Dr Kylie James
Conjoint Senior Lecturer

Dr Kylie James

PhD (Immunology), University of Queensland, 2016
BSc (Hons), University of Queensland, 2011

Medicine & Health
School of Medical Sciences

Dr Kylie James is Group Leader of the Immunogenomics of Inflammatory Bowel Disease team at the Garvan Institute of Medical Research. She completed her PhD at University of Queensland working with Dr Ashraful Haque at QIMR Berghofer Medical Research Institute. In this role, she determined the response kinetics of T helper cells during blood-stage malaria. Kylie then continued to pursue her interest in the immune system as a postdoctoral researcher with Dr Sarah Teichmann at the Wellcome Sanger Institute and Junior Research Fellow at Christ’s College, University of Cambridge, UK. Her work redefined our understanding of the balance of immune and microbial cells across the healthy human colon. In 2021, Kylie returned to Australia to start her own team as Spinak Fellow and supported by an NHMRC Investigator Grant.

Her team investigates how environmental factors shape gut immune cell and microbial landscapes in health and disease. To achieve this goal, the team apply single-cell genomics and computational approaches to reconstruct cellular microenvironments, developmental hierarchies and interactions.

Location
The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, 370 Victoria St, Darlinghurst NSW 2010
  • Books | 2020
    Efremova M; Vento-Tormo R; Park JE; Teichmann SA; James KR, 2020, Immunology in the Era of Single-Cell Technologies, http://dx.doi.org/10.1146/annurev-immunol-090419-020340
  • Journal articles | 2022
    Bolton C; Smillie CS; Pandey S; Elmentaite R; Wei G; Argmann C; Aschenbrenner D; James KR; McGovern DPB; Macchi M; Cho J; Shouval DS; Kammermeier J; Koletzko S; Bagalopal K; Capitani M; Cavounidis A; Pires E; Weidinger C; McCullagh J; Arkwright PD; Haller W; Siegmund B; Peters L; Jostins L; Travis SPL; Anderson CA; Snapper S; Klein C; Schadt E; Zilbauer M; Xavier R; Teichmann S; Muise AM; Regev A; Uhlig HH, 2022, 'An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease', Gastroenterology, vol. 162, pp. 859 - 876, http://dx.doi.org/10.1053/j.gastro.2021.11.014
    Journal articles | 2022
    James KR; Elmentaite R; Teichmann SA; Hold GL, 2022, 'Correction to: Redefining intestinal immunity with single-cell transcriptomics (Mucosal Immunology, (2021), 10.1038/s41385-021-00470-y)', Mucosal Immunology, vol. 15, pp. 526, http://dx.doi.org/10.1038/s41385-022-00483-1
    Journal articles | 2021
    Elmentaite R; Kumasaka N; Roberts K; Fleming A; Dann E; King HW; Kleshchevnikov V; Dabrowska M; Pritchard S; Bolt L; Vieira SF; Mamanova L; Huang N; Perrone F; Goh Kai’En I; Lisgo SN; Katan M; Leonard S; Oliver TRW; Hook CE; Nayak K; Campos LS; Domínguez Conde C; Stephenson E; Engelbert J; Botting RA; Polanski K; van Dongen S; Patel M; Morgan MD; Marioni JC; Bayraktar OA; Meyer KB; He X; Barker RA; Uhlig HH; Mahbubani KT; Saeb-Parsy K; Zilbauer M; Clatworthy MR; Haniffa M; James KR; Teichmann SA, 2021, 'Cells of the human intestinal tract mapped across space and time', Nature, vol. 597, pp. 250 - 255, http://dx.doi.org/10.1038/s41586-021-03852-1
    Journal articles | 2021
