Macrophage Lab | Katharine Irvine and David Hume

@article{pmid37167456,

title = {Macrophage deficiency in CSF1R-knockout rat embryos does not compromise placental or embryo development},

author = {David A Hume and Ngari Teakle and Sahar Keshvari and Katharine M Irvine},

doi = {10.1093/jleuko/qiad052},

issn = {1938-3673},

year  = {2023},

date = {2023-05-01},

journal = {J Leukoc Biol},

abstract = {Macrophages are an abundant cell population in the placenta and developing embryo and appear to be involved in processes of vascularisation, morphogenesis, organogenesis and hematopoiesis. The proliferation, differentiation and survival is dependent upon 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 analysed 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 centre 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37059596,

title = {Intraperitoneal transfer of wild-type bone marrow repopulates tissue macrophages in the Csf1r knockout rat without contributing to monocytopoiesis},

author = {Anuj Sehgal and Dylan Carter-Cusack and Sahar Keshvari and Omkar Patkar and Stephen Huang and Kim M Summers and David A Hume and Katharine M Irvine},

doi = {10.1002/eji.202250312},

issn = {1521-4141},

year  = {2023},

date = {2023-04-01},

journal = {Eur J Immunol},

pages = {e2250312},

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 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 ) origin. An mApple 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 , IBA1 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36327947,

title = {Serum CC-Chemokine Ligand 2 Is Associated with Visceral Adiposity but Not Fibrosis in Patients with Non-Alcoholic Fatty Liver Disease},

author = {Michelle Ferrari-Cestari and Satomi Okano and Preya J Patel and Leigh U Horsfall and Sahar Keshvari and David A Hume and Suzanne Williams and Anthony Russell and Elizabeth E Powell and Katharine M Irvine},

doi = {10.1159/000527784},

issn = {1421-9875},

year  = {2023},

date = {2023-01-01},

journal = {Dig Dis},

volume = {41},

number = {3},

pages = {439--446},

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.nnMETHODS: 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.nnRESULTS: 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.nnCONCLUSION: Circulating CCL2 and FABP2 are associated with NAFLD comorbidities but not liver disease progression in patients with NAFLD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36197652,

title = {CSF1R as a Therapeutic Target in Bone Diseases: Obvious but Not so Simple},

author = {David A Hume and Lena Batoon and Anuj Sehgal and Sahar Keshvari and Katharine M Irvine},

doi = {10.1007/s11914-022-00757-4},

issn = {1544-2241},

year  = {2022},

date = {2022-12-01},

journal = {Curr Osteoporos Rep},

volume = {20},

number = {6},

pages = {516--531},

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.nnRECENT 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35333324,

title = {A kinase-dead Csf1r mutation associated with adult-onset leukoencephalopathy has a dominant inhibitory impact on CSF1R signalling},

author = {Jennifer Stables and Emma K Green and Anuj Sehgal and Omkar L Patkar and Sahar Keshvari and Isis Taylor and Maisie E Ashcroft and Kathleen Grabert and Evi Wollscheid-Lengeling and Stefan Szymkowiak and Barry W McColl and Antony Adamson and Neil E Humphreys and Werner Mueller and Hana Starobova and Irina Vetter and Sepideh Kiani Shabestari and Matthew M Blurton-Jones and Kim M Summers and Katharine M Irvine and Clare Pridans and David A Hume},

doi = {10.1242/dev.200237},

issn = {1477-9129},

year  = {2022},

date = {2022-04-01},

journal = {Development},

volume = {149},

number = {8},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35169835,

title = {Therapeutic potential of macrophage colony-stimulating factor (CSF1) in chronic liver disease},

author = {Sahar Keshvari and Berit Genz and Ngari Teakle and Melanie Caruso and Michelle F Cestari and Omkar L Patkar and Brian W C Tse and Kamil A Sokolowski and Hilmar Ebersbach and Julia Jascur and Kelli P A MacDonald and Gregory Miller and Grant A Ramm and Allison R Pettit and Andrew D Clouston and Elizabeth E Powell and David A Hume and Katharine M Irvine},

doi = {10.1242/dmm.049387},

issn = {1754-8411},

year  = {2022},

date = {2022-02-01},

journal = {Dis Model Mech},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{batoon_treatment_2021b,

title = {Treatment with a long-acting chimeric CSF1 molecule enhances fracture healing of healthy and osteoporotic bones},

author = {Lena Batoon and Susan M. Millard and Liza J. Raggatt and Cheyenne Sandrock and Edmund Pickering and Kyle Williams and Lucas W. H. Sun and Andy C. Wu and Katharine M. Irvine and Peter Pivonka and Vaida Glatt and Martin E. Wullschleger and David A. Hume and Allison R. Pettit},

url = {https://www.sciencedirect.com/science/article/pii/S0142961221002921},

doi = {10.1016/j.biomaterials.2021.120936},

issn = {0142-9612},

year  = {2021},

date = {2021-08-01},

urldate = {2021-08-06},

journal = {Biomaterials},

volume = {275},

pages = {120936},

abstract = {Macrophage-targeted therapies, including macrophage colony-stimulating factor 1 (CSF1), have been shown to have pro-repair impacts post-fracture. Preclinical/clinical applications of CSF1 have been expedited by development of chimeric CSF1-Fc which has extended circulating half-life. Here, we used mouse models to investigate the bone regenerative potential of CSF1-Fc in healthy and osteoporotic fracture. We also explored whether combination of CSF1-Fc with interleukin (IL)-4 provided additional fracture healing benefit in osteopenic bone. Micro-computed tomography, in situ histomorphometry, and bone mechanical parameters were used to assess systemic impacts of CSF1-Fc therapy in naive mice (male and female young, adult and geriatric). An intermittent CSF1-Fc regimen was optimized to mitigate undesirable impacts on bone resorption and hepatosplenomegaly, irrespective of age or gender. The intermittent CSF1-Fc regimen was tested in a mid-diaphyseal femoral fracture model in healthy bones with treatment initiated 1-day post-fracture. Weekly CSF1-Fc did not impact osteoclasts but increased osteal macrophages and improved fracture strength. Importantly, this treatment regimen also improved fracture union and strength in an ovariectomy-model of delayed fracture repair. Combining CSF1-Fc with IL-4 initiated 1-week post-fracture reduced the efficacy of CSF1-Fc. This study describes a novel strategy to specifically achieve bone regenerative actions of CSF1-Fc that has the potential to alleviate fragility fracture morbidity and mortality.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{keshvari_csf1r-dependent_2021b,

title = {CSF1R-dependent macrophages control postnatal somatic growth and organ maturation},

author = {Sahar Keshvari and Melanie Caruso and Ngari Teakle and Lena Batoon and Anuj Sehgal and Omkar L. Patkar and Michelle Ferrari-Cestari and Cameron E. Snell and Chen Chen and Alex Stevenson and Felicity M. Davis and Stephen J. Bush and Clare Pridans and Kim M. Summers and Allison R. Pettit and Katharine M. Irvine and David A. Hume},

editor = {Gregory S. Barsh},

url = {https://dx.plos.org/10.1371/journal.pgen.1009605},

doi = {10.1371/journal.pgen.1009605},

issn = {1553-7404},

year  = {2021},

date = {2021-06-01},

urldate = {2021-10-21},

journal = {PLOS Genetics},

volume = {17},

number = {6},

pages = {e1009605},

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, CD43 

 hi 

 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hume_mononuclear_2021,

title = {The Mononuclear Phagocyte System of the Rat},

author = {David A. Hume and Melanie Caruso and Sahar Keshvari and Omkar L. Patkar and Anuj Sehgal and Stephen J. Bush and Kim M. Summers and Clare Pridans and Katharine M. Irvine},

