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Early immune pressure imposed by tissue resident memory T cells sculpts tumour evolution in non-small cell lung cancer

View ORCID ProfileClare E Weeden, View ORCID ProfileVelimir Gayevskiy, Marie Trussart, Claire Marceaux, Nina Tubau Ribera, Daniel Batey, View ORCID ProfileCharis E Teh, View ORCID ProfileAndrew J Mitchell, View ORCID ProfilePhillip Antippa, View ORCID ProfileTracy Leong, View ORCID ProfileDaniel Steinfort, Louis Irving, View ORCID ProfileClaire L Gordon, View ORCID ProfileCharles Swanton, View ORCID ProfileTerence P Speed, View ORCID ProfileDaniel HD Gray, View ORCID ProfileMarie-Liesse Asselin-Labat
doi: https://doi.org/10.1101/2021.04.20.440373
Clare E Weeden
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
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  • ORCID record for Clare E Weeden
Velimir Gayevskiy
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
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Marie Trussart
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
3School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
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Claire Marceaux
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
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Nina Tubau Ribera
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
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Daniel Batey
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
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Charis E Teh
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
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Andrew J Mitchell
4Materials Characterisation and Fabrication Platform, Department of Chemical Engineering, The University of Melbourne, Parkville, Australia
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Phillip Antippa
5Department of Surgery, The University of Melbourne, Parkville, Australia
7The Royal Melbourne Hospital, Parkville, Australia
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Tracy Leong
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
8Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, Australia
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Daniel Steinfort
6Department of Medicine, The University of Melbourne, Parkville, Australia
7The Royal Melbourne Hospital, Parkville, Australia
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Louis Irving
6Department of Medicine, The University of Melbourne, Parkville, Australia
7The Royal Melbourne Hospital, Parkville, Australia
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Claire L Gordon
9Department of Infectious Diseases, Austin Health, Heidelberg, Australia
10Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
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Charles Swanton
11Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
12Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
13University College London Hospitals, London, UK
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Terence P Speed
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
3School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
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Daniel HD Gray
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
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  • For correspondence: labat@wehi.edu.au dgray@wehi.edu.au
Marie-Liesse Asselin-Labat
1The Walter and Eliza Hall Institute of Medical Research, Parkille, Australia
2Department of Medical Biology, The University of Melbourne, Parkville, Australia
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  • For correspondence: labat@wehi.edu.au dgray@wehi.edu.au
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Abstract

Tissue-resident memory T cells (TRM) provide immune defence against local infection and can inhibit cancer progression. However, it is unclear to what extent chronic inflammation impacts TRM activation and how the immune pressure exerted by TRM affects developing tumours in humans. We performed deep profiling of lung cancers arising in never-smokers (NS) and ever-smokers (ES), finding evidence of enhanced TRM immunosurveillance in ES lung. Only tumours arising in ES patients underwent clonal immune escape, even when evaluating cancers with similar tumour mutational burden to NS patients, suggesting that the timing of immune pressure exerted by TRM is a critical factor in the evolution of tumour immune evasion. Tumours grown in T cell quiescent NS lungs displayed little evidence of immune evasion and had fewer neoantigens with low diversity, paradoxically making them amenable to treatment with agonist of the costimulatory molecule, ICOS. These data demonstrate local environmental insults enhance TRM immunosurveillance of human tissue, shape the evolution of tumour immunogenicity and that this interplay informs effective immunotherapeutic modalities.

Competing Interest Statement

C.S. acknowledges grant support from Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer-Ingelheim, Archer Dx Inc (collaboration in minimal residual disease sequencing technologies) and Ono Pharmaceutical, is an AstraZeneca Advisory Board member and Chief Investigator for the MeRmaiD1 clinical trial. C.S has consulted for Amgen, AstraZeneca, Bicycle Therapeutics, Bristol Myers Squibb, Celgene, Genentech, GlaxoSmithKline, GRAIL, Illumina, Medixci, MSD, Novartis, Pfizer, Roche-Ventana and Sarah Cannon Research Institute. C.S. has stock options in Apogen Biotechnologies, Epic Biosciences, GRAIL, and has stock options and is co-founder of Achilles Therapeutics. The other authors declare that they have no competing interests.

Footnotes

  • Author conflicts of interest Correction of Fig 6h

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Early immune pressure imposed by tissue resident memory T cells sculpts tumour evolution in non-small cell lung cancer
Clare E Weeden, Velimir Gayevskiy, Marie Trussart, Claire Marceaux, Nina Tubau Ribera, Daniel Batey, Charis E Teh, Andrew J Mitchell, Phillip Antippa, Tracy Leong, Daniel Steinfort, Louis Irving, Claire L Gordon, Charles Swanton, Terence P Speed, Daniel HD Gray, Marie-Liesse Asselin-Labat
bioRxiv 2021.04.20.440373; doi: https://doi.org/10.1101/2021.04.20.440373
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Early immune pressure imposed by tissue resident memory T cells sculpts tumour evolution in non-small cell lung cancer
Clare E Weeden, Velimir Gayevskiy, Marie Trussart, Claire Marceaux, Nina Tubau Ribera, Daniel Batey, Charis E Teh, Andrew J Mitchell, Phillip Antippa, Tracy Leong, Daniel Steinfort, Louis Irving, Claire L Gordon, Charles Swanton, Terence P Speed, Daniel HD Gray, Marie-Liesse Asselin-Labat
bioRxiv 2021.04.20.440373; doi: https://doi.org/10.1101/2021.04.20.440373

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