Agent-Based Modelling of Gene Networks to model clonal selection in the tumour microenvironment and predict therapeutic resistance

Project Information

MicroC

Grant agreement ID: 772970

DOI

10.3030/772970

Project closed

EC signature date 7 March 2018

Start date 1 June 2018

End date 30 November 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 996 325,00

EU contribution

€ 1 996 325,00

Coordinated by

UNIVERSITA COMMERCIALE LUIGI BOCCONI
Italy

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (25)

Defining hypoxia in cancer: A landmark evaluation of hypoxia gene expression signatures

Author(s): Matteo Di Giovannantonio, Fiona Hartley, Badran Elshenawy, Alessandro Barberis, Dan Hudson, Hana S. Shafique, Vincent E.S. Allott, David A. Harris, Simon R. Lord, Syed Haider, Adrian L. Harris, Francesca M. Buffa, Benjamin H.L. Harris
Published in: Cell Genomics, Issue 5, 2025, Page(s) 100764, ISSN 2666-979X
Publisher: Cell
DOI: 10.1016/j.xgen.2025.100764

A Structural Characterisation of the Mitogen-Activated Protein Kinase Network in Cancer

Author(s): Evangelos Chatzaroulas, Vytenis Sliogeris, Pedro Victori, Francesca M. Buffa, Sotiris Moschoyiannis, Roman Bauer
Published in: Symmetry, Issue 14, 2025, Page(s) 1009, ISSN 2073-8994
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/sym14051009

A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation

Author(s): Hira Javaid, Alessandro Barberis, Olga Chervova, Isar Nassiri, Vitaly Voloshin, Yusuke Sato, Seishi Ogawa, Benjamin Fairfax, Francesca Buffa, Timothy C. Humphrey
Published in: BMC Cancer, Issue 23, 2024, ISSN 1471-2407
Publisher: BioMed Central
DOI: 10.1186/s12885-023-11162-0

Single cell RNA‐sequencing: A powerful yet still challenging technology to study cellular heterogeneity

Author(s): May Ke, Badran Elshenawy, Helen Sheldon, Anjali Arora, Francesca M Buffa
Published in: BioEssays, Issue 44, 2023, ISSN 0265-9247
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/bies.202200084

Transcriptomic analysis of human primary breast cancer identifies fatty acid oxidation as a target for metformin

Author(s): Simon R. Lord, Jennifer M. Collins, Wei-Chen Cheng, Syed Haider, Simon Wigfield, Edoardo Gaude, Barbara A. Fielding, Katherine E. Pinnick, Ulrike Harjes, Ashvina Segaran, Pooja Jha, Gerald Hoefler, Michael N. Pollak, Alastair M. Thompson, Pankaj G. Roy, Ruth. English, Rosie F. Adams, Christian Frezza, Francesca M. Buffa, Fredrik Karpe, Adrian L. Harris
Published in: British Journal of Cancer, Issue 122, 2024, Page(s) 258-265, ISSN 0007-0920
Publisher: Nature Publishing Group
DOI: 10.1038/s41416-019-0665-5

MAGNETO: Cell type marker panel generator from single-cell transcriptomic data

Author(s): Andrea Tangherloni, Simone G. Riva, Brynelle Myers, Francesca M. Buffa, Paolo Cazzaniga
Published in: Journal of Biomedical Informatics, Issue 147, 2024, Page(s) 104510, ISSN 1532-0464
Publisher: Academic Press
DOI: 10.1016/j.jbi.2023.104510

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post‐radiotherapy, and those with de novo metastatic disease

Author(s): Philip Vincent Charlton, Dawn O'Reilly, Yiannis Philippou, Srinivasa Rao Rao, Alastair David Gordon Lamb, Ian Geoffrey Mills, Geoff Stuart Higgins, Freddie Charles Hamdy, Clare Verrill, Francesca Meteora Buffa, Richard John Bryant
Published in: The Prostate, Issue 84, 2024, Page(s) 977-990, ISSN 0270-4137
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/pros.24715

Integrated Pharmacodynamic Analysis Identifies Two Metabolic Adaption Pathways to Metformin in Breast Cancer