    Haniffa M; Taylor D; Linnarsson S; Aronow BJ; Bader GD; Barker RA; Camara PG; Camp JG; Chédotal A; Copp A; Etchevers HC; Giacobini P; Göttgens B; Guo G; Hupalowska A; James KR; Kirby E; Kriegstein A; Lundeberg J; Marioni JC; Meyer KB; Niakan KK; Nilsson M; Olabi B; Pe’er D; Regev A; Rood J; Rozenblatt-Rosen O; Satija R; Teichmann SA; Treutlein B; Vento-Tormo R; Webb S; Barbry P; Bayraktar O; Behjati S; Bosio A; Canque B; Chalmel F; Gitton Y; Henderson D; Jorgensen A; Lisgo S; Liu J; Lundberg E; Maitre JL; Mazaud-Guittot S; Robertson E; Rolland A; Scharfmann R; Souyri M; Sundström E; Zaffran S; Zilbauer M, 2021, 'A roadmap for the Human Developmental Cell Atlas', Nature, vol. 597, pp. 196 - 205, http://dx.doi.org/10.1038/s41586-021-03620-1
    Journal articles | 2021
    James KR; Elmentaite R; Teichmann SA; Hold GL, 2021, 'Redefining intestinal immunity with single-cell transcriptomics', Mucosal Immunology, http://dx.doi.org/10.1038/s41385-021-00470-y
    Journal articles | 2020
    Beumer J; Puschhof J; Bauzá -Martinez J; Martínez-Silgado A; Elmentaite R; James KR; Ross A; Hendriks D; Artegiani B; Busslinger GA; Ponsioen B; Andersson-Rolf A; Saftien A; Boot C; Kretzschmar K; Geurts MH; Bar-Ephraim YE; Pleguezuelos-Manzano C; Post Y; Begthel H; van der Linden F; Lopez-Iglesias C; van de Wetering WJ; van der Linden R; Peters PJ; Heck AJR; Goedhart J; Snippert H; Zilbauer M; Teichmann SA; Wu W; Clevers H, 2020, 'Erratum: High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells (Cell (2020) 181(6) (1291–1306.e19), (S0092867420305018), (10.1016/j.cell.2020.04.036))', Cell, vol. 182, pp. 1062 - 1064, http://dx.doi.org/10.1016/j.cell.2020.08.005
    Journal articles | 2020
    Beumer J; Puschhof J; Bauzá-Martinez J; Martínez-Silgado A; Elmentaite R; James KR; Ross A; Hendriks D; Artegiani B; Busslinger GA; Ponsioen B; Andersson-Rolf A; Saftien A; Boot C; Kretzschmar K; Geurts MH; Bar-Ephraim YE; Pleguezuelos-Manzano C; Post Y; Begthel H; van der Linden F; Lopez-Iglesias C; van de Wetering WJ; van der Linden R; Peters PJ; Heck AJR; Goedhart J; Snippert H; Zilbauer M; Teichmann SA; Wu W; Clevers H, 2020, 'High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells', Cell, vol. 181, pp. 1291 - 1306.e19, http://dx.doi.org/10.1016/j.cell.2020.04.036
    Journal articles | 2020
    Elmentaite R; Ross ADB; Roberts K; James KR; Ortmann D; Gomes T; Nayak K; Tuck L; Pritchard S; Bayraktar OA; Heuschkel R; Vallier L; Teichmann SA; Zilbauer M, 2020, 'Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease', Developmental Cell, vol. 55, pp. 771 - 783.e5, http://dx.doi.org/10.1016/j.devcel.2020.11.010
    Journal articles | 2020
    Hewitson JP; West KA; James KR; Rani GF; Dey N; Romano A; Brown N; Teichmann SA; Kaye PM; Lagos D, 2020, 'MALAT1 suppresses immunity to infection through promoting expression of Maf and IL-10 in Th cells', Journal of Immunology, vol. 204, pp. 2949 - 2960, http://dx.doi.org/10.4049/jimmunol.1900940
    Journal articles | 2020
    James KR; Gomes T; Elmentaite R; Kumar N; Gulliver EL; King HW; Stares MD; Bareham BR; Ferdinand JR; Petrova VN; Polański K; Forster SC; Jarvis LB; Suchanek O; Howlett S; James LK; Jones JL; Meyer KB; Clatworthy MR; Saeb-Parsy K; Lawley TD; Teichmann SA, 2020, 'Distinct microbial and immune niches of the human colon', Nature Immunology, vol. 21, pp. 343 - 353, http://dx.doi.org/10.1038/s41590-020-0602-z
    Journal articles | 2020
    James KR; King HW, 2020, 'Germs and germlines: how “public” B-cell clones evolve in the gut', Immunology and Cell Biology, vol. 98, pp. 428 - 430, http://dx.doi.org/10.1111/imcb.12340
