in models of acute hepatic injury in mice. Here we investigated the impact of CSF1-Fc on resolution of advanced fibrosis and liver regeneration, utilizing a non-resolving toxin-induced model of chronic liver injury and fibrosis in C57BL/6J mice. Co-administration of CSF1-Fc with exposure to thioacetamide (TAA) exacerbated inflammation consistent with monocyte contributions to initiation of pathology. After removal of TAA, either acute or chronic CSF1-Fc treatment promoted liver growth, prevented progression and promoted resolution of fibrosis. Acute CSF1-Fc treatment was also anti-fibrotic and pro-regenerative in a model of partial hepatectomy in mice with established fibrosis. The beneficial impacts of CSF1-Fc treatment were associated with monocyte-macrophage recruitment and increased expression of remodeling enzymes and growth factors. These studies indicate that CSF1-dependent macrophages contribute to both initiation and resolution of fibrotic injury and that CSF1-Fc has therapeutic potential in human liver disease.
Collapse
Affiliation(s)
- Sahar Keshvari
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Berit Genz
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ngari Teakle
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Caruso
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Michelle F Cestari
- 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
| | - 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
| | - Hilmar Ebersbach
- Novartis Institutes for Biomedical Research (NIBR), Fabrikstrasse 2, Novartis Campus, CH-4056 Basel, Switzerland
| | - Julia Jascur
- Novartis Institutes for Biomedical Research (NIBR), Fabrikstrasse 2, Novartis Campus, CH-4056 Basel, Switzerland
| | | | | | - Grant A Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Allison R Pettit
- Mater Research Institute-The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Andrew D Clouston
- Envoi Specialist Pathologists, Brisbane, Qld, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Elizabeth E Powell
- Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, 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
| |
Collapse
|
25
|
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: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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.
| |
Collapse
|
26
|
Wu Z, Hu T, Chintoan-Uta C, Macdonald J, Stevens MP, Sang H, Hume DA, Kaiser P, Balic A. Development of novel reagents to chicken FLT3, XCR1 and CSF2R for the identification and characterization of avian conventional dendritic cells. Immunology 2021; 165:171-194. [PMID: 34767637 DOI: 10.1111/imm.13426] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/30/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Conventional dendritic cells (cDC) are bone marrow-derived immune cells that play a central role in linking innate and adaptive immunity. cDCs efficiently uptake, process and present antigen to naïve T cells, driving clonal expansion of antigen-specific T-cell responses. In chicken, vital reagents are lacking for the efficient and precise identification of cDCs. In this study, we have developed several novel reagents for the identification and characterization of chicken cDCs. Chicken FLT3 cDNA was cloned and a monoclonal antibody to cell surface FLT3 was generated. This antibody identified a distinct FLT3HI splenic subset which lack expression of signature markers for B cells, T cells or monocyte/macrophages. By combining anti-FLT3 and CSF1R-eGFP transgenic expression, three major populations within the mononuclear phagocyte system were identified in the spleen. The cDC1 subset of mammalian cDCs express the chemokine receptor XCR1. To characterize chicken cDCs, a synthetic chicken chemokine (C motif) ligand (XCL1) peptide conjugated to Alexa Fluor 647 was developed (XCL1AF647 ). Flow cytometry staining of XCL1AF647 on splenocytes showed that all chicken FLT3HI cells exclusively express XCR1, supporting the hypothesis that this population comprises bona fide chicken cDCs. Further analysis revealed that chicken cDCs expressed CSF1R but lacked the expression of CSF2R. Collectively, the cell surface phenotypes of chicken cDCs were partially conserved with mammalian XCR1+ cDC1, with distinct differences in CSF1R and CSF2R expression compared with mammalian orthologues. These original reagents allow the efficient identification of chicken cDCs to investigate their important roles in the chicken immunity and diseases.
