Re(defining) CD4+ T Cell Identities One Cell at a Time

Project Information

ThDEFINE

Grant agreement ID: 646794

DOI 10.3030/646794

Project closed

EC signature date 19 October 2015

Start date 1 January 2016

End date 30 June 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 980 685,00

EU contribution € 1 980 685,00

Coordinated by

GENOME RESEARCH LIMITED
United Kingdom

Publications

Peer reviewed articles (16)

The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation

Author(s): Jhuma Pramanik; Xi Chen; Gozde Kar; Tomás Gomes; Johan Henriksson; Zhichao Miao; Kedar Nath Natarajan; McKenzie Anj.; Bidesh Mahata; Sarah A. Teichmann
Published in: Genome Medicine, Issue 5, 2018, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1101/235010

Distinct microbial and immune niches of the human colon

Author(s): Kylie R. James, Tomas Gomes, Rasa Elmentaite, Nitin Kumar, Emily L. Gulliver, Hamish W. King, Mark D. Stares, Bethany R. Bareham, John R. Ferdinand, Velislava N. Petrova, Krzysztof Polański, Samuel C. Forster, Lorna B. Jarvis, Ondrej Suchanek, Sarah Howlett, Louisa K. James, Joanne L. Jones, Kerstin B. Meyer, Menna R. Clatworthy, Kourosh Saeb-Parsy, Trevor D. Lawley, Sarah A. Teichmann
Published in: Nature Immunology, Issue 21/3, 2020, Page(s) 343-353, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-020-0602-z

Cross-tissue immune cell analysis reveals tissue-specfic features in humans

Author(s): Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Wells SB, Gomes T, Howlett SK, Suchanek O, Polanski K, King HW, Mamanova L, Huang N, Szabo PA, Richardson L, Bolt L, Fasouli ES, Mahbubani KT, Prete M, Tuck L, Richoz N, Tuong ZK, Campos L, Mousa HS, Needham EJ, Pritchard S, Li T, Elmentaite R, Park J, Rahmani E, Chen D, Menon DK, Bayraktar OA, James LK, Meyer KB, Yosef N, Clatworthy MR, Sims PA, Fa
Published in: Science, 2022, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abl5197

A cell atlas of human thymic development defines T cell repertoire formation.

Author(s): Jong-Eun Park; Rachel A. Botting; Cecilia Domínguez Conde; Dorin-Mirel Popescu; Marieke Lavaert; Daniel J Kunz; Daniel J Kunz; Daniel J Kunz; Issac Goh; Emily Stephenson; Roberta Ragazzini; Roberta Ragazzini; Elizabeth Tuck; Anna Wilbrey-Clark; Kenny Roberts; Veronika R. Kedlian; John R. Ferdinand; Xiaoling He; Simone Webb; Daniel Maunder; Niels Vandamme; Krishnaa T. Mahbubani; Krzysztof Polanski
Published in: Science, Issue 1, 2020, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aay3224

Tumors induce de novo steroid biosynthesis in T cells to evade immunity

Author(s): Bidesh Mahata; Jhuma Pramanik; Louise van der Weyden; Krzysztof Polanski; Gozde Kar; Angela Riedel; Xi Chen; Nuno A. Fonseca; Kousik Kundu; Lia S. Campos; Edward Ryder; Graham Duddy; Izabela Walczak; Klaus Okkenhaug; David J. Adams; Jacqueline D. Shields; Sarah A. Teichmann
Published in: Nature Communications, Issue 1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/471359

A rapid and robust method for single cell chromatin accessibility profiling

Author(s): Chen X, Miragaia RJ, Natarajan KN, Teichmann SA.
Published in: Nature Communications, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07771-0

Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory

Author(s): Megan S. F. Soon, Hyun Jae Lee, Jessica A. Engel, Jasmin Straube, Bryce S. Thomas, Clara P. S. Pernold, Lachlan S. Clarke, Pawat Laohamonthonkul, Rohit N. Haldar, Cameron G. Williams, Lianne I. M. Lansink, Marcela L. Moreira, Michael Bramhall, Lambros T. Koufariotis, Scott Wood, Xi Chen, Kylie R. James, Tapio Lönnberg, Steven W. Lane, Gabrielle T. Belz, Christian R. Engwerda, David S. Khoury, Mil
Published in: Nature Immunology, Issue 21/12, 2020, Page(s) 1597-1610, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-020-0800-8

CLICK-enabled analogues reveal pregnenolone interactomes in cancer and immune cells