url = {http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.2100136},

doi = {10.4049/jimmunol.2100136},

issn = {0022-1767, 1550-6606},

year  = {2021},

date = {2021-05-01},

urldate = {2021-10-21},

journal = {The Journal of Immunology},

volume = {206},

number = {10},

pages = {2251--2263},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34742624,

title = {Functions of macrophage colony-stimulating factor (CSF1) in development, homeostasis, and tissue repair},

author = {Anuj Sehgal and Katharine M Irvine and David A Hume},

doi = {10.1016/j.smim.2021.101509},

issn = {1096-3618},

year  = {2021},

date = {2021-04-01},

journal = {Semin Immunol},

volume = {54},

pages = {101509},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{keshvari_csf1r-dependent_2021,

title = {CSF1R-dependent macrophages control postnatal somatic growth and organ maturation},

author = {Sahar Keshvari and Melanie Caruso and Ngari Teakle and Lena Batoon and Anuj Sehgal and Omkar L Patkar and Michelle Ferrari-Cestari and Cameron E Snell and Chen Chen and Alex Stevenson and Felicity M Davis and Stephen J Bush and Clare Pridans and Kim M Summers and Allison R Pettit and Katharine M Irvine and David A Hume},

url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009605},

doi = {10.1371/journal.pgen.1009605},

issn = {1553-7404},

year  = {2021},

date = {2021-01-01},

urldate = {2021-08-06},

journal = {PLOS Genetics},

volume = {17},

number = {6},

pages = {e1009605},

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.},

note = {Publisher: Public Library of Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{batoon_treatment_2021,

title = {Treatment with a long-acting chimeric CSF1 molecule enhances fracture healing of healthy and osteoporotic bones},

author = {Lena Batoon and Susan M Millard and Liza J Raggatt and Cheyenne Sandrock and Edmund Pickering and Kyle Williams and Lucas W H Sun and Andy C Wu and Katharine M Irvine and Peter Pivonka and Vaida Glatt and Martin E Wullschleger and David A Hume and Allison R Pettit},

url = {https://www.sciencedirect.com/science/article/pii/S0142961221002921},

doi = {10.1016/j.biomaterials.2021.120936},

issn = {0142-9612},

year  = {2021},

date = {2021-01-01},

urldate = {2021-08-06},

journal = {Biomaterials},

volume = {275},

pages = {120936},

abstract = {Macrophage-targeted therapies, including macrophage colony-stimulating factor 1 (CSF1), have been shown to have pro-repair impacts post-fracture. Preclinical/clinical applications of CSF1 have been expedited by development of chimeric CSF1-Fc which has extended circulating half-life. Here, we used mouse models to investigate the bone regenerative potential of CSF1-Fc in healthy and osteoporotic fracture. We also explored whether combination of CSF1-Fc with interleukin (IL)-4 provided additional fracture healing benefit in osteopenic bone. Micro-computed tomography, in situ histomorphometry, and bone mechanical parameters were used to assess systemic impacts of CSF1-Fc therapy in naive mice (male and female young, adult and geriatric). An intermittent CSF1-Fc regimen was optimized to mitigate undesirable impacts on bone resorption and hepatosplenomegaly, irrespective of age or gender. The intermittent CSF1-Fc regimen was tested in a mid-diaphyseal femoral fracture model in healthy bones with treatment initiated 1-day post-fracture. Weekly CSF1-Fc did not impact osteoclasts but increased osteal macrophages and improved fracture strength. Importantly, this treatment regimen also improved fracture union and strength in an ovariectomy-model of delayed fracture repair. Combining CSF1-Fc with IL-4 initiated 1-week post-fracture reduced the efficacy of CSF1-Fc. This study describes a novel strategy to specifically achieve bone regenerative actions of CSF1-Fc that has the potential to alleviate fragility fracture morbidity and mortality.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34818538,

title = {Fragmentation of tissue-resident macrophages during isolation confounds analysis of single-cell preparations from mouse hematopoietic tissues},

author = {Susan M Millard and Ostyn Heng and Khatora S Opperman and Anuj Sehgal and Katharine M Irvine and Simranpreet Kaur and Cheyenne J Sandrock and Andy C Wu and Graham W Magor and Lena Batoon and Andrew C Perkins and Jacqueline E Noll and Andrew C W Zannettino and David P Sester and Jean-Pierre Levesque and David A Hume and Liza J Raggatt and Kim M Summers and Allison R Pettit},

doi = {10.1016/j.celrep.2021.110058},

issn = {2211-1247},

year  = {2021},

date = {2021-01-01},

journal = {Cell Rep},

volume = {37},

number = {8},

pages = {110058},

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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{patkar_analysis_2021,

title = {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},

author = {O. L. Patkar and M. Caruso and N. Teakle and S. Keshvari and S. J. Bush and C. Pridans and A. Belmer and K. M. Summers and K. M. Irvine and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099616799&doi=10.1016%2fj.nbd.2021.105268&partnerID=40&md5=b1a09a2930f62a2ec0fc08fd98da6279},

doi = {10.1016/j.nbd.2021.105268},

issn = {09699961},

year  = {2021},

date = {2021-01-01},

journal = {Neurobiology of Disease},

volume = {151},

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. © 2021 The Authors},

note = {Publisher: Academic Press Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pridans_transcriptomic_2021,

title = {Transcriptomic Analysis of Rat Macrophages},

author = {C. Pridans and K. M. Irvine and G. M. Davis and L. Lefevre and S. J. Bush and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100832173&doi=10.3389%2ffimmu.2020.594594&partnerID=40&md5=04750fcce24d9c186af9bbb8e2b54e24},

doi = {10.3389/fimmu.2020.594594},

issn = {16643224},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Immunology},

volume = {11},

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). © Copyright © 2021 Pridans, Irvine, Davis, Lefevre, Bush and Hume.},

note = {Publisher: Frontiers Media S.A.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{grabert_transgenic_2020,

title = {A Transgenic Line That Reports CSF1R Protein Expression Provides a Definitive Marker for the Mouse Mononuclear Phagocyte System},

author = {Kathleen Grabert and Anuj Sehgal and Katharine M. Irvine and Evi Wollscheid-Lengeling and Derya D. Ozdemir and Jennifer Stables and Garry A. Luke and Martin D. Ryan and Antony Adamson and Neil E. Humphreys and Cheyenne J. Sandrock and Rocio Rojo and Veera A. Verkasalo and Werner Mueller and Peter Hohenstein and Allison R. Pettit and Clare Pridans and David A. Hume},

url = {http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.2000835},

doi = {10.4049/jimmunol.2000835},

issn = {0022-1767, 1550-6606},

year  = {2020},

date = {2020-12-01},

urldate = {2021-10-21},

journal = {The Journal of Immunology},

volume = {205},

number = {11},

pages = {3154--3166},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{irvine_analysis_2020,

title = {Analysis of the impact of CSF‐1 administration in adult rats using a novel textitCsf1r ‐mApple reporter gene},

author = {Katharine M. Irvine and Melanie Caruso and Michelle Ferrari Cestari and Gemma M. Davis and Sahar Keshvari and Anuj Sehgal and Clare Pridans and David A. Hume},

url = {https://onlinelibrary.wiley.com/doi/10.1002/JLB.MA0519-149R},

doi = {10.1002/JLB.MA0519-149R},

issn = {0741-5400, 1938-3673},

year  = {2020},

date = {2020-02-01},

urldate = {2021-10-21},

journal = {Journal of Leukocyte Biology},

volume = {107},

number = {2},

pages = {221--235},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hume_phenotypic_2020,

title = {Phenotypic impacts of CSF1R deficiencies in humans and model organisms},

author = {D. A. Hume and M. Caruso and M. Ferrari-Cestari and K. M. Summers and C. Pridans and K. M. Irvine},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075575069&doi=10.1002%2fJLB.MR0519-143R&partnerID=40&md5=4140a7666153d4ddbdafb8e7987f8c2f},