Collapse
Affiliation(s)
- Zhiguang Wu
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Tuanjun Hu
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | | | - Joni Macdonald
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Mark P Stevens
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Helen Sang
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | - David A Hume
- Translational Research Institute, Mater Research Institute-University of Queensland, Woolloongabba, Qld, Australia
| | - Pete Kaiser
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Adam Balic
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK
| |
Collapse
|
27
|
Sehgal A, Irvine KM, Hume DA. Functions of macrophage colony-stimulating factor (CSF1) in development, homeostasis, and tissue repair. Semin Immunol 2021; 54:101509. [PMID: 34742624 DOI: 10.1016/j.smim.2021.101509] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/23/2021] [Indexed: 12/16/2022]
Abstract
Macrophage colony-stimulating factor (CSF1) is the primary growth factor required for the control of monocyte and macrophage differentiation, survival, proliferation and renewal. Although the cDNAs encoding multiple isoforms of human CSF1 were cloned in the 1980s, and recombinant proteins were available for testing in humans, CSF1 has not yet found substantial clinical application. Here we present an overview of CSF1 biology, including evolution, regulation and functions of cell surface and secreted isoforms. CSF1 is widely-expressed, primarily by cells of mesenchymal lineages, in all mouse tissues. Cell-specific deletion of a floxed Csf1 allele in mice indicates that local CSF1 production contributes to the maintenance of tissue-specific macrophage populations but is not saturating. CSF1 in the circulation is controlled primarily by receptor-mediated clearance by macrophages in liver and spleen. Administration of recombinant CSF1 to humans or animals leads to monocytosis and expansion of tissue macrophage populations and growth of the liver and spleen. In a wide variety of tissue injury models, CSF1 administration promotes monocyte infiltration, clearance of damaged cells and repair. We suggest that CSF1 has therapeutic potential in regenerative medicine.
Collapse
Affiliation(s)
- Anuj Sehgal
- 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.
| |
Collapse
|
28
|
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.
Collapse
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)
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Patkar OL, Mohamed AZ, Narayanan A, Mardon K, Cowin G, Bhalla R, Stimson DHR, Kassiou M, Beecher K, Belmer A, Alvarez Cooper I, Morgan M, Hume DA, Irvine KM, Bartlett SE, Nasrallah F, Cumming P. A binge high sucrose diet provokes systemic and cerebral inflammation in rats without inducing obesity. Sci Rep 2021; 11:11252. [PMID: 34045616 PMCID: PMC8160215 DOI: 10.1038/s41598-021-90817-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023] Open
Abstract
While the dire cardiometabolic consequences of the hypercaloric modern 'Western' diet are well known, there is not much information on the health impact of a high sucrose diet not inducing weight gain. Here, we tested the hypothesis that rats reared with intermittent binge access to sucrose in addition to normal chow would develop an inflammatory response in brain. To test this hypothesis, we undertook serial PET/MRI scans with the TSPO ligand [18F]DPA714 in a group of (n=9) rats at baseline and again after voluntarily consuming 5% sucrose solution three days a week for three months. Compared to a control group fed with normal chow (n=9), the sucrose rats indeed showed widespread increases in the availability of cerebral binding sites for the microglial marker, despite normal weight gain compared to the control diet group. Subsequent immunofluorescence staining of the brains confirmed the PET findings, showing a widespread 20% increase in the abundance of IBA-1-positive microglia with characteristic 'semi-activated' morphology in the binge sucrose rats, which had 23% lower density of microglial endpoints and 25% lower mean process length compared to microglia in the control rats with ordinary feeding. GFAP immunofluorescence showed no difference in astroglial coverage in the sucrose rats, except for a slight reduction in hypothalamus. The binge sucrose diet-induced neuroinflammation was associated with a significant elevation of white blood cell counts. Taking these results together, we find that long-term intake of sucrose in a binge paradigm, similar in sucrose content to the contemporary Western diet, triggered a low-grade systemic and central inflammation in non-obese rats. The molecular mechanism of this phenomenon remains to be established.
