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Analysis of the impact of CSF-1 administration in adult rats using a novel Csf1r-mApple reporter gene.

Irvine KM, Caruso M, Cestari MF, Davis GM, Keshvari S, Sehgal A, Pridans C, Hume DA.

J Leukoc Biol. 2019 Aug 8. doi: 10.1002/JLB.MA0519-149R. [Epub ahead of print]


Phenotypic impacts of CSF1R deficiencies in humans and model organisms.

Hume DA, Caruso M, Ferrari-Cestari M, Summers KM, Pridans C, Irvine KM.

J Leukoc Biol. 2019 Jul 22. doi: 10.1002/JLB.MR0519-143R. [Epub ahead of print] Review.


Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations.

Rojo R, Raper A, Ozdemir DD, Lefevre L, Grabert K, Wollscheid-Lengeling E, Bradford B, Caruso M, Gazova I, Sánchez A, Lisowski ZM, Alves J, Molina-Gonzalez I, Davtyan H, Lodge RJ, Glover JD, Wallace R, Munro DAD, David E, Amit I, Miron VE, Priller J, Jenkins SJ, Hardingham GE, Blurton-Jones M, Mabbott NA, Summers KM, Hohenstein P, Hume DA, Pridans C.

Nat Commun. 2019 Jul 19;10(1):3215. doi: 10.1038/s41467-019-11053-8.


Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait.

Chundru VK, Marioni RE, Prendergast JGD, Vallerga CL, Lin T, Beveridge AJ; SGPD Consortium, Gratten J, Hume DA, Deary IJ, Wray NR, Visscher PM, McRae AF.

Genetics. 2019 Jul;212(3):577-586. doi: 10.1534/genetics.118.301861. Epub 2019 Apr 30.


Correction: Pleiotropic Impacts of Macrophage and Microglial Deficiency on Development in Rats with Targeted Mutation of the Csf1r Locus.

Pridans C, Raper A, Davis GM, Alves J, Sauter KA, Lefevre L, Regan T, Meek S, Sutherland L, Thomson AJ, Clohisey S, Bush SJ, Rojo R, Lisowski ZM, Wallace R, Grabert K, Upton KR, Tsai YT, Brown D, Smith LB, Summers KM, Mabbott NA, Piccardo P, Cheeseman MT, Burdon T, Hume DA.

J Immunol. 2019 Jun 1;202(11):3334-3335. doi: 10.4049/jimmunol.1900420. Epub 2019 Apr 26. No abstract available.


Corrigendum: Causes and Consequences of Innate Immune Dysfunction in Cirrhosis.

Irvine KM, Ratnasekera I, Powell EE, Hume DA.

Front Immunol. 2019 Apr 9;10:818. doi: 10.3389/fimmu.2019.00818. eCollection 2019.


The Effect of Race Training on the Basal Gene Expression of Alveolar Macrophages Derived From Standardbred Racehorses.

Karagianni AE, Summers KM, Couroucé A, Depecker M, McGorum BC, Hume DA, Pirie RS.

J Equine Vet Sci. 2019 Apr;75:48-54. doi: 10.1016/j.jevs.2019.01.010. Epub 2019 Jan 29.


Causes and Consequences of Innate Immune Dysfunction in Cirrhosis.

Irvine KM, Ratnasekera I, Powell EE, Hume DA.

Front Immunol. 2019 Feb 25;10:293. doi: 10.3389/fimmu.2019.00293. eCollection 2019. Review. Erratum in: Front Immunol. 2019 Apr 09;10:818.


Linked Mutations at Adjacent Nucleotides Have Shaped Human Population Differentiation and Protein Evolution.

Prendergast JGD, Pugh C, Harris SE, Hume DA, Deary IJ, Beveridge A.

Genome Biol Evol. 2019 Mar 1;11(3):759-775. doi: 10.1093/gbe/evz014.


Measurement of serum macrophage migration inhibitory factor (MIF) and correlation with severity and pruritus scores in client owned dogs with atopic dermatitis.

Gow DJ, Jackson H, Forsythe P, Gow AG, Mellanby RJ, Hume DA, Nuttall T.