doi = {10.1002/JLB.MR0519-143R},

issn = {07415400},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Leukocyte Biology},

volume = {107},

number = {2},

pages = {205--219},

abstract = {Mϕ proliferation, differentiation, and survival are controlled by signals from the Mϕ CSF receptor (CSF1R). Mono-allelic gain-of-function mutations in CSF1R in humans are associated with an autosomal-dominant leukodystrophy and bi-allelic loss-of-function mutations with recessive skeletal dysplasia, brain disorders, and developmental anomalies. Most of the phenotypes observed in these human disease states are also observed in mice and rats with loss-of-function mutations in Csf1r or in Csf1 encoding one of its two ligands. Studies in rodent models also highlight the importance of genetic background and likely epistatic interactions between Csf1r and other loci. The impacts of Csf1r mutations on the brain are usually attributed solely to direct impacts on microglial number and function. However, analysis of hypomorphic Csf1r mutants in mice and several other lines of evidence suggest that primary hydrocephalus and loss of the physiological functions of Mϕs in the periphery contribute to the development of brain pathology. In this review, we outline the evidence that CSF1R is expressed exclusively in mononuclear phagocytes and explore the mechanisms linking CSF1R mutations to pleiotropic impacts on postnatal growth and development. © 2019 The Authors. Journal of Leukocyte Biology published by Wiley Periodicals, Inc. on behalf of Society for Leukocyte Biology},

note = {Publisher: John Wiley and Sons Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hume_mononuclear_2019,

title = {The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages},

author = {D. A. Hume and K. M. Irvine and C. Pridans},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058630239&doi=10.1016%2fj.it.2018.11.007&partnerID=40&md5=c4284bc6f921ae0774a96d0ea1848ce6},

doi = {10.1016/j.it.2018.11.007},

issn = {14714906},

year  = {2019},

date = {2019-01-01},

journal = {Trends in Immunology},

volume = {40},

number = {2},

pages = {98--112},

abstract = {The mononuclear phagocyte system (MPS) is defined as a cell lineage in which committed marrow progenitors give rise to blood monocytes and tissue macrophages. Here, we discuss the concept of self-proscribed macrophage territories and homeostatic regulation of tissue macrophage abundance through growth factor availability. Recent studies have questioned the validity of the MPS model and argued that tissue-resident macrophages are a separate lineage seeded during development and maintained by self-renewal. We address this issue; discuss the limitations of inbred mouse models of monocyte-macrophage homeostasis; and summarize the evidence suggesting that during postnatal life, monocytes can replace resident macrophages in all major organs and adopt their tissue-specific gene expression. We conclude that the MPS remains a valid and accurate framework for understanding macrophage development and homeostasis. © 2018 Elsevier Ltd},

note = {Publisher: Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{irvine_corrigendum_2019,

title = {Corrigendum: Causes and consequences of innate immune dysfunction in cirrhosis (Frontiers in Immunology (2019) 10 (293) DOI: 10.3389/fimmu.2019.00293)},

author = {K. M. Irvine and I. Ratnasekera and E. E. Powell and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065394406&doi=10.3389%2ffimmu.2019.00818&partnerID=40&md5=3c8593ea05366e4515e7f3c1fc25acdf},

doi = {10.3389/fimmu.2019.00818},

issn = {16643224},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Immunology},

volume = {10},

number = {APR},

abstract = {In the original article, we neglected to include the funder "Equity Trustees." The funding statement has therefore been revised as follows: "KI, IR, and DH are grateful for research funding support from the Mater Research Foundation and Equity Trustees, Australia." The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated. Copyright © 2019 Irvine, Ratnasekera, Powell and Hume.},

note = {Publisher: Frontiers Media S.A.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{irvine_casuses_2019,

title = {Casuses and consequences of innate immune dysfucntion in cirrhosis},

author = {K. M. Irvine and I. Ratnasekera and E. E. Powell and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062959223&doi=10.3389%2ffimmu.2019.00293&partnerID=40&md5=5d5b49a795347ded8d993e874cb9a1cf},

doi = {10.3389/fimmu.2019.00293},

issn = {16643224},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Immunology},

volume = {10},

number = {FEB},

abstract = {Liver cirrhosis is an increasing health burden and public health concern. Regardless of etiology, patients with cirrhosis are at risk of a range of life-threatening complications, including the development of infections, which are associated with high morbidity and mortality and frequent hospital admissions. The term Cirrhosis-Associated Immune Dysfunction (CAID) refers to a dynamic spectrum of immunological perturbations that develop in patients with cirrhosis, which are intimately linked to the underlying liver disease, and negatively correlated with prognosis. At the two extremes of the CAID spectrum are systemic inflammation, which can exacerbate clinical manifestations of cirrhosis such as hemodynamic derangement and kidney injury; and immunodeficiency, which contributes to the high rate of infection in patients with decompensated cirrhosis. Innate immune cells, in particular monocytes/macrophages and neutrophils, are pivotal effector and target cells in CAID. This review focuses on the pathophysiological mechanisms leading to impaired innate immune function in cirrhosis. Knowledge of the phenotypic manifestation and pathophysiological mechanisms of cirrhosis associated immunosuppression may lead to immune targeted therapies to reduce susceptibility to infection in patients with cirrhosis, and better biomarkers for risk stratification, and assessment of efficacy of novel immunotherapies. © 2019 Frew.},

note = {Publisher: Frontiers Media S.A.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{waddell_adgre1_2018,

title = {ADGRE1 (EMR1, F4/80) is a rapidly-evolving gene expressed in mammalian monocyte-macrophages},

author = {L. A. Waddell and L. Lefevre and S. J. Bush and A. Raper and R. Young and Z. M. Lisowski and M. E. B. McCulloch and C. Muriuki and K. A. Sauter and E. L. Clark and K. M. Irvine and C. Pridans and J. C. Hope and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85055075237&doi=10.3389%2ffimmu.2018.02246&partnerID=40&md5=05b22fa95491209153f33a6bdd18e794},

doi = {10.3389/fimmu.2018.02246},

issn = {16643224},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Immunology},

volume = {9},

number = {OCT},

abstract = {The F4/80 antigen, encoded by the Adgre1 locus, has been widely-used as a monocyte-macrophage marker in mice, but its value as a macrophage marker in other species is unclear, and has even been questioned. ADGRE1 is a seven transmembrane G protein-coupled receptor with an extracellular domain containing repeated Epidermal Growth Factor (EGF)-like calcium binding domains. Using a new monoclonal antibody, we demonstrated that ADGRE1 is a myeloid differentiation marker in pigs, absent from progenitors in bone marrow, highly-expressed in mature granulocytes, monocytes, and tissue macrophages and induced by macrophage colony-stimulating factor (CSF1) treatment in vivo. Based upon these observations, we utilized RNA-Seq to assess the expression of ADGRE1 mRNA in bone marrow or monocyte-derived macrophages (MDM) and alveolar macrophages from 8 mammalian species including pig, human, rat, sheep, goat, cow, water buffalo, and horse. ADGRE1 mRNA was expressed by macrophages in each species, with inter-species variation both in expression level and response to lipopolysaccharide (LPS) stimulation. Analysis of the RNA-Seq data also revealed additional exons in several species compared to current Ensembl annotations. The ruminant species and horses appear to encode a complete duplication of the 7 EGF-like domains. In every species, Sashimi plots revealed evidence of exon skipping of the EGF-like domains, which are highly-variable between species and polymorphic in humans. Consistent with these expression patterns, key elements of the promoter and a putative enhancer are also conserved across all species. The rapid evolution of this molecule and related ADGRE family members suggests immune selection and a role in pathogen recognition. © 2018 Waddell, Lefevre, Bush, Raper, Young, Lisowski, McCulloch, Muriuki, Sauter, Clark, Irvine, Pridans, Hope and Hume.},

