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Quantitative T cell Immunology and Immunotherapy

Deliverables

Individual research project descriptions

Individual research project descriptions

Bar-coded TCR sequence reads of human memory T cell subsets (blood and BM) (preliminary and final)

Preliminary by M36

Preliminary and validated compartmental model and code of CD8+ T cell infiltration into tumour environments

Preliminary by M36

Reference database of immune receptor alleles in healthy humans

Reference database of immune receptor alleles in healthy humans

Preliminary and validated mechanistic models of TCR repertoire dynamics and cross-reactivity

Preliminary by M36

Preliminary and validated stochastic model of the signals regulating naive T cell maintenance

Preliminary by M36

Preliminary and validated mathematical model of thymic T cell development from D1.1

Preliminary by M36

Renewal rates and lifespans of human T cell subsets (blood and BM) from D1.4 (preliminary and final)

Preliminary by M36

A review report per WP (draft and final)

A review report per WP draft and final review M36

Preliminary and validated compartmental model of human naive and memory T cell maintenance

Preliminary by M36

Estimates of diversity and uniqueness of memory T cell (blood and BM) repertoires from D2.1

Estimates of diversity and uniqueness of memory T cell blood and BM repertoires from D21

Labelling data of human memory T cell subsets in blood and bone marrow (BM) (preliminary and final)

Preliminary by M36

Personal career development plans (in place and reviews)

Reviews at M7 M19 M31

15 trained ESRs with two secondments each

15 trained ESRs with two secondments each

Preliminary and validated probabilistic model of T cell signal integration

Preliminary by M36

Preliminary and validated computational model and code of impact of anti-cancer treatment on T cells

Preliminary by M36

Preliminary and validated computational model and code of TCR repertoire response to tumour

Preliminary by M36

Two journal articles per ESR

Two journal articles per ESR

Data set of thymocyte competition (preliminary and final)

Preliminary by M36

Preliminary and validated computational model of the effect of checkpoint inhibitors on T cells in cancer

Preliminary by M36

Public engagement activities carried out by ESRs

Public engagement activities carried out by ESRs

Two individual videos per ESR

Two individual videos per ESR

Launch of QuanTII website

Launch of QuanTII website

Dissemination of results and methods by QuanTII website

Dissemination of results and methods by QuanTII website

Complementary skill workshop (T4, T5 and T6)

Complementary skill workshop (T4, T5 and T6)

Recruitment strategy in place

Recruitment strategy in place

Publications

Mathematical models of cell signalling in heterogeneous populations

Author(s): Léa Sta
Published in: 2023
Publisher: University of Leeds

Network models of T cell receptor repertoires, cross-reactivity, and viral infection

Author(s): Daniel Luque Duque
Published in: 2023
Publisher: University of Leeds

Stochastic models of cell population dynamics and tick-borne virus transmission

Author(s): Giulia Belluccini
Published in: 2023
Publisher: University of Leeds

Statistical analysis and mathematical modelling of lymphocyte population dynamics

Author(s): HoChan Cheon
Published in: 2023
Publisher: Maynooth University

Counting generations in birth and death processes with competing Erlang and exponential waiting times

Author(s): Giulia Belluccini, Martın Lopez-Garcia, Grant Lythe, Carmen Molina-Paris
Published in: Scientific Reports, 2022, Page(s) 12:11289, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-14202-0

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses.

Author(s): Stephan Wilmes; Polly-Anne Jeffrey; Jonathan Martinez-Fabregas; Maximillian Hafer; Paul K. Fyfe; Elizabeth Pohler; Silvia Gaggero; Martín López-García; Grant Lythe; Charles Taylor; T. Guerrier; David Launay; Suman Mitra; Jacob Piehler; Carmen Molina-París; Carmen Molina-París; Ignacio Moraga
Published in: eLife, Issue 1, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.66014

Innate receptors modulating adaptive T cell responses: KIR-HLA interactions and T cell-mediated control of chronic viral infections

Author(s): Mora-Bitria, L., Asquith, B
Published in: Immunogenetics, 2023, Page(s) 269–282, ISSN 0093-7711
Publisher: Springer Verlag
DOI: 10.1007/s00251-023-01293-w

Why are cell populations maintained via multiple compartments?