Vet Dermatol. 2019 Jan 23. doi: 10.1111/vde.12721. [Epub ahead of print]


Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity.

Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL.

Nat Commun. 2019 Jan 16;10(1):260. doi: 10.1038/s41467-018-08260-0.


Characterization of Subpopulations of Chicken Mononuclear Phagocytes That Express TIM4 and CSF1R.

Hu T, Wu Z, Bush SJ, Freem L, Vervelde L, Summers KM, Hume DA, Balic A, Kaiser P.

J Immunol. 2019 Feb 15;202(4):1186-1199. doi: 10.4049/jimmunol.1800504. Epub 2019 Jan 9.


A chicken bioreactor for efficient production of functional cytokines.

Herron LR, Pridans C, Turnbull ML, Smith N, Lillico S, Sherman A, Gilhooley HJ, Wear M, Kurian D, Papadakos G, Digard P, Hume DA, Gill AC, Sang HM.

BMC Biotechnol. 2018 Dec 29;18(1):82. doi: 10.1186/s12896-018-0495-1.


The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages.

Hume DA, Irvine KM, Pridans C.

Trends Immunol. 2019 Feb;40(2):98-112. doi: 10.1016/ Epub 2018 Dec 19. Review.


Dissecting the Genomic Architecture of Resistance to Eimeria maxima Parasitism in the Chicken.

Boulton K, Nolan MJ, Wu Z, Riggio V, Matika O, Harman K, Hocking PM, Bumstead N, Hesketh P, Archer A, Bishop SC, Kaiser P, Tomley FM, Hume DA, Smith AL, Blake DP, Psifidi A.

Front Genet. 2018 Nov 26;9:528. doi: 10.3389/fgene.2018.00528. eCollection 2018.


Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression.

Bush SJ, McCulloch MEB, Muriuki C, Salavati M, Davis GM, Farquhar IL, Lisowski ZM, Archibald AL, Hume DA, Clark EL.

G3 (Bethesda). 2019 Feb 7;9(2):359-373. doi: 10.1534/g3.118.200810.


Species-Specific Transcriptional Regulation of Genes Involved in Nitric Oxide Production and Arginine Metabolism in Macrophages.

Young R, Bush SJ, Lefevre L, McCulloch MEB, Lisowski ZM, Muriuki C, Waddell LA, Sauter KA, Pridans C, Clark EL, Hume DA.

Immunohorizons. 2018 Jan 1;2(1):27-37. doi: 10.4049/immunohorizons.1700073.


Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis.

Boulton K, Nolan MJ, Wu Z, Psifidi A, Riggio V, Harman K, Bishop SC, Kaiser P, Abrahamsen MS, Hawken R, Watson KA, Tomley FM, Blake DP, Hume DA.

Genet Sel Evol. 2018 Nov 21;50(1):63. doi: 10.1186/s12711-018-0433-7.


Assembly of a Parts List of the Human Mitotic Cell Cycle Machinery.

Giotti B, Chen SH, Barnett MW, Regan T, Ly T, Wiemann S, Hume DA, Freeman TC.

J Mol Cell Biol. 2018 Nov 17. doi: 10.1093/jmcb/mjy063. [Epub ahead of print]


ADGRE1 (EMR1, F4/80) Is a Rapidly-Evolving Gene Expressed in Mammalian Monocyte-Macrophages.

Waddell LA, Lefevre L, Bush SJ, Raper A, Young R, Lisowski ZM, McCulloch MEB, Muriuki C, Sauter KA, Clark EL, Irvine KM, Pridans C, Hope JC, Hume DA.

Front Immunol. 2018 Oct 1;9:2246. doi: 10.3389/fimmu.2018.02246. eCollection 2018.


Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumors.

Nirmal AJ, Regan T, Shih BB, Hume DA, Sims AH, Freeman TC.

Cancer Immunol Res. 2018 Nov;6(11):1388-1400. doi: 10.1158/2326-6066.CIR-18-0342. Epub 2018 Sep 28.


Pleiotropic Impacts of Macrophage and Microglial Deficiency on Development in Rats with Targeted Mutation of the Csf1r Locus.