note = {Publisher: Frontiers Media S.A.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pridans_macrophage_2018,

title = {Macrophage colony-stimulating factor increases hepatic macrophage content, liver growth, and lipid accumulation in neonatal rats},

author = {C. Pridans and K. A. Sauter and K. M. Irvine and G. M. Davis and L. Lefevre and A. Raper and R. Rojo and A. J. Nirmal and P. Beard and M. Cheeseman and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043572074&doi=10.1152%2fajpgi.00343.2017&partnerID=40&md5=884917bf2187b3dc12308991fd5f26eb},

doi = {10.1152/ajpgi.00343.2017},

issn = {01931857},

year  = {2018},

date = {2018-01-01},

journal = {American Journal of Physiology - Gastrointestinal and Liver Physiology},

volume = {314},

number = {3},

pages = {G388--G398},

abstract = {Signaling via the colony-stimulating factor 1 receptor (CSF1R) controls the survival, differentiation, and proliferation of macrophages. Mutations in CSF1 or CSF1R in mice and rats have pleiotropic effects on postnatal somatic growth. We tested the possible application of pig CSF1-Fc fusion protein as a therapy for low birth weight (LBW) at term, using a model based on maternal dexamethasone treatment in rats. Neonatal CSF1-Fc treatment did not alter somatic growth and did not increase the blood monocyte count. Instead, there was a substantial increase in the size of liver in both control and LBW rats, and the treatment greatly exacerbated lipid droplet accumulation seen in the dexamethasone LBW model. These effects were reversed upon cessation of treatment. Transcriptional profiling of the livers supported histochemical evidence of a large increase in macrophages with a resident Kupffer cell phenotype and revealed increased expression of many genes implicated in lipid droplet formation. There was no further increase in hepatocyte proliferation over the already high rates in neonatal liver. In conclusion, treatment of neonatal rats with CSF1-Fc caused an increase in liver size and hepatic lipid accumulation, due to Kupffer cell expansion and/or activation rather than hepatocyte proliferation. Increased liver macrophage numbers and expression of endocytic receptors could mitigate defective clearance functions in neonates. NEW & NOTEWORTHY This study is based on extensive studies in mice and pigs of the role of CSF1/CSF1R in macrophage development and postnatal growth. We extended the study to neonatal rats as a possible therapy for low birth weight. Unlike our previous studies in mice and pigs, there was no increase in hepatocyte proliferation and no increase in monocyte numbers. Instead, neonatal rats treated with CSF1 displayed reversible hepatic steatosis and Kupffer cell expansion. © 2018 American Physiological Society.},

note = {Publisher: American Physiological Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{shakespear_histone_2013,

title = {Histone deacetylase 7 promotes toll-like receptor 4-dependent proinflammatory gene expression in macrophages},

author = {M. R. Shakespear and D. M. Hohenhaus and G. M. Kelly and N. A. Kamal and P. Gupta and L. I. Labzin and K. Schroder and V. Garceau and S. Barbero and A. Iyer and D. A. Hume and R. C. Reid and K. M. Irvine and D. P. Fairlie and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84883336983&doi=10.1074%2fjbc.M113.496281&partnerID=40&md5=d103c9b4c6933bcf8f2d7e286bc1d92b},

doi = {10.1074/jbc.M113.496281},

issn = {00219258},

year  = {2013},

date = {2013-01-01},

journal = {Journal of Biological Chemistry},

volume = {288},

number = {35},

pages = {25362--25374},

abstract = {Background: Histone deacetylase (HDAC) inhibitors reduce LPS-induced inflammatory mediator production from macrophages, but the relevant HDAC targets are unknown. Results: A specific isoform of Hdac7 amplifies expression of LPS-inducible genes via a HIF-1α-dependent mechanism in macrophages. Conclusion: The class IIa HDAC Hdac7 promotes inflammatory responses in macrophages. Significance: Hdac7 may be a viable target for developing new anti-inflammatory drugs. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{schroder_conservation_2012,

title = {Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages},

author = {K. Schroder and K. M. Irvine and M. S. Taylor and N. J. Bokil and K. -A. Le Cao and K. -A. Masterman and L. I. Labzin and C. A. Semple and R. Kapetanovic and L. Fairbairn and A. Akalin and G. J. Faulkner and J. K. Baillie and M. Gongora and C. O. Daub and H. Kawaji and G. J. McLachlan and N. Goldman and S. M. Grimmond and P. Carninci and H. Suzuki and Y. Hayashizaki and B. Lenhard and D. A. Hume and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859993180&doi=10.1073%2fpnas.1110156109&partnerID=40&md5=14a95ac83f504b1327ba71db30a3478b},

doi = {10.1073/pnas.1110156109},

issn = {00278424},

year  = {2012},

date = {2012-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {109},

number = {16},

pages = {E944--E953},

abstract = {Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies differences in the transcriptional responses of primary human and mouse macrophages to the Toll-like receptor (TLR)-4 agonist lipopolysaccharide (LPS). By using a custom platform permitting crossspecies interrogation coupled with deep sequencing of mRNA 5′ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologues were identified as "divergently regulated"). We further demonstrate concordant regulation of human-specific LPS target genes in primary pig macrophages. Divergently regulated orthologues were enriched for genes encoding cellular "inputs" such as cell surface receptors (e.g., TLR6, IL-7Rα) and functional "outputs"such as inflammatory cytokines/chemokines (e.g., CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. Functional consequences of divergent gene regulation were confirmed by showing LPS pretreatment boosts subsequent TLR6 responses in mouse but not human macrophages, in keeping with mouse-specific TLR6 induction. Divergently regulated genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced interspecies promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{van_zuylen_macrophage_2011,

title = {Macrophage activation and differentiation signals regulate Schlafen-4 gene expression: Evidence for Schlafen-4 as a modulator of myelopoiesis},

author = {W. J. Zuylen and V. Garceau and A. Idris and K. Schroder and K. M. Irvine and J. E. Lattin and D. A. Ovchinnikov and A. C. Perkins and A. D. Cook and J. A. Hamilton and P. J. Hertzog and K. J. Stacey and S. Kellie and D. A. Hume and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79251561568&doi=10.1371%2fjournal.pone.0015723&partnerID=40&md5=3187d5e2092c8494686d2787cbe52fcb},

doi = {10.1371/journal.pone.0015723},

issn = {19326203},

year  = {2011},

date = {2011-01-01},

journal = {PLoS ONE},

volume = {6},

number = {1},

abstract = {Background: The ten mouse and six human members of the Schlafen (Slfn) gene family all contain an AAA domain. Little is known of their function, but previous studies suggest roles in immune cell development. In this report, we assessed Slfn regulation and function in macrophages, which are key cellular regulators of innate immunity. Methodology/Principal Findings: Multiple members of the Slfn family were up-regulated in mouse bone marrow-derived macrophages (BMM) by the Toll-like Receptor (TLR)4 agonist lipopolysaccharide (LPS), the TLR3 agonist Poly(I:C), and in disease-affected joints in the collagen-induced model of rheumatoid arthritis. Of these, the most inducible was Slfn4. TLR agonists that signal exclusively through the MyD88 adaptor protein had more modest effects on Slfn4 mRNA levels, thus implicating MyD88-independent signalling and autocrine interferon (IFN)-β in inducible expression. This was supported by the substantial reduction in basal and LPS-induced Slfn4 mRNA expression in IFNAR-1-/- BMM. LPS causes growth arrest in macrophages, and other Slfn family genes have been implicated in growth control. Slfn4 mRNA levels were repressed during macrophage colony-stimulating factor (CSF-1)-mediated differentiation of bone marrow progenitors into BMM. To determine the role of Slfn4 in vivo, we over-expressed the gene specifically in macrophages in mice using a csf1r promoterdriven binary expression system. Transgenic over-expression of Slfn4 in myeloid cells did not alter macrophage colony formation or proliferation in vitro. Monocyte numbers, as well as inflammatory macrophages recruited to the peritoneal cavity, were reduced in transgenic mice that specifically over-expressed Slfn4, while macrophage numbers and hematopoietic activity were increased in the livers and spleens. Conclusions: Slfn4 mRNA levels were up-regulated during macrophage activation but down-regulated during differentiation. Constitutive Slfn4 expression in the myeloid lineage in vivo perturbs myelopoiesis. We hypothesise that the down-regulation of Slfn4 gene expression during macrophage differentiation is a necessary step in development of this lineage. © 2011 van Zuylen et al.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kubosaki_combination_2010,

