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Using regulatory variants to detect gene-gene interactions identifies networks of genes linked to cell immortalisation.

Wragg D, Liu Q, Lin Z, Riggio V, Pugh CA, Beveridge AJ, Brown H, Hume DA, Harris SE, Deary IJ, Tenesa A, Prendergast JGD.

Nat Commun. 2020 Jan 17;11(1):343. doi: 10.1038/s41467-019-13762-6.


Regulation and function of macrophage colony-stimulating factor (CSF1) in the chicken immune system.

Wu Z, Harne R, Chintoan-Uta C, Hu TJ, Wallace R, MacCallum A, Stevens MP, Kaiser P, Balic A, Hume DA.

Dev Comp Immunol. 2020 Apr;105:103586. doi: 10.1016/j.dci.2019.103586. Epub 2019 Dec 20.


Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens.

Freem L, Summers KM, Gheyas AA, Psifidi A, Boulton K, MacCallum A, Harne R, O'Dell J, Bush SJ, Hume DA.

Front Genet. 2019 Nov 14;10:1032. doi: 10.3389/fgene.2019.01032. eCollection 2019.


Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions.

Halachev M, Meynert A, Taylor MS, Vitart V, Kerr SM, Klaric L; S. G. P. Consortium, Aitman TJ, Haley CS, Prendergast JG, Pugh C, Hume DA, Harris SE, Liewald DC, Deary IJ, Semple CA, Wilson JF.

PLoS Genet. 2019 Nov 25;15(11):e1008480. doi: 10.1371/journal.pgen.1008480. eCollection 2019 Nov.


Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep.

Banos G, Clark EL, Bush SJ, Dutta P, Bramis G, Arsenos G, Hume DA, Psifidi A.

PLoS One. 2019 Nov 25;14(11):e0214346. doi: 10.1371/journal.pone.0214346. eCollection 2019.


A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus).

Muriuki C, Bush SJ, Salavati M, McCulloch MEB, Lisowski ZM, Agaba M, Djikeng A, Hume DA, Clark EL.

Front Genet. 2019 Nov 4;10:1080. doi: 10.3389/fgene.2019.01080. eCollection 2019.


Developmental Stage-Specific Distribution of Macrophages in Mouse Mammary Gland.

Stewart TA, Hughes K, Hume DA, Davis FM.

Front Cell Dev Biol. 2019 Oct 24;7:250. doi: 10.3389/fcell.2019.00250. eCollection 2019.


Antigen Sampling CSF1R-Expressing Epithelial Cells Are the Functional Equivalents of Mammalian M Cells in the Avian Follicle-Associated Epithelium.

Balic A, Chintoan-Uta C, Vohra P, Sutton KM, Cassady-Cain RL, Hu T, Donaldson DS, Stevens MP, Mabbott NA, Hume DA, Sang HM, Vervelde L.

Front Immunol. 2019 Oct 22;10:2495. doi: 10.3389/fimmu.2019.02495. eCollection 2019.


Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep.

Salavati M, Bush SJ, Palma-Vera S, McCulloch MEB, Hume DA, Clark EL.

Front Genet. 2019 Sep 19;10:863. doi: 10.3389/fgene.2019.00863. eCollection 2019.


Functional evolution of the colony-stimulating factor 1 receptor (CSF1R) and its ligands in birds.

Hume DA, Gutowska-Ding MW, Garcia-Morales C, Kebede A, Bamidele O, Trujillo AV, Gheyas AA, Smith J.

J Leukoc Biol. 2020 Feb;107(2):237-250. doi: 10.1002/JLB.6MA0519-172R. Epub 2019 Sep 5.


A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis).

Young R, Lefevre L, Bush SJ, Joshi A, Singh SH, Jadhav SK, Dhanikachalam V, Lisowski ZM, Iamartino D, Summers KM, Williams JL, Archibald AL, Gokhale S, Kumar S, Hume DA.

Front Genet. 2019 Jul 24;10:668. doi: 10.3389/fgene.2019.00668. eCollection 2019.


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. 2020 Feb;107(2):221-235. doi: 10.1002/JLB.MA0519-149R. Epub 2019 Aug 8.


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. 2020 Feb;107(2):205-219. doi: 10.1002/JLB.MR0519-143R. Epub 2019 Jul 22. 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. 2019 Aug 19;11(8):703-718. doi: 10.1093/jmcb/mjy063.


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.

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