Collapse
Affiliation(s)
- Omkar L Patkar
- Macrophage Biology Group, Mater Research, Translational Research Institute, Brisbane, QLD, Australia
- Department of Nuclear Medicine, Inselspital, Bern University, Bern, Switzerland
| | - Abdalla Z Mohamed
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ashwin Narayanan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Karine Mardon
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Gary Cowin
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Rajiv Bhalla
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Damion H R Stimson
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Kassiou
- School of Chemistry, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kate Beecher
- Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia
| | - Arnauld Belmer
- Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia
| | - Ignatius Alvarez Cooper
- Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia
| | - Michael Morgan
- Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, Australia
| | - David A Hume
- Macrophage Biology Group, Mater Research, Translational Research Institute, Brisbane, QLD, Australia
| | - Katharine M Irvine
- Macrophage Biology Group, Mater Research, Translational Research Institute, Brisbane, QLD, Australia
| | - Selena E Bartlett
- Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia
| | - Fatima Nasrallah
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Paul Cumming
- Department of Nuclear Medicine, Inselspital, Bern University, Bern, Switzerland.
- School of Psychology and Counselling, Queensland University of Technology, Brisbane, Australia.
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Wiener P, Robert C, Ahbara A, Salavati M, Abebe A, Kebede A, Wragg D, Friedrich J, Vasoya D, Hume DA, Djikeng A, Watson M, Prendergast JGD, Hanotte O, Mwacharo JM, Clark EL. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biol Evol 2021; 13:evab014. [PMID: 33501931 PMCID: PMC7955157 DOI: 10.1093/gbe/evab014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
Collapse
Affiliation(s)
- Pamela Wiener
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Christelle Robert
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, United Kingdom
- Department of Zoology, Misurata University, Misurata, Libya
| | - Mazdak Salavati
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - David Wragg
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Juliane Friedrich
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Deepali Vasoya
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Appolinaire Djikeng
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - James G D Prendergast
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- School of Life Sciences, University of Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- Animal and Veterinary Sciences Group, Scotland’s Rural College (SRUC), Midlothian, United Kingdom
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Emily L Clark
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| |
Collapse
|
33
|
Lisowski ZM, Lefevre L, Mair TS, Clark EL, Hudson NPH, Hume DA, Pirie RS. Use of quantitative real-time PCR to determine the local inflammatory response in the intestinal mucosa and muscularis of horses undergoing small intestinal resection. Equine Vet J 2021; 54:52-62. [PMID: 33524178 DOI: 10.1111/evj.13429] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/30/2020] [Accepted: 01/22/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Studies in rodents and humans have demonstrated that intestinal manipulation or surgical trauma initiates an inflammatory response in the intestine which results in leucocyte recruitment to the muscularis externa causing smooth muscle dysfunction. OBJECTIVES To examine the intestinal inflammatory response in horses undergoing colic surgery by measuring relative differential gene expression in intestinal tissues harvested from surgical colic cases and control horses. STUDY DESIGN Prospective case-control study. METHODS Mucosa and muscularis externa were harvested from healthy margins of resected small intestine from horses undergoing colic surgery (n = 12) and from intestine derived from control horses euthanised for reasons unrelated to the gastrointestinal tract (n = 6). Tissue was analysed for genes encoding proteins involved in the inflammatory response: interleukin (IL) 6 and IL1β, C-C motif chemokine ligand 2 (CCL2), tumour necrosis factor (TNF), prostaglandin-endoperoxide synthase 2 (PTGS2) and indoleamine 2,3-dioxygenase (IDO1). Relative expression of these genes was compared between the two groups. Further analysis was applied to the colic cases to determine whether the magnitude of relative gene expression was associated with the subsequent development of post-operative reflux (POR). RESULTS Samples obtained from colic cases had increased relative expression of IL1β, IL6, CCL2 and TNF in the mucosa and muscularis externa when compared with the control group. There was no difference in relative gene expression between proximal and distal resection margins and no association between duration of colic, age, resection length, short-term survival and the presence of pre-operative reflux and the relative expression of the genes of interest. Horses that developed POR had significantly greater relative gene expression of TNF in the mucosa compared with horses that did not develop POR. MAIN LIMITATIONS Small sample size per group and variation within the colic cases. CONCLUSIONS These preliminary data support an upregulation of inflammatory genes in the intestine of horses undergoing colic surgery.