title = {The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells},

author = {A. Kubosaki and G. Lindgren and M. Tagami and C. Simon and Y. Tomaru and H. Miura and T. Suzuki and E. Arner and A. R. R. Forrest and K. M. Irvine and K. Schroder and Y. Hasegawa and M. Kanamori-Katayama and M. Rehli and D. A. Hume and J. Kawai and M. Suzuki and H. Suzuki and Y. Hayashizaki},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955419023&doi=10.1016%2fj.molimm.2010.05.289&partnerID=40&md5=51bc8194ce2f4de287ab9fbbaa78b02b},

doi = {10.1016/j.molimm.2010.05.289},

issn = {01615890},

year  = {2010},

date = {2010-01-01},

journal = {Molecular Immunology},

volume = {47},

number = {14},

pages = {2295--2302},

abstract = {Gene regulatory networks in living cells are controlled by the interaction of multiple cell type-specific transcription regulators with DNA binding sites in target genes. Interferon regulatory factor 8 (IRF8), also known as interferon consensus sequence binding protein (ICSBP), is a transcription factor expressed predominantly in myeloid and lymphoid cell lineages. To find the functional direct target genes of IRF8, the gene expression profiles of siRNA knockdown samples and genome-wide binding locations by ChIP-chip were analyzed in THP-1 myelomonocytic leukemia cells. Consequently, 84 genes were identified as functional direct targets. The ETS family transcription factor PU.1, also known as SPI1, binds to IRF8 and regulates basal transcription in macrophages. Using the same approach, we identified 53 direct target genes of PU.1; these overlapped with 19 IRF8 targets. These 19 genes included key molecules of IFN signaling such as OAS1 and IRF9, but excluded other IFN-related genes amongst the IRF8 functional direct target genes. We suggest that IRF8 and PU.1 can have both combined, and independent actions on different promoters in myeloid cells. © 2010 Elsevier Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{halili_differential_2010,

title = {Differential effects of selective HDAC inhibitors on macrophage inflammatory responses to the Toll-like receptor 4 agonist LPS},

author = {M. A. Halili and M. R. Andrews and L. I. Labzin and K. Schroder and G. Matthias and C. Cao and E. Lovelace and R. C. Reid and G. T. Le and D. A. Hume and K. M. Irvine and P. Matthias and D. P. Fairlie and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77954013043&doi=10.1189%2fjlb.0509363&partnerID=40&md5=c860a9f2d2c4adc2f99ebd2df5a8b5e9},

doi = {10.1189/jlb.0509363},

issn = {07415400},

year  = {2010},

date = {2010-01-01},

journal = {Journal of Leukocyte Biology},

volume = {87},

number = {6},

pages = {1103--1114},

abstract = {Broad-spectrum inhibitors of HDACs are therapeutic in many inflammatory disease models but exacerbated disease in a mouse model of atherosclerosis. HDAC inhibitors have anti- and proinflammatory effects on macrophages in vitro. We report here that several broad-spectrum HDAC inhibitors, including TSA and SAHA, suppressed the LPS-induced mRNA expression of the proinflammatory mediators Edn-1, Ccl-7/MCP-3, and Il-12p40 but amplified the expression of the proatherogenic factors Cox-2 and Pai-1/serpine1 in primary mouse BMM. Similar effects were also apparent in LPS-stimulated TEPM and HMDM. The pro- and anti-inflammatory effects of TSA were separable over a concentration range, implying that individual HDACs have differential effects on macrophage inflammatory responses. The HDAC1-selective inhibitor, MS-275, retained proinflammatory effects (amplification of LPS-induced expression of Cox-2 and Pai-1 in BMM) but suppressed only some inflammatory responses. In contrast, 17a (a reportedly HDAC6-selective inhibitor) retained anti-inflammatory but not proinflammatory properties. Despite this, HDAC6-/- macrophages showed normal LPS-induced expression of HDAC-dependent inflammatory genes, arguing that the anti-inflammatory effects of 17a are not a result of inhibition of HDAC6 alone. Thus, 17a provides a tool to identify individual HDACs with proinflammatory properties. © Society for Leukocyte Biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{goh_selective_2009,

title = {Selective induction of the Notch ligand Jagged-1 in macrophages by soluble egg antigen from Schistosoma mansoni involves ERK signalling},

author = {F. Goh and K. M. Irvine and E. Lovelace and S. Donnelly and M. K. Jones and K. Brion and D. A. Hume and A. C. Kotze and J. P. Dalton and A. Ingham and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66549095477&doi=10.1111%2fj.1365-2567.2008.02979.x&partnerID=40&md5=bc2694bc6a19a0b4e3973d71141c49c8},

doi = {10.1111/j.1365-2567.2008.02979.x},

issn = {00192805},

year  = {2009},

date = {2009-01-01},

journal = {Immunology},

volume = {127},

number = {3},

pages = {326--337},

abstract = {Summary Soluble egg antigen (SEA) from the helminth Schistosoma mansoni promotes T helper type 2 (Th2) responses by modulating antigen-presenting cell function. The Jagged/Notch pathway has recently been implicated in driving Th2 development. We show here that SEA rapidly up-regulated mRNA and protein expression of the Notch ligand Jagged-1 in both murine bone marrow-derived macrophages (BMMs) and human monocyte-derived macrophages (HMDMs). Another potential Th2-promoting factor, interleukin (IL)-33, was not transcriptionally induced by SEA in BMMs. Up-regulation of Jagged-1 mRNA by SEA was also apparent in conventional dendritic cells (DCs), although the effect was less striking than in BMMs. Conversely, SEA-pulsed DCs, but not BMMs, promoted IL-4 production upon T-cell activation, suggesting that Jagged-1 induction alone is insufficient for instructing Th2 development. A comparison of the responses initiated in BMMs by SEA and the bacterial endotoxin lipopolysaccharide (LPS) revealed common activation of extracellular signal-regulated kinase-1/2 (ERK-1/2) and p38 phosphorylation, as well as induction of Jagged-1 mRNA. However, only LPS triggered IκB degradation, phosphorylation of c-Jun N-terminal kinase (Jnk) and signal transducer and activator of transcription 1 (Stat1) Tyr701, and IL-33 and IL-12p40 mRNA up-regulation. Inducible gene expression was modified by the presence of the macrophage growth factor colony-stimulating factor (CSF)-1, which inhibited Jagged-1 induction by SEA and LPS, but enhanced LPS-induced IL-12p40 expression. Unlike LPS, SEA robustly activated signalling in HEK293 cells expressing either Toll-like receptor 2 (TLR2) or TLR4/MD2. Pharmacological inhibition of the ERK-1/2 pathway impaired SEA- and LPS-inducible Jagged-1 expression in BMMs. Taken together, our data suggest that Jagged-1 is an ERK-dependent target of TLR signalling that has a macrophage-specific function in the response to SEA. © 2008 Blackwell Publishing Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{faulkner_regulated_2009,