Pridans C, Raper A, Davis GM, Alves J, Sauter KA, Lefevre L, Regan T, Meek S, Sutherland L, Thomson AJ, Clohisey S, Bush SJ, Rojo R, Lisowski ZM, Wallace R, Grabert K, Upton KR, Tsai YT, Brown D, Smith LB, Summers KM, Mabbott NA, Piccardo P, Cheeseman MT, Burdon T, Hume DA.

J Immunol. 2018 Nov 1;201(9):2683-2699. doi: 10.4049/jimmunol.1701783. Epub 2018 Sep 24. Erratum in: J Immunol. 2019 Jun 1;202(11):3334-3335.


Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.

Bush SJ, Freem L, MacCallum AJ, O'Dell J, Wu C, Afrasiabi C, Psifidi A, Stevens MP, Smith J, Summers KM, Hume DA.

BMC Genomics. 2018 Aug 7;19(1):594. doi: 10.1186/s12864-018-4972-7.


The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages.

Scott CL, T'Jonck W, Martens L, Todorov H, Sichien D, Soen B, Bonnardel J, De Prijck S, Vandamme N, Cannoodt R, Saelens W, Vanneste B, Toussaint W, De Bleser P, Takahashi N, Vandenabeele P, Henri S, Pridans C, Hume DA, Lambrecht BN, De Baetselier P, Milling SWF, Van Ginderachter JA, Malissen B, Berx G, Beschin A, Saeys Y, Guilliams M.

Immunity. 2018 Aug 21;49(2):312-325.e5. doi: 10.1016/j.immuni.2018.07.004. Epub 2018 Jul 31.


Self-repopulating recipient bone marrow resident macrophages promote long-term hematopoietic stem cell engraftment.

Kaur S, Raggatt LJ, Millard SM, Wu AC, Batoon L, Jacobsen RN, Winkler IG, MacDonald KP, Perkins AC, Hume DA, Levesque JP, Pettit AR.

Blood. 2018 Aug 16;132(7):735-749. doi: 10.1182/blood-2018-01-829663. Epub 2018 Jun 26.


Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing.

Pandit RJ, Hinsu AT, Patel NV, Koringa PG, Jakhesara SJ, Thakkar JR, Shah TM, Limon G, Psifidi A, Guitian J, Hume DA, Tomley FM, Rank DN, Raman M, Tirumurugaan KG, Blake DP, Joshi CG.

Microbiome. 2018 Jun 23;6(1):115. doi: 10.1186/s40168-018-0501-9.


Environmentally enriched pigs have transcriptional profiles consistent with neuroprotective effects and reduced microglial activity.

Brown SM, Bush SJ, Summers KM, Hume DA, Lawrence AB.

Behav Brain Res. 2018 Sep 17;350:6-15. doi: 10.1016/j.bbr.2018.05.015. Epub 2018 May 17.


Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.

Bush SJ, Muriuki C, McCulloch MEB, Farquhar IL, Clark EL, Hume DA.

Genet Sel Evol. 2018 Apr 24;50(1):20. doi: 10.1186/s12711-018-0391-0.


The preterm labor associated ADAMTS2 gene is induced by glucocorticoids.

Jubb AW, Hofer TP, Hume DA, Ziegler-Heitbrock L.

Am J Obstet Gynecol. 2018 Jul;219(1):122-123. doi: 10.1016/j.ajog.2018.03.024. Epub 2018 Mar 28. No abstract available.


The role of CSF1R-dependent macrophages in control of the intestinal stem-cell niche.

Sehgal A, Donaldson DS, Pridans C, Sauter KA, Hume DA, Mabbott NA.

Nat Commun. 2018 Mar 28;9(1):1272. doi: 10.1038/s41467-018-03638-6.


Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA.

PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar.


Csf1r-mApple Transgene Expression and Ligand Binding In Vivo Reveal Dynamics of CSF1R Expression within the Mononuclear Phagocyte System.

Hawley CA, Rojo R, Raper A, Sauter KA, Lisowski ZM, Grabert K, Bain CC, Davis GM, Louwe PA, Ostrowski MC, Hume DA, Pridans C, Jenkins SJ.