Author(s): Simon R. Lord, Wei-Chen Cheng, Dan Liu, Edoardo Gaude, Syed Haider, Tom Metcalf, Neel Patel, Eugene J. Teoh, Fergus Gleeson, Kevin Bradley, Simon Wigfield, Christos Zois, Daniel R. McGowan, Mei-Lin Ah-See, Alastair M. Thompson, Anand Sharma, Luc Bidaut, Michael Pollak, Pankaj G. Roy, Fredrik Karpe, Tim James, Ruth English, Rosie F. Adams, Leticia Campo, Lisa Ayers, Cameron Snell, Ioannis Roxanis,
Published in: Cell Metabolism, Issue 28, 2024, Page(s) 679-688.e4, ISSN 1550-4131
Publisher: Cell Press
DOI: 10.1016/j.cmet.2018.08.021

Robustness and reproducibility for AI learning in biomedical sciences: RENOIR

Author(s): Alessandro Barberis, Hugo J. W. L. Aerts, Francesca M. Buffa
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-51381-4

A machine learning and directed network optimization approach to uncover TP53 regulatory patterns

Author(s): Charalampos P. Triantafyllidis, Alessandro Barberis, Fiona Hartley, Ana Miar Cuervo, Enio Gjerga, Philip Charlton, Linda van Bijsterveldt, Julio Saez Rodriguez, Francesca M. Buffa
Published in: iScience, Issue 26, 2025, Page(s) 108291, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2023.108291

The many faces of mathematical modelling in oncology

Author(s): Pedro Victori, Francesca M Buffa
Published in: The British Journal of Radiology, Issue 92, 2024, ISSN 0007-1285
Publisher: British Institute of Radiology
DOI: 10.1259/bjr.20180856

Guidelines for using sigQC for systematic evaluation of gene signatures

Author(s): Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Published in: Nature Protocols, Issue 14/5, 2019, Page(s) 1377-1400, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-019-0136-8

Modeling genotypes in their microenvironment to predict single- and multi-cellular behavior

Author(s): Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Francesca M Buffa
Published in: GigaScience, Issue 8/3, 2019, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giz010

Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors

Author(s): Andrew Dhawan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07657-1

Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation

Author(s): Zhuoyao Chen, Rafael M. Ioris, Stacey Richardson, Ava N. Van Ess, Iolanda Vendrell, Benedikt M. Kessler, Francesca M. Buffa, Luca Busino, Steven C. Clifford, Alex N. Bullock, Vincenzo D’Angiolella
Published in: Cell Death & Differentiation, Issue 29, 2022, Page(s) 1955-1969, ISSN 1350-9047
Publisher: Nature Publishing Group
DOI: 10.1038/s41418-022-00983-4

Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures

Author(s): Umair Mahmood, Andrew Blake, Sanjay Rathee, Leslie Samuel, Graeme Murray, David Sebag-Montefiore, Simon Gollins, Nicholas P. West, Rubina Begum, Simon P. Bach, Susan D. Richman, Phil Quirke, Keara L. Redmond, Manuel Salto-Tellez, Viktor H. Koelzer, Simon J. Leedham, Ian Tomlinson, Philip D. Dunne, Francesca M. Buffa, null null, Tim S. Maughan, Enric Domingo
Published in: Cancer Research Communications, Issue 4, 2024, Page(s) 1765-1776, ISSN 2767-9764
Publisher: AACR journals
DOI: 10.1158/2767-9764.crc-23-0502

Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFβ as key predictors

Author(s): Enric Domingo, Sanjay Rathee, Andrew Blake, Leslie Samuel, Graeme Murray, David Sebag-Montefiore, Simon Gollins, Nicholas West, Rubina Begum, Susan Richman, Phil Quirke, Keara Redmond, Aikaterini Chatzipli, Alessandro Barberis, Sylvana Hassanieh, Umair Mahmood, Michael Youdell, Ultan McDermott, Viktor Koelzer, Simon Leedham, Ian Tomlinson, Philip Dunne, Andrew Blake, Francesca Buffa, Enric Domingo
Published in: eBioMedicine, Issue 106, 2024, Page(s) 105228, ISSN 2352-3964
Publisher: Elsevier BV
DOI: 10.1016/j.ebiom.2024.105228

