Project Publications

COLOSSUS publications will be added here as articles are published.

  1. Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandrı, Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, & Francesca Cordero. CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinformatics. 2023 May 4;39(5):btad201. DOI: https://doi.org/10.1093/bioinformatics/btad201 Download the PDF here.
  2. Simonetta M. Leto, Martina Ferri, Francesco Sassi, Eugenia R. Zanella, Francesca Cottino, Valentina Vurchio, Irene Catalano, Alessandro Ferrero, Caterina C. Zingaretti, Caterina Marchiò, Elena Grassi, Livio Trusolino, and Andrea Bertotti, Synthetic Lethal Interaction with BCL-XL Blockade Deepens Response to Cetuximab in Patient-Derived Models of Metastatic Colorectal Cancer, Clin Cancer Res 2023;29:1102–13, DOI: https://doi.org/10.1158/1078-0432.CCR-22-2550 Download the PDF here.
  3. Zanella ER, Grassi E, Trusolino L. Towards precision oncology with patient-derived xenografts. Nat Rev Clin Oncol. 2022 Nov;19(11):719-732. Epub 2022 Sep 23. DOI: 10.1038/s41571-022-00682-6 PMID: 36151307. Download the PDF here.
  4. PMyer PA, Kim H, Blümel AM, Finnegan E, Kel A, Thompson TV, Greally JM, Prehn JH, O’Connor DP, Friedman RA, Floratos A, Das S. Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer. Gastro Hep Adv. 2022;1(3):328-341. DOI: 10.1016/j.gastha.2022.01.004. PMID: 35711675 Download the pdf here.
  5. Di Nicolantonio F, Vitiello PP, Marsoni S, Siena S, Tabernero J, Trusolino L, Bernards R, Bardelli A. Precision Oncology in Metastatic Colorectal Cancer – From Biology to Medicine. Nat Rev Clin Oncol. 2021;18:506-525. doi: 10.1038/s41571-021-00495-z. Link to repository: https://hdl.handle.net/2318/1829279
  6. Avolio M, Trusolino L. Rational Treatment of Metastatic Colorectal Cancer: A Reverse Tale of Men, Mice, and Culture Dishes. Cancer Discov. 2021;11:1644-1660. doi: 10.1158/2159-8290.CD-20-1531 Download the pdf here.
  7. Pinnelli M, Trusolino L. The gRASs is Greener: Potential New Therapies in Lung Cancer with Acquired Resistance to KRAS G12C Inhibitors. Cancer Discov. 2021;11:1874-1876. doi: 10.1158/2159-8290.CD-21-0609. Download the pdf here.
  8. Ponsioen B, Post JB, Buissant des Amorie JR, Laskaris D, van Ineveld RL, Kersten S, Bertotti A, Sassi F, Sipieter F, Cappe B, Mertens S, Verlaan-Klink I, Boj SF, Vries RGJ, Rehmann H, Vandenabeele P, Riquet FB, Trusolino L, Bos JL, Snippert HJG. Quantifying Single-Cell ERK Dynamics in Colorectal Cancer Organoids Reveals EGFR as an Amplifier of Oncogenic MAPK Pathway Signalling. Nat Cell Biol. 2021;23:377-390. doi: 10.1038/s41556-021-00654-5. Download the pdf here.
  9. Tedesco M, Giannese F, Lazarević D, Giansanti V, Rosano D, Monzani S, Catalano I, Grassi E, Zanella ER, Botrugno OA, Morelli L, Panina Bordignon P, Caravagna G, Bertotti A, Martino G, Aldrighetti L, Pasqualato S, Trusolino L, Cittaro D, Tonon G. Chromatin Velocity Reveals Epigenetic Dynamics by Single-Cell Profiling of Heterochromatin and Euchromatin. Nat Biotechnol. 2022;40:235-244. doi: 10.1038/s41587-021-01031-1 Download the PDF here.
