Subclonal immune evasion in non-small cell lung cancer

Krijn K Dijkstra; Roberto Vendramin; Despoina Karagianni; Maartje Witsen; Felipe Gálvez-Cancino; Mark S Hill; Kane A Foster; Vittorio Barbè; Mihaela Angelova; Robert E Hynds; David R Pearce; Carlos Martínez-Ruiz; James R M Black; Ariana Huebner; Oriol Pich; Andrew Rowan; Marcellus Augustine; Clare Puttick; David A Moore; Lydia L Liu; Sadegh Saghafinia; Joris van de Haar; Selvaraju Veeriah; Cristina Naceur-Lombardelli; Antonia Toncheva; Supreet Kaur Bola; Crispin T Hiley; Mariam Jamal-Hanjani; Nicholas McGranahan; Kevin Litchfield; James L Reading; Benny Chain; TRACERx consortium; Sergio A Quezada; Emile E Voest; Charles Swanton

doi:10.1016/j.ccell.2025.06.012

Subclonal immune evasion in non-small cell lung cancer

Cancer Cell. 2025 Oct 13;43(10):1833-1849.e10. doi: 10.1016/j.ccell.2025.06.012. Epub 2025 Jul 3.

Authors

Krijn K Dijkstra¹, Roberto Vendramin², Despoina Karagianni³, Maartje Witsen⁴, Felipe Gálvez-Cancino⁵, Mark S Hill⁶, Kane A Foster⁷, Vittorio Barbè⁶, Mihaela Angelova⁸, Robert E Hynds⁹, David R Pearce⁶, Carlos Martínez-Ruiz⁶, James R M Black⁶, Ariana Huebner⁶, Oriol Pich⁶, Andrew Rowan⁸, Marcellus Augustine¹⁰, Clare Puttick¹¹, David A Moore¹², Lydia L Liu⁶, Sadegh Saghafinia⁶, Joris van de Haar⁴, Selvaraju Veeriah⁶, Cristina Naceur-Lombardelli⁶, Antonia Toncheva⁶, Supreet Kaur Bola³, Crispin T Hiley⁶, Mariam Jamal-Hanjani¹³, Nicholas McGranahan¹⁴, Kevin Litchfield¹⁵, James L Reading¹⁶, Benny Chain¹⁷; TRACERx consortium; Sergio A Quezada¹⁸, Emile E Voest¹⁹, Charles Swanton²⁰