Collapse
Affiliation(s)
- Zofia M Lisowski
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - Lucas Lefevre
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - Tim S Mair
- The Bell Equine Veterinary Clinic, Maidstone, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - Neil P H Hudson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - David A Hume
- Mater Research Institute-University of Queensland, South Brisbane, QLD, Australia
| | - R Scott Pirie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| |
Collapse
|
34
|
Abstract
The laboratory rat is widely used as a model for human diseases. Many of these diseases involve monocytes and tissue macrophages in different states of activation. Whilst methods for in vitro differentiation of mouse macrophages from embryonic stem cells (ESC) and bone marrow (BM) are well established, these are lacking for the rat. The gene expression profiles of rat macrophages have also not been characterised to the same extent as mouse. We have established the methodology for production of rat ESC-derived macrophages and compared their gene expression profiles to macrophages obtained from the lung and peritoneal cavity and those differentiated from BM and blood monocytes. We determined the gene signature of Kupffer cells in the liver using rats deficient in macrophage colony stimulating factor receptor (CSF1R). We also examined the response of BM-derived macrophages to lipopolysaccharide (LPS). The results indicate that many, but not all, tissue-specific adaptations observed in mice are conserved in the rat. Importantly, we show that unlike mice, rat macrophages express the CSF1R ligand, colony stimulating factor 1 (CSF1).
Collapse
Affiliation(s)
- Clare Pridans
- Centre for Inflammation Research, University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M. Irvine
- Mater Research Institute Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
| | - Gemma M. Davis
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Lucas Lefevre
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Headington, United Kingdom
| | - David A. Hume
- Mater Research Institute Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
35
|
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.
Collapse
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.
| |
Collapse
|
36
|
Kaur S, Sehgal A, Wu AC, Millard SM, Batoon L, Sandrock CJ, Ferrari-Cestari M, Levesque JP, Hume DA, Raggatt LJ, Pettit AR. Stable colony-stimulating factor 1 fusion protein treatment increases hematopoietic stem cell pool and enhances their mobilisation in mice. J Hematol Oncol 2021; 14:3. [PMID: 33402221 PMCID: PMC7786999 DOI: 10.1186/s13045-020-00997-w] [Citation(s) in RCA: 9] [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: 09/14/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
Background Prior chemotherapy and/or underlying morbidity commonly leads to poor mobilisation of hematopoietic stem cells (HSC) for transplantation in cancer patients. Increasing the number of available HSC prior to mobilisation is a potential strategy to overcome this deficiency. Resident bone marrow (BM) macrophages are essential for maintenance of niches that support HSC and enable engraftment in transplant recipients. Here we examined potential of donor treatment with modified recombinant colony-stimulating factor 1 (CSF1) to influence the HSC niche and expand the HSC pool for autologous transplantation. Methods We administered an acute treatment regimen of CSF1 Fc fusion protein (CSF1-Fc, daily injection for 4 consecutive days) to naive C57Bl/6 mice. Treatment impacts on macrophage and HSC number, HSC function and overall hematopoiesis were assessed at both the predicted peak drug action and during post-treatment recovery. A serial treatment strategy using CSF1-Fc followed by granulocyte colony-stimulating factor (G-CSF) was used to interrogate HSC mobilisation impacts. Outcomes were assessed by in situ imaging and ex vivo standard and imaging flow cytometry with functional validation by colony formation and competitive transplantation assay. Results CSF1-Fc treatment caused a transient expansion of monocyte-macrophage cells within BM and spleen at the expense of BM B lymphopoiesis and hematopoietic stem and progenitor cell (HSPC) homeostasis. During the recovery phase after cessation of CSF1-Fc treatment, normalisation of hematopoiesis was accompanied by an increase in the total available HSPC pool. Multiple approaches confirmed that CD48−CD150+ HSC do not express the CSF1 receptor, ruling out direct action of CSF1-Fc on these cells. In the spleen, increased HSC was associated with expression of the BM HSC niche macrophage marker CD169 in red pulp macrophages, suggesting elevated spleen engraftment with CD48−CD150+ HSC was secondary to CSF1-Fc macrophage impacts. Competitive transplant assays demonstrated that pre-treatment of donors with CSF1-Fc increased the number and reconstitution potential of HSPC in blood following a HSC mobilising regimen of G-CSF treatment. Conclusion These results indicate that CSF1-Fc conditioning could represent a therapeutic strategy to overcome poor HSC mobilisation and subsequently improve HSC transplantation outcomes.