title = {The regulated retrotransposon transcriptome of mammalian cells},

author = {G. J. Faulkner and Y. Kimura and C. O. Daub and S. Wani and C. Plessy and K. M. Irvine and K. Schroder and N. Cloonan and A. L. Steptoe and T. Lassmann and K. Waki and N. Hornig and T. Arakawa and H. Takahashi and J. Kawai and A. R. R. Forrest and H. Suzuki and Y. Hayashizaki and D. A. Hume and V. Orlando and S. M. Grimmond and P. Carninci},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-67349173665&doi=10.1038%2fng.368&partnerID=40&md5=1e5e869547f5181996c4ea6caa1a6c7e},

doi = {10.1038/ng.368},

issn = {10614036},

year  = {2009},

date = {2009-01-01},

journal = {Nature Genetics},

volume = {41},

number = {5},

pages = {563--571},

abstract = {Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6-30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5′ of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3′ UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome. © 2009 Nature America, Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{suzuki_transcriptional_2009,

title = {The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line},

author = {H. Suzuki and A. R. R. Forrest and E. Van Nimwegen and C. O. Daub and P. J. Balwierz and K. M. Irvine and T. Lassmann and T. Ravasi and Y. Hasegawa and M. J. L. De Hoon and S. Katayama and K. Schroder and P. Carninci and Y. Tomaru and M. Kanamori-Katayama and A. Kubosaki and A. Akalin and Y. Ando and E. Arner and M. Asada and H. Asahara and T. Bailey and V. B. Bajic and D. Bauer and A. G. Beckhouse and N. Bertin and J. Björkegren and F. Brombacher and E. Bulger and A. M. Chalk and J. Chiba and N. Cloonan and A. Dawe and J. Dostie and P. G. Engström and M. Essack and G. J. Faulkner and J. L. Fink and D. Fredman and K. Fujimori and M. Furuno and T. Gojobori and J. Gough and S. M. Grimmond and M. Gustafsson and M. Hashimoto and T. Hashimoto and M. Hatakeyama and S. Heinzel and W. Hide and O. Hofmann and M. Hörnquist and L. Huminiecki and K. Ikeo and N. Imamoto and S. Inoue and Y. Inoue and R. Ishihara and T. Iwayanagi and A. Jacobsen and M. Kaur and H. Kawaji and M. C. Kerr and R. Kimura and S. Kimura and Y. Kimura and H. Kitano and H. Koga and T. Kojima and S. Kondo and T. Konno and A. Krogh and A. Kruger and A. Kumar and B. Lenhard and A. Lennartsson and M. Lindow and M. Lizio and C. MacPherson and N. Maeda and C. A. Maher and M. Maqungo and J. Mar and N. A. Matigian and H. Matsuda and J. S. Mattick and S. Meier and S. Miyamoto and E. Miyamoto-Sato and K. Nakabayashi and Y. Nakachi and M. Nakano and S. Nygaard and T. Okayama and Y. Okazaki and H. Okuda-Yabukami and V. Orlando and J. Otomo and M. Pachkov and N. Petrovsky and C. Plessy and J. Quackenbush and A. Radovanovic and M. Rehli and R. Saito and A. Sandelin and S. Schmeier and C. Schönbach and A. S. Schwartz and C. A. Semple and M. Sera and J. Severin and K. Shirahige and C. Simons and G. St. Laurent and M. Suzuki and T. Suzuki and M. J. Sweet and R. J. Taft and S. Takeda and Y. Takenaka and K. Tan and M. S. Taylor and R. D. Teasdale and J. Tegnér and S. Teichmann and E. Valen and C. Wahlestedt and K. Waki and A. Waterhouse and C. A. Wells and O. Winther and L. Wu and K. Yamaguchi and H. Yanagawa and J. Yasuda and M. Zavolan and D. A. Hume and T. Arakawa and S. Fukuda and K. Imamura and C. Kai and A. Kaiho and T. Kawashima and C. Kawazu and Y. Kitazume and M. Kojima and H. Miura and K. Murakami and M. Murata and N. Ninomiya and H. Nishiyori and S. Noma and C. Ogawa and T. Sano and C. Simon and M. Tagami and Y. Takahashi and J. Kawai and Y. Hayashizaki},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-65149083962&doi=10.1038%2fng.375&partnerID=40&md5=5372db2b6f8078fb8376fb15d03d19be},

doi = {10.1038/ng.375},

issn = {10614036},

year  = {2009},

date = {2009-01-01},

journal = {Nature Genetics},

volume = {41},

number = {5},

pages = {553--562},

abstract = {Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process. © 2009 Nature America, Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mar_data-driven_2009,

title = {Data-driven normalization strategies for high-throughput quantitative RT-PCR},

author = {J. C. Mar and Y. Kimura and K. Schroder and K. M. Irvine and Y. Hayashizaki and H. Suzuki and D. Hume and J. Quackenbush},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-65549139459&doi=10.1186%2f1471-2105-10-110&partnerID=40&md5=cd13c70a928bcb7036a15714639b0326},

doi = {10.1186/1471-2105-10-110},

issn = {14712105},

year  = {2009},

date = {2009-01-01},

journal = {BMC Bioinformatics},

volume = {10},

abstract = {Background: High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage technology allows the acquisition of profiles for a moderate number of genes (50 to a few thousand), and this number continues to grow. The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline. Results: We present and evaluate two data-driven normalization methods that directly correct for technical variation and represent robust alternatives to standard housekeeping gene-based approaches. We evaluated the performance of these methods against a single gene housekeeping gene method and our results suggest that quantile normalization performs best. These methods are implemented in freely-available software as an R package qpcrNorm distributed through the Bioconductor project. Conclusion: The utility of the approaches that we describe can be demonstrated most clearly in situations where standard housekeeping genes are regulated by some experimental condition. For large qPCR-based data sets, our approaches represent robust, data-driven strategies for normalization. © 2009 Mar et al; licensee BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kawaji_fantom_2009,

title = {The FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulation},

author = {H. Kawaji and J. Severin and M. Lizio and A. Waterhouse and S. Katayama and K. M. Irvine and D. A. Hume and A. R. R. Forrest and H. Suzuki and P. Carninci and Y. Hayashizaki and C. O. Daub},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-65549128370&doi=10.1186%2fgb-2009-10-4-r40&partnerID=40&md5=5988ef9566b8651b3f4610702aed8910},

doi = {10.1186/gb-2009-10-4-r40},

issn = {14747596},

year  = {2009},

date = {2009-01-01},

journal = {Genome Biology},

volume = {10},

number = {4},

abstract = {In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5′-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource. © 2009 Kawaji et al.; licensee BioMed Central Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{irvine_colony-stimulating_2009,

title = {Colony-stimulating factor-1 (CSF-1) delivers a proatherogenic signal to human macrophages},

author = {K. M. Irvine and M. R. Andrews and M. A. Fernandez-Rojo and K. Schroder and C. J. Burns and S. Su and A. F. Wilks and R. G. Parton and D. A. Hume and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-59649091219&doi=10.1189%2fjlb.0808497&partnerID=40&md5=e8f44bf21620fd7a76cc07e93aa23570},

