Dissecting and exploiting functional interactions between cancer and the immune system
Authors:   , Ibáñez Molero Sofía 
Published: December 2024

In 2018, coinciding with the start of the work described in this thesis, the Nobel Prize
in Physiology or Medicine was jointly awarded to James P. Allison and Tasuku Honjo
for “their discovery of cancer therapy by inhibition of negative immune regulation”.
Indeed, the advent of immunotherapy has revolutionized cancer treatment, evoking
an enormous enthusiasm within the scientific community. However, although
the clinical results are encouraging, a thorough understanding of resistance
mechanisms and personalizing therapies for individual patients are both still part of
an ongoing mission.
This thesis describes several studies aiming to investigate the interplay between T
cells and tumor cells as a key element of cancer immunosurveillance, and failure
thereof. In Chapter 1 I will review the clinical impact of T cell-tumor cell interactions,
both within and outside the tumor microenvironment. Thanks to rapidly advancing
techniques developed in recent years, we now have a better understanding of the
mechanisms governing this particular dialogue, which has clinical consequences.
When T cells recognize cancer cells, they can secrete cytokines that trigger an
apoptotic cascade in the targeted cells. I have studied the mechanisms of actions of
two of these cytokines: Granzyme B and IFNG. In Chapter 2, I describe the genetic
profiling of a cancer cell line panel exhibiting varying degrees of susceptibility to T cellmediated cytotoxicity. In this project I uncovered SERPINB9, an inhibitor of Granzyme
B, as a key mechanism of cancer cell resistance to T cell killing. In Chapter 3, I analyze
the results from a sort-based CRISPRCas9 screen, identifying TM2D proteins as new
regulators of IFNG Receptor 1 (IFNGR1).
Several genetic approaches have been used to increase our understanding of T celltumor
cell communication, including the ones utilized in Chapters 1 and 2. To expand
these efforts, I have also developed a proteomic strategy with a new method described
in Chapter 4. I have termed this technique HySic (for Hybrid quantification of SILACbarcoded interacting cells), which evaluates protein translation and phosphorylation
and is especially suited for cocultures of heterotypic cells. This approach has led to
the identification of new proteins involved in T cell interactions, like PAK1.
In Chapter 5, I study T cells interacting with tumor cells and antigen-presenting cells
(APCs) through the analysis of cell clusters isolated from clinical cancer specimens.
This study was based on the ability of TCR-matched T cells to be enriched in cancer
cell conjugates, as I observed. This new methodology enables the identification of T cell, tumor and APC phenotypes encapsulated in cell clusters, which could shed light
into the functional mechanisms of T cell activation and tumor killing. In addition,
this project holds a translational goal: identifying and isolating tumor-reactive T cells
from patients, to lay the preclinical foundation for new T cell therapy strategies.
Lastly, in Chapter 6, the data presented in this thesis will be summarized, reviewed
and future perspectives will be discussed.