Collapse
Affiliation(s)
- Simranpreet Kaur
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Anuj Sehgal
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Andy C Wu
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Susan M Millard
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Lena Batoon
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Cheyenne J Sandrock
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Michelle Ferrari-Cestari
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Jean-Pierre Levesque
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - David A Hume
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Liza J Raggatt
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia
| | - Allison R Pettit
- Mater Research Institute-The University of Queensland, Faculty of Medicine, Translational Research Institute, 37 Kent St, Woolloongabba, 4102, Australia.
| |
Collapse
|
37
|
Munro DAD, Bradford BM, Mariani SA, Hampton DW, Vink CS, Chandran S, Hume DA, Pridans C, Priller J. CNS macrophages differentially rely on an intronic Csf1r enhancer for their development. Development 2020; 147:147/23/dev194449. [PMID: 33323375 PMCID: PMC7758622 DOI: 10.1242/dev.194449] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/26/2020] [Indexed: 12/29/2022]
Abstract
The central nervous system hosts parenchymal macrophages, known as microglia, and non-parenchymal macrophages, collectively termed border-associated macrophages (BAMs). Microglia, but not BAMs, were reported to be absent in mice lacking a conserved Csf1r enhancer: the fms-intronic regulatory element (FIRE). However, it is unknown whether FIRE deficiency also impacts BAM arrival and/or maintenance. Here, we show that macrophages in the ventricular system of the brain, including Kolmer's epiplexus macrophages, are absent in Csf1rΔFIRE/ΔFIRE mice. Stromal choroid plexus BAMs are also considerably reduced. During normal development, we demonstrate that intracerebroventricular macrophages arrive from embryonic day 10.5, and can traverse ventricular walls in embryonic slice cultures. In Csf1rΔFIRE/ΔFIRE embryos, the arrival of both primitive microglia and intracerebroventricular macrophages was eliminated, whereas the arrival of cephalic mesenchyme and stromal choroid plexus BAMs was only partially restricted. Our results provide new insights into the development and regulation of different CNS macrophage populations. Summary: Deletion of the fms-intronic regulatory element of Csf1r in mouse disrupts the engraftment and maintenance of central nervous system macrophages in a compartment-specific manner.
Collapse
Affiliation(s)
- David A D Munro
- UK Dementia Research Institute at The University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK
| | - Barry M Bradford
- The Roslin Institute & Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Samanta A Mariani
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - David W Hampton
- Euan MacDonald Centre for MND Research, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Chris S Vink
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at The University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK.,Euan MacDonald Centre for MND Research, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - David A Hume
- Mater Research Institute, University of Queensland, Translational Research Institute, Woolloongabba Q4102, Australia
| | - Clare Pridans
- The 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, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Josef Priller
- UK Dementia Research Institute at The University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK .,Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| |
Collapse
|
38
|
Grabert K, Sehgal A, Irvine KM, Wollscheid-Lengeling E, Ozdemir DD, Stables J, Luke GA, Ryan MD, Adamson A, Humphreys NE, Sandrock CJ, Rojo R, Verkasalo VA, Mueller W, Hohenstein P, Pettit AR, Pridans C, Hume DA. A Transgenic Line That Reports CSF1R Protein Expression Provides a Definitive Marker for the Mouse Mononuclear Phagocyte System. J I 2020; 205:3154-3166. [DOI: 10.4049/jimmunol.2000835] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
|
39
|
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.