Author(s): Flavia Feliciangeli, Hanan Dreiwi, Martín López-García, Mario Castro Ponce, Carmen Molina-París and Grant Lythe
Published in: Journal of the Royal Society Interface, Issue 17425689, 2022, Page(s) 20220629, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2022.0629

Cyton2: A Model of Immune Cell Population Dynamics That Includes Familial Instructional Inheritance

Author(s): HoChan Cheon, Andrey Kan, Giulio Prevedello, Simone C. Oostindie, Simon J. Dovedi, Edwin D. Hawkins, Julia M. Marchingo, Susanne Heinzel, Ken R. Duffy, Philip D. Hodgkin
Published in: Frontiers in Bioinformatics, Issue 1, 2021, ISSN 2673-7647
Publisher: Frontiers Media SA
DOI: 10.3389/fbinf.2021.723337

KIR-HLA interactions extend human CD8+ T cell lifespan in vivo

Author(s): Yan Zhang, Ada W.C. Yan, Lies Boelen, Linda Hadcocks, Arafa Salam, Daniel Padrosa Gispert, Loiza Spanos, Laura Mora Bitria, Neda Nemat-Gorgani, James A. Traherne, Chrissy Roberts, Danai Koftori, Graham P. Taylor, Daniel Forton, Paul J. Norman, Steven G.E. Marsh, Robert Busch, Derek C. Macallan, and Becca Asquith
Published in: The Journal of Clinical Investigation, Issue 2023;133(12):e169496, 2023, ISSN 0021-9738
Publisher: American Society for Clinical Investigation
DOI: 10.1172/jci169496

Quantifying T Cell Cross-Reactivity: Influenza and Coronaviruses

Author(s): Jessica Ann Gaevert, Daniel Luque Duque, Grant Lythe, Carmen Molina-París, Paul Glyndwr Thomas
Published in: Viruses, Issue 13/9, 2021, Page(s) 1786, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13091786

Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T cell development

Author(s): Stefanie Scherer, Susanne G Oberle, Kristiyan Kanev, Ann-Katrin Gerullis, Ming Wu, Gustavo P de Almeida, Daniel J Puleston, Francesc Baixauli, Lilian Aly, Alessandro Greco, Tamar Nizharadze, Nils B Becker, Madlaina V Hoesslin, Lara V Donhauser, Jacqueline Berner, Talyn Chu, Hayley A McNamara, Zeynep Esencan, Patrick Roelli, Christine Wurmser, Ingo Kleiter, Maria J G T Vehreschild, Christoph A Maye
Published in: Nature Communications, Issue 24(3), 2023, Page(s) 501-515, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-023-01436-x

Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding

Author(s): Weike Pei, Fuwei Shang, Xi Wang, Ann-Kathrin Fanti, Alessandro Greco, Katrin Busch, Kay Klapproth, Qin Zhang, Claudia Quedenau, Sascha Sauer, Thorsten B. Feyerabend, Thomas Höfer, Hans-Reimer Rodewald
Published in: Cell Stem Cell, Issue 27/3, 2020, Page(s) 383-395.e8, ISSN 1934-5909
Publisher: Cell Press
DOI: 10.1016/j.stem.2020.07.018

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

Author(s): María Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra M. Walczak
Published in: PLOS Genetics, 2023, ISSN 1553-7390
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1010652

Differentiation-based model of hematopoietic stem cell functions and lineage pathways

Author(s): Thomas Höfer, Hans-Reimer Rodewald
Published in: Blood, Issue 132/11, 2018, Page(s) 1106-1113, ISSN 0006-4971
Publisher: American Society of Hematology
DOI: 10.1182/blood-2018-03-791517

Fate of a Naive T Cell: A Stochastic Journey

Author(s): Luis de la Higuera, Martín López-García, Mario Castro, Niloufar Abourashchi, Grant Lythe, Carmen Molina-París
Published in: Frontiers in Immunology, Issue 10, 2019, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2019.00194

IL7 receptor signaling in T cells: A mathematical modeling perspective

Author(s): Jung‐Hyun Park, Adam T. Waickman, Joseph Reynolds, Mario Castro, Carmen Molina‐París
Published in: Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Issue 11/5, 2019, ISSN 1939-5094
Publisher: John Wiley and Sons Inc.
DOI: 10.1002/wsbm.1447

Step‐by‐step comparison of ordinary differential equation and agent‐based approaches to pharmacokinetic‐pharmacodynamic models

Author(s): Van Thuy Truong, Paul G. Baverel, Grant D. Lythe, Paolo Vicini, James W. T. Yates, Vincent F. S. Dubois
Published in: CPT: Pharmacometrics & Systems Pharmacology, 2021, ISSN 2163-8306
Publisher: Nature Publishing Group
DOI: 10.1002/psp4.12703

Fate mapping of hematopoietic stem cells reveals two pathways of native thrombopoiesis

Author(s): Mina N. F. Morcos; Congxin Li; Clara M. Munz; Alessandro Greco; Nicole Dressel; Susanne Reinhardt; Katrin Sameith; Andreas Dahl; Nils B. Becker; Axel Roers; Thomas Höfer; Alexander Gerbaulet
Published in: Nature Communications, Issue 20411723, 2022, Page(s) 4504, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31914-z