  10. Patricia Jaaks, Elizabeth A. Coker, Daniel J. Vis, Olivia Edwards, Emma F. Carpenter, Simonetta M. Leto, Lisa Dwane, Francesco Sassi, Howard Lightfoot, Syd Barthorpe, Dieudonne van der Meer, Wanjuan Yang, Alexandra Beck, Tatiana Mironenko, Caitlin Hall, James Hall, Iman Mali, Laura Richardson, Charlotte Tolley, James Morris, Frances Thomas, Ermira Lleshi, Nanne Aben, Cyril H. Benes, Andrea Bertotti, Livio Trusolino, Lodewyk Wessels and Mathew J. Garnett. Effective drug combinations in breast, colon and pancreatic cancer cells, Nature 603, 166–173 (2022). https://doi.org/10.1038/s41586-022-04437-2. Download the pdf here.

  11. Adam Lafferty, Alice C O’Farrell, Giorgia Migliardi, Niraj Khemka, Andreas U Lindner, Francesco Sassi, Eugenia R Zanella, Manuela Salvucci, Evy Vanderheyden, Elodie Modave, Bram Boeckx, Luise Halang, Johannes Betge, Matthias P A Ebert, Patrick Dicker, Guillem Argilés, Josep Tabernero, Rodrigo Dienstmann, Enzo Medico, Diether Lambrechts, Andrea Bertotti, Claudio Isella, Livio Trusolino, Jochen H M Prehn, Annette T Byrne, Molecular Subtyping Combined with Biological Pathway Analyses to Study Regorafenib Response in Clinically Relevant Mouse Models of Colorectal Cancer, Clin Cancer Res(2021) 27 (21): 5979–5992. DOI: https://doi.org/10.1158/1078-0432.CCR-21-0818 Download the pdf here.

  12. Annabelle Nwaokorie and Dirk Fey. Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models, Int. J. Mol. Sci. 2021, 22(18), 9970; https://doi.org/10.3390/ijms22189970. Download the pdf here.
  13. Aoife Nolan, N.K. Aboud, Walter Kolch, and David Matallanas. Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling (Genes 2021, 12, 553), 10 April 2021. https://doi.org/10.3390/genes12040553 Download the pdf here.
  14. Xing Yi Woo, Jessica Giordano, Anuj Srivastava, Zi-Ming Zhao, Michael W. Lloyd, Roebi de Bruijn, Yun-Suhk Suh, Rajesh Patidar, Li Chen, Sandra Scherer, Matthew H. Bailey, Chieh-Hsiang Yang, Emilio Cortes-Sanchez, Yuanxin Xi, Jing Wang, Jayamanna Wickramasinghe, Andrew V. Kossenkov, Vito W. Rebecca, Hua Sun, R. Jay Mashl, Sherri R. Davies, Ryan Jeon, Christian Frech, Jelena Randjelovic, Jacqueline Rosains, Francesco Galimi, Andrea Bertotti, Adam Lafferty, Alice C. O’Farrell, Elodie Modave, Diether Lambrechts, Petra ter Brugge, Violeta Serra, Elisabetta Marangoni, Rania El Botty, Hyunsoo Kim, Jong-Il Kim, Han-Kwang Yang, Charles Lee, Dennis A. Dean II, Brandi Davis-Dusenbery, Yvonne A. Evrard, James H. Doroshow, Alana L. Welm, Bryan E. Welm, Michael T. Lewis, Bingliang Fang, Jack A. Roth, Funda Meric-Bernstam, Meenhard Herlyn, Michael A. Davies, Li Ding, Shunqiang Li, Ramaswamy Govindan, Claudio Isella, Jeffrey A. Moscow, Livio Trusolino, Annette T. Byrne, Jos Jonkers, Carol J. Bult, Enzo Medico, Jeffrey H. Chuang, PDXNET Consortium & EurOPDX Consortium, Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nat Genet 53, 86–99 (2021). DOI: https://doi.org/10.1038/s41588-020-00750-6 Download the PDF here.