Collapse
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:
| |
Collapse
|
40
|
Karagianni AE, Lisowski ZM, Hume DA, Scott Pirie R. The equine mononuclear phagocyte system: The relevance of the horse as a model for understanding human innate immunity. Equine Vet J 2020; 53:231-249. [PMID: 32881079 DOI: 10.1111/evj.13341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/07/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022]
Abstract
The mononuclear phagocyte system (MPS) is a family of cells of related function that includes bone marrow progenitors, blood monocytes and resident tissue macrophages. Macrophages are effector cells in both innate and acquired immunity. They are a major resident cell population in every organ and their numbers increase in response to proinflammatory stimuli. Their function is highly regulated by a wide range of agonists, including lymphokines, cytokines and products of microorganisms. Macrophage biology has been studied most extensively in mice, yet direct comparisons of rodent and human macrophages have revealed many functional differences. In this review, we provide an overview of the equine MPS, describing the variation in the function and phenotype of macrophages depending on their location and the similarities and differences between the rodent, human and equine immune response. We discuss the use of the horse as a large animal model in which to study macrophage biology and pathological processes shared with humans. Finally, following the recent update to the horse genome, facilitating further comparative analysis of regulated gene expression between the species, we highlight the importance of future transcriptomic macrophage studies in the horse, the findings of which may also be applicable to human as well as veterinary research.
Collapse
Affiliation(s)
- Anna E Karagianni
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Zofia M Lisowski
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, 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, Midlothian, UK
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Gow DJ, Jackson H, Forsythe P, Nuttall T, Gow AG, Mellanby RJ, Hume DA. Measurement of serum Interleukin 34 (IL‐34) and correlation with severity and pruritus scores in client‐owned dogs with atopic dermatitis. Vet Dermatol 2020; 31:359-e94. [PMID: 32794277 DOI: 10.1111/vde.12873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Deborah J. Gow
- R(D)SVS and The Roslin Institute Hospital for Small Animals The University of Edinburgh Edinburgh EH25 9RG Scotland, UK
| | - Hilary Jackson
- The Dermatology Referral Service 528 Paisley Road West Glasgow G51 1RN UK
| | - Peter Forsythe
- The Dermatology Referral Service 528 Paisley Road West Glasgow G51 1RN UK
| | - Tim Nuttall
- R(D)SVS and The Roslin Institute Hospital for Small Animals The University of Edinburgh Edinburgh EH25 9RG Scotland, UK
| | - Adam G. Gow
- R(D)SVS and The Roslin Institute Hospital for Small Animals The University of Edinburgh Edinburgh EH25 9RG Scotland, UK
| | - Richard J. Mellanby
- R(D)SVS and The Roslin Institute Hospital for Small Animals The University of Edinburgh Edinburgh EH25 9RG Scotland, UK
| | - David A. Hume
- R(D)SVS and The Roslin Institute Hospital for Small Animals The University of Edinburgh Edinburgh EH25 9RG Scotland, UK
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 2020; 9:5858065. [PMID: 32543654 PMCID: PMC7448572 DOI: 10.1093/gigascience/giaa051] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [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: 10/28/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 01/05/2023] Open
Abstract
Background The domestic pig (Sus scrofa) is important both as a food source and
as a biomedical model given its similarity in size, anatomy, physiology, metabolism,
pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a
purebred Duroc female pig established using older clone-based sequencing methods was
incomplete, and unresolved redundancies, short-range order and orientation errors, and
associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created
with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the
same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0).
