Grasping the Complexity of Anti-Tumor Immunity
Authors:   , Veninga Vivien 
Published: March 2024

This thesis aims to understand the anti-tumor potential of different immune cell types while carefully considering the complexity of tumor-immune cell interactions. To investigate anti-tumor immunity in a personalized manner, which may support clinical translation, choosing the right model system is of high importance. Patient-derived tumor organoids (PDTOs) resemble the phenotypic and genetic characteristics of the original tumor and allow for the readout of autologous immune responses. As PDTOs are fundamental to the research of this thesis, Chapter 2 will highlight the opportunities and challenges associated with the model system concerning precision medicine.

Chapter 3 reports on our attempt to perform whole-genome CRISPR Cas9 knockout screens on PDTOs to identify modulators of autologous CD8+ T cell killing. Based on two independent fully autologous screens of microsatellite instable colorectal cancer (MSI CRC) PDTOs and expanded tumor-reactive CD8+ T cells, sensitizers and resistors to T cell killing were identified and validated.
In line with the goal to better understand T cell killing and reactivity, Chapter 4 dissects T cell dynamics during co-culture with PDTOs, albeit at a much smaller scale. Here, we aimed to understand differences in T cell reactivity based on expression and chromatin accessibility profiles.

Chapter 5 sheds light on how tumors, invisible to CD8+ T cells, can respond to ICI treatment. Following a comprehensive multi-omics analysis of mismatch repair-deficient (MMR-d) B2M mutant CRC tumors and patient cohorts, we identified γδ T cells as effectors of ICI response. Differential gene expression analysis of two independent patient cohorts treated with ICI, surface marker phenotyping, and single-cell RNA analysis of tumor-infiltrating γδ T cells, along with in vitro experiments using CRC cell lines as well as isogenic B2M mutant/knockout PDTOs, confirmed a cytotoxic phenotype and enhanced reactivity of Vδ1/3 T cells towards B2M mutant MMR-d CRC tumors.

Taking the discoveries of Chapter 5 one step further, we asked whether our findings of enhanced γδ T cell tumor reactivity in the context of MMR-d CRC can be translated to MMR-p CRC. These tumors generally do not respond well to ICI treatment, and any advancement in initiating a better immune response would be a promising step forward. Chapter 6 summarizes our most recent findings on introducing a B2M mutation in MMR-p CRC as an effort to increase γδ T cell reactivity.

Lastly, Chapter 7 explores hematopoietic stem and progenitor cell-derived NK cell (HSPC-NK cells) reactivity towards PDTOs to characterize activating and inhibiting ligands, as well as the investigating the role of IFNγ on tumor recognition. Moreover, using pairs of CRC PDTOs derived before and after ICI treatment revealed reduced HSPC-NK cell reactivity towards post ICI treatment-derived PDTOs. In line with Chapter 4, this could point towards the involvement of immune cells, other than conventional T cells, to ICI response.

Taken together, the thesis embodies a journey through the complexity of anti-tumor immunity, which, I believe, we are just beginning to grasp.