J Immunol. 2018 Mar 15;200(6):2209-2223. doi: 10.4049/jimmunol.1701488. Epub 2018 Feb 12.


Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages.

Regan T, Gill AC, Clohisey SM, Barnett MW, Pariante CM, Harrison NA; MRC Immunopsychiatry Consortium, Hume DA, Bullmore ET, Freeman TC.

J Leukoc Biol. 2018 Apr;103(4):681-692. doi: 10.1002/JLB.3A0617-261R. Epub 2018 Jan 26.


Macrophage colony-stimulating factor increases hepatic macrophage content, liver growth, and lipid accumulation in neonatal rats.

Pridans C, Sauter KA, Irvine KM, Davis GM, Lefevre L, Raper A, Rojo R, Nirmal AJ, Beard P, Cheeseman M, Hume DA.

Am J Physiol Gastrointest Liver Physiol. 2018 Mar 1;314(3):G388-G398. doi: 10.1152/ajpgi.00343.2017. Epub 2017 Dec 21.


An update on equine post-operative ileus: Definitions, pathophysiology and management.

Lisowski ZM, Pirie RS, Blikslager AT, Lefebvre D, Hume DA, Hudson NPH.

Equine Vet J. 2018 May;50(3):292-303. doi: 10.1111/evj.12801. Epub 2018 Jan 29. Review.


Glucocorticoid Receptor Binding Induces Rapid and Prolonged Large-Scale Chromatin Decompaction at Multiple Target Loci.

Jubb AW, Boyle S, Hume DA, Bickmore WA.

Cell Rep. 2017 Dec 12;21(11):3022-3031. doi: 10.1016/j.celrep.2017.11.053.


The evolution of the macrophage-specific enhancer (Fms intronic regulatory element) within the CSF1R locus of vertebrates.

Hume DA, Wollscheid-Lengeling E, Rojo R, Pridans C.

Sci Rep. 2017 Dec 7;7(1):17115. doi: 10.1038/s41598-017-15999-x.


CD169+ macrophages are critical for osteoblast maintenance and promote intramembranous and endochondral ossification during bone repair.

Batoon L, Millard SM, Wullschleger ME, Preda C, Wu AC, Kaur S, Tseng HW, Hume DA, Levesque JP, Raggatt LJ, Pettit AR.

Biomaterials. 2019 Mar;196:51-66. doi: 10.1016/j.biomaterials.2017.10.033. Epub 2017 Oct 22.


Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology.

Macdonald SE, Nolan MJ, Harman K, Boulton K, Hume DA, Tomley FM, Stabler RA, Blake DP.

PLoS One. 2017 Sep 21;12(9):e0184890. doi: 10.1371/journal.pone.0184890. eCollection 2017.


A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA.

PLoS Genet. 2017 Sep 15;13(9):e1006997. doi: 10.1371/journal.pgen.1006997. eCollection 2017 Sep.


FANTOM5 CAGE profiles of human and mouse samples.

Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Kanamori-Katayama M, Kawashima T, Kojima M, Kubosaki A, Manabe RI, Murata M, Nagao-Sato S, Nakazato K, Ninomiya N, Nishiyori-Sueki H, Noma S, Saijyo E, Saka A, Sakai M, Simon C, Suzuki N, Tagami M, Watanabe S, Yoshida S, Arner P, Axton RA, Babina M, Baillie JK, Barnett TC, Beckhouse AG, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Carlisle AJ, Clevers HC, Davis CA, Detmar M, Dohi T, Edge ASB, Edinger M, Ehrlund A, Ekwall K, Endoh M, Enomoto H, Eslami A, Fagiolini M, Fairbairn L, Farach-Carson MC, Faulkner GJ, Ferrai C, Fisher ME, Forrester LM, Fujita R, Furusawa JI, Geijtenbeek TB, Gingeras T, Goldowitz D, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Hasegawa Y, Herlyn M, Heutink P, Hitchens KJ, Hume DA, Ikawa T, Ishizu Y, Kai C, Kawamoto H, Kawamura YI, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klein S, Klinken SP, Knox AJ, Kojima S, Koseki H, Koyasu S, Lee W, Lennartsson A, Mackay-Sim A, Mejhert N, Mizuno Y, Morikawa H, Morimoto M, Moro K, Morris KJ, Motohashi H, Mummery CL, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nozaki T, Ogishima S, Ohkura N, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Passier R, Patrikakis M, Pombo A, Pradhan-Bhatt S, Qin XY, Rehli M, Rizzu P, Roy S, Sajantila A, Sakaguchi S, Sato H, Satoh H, Savvi S, Saxena A, Schmidl C, Schneider C, Schulze-Tanzil GG, Schwegmann A, Sheng G, Shin JW, Sugiyama D, Sugiyama T, Summers KM, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tomoiu A, Toyoda H, van de Wetering M, van den Berg LM, Verardo R, Vijayan D, Wells CA, Winteringham LN, Wolvetang E, Yamaguchi Y, Yamamoto M, Yanagi-Mizuochi C, Yoneda M, Yonekura Y, Zhang PG, Zucchelli S, Abugessaisa I, Arner E, Harshbarger J, Kondo A, Lassmann T, Lizio M, Sahin S, Sengstag T, Severin J, Shimoji H, Suzuki M, Suzuki H, Kawai J, Kondo N, Itoh M, Daub CO, Kasukawa T, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y.

Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.


The genomic architecture of mastitis resistance in dairy sheep.

Banos G, Bramis G, Bush SJ, Clark EL, McCulloch MEB, Smith J, Schulze G, Arsenos G, Hume DA, Psifidi A.

BMC Genomics. 2017 Aug 16;18(1):624. doi: 10.1186/s12864-017-3982-1.


Transcriptional mechanisms that control expression of the macrophage colony-stimulating factor receptor locus.

Rojo R, Pridans C, Langlais D, Hume DA.

Clin Sci (Lond). 2017 Jul 31;131(16):2161-2182. doi: 10.1042/CS20170238. Print 2017 Aug 15. Review.


Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data.

Summers KM, Hume DA.

J Leukoc Biol. 2017 Oct;102(4):1081-1092. doi: 10.1189/jlb.1A0417-150RR. Epub 2017 Jul 27.


CCR2-dependent monocyte-derived macrophages resolve inflammation and restore gut motility in postoperative ileus.

Farro G, Stakenborg M, Gomez-Pinilla PJ, Labeeuw E, Goverse G, Di Giovangiulio M, Stakenborg N, Meroni E, D'Errico F, Elkrim Y, Laoui D, Lisowski ZM, Sauter KA, Hume DA, Van Ginderachter JA, Boeckxstaens GE, Matteoli G.

Gut. 2017 Dec;66(12):2098-2109. doi: 10.1136/gutjnl-2016-313144. Epub 2017 Jun 14. Erratum in: Gut. 2019 Sep;68(9):1726.


Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries.

Bush SJ, McCulloch MEB, Summers KM, Hume DA, Clark EL.

BMC Bioinformatics. 2017 Jun 13;18(1):301. doi: 10.1186/s12859-017-1714-9.


Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions.

Kwok J, O'Shea M, Hume DA, Lengeling A.

Front Genet. 2017 Mar 16;8:32. doi: 10.3389/fgene.2017.00032. eCollection 2017. Review.


Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Faulkner GJ, Wells CA, Rehli M, Pavli P, Summers KM, Hume DA.

PLoS Genet. 2017 Mar 6;13(3):e1006641. doi: 10.1371/journal.pgen.1006641. eCollection 2017 Mar.


Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes.

Psifidi A, Banos G, Matika O, Desta TT, Bettridge J, Hume DA, Dessie T, Christley R, Wigley P, Hanotte O, Kaiser P.

Genet Sel Evol. 2016 Sep 29;48(1):74.


Resting and injury-induced inflamed periosteum contain multiple macrophage subsets that are located at sites of bone growth and regeneration.

Alexander KA, Raggatt LJ, Millard S, Batoon L, Chiu-Ku Wu A, Chang MK, Hume DA, Pettit AR.

Immunol Cell Biol. 2017 Jan;95(1):7-16. doi: 10.1038/icb.2016.74. Epub 2016 Nov 15.


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