Author(s): Sougata Roy; Sougata Roy; Sougata Roy; James Sipthorp; Bidesh Mahata; Bidesh Mahata; Bidesh Mahata; Jhuma Pramanik; Jhuma Pramanik; Marco L. Hennrich; Anne-Claude Gavin; Anne-Claude Gavin; Anne-Claude Gavin; Steven V. Ley; Sarah A. Teichmann
Published in: iScience, Vol 24, Iss 5, Pp 102485- (2021), Issue 1, 2021, ISSN 2589-0042
Publisher: iScience Cell Press
DOI: 10.1101/800649

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

Author(s): Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B. Meyer, Ricardo Miragaia, Graham Duddy, Jhuma Pramanik, Kosuke Yusa, Riitta Lahesmaa, Sarah A. Teichmann
Published in: Cell, Issue 176/4, 2019, Page(s) 882-896.e18, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2018.11.044

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation.

Author(s): Ricardo J. Miragaia; Tomás Gomes; Agnieszka Chomka; Laura Jardine; Angela Riedel; Ahmed N. Hegazy; Ahmed N. Hegazy; Natasha Whibley; Andrea Tucci; Xi Chen; Ida Lindeman; Guy Emerton; Thomas Krausgruber; Thomas Krausgruber; Jacqueline D. Shields; Muzlifah Haniffa; Fiona Powrie; Fiona Powrie; Sarah A. Teichmann; Sarah A. Teichmann; Sarah A. Teichmann
Published in: Immunity, Issue 9, 2019, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2019.01.001

A cell atlas of human thymic development defines T cell repertoire formation

Author(s): Jong-Eun Park; Rachel A. Botting; Cecilia Domínguez Conde; Dorin-Mirel Popescu; Marieke Lavaert; Daniel J Kunz; Daniel J Kunz; Daniel J Kunz; Emily Stephenson; Roberta Ragazzini; Elizabeth Tuck; Anna Wilbrey-Clark; John R. Ferdinand; Simone Webb; Daniel Maunder; Niels Vandamme; Krishnaa T. Mahbubani; Krzysztof Polanski; Lira Mamanova; Andrew Fuller; Andrew Filby; Gary Reynolds; David Dixon; Kouro
Published in: Science, Issue 9, 2020, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1101/2020.01.28.911115

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

Author(s): Ida Lindeman, Guy Emerton, Lira Mamanova, Omri Snir, Krzysztof Polanski, Shuo-Wang Qiao, Ludvig M. Sollid, Sarah A. Teichmann, Michael J. T. Stubbington
Published in: Nature Methods, Issue 15/8, 2018, Page(s) 563-565, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0082-3

Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves T H 1/T FH fate bifurcation in malaria

Author(s): Tapio Lönnberg, Valentine Svensson, Kylie R. James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S. F. Soon, Lily G. Fogg, Arya Sheela Nair, Urijah N. Liligeto, Michael J. T. Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D. Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T. Bunn, Christian R. Engwerda, William R. Heath, Oliver Billker, Oliver Stegle, Ashra
Published in: Science Immunology, Issue 2/9, 2017, Page(s) eaal2192, ISSN 2470-9468
Publisher: AAAS
DOI: 10.1126/sciimmunol.aal2192

T cell fate and clonality inference from single-cell transcriptomes

Author(s): Michael J T Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, Sarah A Teichmann
Published in: Nature Methods, Issue 13/4, 2016, Page(s) 329-332, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/nmeth.3800

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth

Author(s): Sarah Davidson; Mirjana Efremova; Angela Riedel; Bidesh Mahata; Jhuma Pramanik; Jani Huuhtanen; Gozde Kar; Roser Vento-Tormo; Tzachi Hagai; Xi Chen; Muzlifah Haniffa; Jacqueline D. Shields; Sarah A. Teichmann; Sarah A. Teichmann
Published in: Cell Reports, Issue 1, 2020, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.17863/cam.52009

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.

Author(s): Rasa Elmentaite; Alexander Ross; Kenny Roberts; Kylie R. James; Daniel Ortmann; Tomás Gomes; Komal Nayak; Liz Tuck; Sophie Pritchard; Omer Ali Bayraktar; Robert Heuschkel; Ludovic Vallier; Sarah A. Teichmann; Sarah A. Teichmann; Sarah A. Teichmann; Matthias Zilbauer
Published in: Developmental Cell, Issue 1, 2020, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2020.11.010

Other (1)

Germs and germlines: how “public” B‐cell clones evolve in the gut

Author(s): Kylie R. James; Hamish W King
Published in: Immunology & Cell Biology, Issue 2, 2020, ISSN 1440-1711
Publisher: Immunology & Cell Biology
DOI: 10.1111/imcb.12340