  15. V Amodio, R Yaeger, P Arcella, C Cancelliere, S Lamba, A Lorenzato, S Arena, M Montone, B Mussolin, Y Bian, A Whaley, M Pinnelli, YR Murciano-Goroff, E Vakiani, N Valeri, WL Liao, A Bhalkikar, S Thyparambil, HY Zhao, E de Stanchina, S Marsoni, S Siena, A Bertotti, L Trusolino, BT Li, N Rosen, F Di Nicolantonio, A Bardelli, S Misale, EGFR Blockade Reverts Resistance to KRASG12C Inhibition in Colorectal Cancer, Cancer Discov 10:1129-1139, 2020. https://cancerdiscovery.aacrjournals.org/content/10/8/1129 DOI: 10.1158/2159-8290.CD-20-0187 Download the PDF here. Repository link: https://iris.unito.it/handle/2318/1740015#.YAmyMnZKiCg
  16. Aarestrup FM, Albeyatti A, Armitage WJ, Auffray C, Augello L, Balling R, Benhabiles N, Bertolini G, Bjaalie JG, Black M, Blomberg N, Bogaert P, Bubak M, Claerhout B, Clarke L, De Meulder B, D’Errico G, Di Meglio A, Forgo N, Gans-Combe C, Gray AE, Gut I, Gyllenberg A, Hemmrich-Stanisak G, Hjorth L, Ioannidis Y, Jarmalaite S, Kel A, Kherif F, Korbel JO, Larue C, Laszlo M, Maas A, Magalhaes L, Manneh-Vangramberen I, Morley-Fletcher E, Ohmann C, Oksvold P, Oxtoby NP, Perseil I, Pezoulas V, Riess O, Riper H, Roca J, Rosenstiel P, Sabatier P, Sanz F, Tayeb M, Thomassen G, Van Bussel J, Van den Bulcke M, Van Oyen H. Towards a European health research and innovation cloud (HRIC). Genome Med. 2020 Feb 19;12(1):18. DOI: https://doi.org/10.1186/s13073-020-0713-z. Download the pdf here.
  17. Florent Petitprez, Sacha Levy, Cheng-Ming Sun, Maxime Meylan, Christophe Linhard, Etienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catherine Sautès-Fridman, Wolf H. Fridman & Aurélien de Reyniès, The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression, Genome Med 12, 86 (2020). https://doi.org/10.1186/s13073-020-00783-w, DOI: https://doi.org/10.1186/s13073-020-00783-w Download the pdf here.
  18. Alice C. O’Farrell and Monika A. Jarzabek, Andreas U. Lindner, Steven Carberry, Emer Conroy, Ian S. Miller, Kate Connor, Liam Shiels, Eugenia R. Zanella, Federico Lucantoni, Adam Lafferty, Kieron White, Mariangela Meyer Villamandos, Patrick Dicker, William M. Gallagher, Simon A. Keek, Sebastian Sanduleanu, Philippe Lambin, Henry C. Woodruff, Andrea Bertotti, Livio Trusolino, Annette T. Byrne and Jochen H.M. Prehn, Implementing Systems Modelling and Molecular Imaging to Predict the Efficacy of BCL-2 Inhibition in Colorectal Cancer Patient-Derived Xenograft Models, Cancers 2020, 12(10), 2978; https://doi.org/10.3390/cancers12102978 (registering DOI), 14 Oct 2020. Download the pdf here.
  19. Dienstmann R*, Connor K, Byrne AT* and the COLOSSUS consortium (*contributed equally to this work), Precision Therapy in RAS Mutant Colorectal Cancer. Gastroenterology. 2020 Mar;158(4):806-811. DOI: 10.1053/j.gastro.2019.12.051. Download the pdf here.