New role of fat-free mass in cancer risk linked with genetic predisposition

Author(s): Benjamin H. L. Harris, Matteo Di Giovannantonio, Ping Zhang, David A. Harris, Simon R. Lord, Naomi E. Allen, Tim S. Maughan, Richard J. Bryant, Adrian L. Harris, Gareth L. Bond, Francesca M. Buffa
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-54291-7

Obesity: a perfect storm for carcinogenesis

Author(s): Benjamin H. L. Harris, Valentine M. Macaulay, David A. Harris, Paul Klenerman, Fredrik Karpe, Simon R. Lord, Adrian L. Harris, Francesca M. Buffa
Published in: Cancer and Metastasis Reviews, Issue 41, 2022, Page(s) 491-515, ISSN 0167-7659
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10555-022-10046-2

Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study

Author(s): Pahala Gedara Jayathilake, Pedro Victori, Clara E. Pavillet, Chang Heon Lee, Dimitrios Voukantsis, Ana Miar, Anjali Arora, Adrian L. Harris, Karl J. Morten, Francesca M. Buffa
Published in: PLOS Computational Biology, Issue 20, 2024, Page(s) e1011944, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1011944

Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity

Author(s): Samuel B Bader, Tiffany S Ma, Charlotte J Simpson, Jiachen Liang, Sakura Eri B Maezono, Monica M Olcina, Francesca M Buffa, Ester M Hammond
Published in: Nucleic Acids Research, Issue 49, 2021, Page(s) 7492-7506, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab551

E2F1 proteolysis via <scp>SCF</scp> ‐cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition

Author(s): Kamila Burdova, Hongbin Yang, Roberta Faedda, Samuel Hume, Jagat Chauhan, Daniel Ebner, Benedikt M Kessler, Iolanda Vendrell, David H Drewry, Carrow I Wells, Stephanie B Hatch, Grigory L Dianov, Francesca M Buffa, Vincenzo D'Angiolella
Published in: The EMBO Journal, Issue 38, 2023, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2018101443

Cyclin F–EXO1 axis controls cell cycle–dependent execution of double-strand break repair

Author(s): Hongbin Yang, Shahd Fouad, Paul Smith, Eun Young Bae, Yu Ji, Xinhui Lan, Ava Van Ess, Francesca M. Buffa, Roman Fischer, Iolanda Vendrell, Benedikt M. Kessler, Vincenzo D’Angiolella
Published in: Science Advances, Issue 10, 2024, ISSN 2375-2548
Publisher: Science
DOI: 10.1126/sciadv.ado0636

ELTD1 is present in extracellular vesicles derived from endothelial cells as a cleaved extracellular domain which induces in vivo angiogenesis

Author(s): Helen Sheldon, Wei Zhang, Esther Bridges, Koon Hwee Ang, Salwa Lin, Massimo Masiero, Demin Li, Penny A. Handford, Pat Whiteman, Roman Fischer, Francesca Buffa, Manu Vatish, Alison H. Banham, Adrian L. Harris
Published in: Journal of Extracellular Biology, Issue 1, 2023, ISSN 2768-2811
Publisher: Wiley
DOI: 10.1002/jex2.52

Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits

Author(s): Matteo Di Giovannantonio, Benjamin HL Harris, Ping Zhang, Isaac Kitchen-Smith, Lingyun Xiong, Natasha Sahgal, Giovanni Stracquadanio, Marsha Wallace, Sarah Blagden, Simon Lord, David Harris, Adrian H.L. Harris, Francesca M. Buffa, Gareth L. Bond
Published in: Journal of Medical Genetics, 2020, Page(s) jmedgenet-2019-106799, ISSN 0022-2593
Publisher: British Medical Association
DOI: 10.1136/jmedgenet-2019-106799

Book chapters (1)

Machine Learning Using Gene-Sets to Infer miRNA Function

Author(s): Andrew Dhawan, Francesca M. Buffa
Published in: Advances in Experimental Medicine and Biology, Systems Biology of MicroRNAs in Cancer, 2022, Page(s) 229-240
Publisher: Springer International Publishing
DOI: 10.1007/978-3-031-08356-3_8