doi = {10.1189/jlb.0808497},

issn = {07415400},

year  = {2009},

date = {2009-01-01},

journal = {Journal of Leukocyte Biology},

volume = {85},

number = {2},

pages = {278--288},

abstract = {M-CSF/CSF-1 supports the proliferation and differentiation of monocytes and macrophages. In mice, CSF-1 also promotes proinflammatory responses in vivo by regulating mature macrophage functions, but little is known about the acute effects ofthis growth factor on mature human macrophages. Here, we show that in contrast to its effects on mouse bone marrow-derived macrophages, CSF-1 did not induce expression of urokinase plasminogen activator mRNA, repress expression of apolipoprotein E mRNA, or prime LPS-induced TNF and IL-6 secretion in human monocyte-derived macrophages (HMDM) from several independent donors. Instead, we show by expression profiling that CSF-1 modulates the HMDM transcriptome to favor a proathero-genic environment. CSF-1 induced expression ofthe proatherogenic chemokines CXCL10/IFN-inducible protein 10, CCL2, and CCL7 but repressed expression of the antiatherogenic chemokine receptor CXCR4. CSF-1 also up-regulated genes encoding enzymes of the cholesterol biosynthetic pathway (HMGCR, MVD, IDI1, FDPS, SQLE, CYP51A1,EBP, NSDHL, DHCR7, and DHCR24), and expression of ABCG1, encoding a cholesterol efflux transporter, was repressed. Consistent with these effects, CSF-1 increased levels offree cholesterol in HMDM, and the selective CSF-1R kinase inhibitor GW2580 ablated this response. These data demonstrate that CSF-1 represents a further link between inflammation and cardiovascular disease and suggest two distinct mechanisms by which CSF-1, which is known to be present in atherosclerotic lesions, may contribute to plaque progression. © Society for Leukocyte Biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{taft_erratum_2009,

title = {Erratum: Tiny RNAs associated with transcription start sites in animals (Nature Genetics (2009) 41 (572-578)).},

author = {R. J. Taft and E. A. Glazov and N. Cloonan and C. Simons and S. Stephen and G. J. Faulkner and T. Lassmann and A. R. R. Forrest and S. M. Grimmond and K. Schroder and K. Irvine and T. Arakawa and M. Nakamura and A. Kubosaki and K. Hayashida and C. Kawazu and M. Murata and H. Nishiyori and S. Fukuda and J. Kawai and C. O. Daub and D. A. Hume and H. Suzuki and V. Orlando and P. Carninci and Y. Hayashizaki and J. S. Mattick},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-67649858457&doi=10.1038%2fng0709-859a&partnerID=40&md5=fd38027ed5a49e2edb9e566c4e929b3c},

doi = {10.1038/ng0709-859a},

issn = {10614036},

year  = {2009},

date = {2009-01-01},

journal = {Nature Genetics},

volume = {41},

number = {7},

pages = {859},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{taft_tiny_2009,

title = {Tiny RNAs associated with transcription start sites in animals},

author = {R. J. Taft and E. A. Glazov and N. Cloonan and C. Simons and S. Stephen and G. J. Faulkner and T. Lassmann and A. R. R. Forrest and S. M. Grimmond and K. Schroder and K. Irvine and T. Arakawa and M. Nakamura and A. Kubosaki and K. Hayashida and C. Kawazu and M. Murata and H. Nishiyori and S. Fukuda and J. Kawai and C. O. Daub and D. A. Hume and H. Suzuki and V. Orlando and P. Carninci and Y. Hayashizaki and J. S. Mattick},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-67349157682&doi=10.1038%2fng.312&partnerID=40&md5=c2b1a4560d94c55fb48fac8d83784276},

doi = {10.1038/ng.312},

issn = {10614036},

year  = {2009},

date = {2009-01-01},

journal = {Nature Genetics},

volume = {41},

number = {5},

pages = {572--578},

abstract = {It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within 60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5′ ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes. © 2009 Nature America, Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{maeda_development_2008,

title = {Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer},

author = {N. Maeda and H. Nishiyori and M. Nakamura and C. Kawazu and M. Murata and H. Sano and K. Hayashida and S. Fukuda and M. Tagami and A. Hasegawa and K. Murakami and K. Schroder and K. Irvine and D. A. Hume and Y. Hayashizaki and P. Carninci and H. Suzuki},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-47949091256&doi=10.2144%2f000112814&partnerID=40&md5=261dacfb8af2de67f09124fdf83dfde8},

doi = {10.2144/000112814},

issn = {07366205},

year  = {2008},

date = {2008-01-01},

journal = {BioTechniques},

volume = {45},

number = {1},

pages = {95--97},

abstract = {CAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5′ end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was limited previously by sequencing technology and the labor-intensive protocol. Here we describe an improved CAGE method for use with a next generation sequencer. This modified method allows the identification of the RNA source of each CAGE tag within a pooled library by introducing DNA tags (barcodes). The method not only drastically improves the sequencing capacity, but also contributes to savings in both time and budget. Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{schroder_differential_2007,

title = {Differential effects of CpG DNA on IFN-β induction and STAT1 activation in murine macrophages versus dendritic cells: Alternatively activated STAT1 negatively regulates TLR signaling in macrophages},

author = {K. Schroder and M. Spille and A. Pilz and J. Lattin and K. A. Bode and K. M. Irvine and A. D. Burrows and T. Ravasi and H. Weighardt and K. J. Stacey and T. Decker and D. A. Hume and A. H. Dalpke and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-35748939086&doi=10.4049%2fjimmunol.179.6.3495&partnerID=40&md5=48c7d2156ddc4b3af6eb7700fc0539f5},

doi = {10.4049/jimmunol.179.6.3495},

issn = {00221767},

year  = {2007},

date = {2007-01-01},

journal = {Journal of Immunology},

volume = {179},

number = {6},

pages = {3495--3503},

abstract = {Classical STAT1 activation in response to TLR agonists occurs by phosphorylation of the Y701 and S727 residues through autocrine type I IFN signaling and p38 MAPK signaling, respectively. In this study, we report that the TLR9 agonist CpG DNA induced Ifn-β mRNA, as well as downstream type I IFN-dependent genes, in a MyD88-dependent manner in mouse myeloid dendritic cells. This pathway was required for maximal TNF and IL-6 secretion, as well as expression of cell surface costimulatory molecules. By contrast, neither A- nor B-type CpG-containing oligonucleotides induced Ifn-β in mouse bone marrow-derived macrophages (BMM) and a CpG-B oligonucleotide did not induce IFn-β in the macrophage-like cell line, J774. In BMM, STAT1 was alternatively activated (phosphorylated on S727, but not Y701), and was retained in the cytoplasm in response to CpG DNA. CpG DNA responses were altered in BMM from STAT1S727A mice; Il-12p40 and Cox-2 mRNAs were more highly induced, whereas Tlr4 and Tlr9 mRNAs were more repressed. The data suggest a novel inhibitory function for cytoplasmic STAT1 in response to TLR agonists that activate p38 MAPK but do not elicit type I IFN production. Indeed, the TLR7 agonist, R837, failed to induce Ifn-β mRNA and consequently triggered STAT1 phosphorylation on S727, but not Y701, in human monocyte-derived macrophages. The differential activation of Ifn-β and STAT1 by CpG DNA in mouse macrophages vs dendritic cells provides a likely mechanism for their divergent roles in priming the adaptive immune response. Copyright © 2007 by The American Association of Immunologists, Inc.},

note = {Publisher: American Association of Immunologists},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{schroder_pu1_2007,

title = {PU.1 and ICSBP control constitutive and IFN-γ-regulated Tlr9 gene expression in mouse macrophages},

author = {K. Schroder and M. Lichtinger and K. M. Irvine and K. Brion and A. Trieu and I. L. Ross and T. Ravasi and K. J. Stacey and M. Rehli and D. A. Hume and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34249665503&doi=10.1189%2fjlb.0107036&partnerID=40&md5=cc8113a6f471c56807af65e03b7ed2fc},