    Journal articles | 2020
    Soon MSF; Lee HJ; Engel JA; Straube J; Thomas BS; Pernold CPS; Clarke LS; Laohamonthonkul P; Haldar RN; Williams CG; Lansink LIM; Moreira ML; Bramhall M; Koufariotis LT; Wood S; Chen X; James KR; Lönnberg T; Lane SW; Belz GT; Engwerda CR; Khoury DS; Davenport MP; Svensson V; Teichmann SA; Haque A, 2020, 'Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory', Nature Immunology, vol. 21, pp. 1597 - 1610, http://dx.doi.org/10.1038/s41590-020-0800-8
    Journal articles | 2019
    Akter J; Khoury DS; Aogo R; Lansink LIM; SheelaNair A; Thomas BS; Laohamonthonkul P; Pernold CPS; Dixon MWA; Soon MSF; Fogg LG; Engel JA; Elliott T; Sebina I; James KR; Cromer D; Davenport MP; Haque A, 2019, 'Plasmodium-specific antibodies block in vivo parasite growth without clearing infected red blood cells', PLoS Pathogens, vol. 15, pp. e1007599, http://dx.doi.org/10.1371/journal.ppat.1007599
    Journal articles | 2018
    James KR; Soon MSF; Sebina I; Fernandez-Ruiz D; Davey G; Liligeto UN; Nair AS; Fogg LG; Edwards CL; Best SE; Lansink LIM; Schroder K; Wilson JAC; Austin R; Suhrbier A; Lane SW; Hill GR; Engwerda CR; Heath WR; Haque A, 2018, 'IFN regulatory factor 3 balances Th1 and t follicular helper immunity during nonlethal blood-Stage plasmodium infection', Journal of Immunology, vol. 200, pp. 1443 - 1456, http://dx.doi.org/10.4049/jimmunol.1700782
    Journal articles | 2018
    Kunz DJ; Gomes T; James KR, 2018, 'Immune cell dynamics unfolded by single-cell technologies', Frontiers in Immunology, vol. 9, http://dx.doi.org/10.3389/fimmu.2018.01435
    Journal articles | 2017
    Fernandez-Ruiz D; Lau LS; Ghazanfari N; Jones CM; Ng WY; Davey GM; Berthold D; Holz L; Kato Y; Enders MH; Bayarsaikhan G; Hendriks SH; Lansink LIM; Engel JA; Soon MSF; James KR; Cozijnsen A; Mollard V; Uboldi AD; Tonkin CJ; De Koning-Ward TF; Gilson PR; Kaisho T; Haque A; Crabb BS; Carbone FR; McFadden GI; Heath WR, 2017, 'Development of a novel CD4+ TCR transgenic line that reveals a dominant role for CD8+ dendritic cells and CD40 signaling in the generation of helper and CTL responses to blood-stage malaria', Journal of Immunology, vol. 199, pp. 4165 - 4179, http://dx.doi.org/10.4049/jimmunol.1700186
    Journal articles | 2017
    Khoury DS; Cromer D; Akter J; Sebina I; Elliott T; Thomas BS; Soon MSF; James KR; Best SE; Haque A; Davenport MP, 2017, 'Host-mediated impairment of parasite maturation during blood-stage Plasmodium infection', Proceedings of the National Academy of Sciences of the United States of America, vol. 114, pp. 7701 - 7706, http://dx.doi.org/10.1073/pnas.1618939114
    Journal articles | 2017
    Khoury DS; Cromer D; Elliott T; Soon MSF; Thomas BS; James KR; Best SE; Aogo RA; Engel JA; Gartlan KH; Akter J; Sebina I; Haque A; Davenport MP, 2017, 'Characterising the effect of antimalarial drugs on the maturation and clearance of murine blood-stage Plasmodium parasites in vivo', International Journal for Parasitology, vol. 47, pp. 913 - 922, http://dx.doi.org/10.1016/j.ijpara.2017.05.009
    Journal articles | 2017
    Lönnberg T; Svensson V; James KR; Fernandez-Ruiz D; Sebina I; Montandon R; Soon MSF; Fogg LG; Nair AS; Liligeto UN; Stubbington MJT; Ly LH; Bagger FO; Zwiessele M; Lawrence ND; Souza-Fonseca-Guimaraes F; Bunn PT; Engwerda CR; Heath WR; Billker O; Stegle O; Haque A; Teichmann SA, 2017, 'Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria', Science Immunology, vol. 2, http://dx.doi.org/10.1126/sciimmunol.aal2192