Collaborators

TRACERx consortium:
Abigail Bunkum, Adam Atkin, Aiman Alzetani, Akshay J Patel, Alan Kirk, Alexander James Procter, Alexander M Frankell, Alexandra Rice, Allan Hackshaw, Amrita Bajaj, Anand Devaraj, Anca Grapa, Andrew G Nicholson, Andrew Kidd, Andrew Rowan, Angela Dwornik, Angela Leek, Angeliki Karamani, Anne-Marie Hacker, Anshuman Chaturvedi, Antonio Paiva-Correia, Aoife Walker, Apostolos Nakas, Ariana Huebner, Arjun Nair, Asia Ahmed, Aya Osman, Azmina Sodha-Ramdeen, Babu Naidu, Benny Chain, Camilla Pilotti, Carla Castignani, Carlos Martínez-Ruiz, Caroline Dive, Catarina Veiga, Charles Swanton, Charles-Antoine Collins-Fekete, Chiara Proli, Chris Bailey, Cian Murphy, Claire Wilson, Clare E Weeden, Clare Puttick, Claudia Lee, Colin R Lindsay, Corentin Richard, Craig Dick, Crispin T Hiley, Cristina Naceur-Lombardelli, Daniel Kaniu, David A Moore, David Chuter, David Lawrence, David R Pearce, Davide Patrini, Dean A Fennell, Despoina Karagianni, Dionysis Papadatos-Pastos, Ekaterini Boleti, Elaine Borg, Elizabeth Keene, Emilia L Lim, Emilie Martinoni Hoogenboom, Emma Colliver, Emma Nye, Eric Lim, Erik Sahai, Eustace Fontaine, Eva Grönroos, Felice Granato, Fiona H Blackhall, Fleur Monk, Francesco Fraioli, Francisco Gimeno-Valiente, Gareth A Wilson, Gary Middleton, Gary Royle, George Kassiotis, Georgia Moth, Georgia Stavrou, Gerald Langman, Gerasimos-Theodoros Mastrokalos, Gillian Price, Gurdeep Matharu, Hanyun Zhang, Harshil Bhayani, Heather Cheyne, Helen L Lowe, Helen Shackleford, Hemangi Chavan, Hilgardt Raubenheimer, Hugo Jwl Aerts, Ieva Usaite, Imran Noorani, Jack Davies Hodgkinson, Jack French, Jacki Goldman, Jacqui A Shaw, James L Reading, James R M Black, James W Holding, James Wilson, Jason F Lester, Jayant K Rane, Jeanette Kittel, Jennifer Whiteley, Jerome Nicod, John A Hartley, John Le Quesne, Jonas Demeulemeester, Jonathan Tugwood, Judith Cave, Juliette Novasio, Junaid Choudhary, Karen Grimes, Karl S Peggs, Katey S S Enfield, Katherine D Brown, Kayalvizhi Selvaraju, Kayleigh Gilbert, Keith M Kerr, Kendadai Rammohan, Kerstin Haase, Kerstin Thol, Kevin G Blyth, Kexin Koh, Khalid AbdulJabbar, Kristiana Grigoriadis, Krupa Thakkar, Kunal Bhakhri, Leah Ensell, Leena Joseph, Lily Robinson, Lucrezia Patruno, Lyn Ambrose, Madava Djearaman, Madeleine Hewish, Magali N Taylor, Mairead MacKenzie, Maise Al Bakir, Mandeesh Sangha, Mansi Shah, Maria Chiara Pisciella, Maria Litovchenko, Maria Zagorulya, Mariam Jamal-Hanjani, Martin D Forster, Mary Falzon, Mathew Carter, Mathew Thomas, Matthew G Krebs, Michael J Shackcloth, Michalina Magala, Michelle M Leung, Mickael Escudero, Mihaela Angelova, Miklos Diossy, Mo Asif, Mohamad Tufail, Mohammed Khalil, Molly Scotland, Monica Sivakumar, Mpho Malima, Nadia Fernandes, Neal Navani, Nicholas McGranahan, Nicola Totton, Nicolai J Birkbak, Nikos Kostoulas, Nnennaya Kanu, Olivia Lucas, Oriol Pich, Pat Gorman, Patricia Georg, Paul Ashford, Paul Bishop, Paulo De Sousa, Pedro Oliveira, Peter Russell, Peter Van Loo, Philip Crosbie, Philip Hobson, Piotr Pawlik, Pratibha Shah, Rachel Rosenthal, Rebecca Boyles, Reena Khiroya, Richard Kevin Stone, Ricky M Thakrar, Rija Zaidi, Robert Bentham, Robert C M Stephens, Roberto Salgado, Roberto Vendramin, Rocco Bilancia, Roland F Schwarz, Sadegh Saghafinia, Salomey Kellet, Sam M Janes, Samuel Gamble, Sara Waplington, Sarah Benafif, Sarah Booth, Sarah Danson, Sean Dulloo, Selvaraju Veeriah, Seng Kuong Anakin Ung, Serena Chee, Sergio A Quezada, Sharon Vanloo, Shirley Richardson, Sian Harries, Silviu I Buderi, Simon Jordan, Simone Zaccaria, Siow Ming Lee, Sofina Begum, Sonya Hessey, Sophia Ward, Sridhar Rathinam, Stefan Boeing, Stephan Beck, Steve Bandula, Supreet Kaur Bola, Takahiro Karasaki, Tamara Denner, Tanya Ahmad, Teresa Marafioti, Theepan Visakan, Thomas B K Watkins, Thomas Patrick Jones, Tom L Kaufmann, Tracey Cruickshank, Victoria Spanswick, Vijay Joshi, Vittorio Barbè, Wei-Ting Lu, William Hill, Wing Kin Liu, Xiaoxi Pan, Yien Ning Sophia Wong, Yin Wu, Yinyin Yuan, Yutaka Naito, Yvonne Summers, Zainab Kalokoh, Zoe Ramsden, Zoltan Kaplar, Zoltan Szallasi

