Dissecting how natural killer cells change in tumours to rationalise immunotherapies

Dean, Isaac William (2023). Dissecting how natural killer cells change in tumours to rationalise immunotherapies. University of Birmingham. Ph.D.

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Abstract

Tumour immuno-evasion is facilitated by dysfunctional effector cells, however, why different tumour infiltrating lymphocytes become defective within the tumour microenvironment remains incompletely understood. T cell exhaustion from chronic antigen exposure is well established, whereas the alteration of other effector cells, including Natural Killer (NK) cells, are not fully defined nor are the mechanisms driving this fully elucidated. NK cells directly target and kill cancer cells by secreting perforin and granzymes. Indirectly, NK cells support the establishment of the CD8 T cell response, recruiting conventional type 1 DC1s (cDC1s) through XCL1 and CCL5, and activating intra-tumoural DCs via IFN-γ and TNF.

Underpinning this study was the use of temporal dynamic labelling of tumour immune cells to distinguish between newly entering and retained NK cells within tumours. This enables tracking of how NK cells change over time within tumours. Single cell RNA-sequencing (scRNA- seq) identified 3 distinct NK clusters; CD11b\(^{+}\) CD49a\(^{-}\) newly infiltrating ‘NK-1’, CD11b\(^{-}\) CD49a\(^{-}\) ‘NK-2’, and CD11b\(^{-}\) CD49a\(^{+}\) resident-like ‘NK-3’ cells which accumulated overtime, and strikingly appeared dysfunctional at the transcriptomic level compared with newly infiltrating cells. Using flow cytometry, these observations were validated in ectopic, orthotopic, and primary models, confirming a universal loss of NK function including CCL5, IFN-γ, and an augmented granzyme repertoire and reduced cytotoxicity.

Targeting NK cells with IL-15:IL-15Rα complexes \(\textit{in vivo}\) partially restored NK functions, inducing a functionally adept CD11b\(^{+}\) CD49a\(^{+}\) subset. However, IL-15:IL-15Rα promoted systemic expression of inhibitory checkpoints suggestive of further negative feedback mechanisms constraining NK cell activation. Collectively, these data reveal a rapid loss of diverse NK cell functions within tumours, providing a unique temporal characterisation of NK cells adapting to the TME, and an investigation into how potential therapeutic interventions impact this process.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):