    Journal articles | 2017
    Sebina I; Fogg LG; James KR; Soon MSF; Akter J; Thomas BS; Hill GR; Engwerda CR; Haque A, 2017, 'IL-6 promotes CD4+ T-cell and B-cell activation during Plasmodium infection', Parasite Immunology, vol. 39, http://dx.doi.org/10.1111/pim.12455
    Journal articles | 2016
    Proserpio V; Piccolo A; Haim-Vilmovsky L; Kar G; Lönnberg T; Svensson V; Pramanik J; Natarajan KN; Zhai W; Zhang X; Donati G; Kayikci M; Kotar J; McKenzie ANJ; Montandon R; James KR; Fernandez-Ruiz D; Heath WR; Haque A; Billker O; Woodhouse S; Cicuta P; Nicodemi M; Teichmann SA, 2016, 'Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation [Genome Biol. 17 (2016) 103]', Genome Biology, vol. 17, http://dx.doi.org/10.1186/s13059-016-0998-9
    Journal articles | 2016
    Sebina I; James KR; Soon MSF; Fogg LG; Best SE; Labastida Rivera FD; Montes de Oca M; Amante FH; Thomas BS; Beattie L; Souza-Fonseca-Guimaraes F; Smyth MJ; Hertzog PJ; Hill GR; Hutloff A; Engwerda CR; Haque A, 2016, 'IFNAR1-Signalling Obstructs ICOS-mediated Humoral Immunity during Non-lethal Blood-Stage Plasmodium Infection', PLoS Pathogens, vol. 12, http://dx.doi.org/10.1371/journal.ppat.1005999
    Journal articles | 2015
    Edwards CL; Best SE; Gun SY; Claser C; James KR; de Oca MM; Sebina I; Rivera FDL; Amante FH; Hertzog PJ; Engwerda CR; Renia L; Haque A, 2015, 'Spatiotemporal requirements for IRF7 in mediating type I IFN-dependent susceptibility to blood-stage Plasmodium infection', European Journal of Immunology, vol. 45, pp. 130 - 141, http://dx.doi.org/10.1002/eji.201444824
    Journal articles | 2015
    Edwards CL; Zhang V; Werder RB; Best SE; Sebina I; James KR; Faleiro RJ; De Labastida Rivera F; Amante FH; Engwerda CR; Phipps S; Haque A, 2015, 'Coinfection with blood-stage Plasmodium promotes systemic type I interferon production during pneumovirus infection but impairs inflammation and viral control in the lung', Clinical and Vaccine Immunology, vol. 22, pp. 477 - 483, http://dx.doi.org/10.1128/CVI.00051-15
    Journal articles | 2015
    Khoury DS; Cromer D; Best SE; James KR; Sebina I; Haque A; Davenport MP, 2015, 'Reduced erythrocyte susceptibility and increased host clearance of young parasites slows Plasmodium growth in a murine model of severe malaria', Scientific Reports, vol. 5, http://dx.doi.org/10.1038/srep09412
    Journal articles | 2014
    Bunn PT; Stanley AC; De Labastida Rivera F; Mulherin A; Sheel M; Alexander CE; Faleiro RJ; Amante FH; De Oca MM; Best SE; James KR; Kaye PM; Haque A; Engwerda CR, 2014, 'Tissue requirements for establishing long-term CD4+ T cell-mediated immunity following Leishmania donovani infection', Journal of Immunology, vol. 192, pp. 3709 - 3718, http://dx.doi.org/10.4049/jimmunol.1300768
    Journal articles | 2014
    Haque A; Best SE; De Oca MM; James KR; Ammerdorffer A; Edwards CL; De Labastida Rivera F; Amante FH; Bunn PT; Sheel M; Sebina I; Koyama M; Varelias A; Hertzog PJ; Kalinke U; Gun SY; Rénia L; Ruedl C; MacDonald KPA; Hill GR; Engwerda CR, 2014, 'Type I IFN signaling in CD8-DCs impairs Th1-dependent malaria immunity', Journal of Clinical Investigation, vol. 124, pp. 2483 - 2496, http://dx.doi.org/10.1172/JCI70698
    Journal articles | 2013
    Anthony BJ; James KR; Gobert GN; Ramm GA; McManus DP, 2013, 'Schistosoma japonicum Eggs Induce a Proinflammatory, Anti-Fibrogenic Phenotype in Hepatic Stellate Cells', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0068479