Affiliations

¹ Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Oncode Institute, Utrecht, the Netherlands. Electronic address: k.dijkstra@nki.nl.
² Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Tumor ImmunoGenomics and Immunosurveillance Laboratory, University College London Cancer Institute, University College London, London, UK.
³ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Cancer Immunology Unit, Immune Regulation and Tumor Immunotherapy Group, Research Department of Haematology, University College London Cancer Institute, London, UK.
⁴ Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
⁵ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Cancer Immunology Unit, Immune Regulation and Tumor Immunotherapy Group, Research Department of Haematology, University College London Cancer Institute, London, UK; Immune Regulation Laboratory, Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
⁶ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK.
⁷ Cancer Immunology Unit, Immune Regulation and Tumor Immunotherapy Group, Research Department of Haematology, University College London Cancer Institute, London, UK.
⁸ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
⁹ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK.
¹⁰ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Tumor ImmunoGenomics and Immunosurveillance Laboratory, University College London Cancer Institute, University College London, London, UK; Division of Medicine, University College London, London, UK.
¹¹ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
¹² Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Department of Cellular Pathology, University College London Hospital, London, UK.
¹³ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
¹⁴ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
¹⁵ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Tumor ImmunoGenomics and Immunosurveillance Laboratory, University College London Cancer Institute, University College London, London, UK.
¹⁶ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Pre-Cancer Immunology Laboratory, University College London Cancer Institute, London, UK.
¹⁷ University College London Cancer Institute, London, UK; Division of Infection and Immunity, University College London, London, UK.
¹⁸ Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Cancer Immunology Unit, Immune Regulation and Tumor Immunotherapy Group, Research Department of Haematology, University College London Cancer Institute, London, UK. Electronic address: s.quezada@ucl.ac.uk.
¹⁹ Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands. Electronic address: e.voest@nki.nl.
²⁰ Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK. Electronic address: charles.swanton@crick.ac.uk.

PMID: 40614739
DOI: 10.1016/j.ccell.2025.06.012

Abstract

Cancers rarely respond completely to immunotherapy. While tumors consist of multiple genetically distinct clones, whether this affects the potential for immune escape remains unclear due to an inability to isolate and propagate individual subclones from human cancers. Here, we leverage the multi-region TRACERx lung cancer evolution study to generate a patient-derived organoid - T cell co-culture platform that allows the functional analysis of subclonal immune escape at single clone resolution. We establish organoid lines from 11 separate tumor regions from three patients, followed by isolation of 81 individual clonal sublines. Co-culture with tumor infiltrating lymphocytes (TIL) or natural killer (NK) cells reveals cancer-intrinsic and subclonal immune escape in all 3 patients. Immune evading subclones represent genetically distinct lineages with a unique evolutionary history. This indicates that immune evading and non-evading subclones can be isolated from the same tumor, suggesting that subclonal tumor evolution directly affects immune escape.

Keywords: T cell; cancer evolution; immune escape; immune evasion; immunosurveillance; immunotherapy; intratumor heterogeneity; non-small cell lung cancer; organoids; tumor evolution; tumor immunology.

MeSH terms

Carcinoma, Non-Small-Cell Lung* / genetics
Carcinoma, Non-Small-Cell Lung* / immunology
Carcinoma, Non-Small-Cell Lung* / pathology
Coculture Techniques
Humans
Immune Evasion*
Killer Cells, Natural / immunology
Lung Neoplasms* / genetics
Lung Neoplasms* / immunology
Lung Neoplasms* / pathology
Lymphocytes, Tumor-Infiltrating / immunology
Organoids / immunology
Tumor Escape* / immunology