Association of the imbalance between early and late differentiated intra-tumor CD4 T cells with mutational burden in non-small cell lung cancer.

person Ehsan Ghorani Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom info_outline Ehsan Ghorani, James L. Reading, Jake Y. Henry, Marc Robert De Massy, Rachel Rosenthal, Andrew J.S. Furness, Assma Ben Aissa, Mariam Jamal-Hanjani, Nicolai Birkbak, Gareth Wilson, Roberto Salgado, Tom Lund, Crispin T. Hiley, Sherene Loi, Allan Hackshaw, Nicholas McGranahan, Benjamin M. Chain, Karl S. Peggs, Charles Swanton, Sergio A. Quezada

Authors person Ehsan Ghorani Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom info_outline Ehsan Ghorani, James L. Reading, Jake Y. Henry, Marc Robert De Massy, Rachel Rosenthal, Andrew J.S. Furness, Assma Ben Aissa, Mariam Jamal-Hanjani, Nicolai Birkbak, Gareth Wilson, Roberto Salgado, Tom Lund, Crispin T. Hiley, Sherene Loi, Allan Hackshaw, Nicholas McGranahan, Benjamin M. Chain, Karl S. Peggs, Charles Swanton, Sergio A. Quezada Organizations Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom, Cancer Immunology Unit, University College London Cancer Institute, London], United Kingdom, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom, Cancer, London, United Kingdom, Center for Oncological Research (CORE) -Campus Sint-Augustinus-University of Antwerp, Antwerpen, Belgium, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom, Peter MacCallum Cancer Centre, Melbourne, Australia, Cancer Research UK & UCL Cancer Trials Centre, London, United Kingdom, Division of Infection and Immunity, University College London, London, United Kingdom, University College London Cancer Institute, London, United Kingdom, Translation Cancer Therapeutics Laboratory, The Francis Crick Institute, London, United Kingdom Abstract Disclosures Research Funding Other Foundation Background: CD4 T helper cells are key orchestrators of immunity in states of persistent antigen exposure. In chronic viral infection, loss of immune control is associated with CD4 differentiation skewing (CD4 ds ) resulting from decline of early progenitors and gain in abundance of exhausted and terminally differentiated subsets. Here, we set out to identify whether a similar process occurs within the tumour microenvironment, contributing to immune dysfunction. Methods: Multiregional samples of tumour and non-tumour lung tissue from patients with untreated, surgically resected non-small cell lung cancer (NSCLC) within the first 100 recruited to the prospective lung TRACERx study were analysed by high dimensional flow cytometry of tumour infiltrating lymphocytes (TILs) and paired bulk tumour exome and RNA sequencing. We additionally reanalysed publically available single T cell and bulk tumour RNA sequencing from patients with NSCLC. Results: Unsupervised clustering and dimension reduction revealed a heterogenous landscape of CD4 TILs, with evidence of CD4 ds in association with tumour mutational burden. Loss of PD1 - CCR7 + T central memory enriched early differentiated cells was accompanied by gain in abundance of PD1 + populations with exhausted (CD57 - ICOS hi CTLA4 hi ) and terminally differentiated effector (CD57 + Eomes + ) phenotypes. Further characterisation of these populations by single cell RNA sequencing revealed differential expression of key genes involved in transcriptional regulation, co-inhibition and co-stimulatory pathways. A validated gene signature of CD4 ds was associated with worse outcomes in TRACERx and TCGA cohorts. Conclusions: Our findings reveal remodelling of the CD4 differentiation landscape in association with tumour genomic characteristics, underscoring how mutational burden in the context of chronic stimulation may lead to loss of immune fitness and elucidating key regulatory pathways in potentially clinically relevant CD4 subsets.