Comparison of blood and lymph node cells after intramuscular injection with HIV envelope immunogens

Author(s): Suzanne Day; Charandeep Kaur; Hannah M. Cheeseman; Emily de Groot; Leon R. McFarlane; Maniola Tanaka; Sofia Coelho; Tom Cole; Nana-Marie Lemm; Adrian Lim; Rogier W. Sanders; Becca Asquith; Robin J. Shattock; Katrina M. Pollock
Published in: Frontiers in Immunology, 2022, Page(s) 13:991509, ISSN 1664-3224
Publisher: Frontiers Media
DOI: 10.3389/fimmu.2022.991509

No evidence that HLA genotype influences the driver mutations that occur in cancer patients

Author(s): Noor Kherreh, Siobhán Cleary, Cathal Seoighe
Published in: Cancer Immunology, Immunotherapy, 2021, ISSN 0340-7004
Publisher: Springer Verlag
DOI: 10.1007/s00262-021-03028-w

RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles

Author(s): Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M. Walczak
Published in: Cell Systems, Issue 12/2, 2021, Page(s) 195-202.e9, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2020.11.005

Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response

Author(s): Chun-Yang Lin, Joshua Wolf, David C. Brice, Yilun Sun, Macauley Locke, Sean Cherry, Ashley H. Castellaw, Marie Wehenkel, Jeremy Chase Crawford, Veronika I. Zarnitsyna, Daniel Duque, Kim J. Allison, E. Kaitlynn Allen, Scott A. Brown, Alexandra H. Mandarano, Jeremie H. Estepp, The SJTRC Study Team, Charles Taylor 5, Carmen Molina-Paris, Stacey Schultz-Cherry, Li Tang, Paul G. Thomas, Maureen A. McGa
Published in: Cell Host and Microbe, 2021, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.12.005

Carbon ion radiotherapy eradicates medulloblastomas with chromothripsis in an orthotopic Li-Fraumeni patient-derived mouse model

Author(s): Milena Simovic, Michiel Bolkestein, Mahmoud Moustafa, John K L Wong, Verena Körber, Sarah Benedetto, Umar Khalid, Hannah Sophia Schreiber, Manfred Jugold, Andrey Korshunov, Daniel Hübschmann, Norman Mack, Stephan Brons, Pei-Chi Wei, Michael O Breckwoldt, Sabine Heiland, Martin Bendszus, Jürgen Debus, Thomas Höfer, Marc Zapatka, Marcel Kool, Stefan M Pfister, Amir Abdollahi, Aurélie Ernst
Published in: Neuro-Oncology, Issue Volume 23, Issue 12, December 2021, 2021, Page(s) 2028–2041, ISSN 1522-8517
Publisher: Duke University Press
DOI: 10.1093/neuonc/noab127

Current estimates of T cell kinetics in humans

Author(s): Derek C. Macallan, Robert Busch, Becca Asquith
Published in: Current Opinion in Systems Biology, Issue 18, 2019, Page(s) 77-86, ISSN 2452-3100
Publisher: Elsevier Ltd
DOI: 10.1016/j.coisb.2019.10.002

COGNITION: a prospective precision oncology trial for patients with early breast cancer at high risk following neoadjuvant chemotherapy

Author(s): C. Pixberg, M. Zapatka, M. Hlevnjak, S. Benedetto, J.P. Suppelna, J. Heil, K. Smetanay, L. Michel, C. Fremd, V. Körber, M. Rübsam, L. Buschhorn, S. Heublein, B. Schäfgen, M. Golatta, C. Gomez, A. von Au, M. Wallwiener, S. Wolf, N. Dikow, C. Schaaf, E. Gutjahr, M. Allgäuer, A. Stenzinger, K. Pfütze, R. Kirsten, D. Hübschmann, H.-P. Sinn, D. Jäger, A. Trumpp, R. Schlenk, T. Höfer, V. Thewes,
Published in: ESMO Open, 2022, ISSN 2059-7029
Publisher: Elsevier
DOI: 10.1016/j.esmoop.2022.100637

Stochastic modelling of the T cell repertoire with epitope affinity

Author(s): Daniel F Luque Duque, Carmen Molina-Paris, Grant Lythe, Martin Lopez Garcia, Paul Glyndwr Thomas and Jessica Gaevert
Published in: The Journal of Immunology, Issue 204 (1 Supplement), 2020, Page(s) 94.18, ISSN 1550-6606
Publisher: The American Association of Immunologists, Inc.

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