Both assemblies are of substantially higher (>90-fold) continuity and accuracy than
Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read
assemblies provide an unprecedented view of the genetic make-up of this important
agricultural and biomedical model species. We propose that the improved Duroc assembly
(Sscrofa11.1) become the reference genome for genomic research in pigs.
Collapse
Affiliation(s)
- Amanda Warr
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Nabeel Affara
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamid Beiki
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lel Eory
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Heather A Finlayson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Carlos G Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Richard Hall
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | | | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane QLD 4104, Australia
| | - Osagie Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristi Kim
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Haibou Liu
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Nancy Manchanda
- Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Dan J Nonneman
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Gary A Rohrer
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Carole A Sargent
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | | | - Ben M Skinner
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Richard Talbot
- Edinburgh Genomics, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Christopher K Tuggle
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA.,Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| |
Collapse
|
46
|
Lisowski ZM, Sauter KA, Waddell LA, Hume DA, Pirie RS, Hudson NPH. Immunohistochemical study of morphology and distribution of CD163 +ve macrophages in the normal adult equine gastrointestinal tract. Vet Immunol Immunopathol 2020; 226:110073. [PMID: 32559524 DOI: 10.1016/j.vetimm.2020.110073] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 04/07/2020] [Accepted: 05/15/2020] [Indexed: 12/20/2022]
Abstract
Intestinal macrophages are the largest group of mononuclear phagocytes in the body and play a role in intestinal innate immunity, neuroimmune interactions and maintaining intestinal homeostasis. Conversely, they also are implicated in numerous pathologies of the gastrointestinal tract, such as postoperative ileus and inflammatory bowel disease. As a result, macrophages could be potential therapeutic targets. To date, there are limited studies on the morphology and distribution of macrophages in the equine gastrointestinal tract (GIT). The aim of this study was to identify the location and abundance of resident macrophages in the equine GIT using CD163 as an immunohistochemical marker. Tissue samples were obtained post-mortem from 14 sites along the gastrointestinal tracts of 10 horses free from gastrointestinal disease; sample sites extended from the stomach to the small colon. CD163+ve cells were present in all regions of the equine GIT from stomach to small colon. CD163+ve cells were also identified in all tissue layers of the intestinal wall, namely, mucosa, submucosa, muscularis externa (ME), myenteric plexus and serosa. Consistent with a proposed function in regulation of intestinal motility, CD163+ve cells were regularly distributed within the ME, with accumulations closely associated with the myenteric plexus and effector cells such as neurons and the interstitial cells of Cajal (ICC).
Collapse
Affiliation(s)
- Zofia M Lisowski
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Kristin A Sauter
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Lindsey A Waddell
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Woolloongabba, QLD, Australia
| | - R Scott Pirie
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil P H Hudson
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
47
|
Wu Z, Harne R, Chintoan-Uta C, Hu TJ, Wallace R, MacCallum A, Stevens MP, Kaiser P, Balic A, Hume DA. Regulation and function of macrophage colony-stimulating factor (CSF1) in the chicken immune system. Dev Comp Immunol 2020; 105:103586. [PMID: 31870792 PMCID: PMC6996135 DOI: 10.1016/j.dci.2019.103586] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 05/11/2023]
Abstract
Macrophage colony-stimulating factor (CSF1) is an essential growth factor to control the proliferation, differentiation and survival of cells of the macrophage lineage in vertebrates. We have previously produced a recombinant chicken CSF1-Fc fusion protein and administrated it to birds which produced a substantial expansion of tissue macrophage populations. To further study the biology of CSF1 in the chicken, here we generated anti-chicken CSF1 antibodies (ROS-AV181 and 183) using CSF1-Fc as an immunogen. The specific binding of each monoclonal antibody was confirmed by ELISA, Western blotting and immunohistochemistry on tissue sections. Using the anti-CSF1 antibodies, we show that chicken bone marrow derived macrophages (BMDM) express CSF1 on their surface, and that the level appears to be regulated further by exogenous CSF1. By capture ELISA circulating CSF1 levels increased transiently in both layer and broiler embryos around the day of hatch. The levels of CSF1 in broilers was higher than in layers during the first week after hatch. Antibody ROS-AV183 was able to block CSF1 biological activity in vitro and treatment of hatchlings using this neutralising antibody in vivo impacted on some tissue macrophage populations, but not blood monocytes. After anti-CSF1 treatment, CSF1R-transgene reporter expressing cells were reduced in the bursa of Fabricius and cecal tonsil and TIM4+ Kupffer cells in the liver were almost completely ablated. Anti-CSF1 treatment also produced a reduction in overall bone density, trabecular volume and TRAP+ osteoclasts. Our novel neutralising antibody provides a new tool to study the roles of CSF1 in birds.