doi = {10.1189/jlb.0107036},

issn = {07415400},

year  = {2007},

date = {2007-01-01},

journal = {Journal of Leukocyte Biology},

volume = {81},

number = {6},

pages = {1577--1590},

abstract = {Macrophages are activated by unmethylated CpG-containing DNA (CpG DNA) via TLR9. IFN-γ and LPS can synergize with CpG DNA to enhance proinflammatory responses in murine macrophages. Here, we show that LPS and IFN-γ up-regulated Tlr9 mRNA in murine bone marrow-derived macrophages (BMM). The ability of LPS and IFN-γ to induce Tlr9 mRNA expression in BMM was dependent on the presence of the growth factor, CSF-1, which is constitutively present in vivo. However, there were clear differences in mechanisms of Tlr9 mRNA induction. LPS stimulation rapidly removed the CSF-1 receptor (CSF-1R) from the cell surface, thereby blocking CSF-1-mediated transcriptional repression and indirectly inducing Tlr9 mRNA expression. By contrast, IFN-γ activated the Tlr9 promoter directly and only marginally affected cell surface CSF-1R expression. An ∼100-bp proximal promoter of the murine Tlr9 gene was sufficient to confer basal and IFN-γ-inducible expression in RAW264.7 cells. A composite IFN regulatory factor (IRF)/PU.1 site upon the major transcription start site was identified. Mutation of the binding sites for PU.1 or IRF impaired basal promoter activity, but only the IRF-binding site was required for IFN-γ induction. The mRNA expression of the IRF family member IFN consensus-binding protein [(ICSBP)/IRF8] was coregulated with Tlr9 in macrophages, and constitutive and IFN-γ-inducible Tlr9 mRNA expression was reduced in ICSBP-deficient BMM. This study therefore characterizes the regulation of mouse Tlr9 expression and defines a molecular mechanism by which IFN-γ amplifies mouse macrophage responses to CpG DNA. © Society for Leukocyte Biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ripoll_gpnmb_2007,

title = {Gpnmb is induced in macrophages by IFN-γ and lipopolysaccharide and acts as a feedback regulator of proinflammatory responses},

author = {V. M. Ripoll and K. M. Irvine and T. Ravasi and M. J. Sweet and D. A. Hume},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34248226374&doi=10.4049%2fjimmunol.178.10.6557&partnerID=40&md5=136c0545c09765af303ce29c88f72640},

doi = {10.4049/jimmunol.178.10.6557},

issn = {00221767},

year  = {2007},

date = {2007-01-01},

journal = {Journal of Immunology},

volume = {178},

number = {10},

pages = {6559--6566},

abstract = {The process of inflammation requires the selective expression of a suite of genes in cells of the macrophage lineage. To identify candidate regulators of inflammation, we used cDNA microarrays to compare the transcriptome of inflammatory macrophages (thioglycolate-elicited peritoneal macrophages), bone marrow-derived macrophages, nonadherent spleen cells, and fibroblasts. We identified genes that were macrophage restricted and further elevated in inflammatory macrophages, and characterized the function of one such gene, gpnmb. Gpnmb mRNA expression was enriched in myelomonocytic cell lines and macrophage-related tissues and strongly up-regulated during macrophage diferentiation. Epitope-tagged GPNMB expressed in RAW264.7 cells exhibited a perinuclear distribution and colocalized with the Golgi marker coat protein β. Upon activation of macrophages with IFN-γ and LPS, GPNMB translocated from the Golgi apparatus to vesicular compartments scattered toward the periphery. Gpnmb overexpression in RAW264.7 cells caused a 2-fold reduction in the production of the cytokines IL-6 and IL-12p40 and the inflammatory mediator NO in response to LPS. DBA mice, which have an inactivating point mutation in the gpnmb gene, exhibited reduced numbers of myeloid cells, elevated numbers of thioglycolate-elicited peritoneal macrophages, and higher levels of proinflammatory cytokines in response to LPS. Thus, GPNMB acts as a negative regulator of macrophage inflammatory responses. Copyright © 2007 by The American Association of Immunologists, Inc.},

note = {Publisher: American Association of Immunologists},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{irvine_csf-1_2006,

title = {A CSF-1 receptor kinase inhibitor targets effector functions and inhibits pro-inflammatory cytokine production from murine macrophage populations},

author = {K. M. Irvine and C. J. Burns and A. F. Wilks and S. Su and D. A. Hume and M. J. Sweet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33845581266&doi=10.1096%2ffj.06-5848fje&partnerID=40&md5=53f3c50c4f84dbf0453429373c6af40a},

doi = {10.1096/fj.06-5848fje},

issn = {08926638},

year  = {2006},

date = {2006-01-01},

journal = {FASEB Journal},

volume = {20},

number = {11},

pages = {E1315--E1326},

abstract = {CSF-1 regulates macrophage differentiation, survival, and function, and is an attractive therapeutic target for chronic inflammation and malignant diseases. Here we describe the effects of a potent and selective inhibitor of CSF-1R - CYC10268 - on CSF-1R-dependent signaling. In in vitro kinase assays, CYC10268 was active in the low nanomolar range and showed selectivity over other kinases such as Abl and Kit. CYC10268 blocked survival mediated by CSF-1R in primary murine bone marrow-derived macrophages (BMM) and in the factor-dependent cell line Ba/F3, in which the CSF-1R was ectopically expressed. CYC10268 also inhibited CSF-1 regulated signaling (Akt, ERK-1/2), gene expression (urokinase plasminogen activator, toll-like receptor 9, and apolipoprotein E), and priming of LPS-inducible cytokine production in BMM. In thioglycollate-elicited peritoneal macrophages (TEPM), which survive in the absence of exogenous CSF-1, CYC10268 impaired LPS-induced cytokine production and regulated expression of known CSF-1 target genes. These observations support the conclusion that TEPM are CSF-1 autocrine and that CSF-1 plays a central role in macrophage effector functions during inflammation. CSF-1R inhibitors such as CYC10268 provide a powerful tool to dissect the role of the CSF-1/CSF-1R signaling system in a range of biological systems and have potential for a number of therapeutic applications. © FASEB.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{irvine_rasputin_2004,

title = {Rasputin, more promiscuous than ever: A review of G3BP},

author = {K. Irvine and R. Stirling and D. Hume and D. Kennedy},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-13144276292&doi=10.1387%2fijdb.041893ki&partnerID=40&md5=02ac347bb651d9b7e8c902f03a964efb},

doi = {10.1387/ijdb.041893ki},

issn = {02146282},

year  = {2004},

date = {2004-01-01},

journal = {International Journal of Developmental Biology},

volume = {48},

number = {10},

pages = {1065--1077},

abstract = {The foregoing discussion highlights what G3BP's domain structure initially suggested; that G3BPs are "scaffolding" proteins linking signal transduction to RNA metabolism. Whilst it is most attractive to hypothesise about G3BP's role in signalling to mRNA metabolism, it is not known whether all G3BP functions impinge on their RNA-binding activities, so any theories are naturally subject to this qualification. It is hypothesised that, in coordination with an array of other proteins, G3BP, in a phosphorylation- dependent manner, is involved in the post-transcriptional regulation of a subset of mRNAs, at least some of which are in common with those regulated by Hu proteins. These transcripts, partially controlled at the post-transcriptional level by G3BPs, code for proteins important in transcription (e.g. c-Myc) and cytoskeletal arrangement (e.g. Tau), amongst other as yet undetermined pathways. The subtle differences between G3BP family members could dictate binding to a variety of signalling proteins, so each of the G3BPs may participate in different, though possibly related mRNPs, which are assembled in response to different stimuli. The combinatorial nature of the mRNP complex offers a powerful means of regulating gene expression, beyond that provided by a simple mRNA sequence. The ways in which mRNP flexibility and specificity may be harnessed to coordinate gene expression of functionally or structurally related mRNAs are not yet fully appreciated. Characterising mRNP composition and the function/s of mRNP components, such as the G3BPs, will aid in the understanding of how post-transcriptional mechanisms contribute to the global regulation of gene expression.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}