Harnessing tumor metabolism to overcome immunosupression

Project Information

ImmunoFit

Grant agreement ID: 773208

DOI

10.3030/773208

Project closed

EC signature date 12 February 2018

Start date 1 July 2018

End date 31 March 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 721,00

EU contribution

€ 1 999 721,00

Coordinated by

VIB VZW
Belgium

Periodic Reporting for period 4 - ImmunoFit (Harnessing tumor metabolism to overcome immunosupression)

Reporting period: 2023-01-01 to 2024-03-31

Summary of the context and overall objectives of the project

Cancer immunotherapy has provided patients with a promising treatment approach harnessing the ability of the immune system to reject the tumor. However, for a subset of tumor types immunotherapy fails to show any clinical benefit. The next challenge is therefore to anticipate the reasons why in certain patients immune intervention does not offer a durable response.
Growing evidence shows that, even in the presence of an immunotherapeutic intervention, specific metabolic features of the tumor microenvironment (TME) can compromise functions and fate of tumor-infiltrating immune cells in a way to favor immunological tolerance and reduce anti-tumor effector functions. Here we propose a holistic, integrative approach to study the metabolic roadmaps and cross-talk between different cell compartments in the TME that lead to immunosuppression and resistance to immunotherapy. The overarching goal of this project is to metabolically modulate the TME or CD8+ T cells in order to restore T cell fitness and anti-tumor effector functions.

We now want to address new important questions: (i) Which are the metabolic alterations that define the composition of an immunosuppressive TME? (ii) Which of the tumor cell compartments and their cross-talk drives these metabolic alterations? (iii) Can we “normalize” the TME to sustain T cell fitness and effector functions? (iv) Can we directly modify the metabolism of T cells to increase their fitness and effector function in the harsh TME? (v) Can this knowledge be exploited for therapeutic purposes in the treatment of cancer and to overcome resistance to immunotherapy?

The society impact of this research will be broad. It is our tradition to attempt to set-up new spinoffs based on academic findings taking care of valorizing our research at the industrial level. This will create new platforms, networks, and working opportunities. All these data will allow to set up new immunotherapeutic regimens that per se trigger the immune system against the tumor and keep under control a possible metastatic relapse, or in the best-case scenario, impose the shrinkage of already established metastatic lesions. Through our findings, many more patients will likely respond to immunotherapy, thus enlarging the population of cancer patients that can benefit from this strategy.

We believe that overcoming the immune suppressive “metabolic checkpoints” of the TME by pharmacologic intervention represents a novel frontier of cancer immunotherapy. The use and combination of patient and mouse datasets is allowing us to have at the same time, a workable, experimental model but also reach clinically relevant conclusions that can be quickly translated to humans. Finally, since other conditions as infections (viral, bacterial, etc.) and autoimmune diseases aim respectively to boost and hinder the immune system, our findings will open up a new avenue for the treatment of several disorders.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

1. Using a novel screening approach we identified CDA, SLC4A4, and HPGDS as potential targets involved in immune checkpoint blockade unresponsiveness. By using single cell RNA sequencing and histological protein evaluation on patient samples in melanoma and PDAC tumors, we disclosed the induction of these targets during immunotherapy resistance. All was confirmed in workable mouse models carrying clinically relevant mutations. We have combined metabolomics, metabolic tracing, mouse genetics, small molecule inhibitors, histology, FACS, and in vitro assays to study the metabolic cross-talk and how the perturbation of these metabolic pathways can change the immune landscape and immune cells functions in mice and in vitro. Besides delivering fundamental biology on tumor metabolism and metabolic cross-talks, we provided proof-of-concept towards innovative anti-cancer therapies to overcome resistance to state-of-the-art immunotherapies.

2. In order to probe in a high throughput fashion, the metabolic and epigenetic networks of T cells in vivo, we have generated tailored CRISPR/Cas9 pooled-gRNA libraries to perturb the metabolism and the epigenome of T cells. Our genetic perturbation platform coupled with adoptive T cells transfer approaches, NGS, and downstream bioinformatic analyses will pinpoint all those genes that, when targeted, do not only increase CD8+ T cells infiltration/fitness within the tumor niches, but also their effector functions. The targets identified in the screens have validated and characterized in a clinically relevant set of tumor models, all corroborated by specific in vitro assays.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The novelty of this project lies in the combination of several cutting-edge approaches for in vivo selection and validation of functionally relevant metabolic targets in different tumor compartments, in casu cancer cells, TAMs, and T cells. The selection and validation steps are supported by unique and innovative (i) tailored metabolic gRNA libraries, (ii) clinically relevant metastatic tumor models as well as surrogate neoantigens, and (iii) transgenic mouse models. With this research, we will shed light on how metabolism and the metabolic cross-talk among cells contribute to the immunosuppressive TME, and it will build novel concepts into T cell metabolism to support T cell fitness in the adverse growth conditions of the TME. With our approach we move far beyond the current concept of targeting cancer metabolism to kill cancer cells directly. Here, we rather aim to hinder a metabolic cross-talk within the TME in order to trigger the action of the immune system.

In the short run, studying the link between metabolism and anti-tumor immunity will disclose a list of pathways and genes that are key regulators of the immunosuppressive properties of cancer cells (CDA, SLC4A4) and TAMs (GS, GLUD1, HPGDS), or that are causative for inefficient T cell fitness within the harsh TME, with particular attention to specific niches such as hypoxic regions, peri-vascular regions, different primary tumor versus metastatic sites (ad hoc designed screenings in CD8+ T cells). We will provide proof-of-concept of pharmacological targeting and initiate drug discovery campaigns within our spinoffs, with VIB Discovery Sciences and the Centre for Drug Design and Discovery, or with external industrial collaborators. Furthermore, studying how metabolism affects T cell fitness directly, will allow us to select for targets that can be safely modified ex vivo in T cells prior ACT. The ground-breaking nature is underscored by the recent green light to use the CRISPR/Cas9 platform to boost the therapeutic efficacy of patient’s T cells. Overall, our approach will not only open a brand-new way of tumor treatment but also offer the possibility to refine current tumor treatment options, as we are implementing immune checkpoint inhibitors and ACT in our experimental settings. Finally, all our effort and analysis of existing and newly generated mouse and, especially, patient samples (blood/plasma, tumor, metastasis, primary cells) will unseal the expression of the target, metabolic profiles, in situ or circulating metabolites, and new cellular neighbourhood descriptions as possible biomarkers to select the best subset of patients responding to current immunotherapies, or to one of our novel immunotherapeutic targets (i.e. companion diagnostic and predictive biomarkers), and to follow-up disease outcome (i.e. prognostic biomarkers).

Graphical Abstract