  20. Barbara Lupo, Francesco Sassi, Marika Pinnelli, Francesco Galimi, Eugenia R. Zanella,Valentina Vurchio, Giorgia Migliardi, Paolo Armando Gagliardi, Alberto Puliafito, Daria Manganaro, Paolo Luraghi, Michael Kragh, Mikkel W. Pedersen, Ivan D. Horak, Carla Boccaccio, Enzo Medico, Luca Primo, Daniel Nichol, Inmaculada Spiteri, Timon Heide, Alexandra Vatsiou, Trevor A. Graham, Elena Élez, Guillem Argiles, Paolo Nuciforo, Andrea Sottoriva, Rodrigo Dienstmann, Diego Pasini, Elena Grassi, Claudio Isella, Andrea Bertotti and Livio Trusolino, Colorectal cancer residual disease at maximal response to EGFR blockade displays a druggable Paneth cell–like phenotype. Science Translational Medicine 05 Aug 2020: Vol. 12, Issue 555, eaax8313 DOI: 10.1126/scitranslmed.aax8313. Repository link: http://hdl.handle.net/2318/1750197. Download the pdf here.
  21. Russo et al. Adaptive mutability of colorectal cancers in response to targeted therapies. Science 2019 Nov 7. pii: eaav4474. DOI: 10.1126/science.aav4474. Download the pdf here.
  22. Irene Catalano, Elena Grassi, Andrea Bertotti, Livio Trusolino, Immunogenomics of Colorectal Tumors: Facts and Hypotheses on an Evolving Saga, Trends in Cancer, December 2019, Vol. 5, No. 12 DOI: https://doi.org/10.1016/j.trecan.2019.10.006. Download the pdf here.
  23. WH Fridman, I Miller, C Sautès-Fridman, AT Byrne, Therapeutic Targeting of the Colorectal Tumor Stroma, Gastroenterology, 14 October 2019, pii: S0016-5085(19)41442-X. DOI: 10.1053/j.gastro.2019.09.045. Download the pdf here.
  24. Elke Burgermeister, Francesca Battaglin, Fagr Eladly, Wen Wu, Frank Herweck , Nadine Schulte, Johannes Betge, Nicolai Härtel, Jakob N. Kather, Cleo-Aron Weis, Timo Gaiser, Alexander Marx, Christel Weiss, Ralf Hofheinz, Ian S. Miller, Fotios Loupakis, Heinz-Josef Lenz, Annette T. Byrne, Matthias P. Ebert, Aryl hydrocarbon receptor nuclear translocator-like (ARNTL/BMAL1) is associated with bevacizumab resistance in colorectal cancer via regulation of vascular endothelial growth factor A, 2019 Jul;45:139-154. DOI: 10.1016/j.ebiom.2019.07.004. Epub 2019 Jul 9. Download the pdf here.
  25. Irene Catalano and Livio Trusolino, The Stromal and Immune Landscape of Colorectal Cancer Progression during Anti-EGFR Therapy, Cancer Cell, Volume 36, Issue 1, 8 July 2019, Pages 1-3, DOI: 10.1016/j.ccell.2019.06.001. Download the pdf here.
  26. Caterina Thomaseth, Dirk Fey, Tapesh Santra, Oleksii S. Rukhlenko, Nicole E. Radde, and Boris N. Kholodenko, Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction, Sci Rep. 2018; 8: 16217. Published online 2018 Nov 1. DOI: 10.1038/s41598-018-34353-3 Download the pdf here.
  27. Florent Petitprez, Cheng-Ming Sun, Laetitia Lacroix, Catherine Sautès-Fridman, Aurélien de Reyniès and Wolf H. Fridman, Quantitative analyses of the tumor microenvironment composition and orientation in the era of precision medicine, Frontiers in Oncology, September 25, 2018, DOI: 10.3389/fonc.2018.00390. Download the pdf here.
  28. M. Sturrock, I. S. Miller, G. Kang, N. Hannis Arba’ie, A. C. O’Farrell, A. Barat, G. Marston, P. L. Coletta, A. T. Byrne, J. H. Prehn, Anti-angiogenic drug scheduling optimisation with application to colorectal cancer, Scientific Reports, V 8, Article number: 11182 (2018). DOI: 10.1038/s41598-018-29318-5 Download the pdf here.