    Journal articles | 2013
    Khoury DS; Cromer D; Best SE; James KR; Kim PS; Engwerda CR; Haque A; Davenport MP, 2013, 'Effect of mature, blood-stage Plasmodium parasite sequestration on pathogen biomass in mathematical and in vivo models of malaria.', Infection and Immunity, vol. 82, pp. 212 - 220, http://dx.doi.org/10.1128/IAI.00705-13
  • Preprints | 2022
    Stewart B; Fergie M; Young M; Jones C; Sachdeva A; Blain A; Bacon C; Rand V; Ferdinand J; James K; Mahbubani K; Hook L; Jonas N; Coleman N; Saeb-Parsy K; Collin M; Clatworthy M; Behjati S; Carey C, 2022, Spatial and molecular profiling of classic Hodgkin lymphoma reveals an immunosuppressive mononuclear phagocyte network, http://dx.doi.org/10.21203/rs.3.rs-1233380/v2
    Preprints | 2017
    Fernandez-Ruiz D; Lau LS; Ghazanfari N; Jones C; Ng WY; Davey G; Berthold D; Holz L; Kato Y; Bayarsaikhan G; Hendriks S; James K; Cozijnsen A; Mollard V; de Koning-Ward T; Gilson P; Kaisho T; Haque A; Crabb B; Carbone F; McFadden G; Heath W, 2017, Development of a Novel CD4+TCR Transgenic Line that Reveals a Dominant Role for CD8+DC and CD40-Signaling in the Generation of Helper and CTL Responses to Blood Stage Malaria, http://dx.doi.org/10.1101/113837
    Preprints |
    Elmentaite R; Ross A; James KR; Ortmann D; Gomes T; Roberts K; Nayak K; Tuck L; Bayraktar OA; Heuschkel R; Vallier L; Teichmann SA; Zilbauer M, Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease, http://dx.doi.org/10.1101/2020.02.06.937110
    Preprints |
    James K, Gut_All Cells_Human v1, http://dx.doi.org/10.17504/protocols.io.q3xdypn
    Preprints |
    James K, Human colon tissue dissociation for immune cells v1, http://dx.doi.org/10.17504/protocols.io.tbfeijn
    Preprints |
    James KR; Gomes T; Elmentaite R; Kumar N; Gulliver EL; King HW; Stares MD; Bareham BR; Ferdinand JR; Petrova VN; Polanski K; Forster SC; Jarvis LB; Suchanek O; Howlett S; James LK; Jones JL; Meyer KB; Clatworthy MR; Saeb-Parsy K; Lawley TD; Teichmann SA, Distinct microbial and immune niches of the human colon, http://dx.doi.org/10.1101/2019.12.12.871657
    Preprints |
    Lönnberg T; Svensson V; James KR; Fernandez-Ruiz D; Sebina I; Montandon R; Soon MSF; Fogg LG; Stubbington MJT; Otzen Bagger F; Zwiessele M; Lawrence N; Souza-Fonseca-Guimaraes F; Heath WR; Billker O; Stegle O; Haque A; Teichmann SA, Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation, http://dx.doi.org/10.1101/074971
    Preprints |
    Soon MSF; Lee HJ; Engel JA; Straube J; Thomas BS; Clarke LS; Laohamonthonkul P; Pernold CPS; Haldar RN; Williams CG; Lansink LIM; Koufariotis R; Lakis V; Wood S; Chen X; James KR; Lönnberg T; Lane SW; Davenport MP; Khoury DS; Svensson V; Teichmann SA; Haque A, Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4+T cells, http://dx.doi.org/10.1101/675967
    Preprints |
    Stewart B; Fergie M; Young M; Jones C; Sachdeva A; Blain A; Bacon C; Rand V; Ferdinand J; James K; Mahbubani K; Hook L; Jonas N; Coleman N; Saeb-Parsy K; Collin M; Clatworthy M; Behjati S; Carey C, Spatial and molecular profiling of the classic Hodgkin lymphoma microenvironment reveals an immunosuppressive mononuclear phagocyte network, http://dx.doi.org/10.21203/rs.3.rs-1233380/v1

NHMRC Investigator Grant (2021-2026)

Spinak Fellowship (2021-2024)

Christ’s College Junior Research Fellowship (2018-2020)