Collapse
Affiliation(s)
- Zhiguang Wu
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Rakhi Harne
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Cosmin Chintoan-Uta
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Tuan-Jun Hu
- The Roslin Institute, 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
| | - Amanda MacCallum
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mark P Stevens
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Pete Kaiser
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Adam Balic
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, 4104, Australia.
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Banos G, Clark EL, Bush SJ, Dutta P, Bramis G, Arsenos G, Hume DA, Psifidi A. Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep. PLoS One 2019; 14:e0214346. [PMID: 31765378 PMCID: PMC6876840 DOI: 10.1371/journal.pone.0214346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 03/07/2019] [Accepted: 10/31/2019] [Indexed: 11/19/2022] Open
Abstract
Milk yield is the most important dairy sheep trait and constitutes the key genetic improvement goal via selective breeding. Mastitis is one of the most prevalent diseases, significantly impacting on animal welfare, milk yield and quality, while incurring substantial costs. Our objectives were to determine the feasibility of a concomitant genetic improvement programme for enhanced milk production and resistance to mastitis. Individual records for milk yield, and four mastitis-related traits (milk somatic cell count, California Mastitis Test score, total viable bacterial count in milk and clinical mastitis presence) were collected monthly throughout lactation for 609 ewes of the Chios breed. All ewes were genotyped with a mastitis specific custom-made 960 single nucleotide polymorphism (SNP) array. We performed targeted genomic association studies, (co)variance component estimation and pathway enrichment analysis, and characterised gene expression levels and the extent of allelic expression imbalance. Presence of heritable variation for milk yield was confirmed. There was no significant genetic correlation between milk yield and mastitis traits. Environmental factors appeared to favour both milk production and udder health. There were no overlapping of SNPs associated with mastitis resistance and milk yield in Chios sheep. Furthermore, four distinct Quantitative Trait Loci (QTLs) affecting milk yield were detected on chromosomes 2, 12, 16 and 19, in locations other than those previously identified to affect mastitis resistance. Five genes (DNAJA1, GHR, LYPLA1, NUP35 and OXCT1) located within the QTL regions were highly expressed in both the mammary gland and milk transcriptome, suggesting involvement in milk synthesis and production. Furthermore, the expression of two of these genes (NUP35 and OXCT1) was enriched in immune tissues implying a potentially pleiotropic effect or likely role in milk production during udder infection, which needs to be further elucidated in future studies. In conclusion, the absence of genetic antagonism between milk yield and mastitis resistance suggests that simultaneous genetic improvement of both traits be achievable.
Collapse
Affiliation(s)
- Georgios Banos
- Scotland’s Rural College, Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Emily L. Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, England, United Kingdom
| | - Prasun Dutta
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Georgios Bramis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Arsenos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - David A. Hume
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Androniki Psifidi
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- Royal Veterinary College, University of London, Hatfield, England, United Kingdom
- * E-mail: ,
| |
Collapse
|
50
|
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.
Collapse
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
| |
Collapse
|