Exploring cell interactions in the tumor microenvironment with dual ribosome profiling

Project Information

DualRP

Grant agreement ID: 759579

DOI

10.3030/759579

Project closed

EC signature date 8 November 2017

Start date 1 June 2018

End date 31 May 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 375,00

EU contribution

€ 1 499 375,00

Coordinated by

DEUTSCHES KREBSFORSCHUNGSZENTRUM HEIDELBERG
Germany

Periodic Reporting for period 4 - DualRP (Exploring cell interactions in the tumor microenvironment with dual ribosome profiling)

Reporting period: 2022-12-01 to 2024-05-31

Summary of the context and overall objectives of the project

This project addresses the critical issue of how tumors adapt metabolically to support their growth. Specifically, it focuses on identifying amino acid shortages within the tumor microenvironment (TME) that could be targeted for therapy. Traditionally, studying the interactions between cancer cells and their surroundings required breaking apart the tumor, a process that can stress cells and alter their natural behavior. To overcome this limitation, the project employs a method called Dual Ribosome Profiling (DualRP), which allows for real-time analysis of how cancer cells interact with their environment in a more natural, in vivo setting.

This research is important for society because understanding and targeting the metabolic needs of tumors could lead to more effective cancer treatments with fewer side effects than current options. Cancer remains one of the leading causes of death worldwide, and many patients face treatment resistance or relapse. By identifying specific amino acid limitations in the TME, researchers can develop therapies that disrupt the metabolic support that tumors rely on to grow. This approach has the potential to improve outcomes for patients, particularly those with cancers that are difficult to treat or resistant to existing therapies.

The main goals of the project are to identify these metabolic vulnerabilities using tools like DualRP and diricore, to understand how cancer cells interact with surrounding stromal cells in ways that promote tumor growth, and to apply these insights to develop new therapies. Ultimately, the project aims to reprogram the TME to block tumor growth and overcome treatment resistance, offering new avenues for cancer treatment.

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

Since the beginning of the project, we have focused on uncovering the metabolic weaknesses of cancer by studying the tumor microenvironment (TME). To achieve this, we developed innovative tools like Dual Ribosome Profiling (DualRP) and diricore, which allow us to explore the metabolic interactions between cancer cells and the surrounding stromal cells. These tools help us understand how cancer cells depend on specific amino acids to grow and survive. DualRP, in particular, enables us to analyze the gene activity of two interacting cell populations within the TME at the same time, giving us valuable insights into how cancer adapts to its environment.

One of our significant findings was that cancer cells and fibroblasts, which support the tumor, experience shortages of key amino acids, such as alanine and glycine, under low glucose conditions. However, when these cells are co-cultured, they manage to overcome this shortage by activating a specific signaling pathway, allowing them to produce the nutrients they need to make proteins. Additionally, we developed mouse models that let us examine different cell types' interactions and metabolic activities in a more natural, living environment. This has been crucial in discovering how amino acid restrictions can affect immune cells, particularly T-cells, during cancer treatment with checkpoint inhibitors. Our research showed that when T-cells lack certain amino acids, their ability to respond to cancer therapies weakens.

Our findings are being shared through scientific publications and conferences, contributing to the broader understanding of cancer metabolism. Moving forward, we aim to develop new therapies that target these metabolic weaknesses, with the hope of improving cancer treatments and overcoming drug resistance. This research sets the stage for future innovations in cancer therapy by shedding light on the complex metabolic interactions within the TME.
Overall, the project has advanced our understanding of the TME's metabolic complexities, setting the stage for future therapeutic innovations in cancer treatment.

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 project has made significant strides in cancer research by developing innovative methods to exploit the metabolic weaknesses of tumors within their microenvironment (TME). One of the key advancements is the creation of Dual Ribosome Profiling (DualRP), a cutting-edge technique that allows for the simultaneous analysis of gene expression in two interacting cell populations within the TME without the need for full tumor dissociation. This overcomes a major limitation of previous methods, which altered gene expression due to the stress of isolating cells. By tagging ribosomes with unique chimera proteins, DualRP provides precise insights into the metabolic interactions between different cellular compartments, offering a more detailed and accurate picture of how tumors sustain themselves.

The project has also uncovered specific metabolic vulnerabilities, particularly in amino acid dependencies. DualRP, in combination with another tool called diricore, identified limitations in amino acids like alanine and glycine in cancer and stromal cells. Interestingly, these limitations were resolved in co-cultures, revealing critical metabolic interactions that could be targeted in future therapies. Additionally, the discovery that the Interferon-β1 signaling pathway plays a role in triggering lysosomal acidification and nutrient generation offers a new understanding of TME dynamics and potential therapeutic interventions.

Further progress has been made using transgenic mouse models, which allow for in vivo studies of these metabolic interactions. These models, with ribosome-tagged immune and cancer cells, provide more physiologically relevant insights than traditional lab-based (in vitro) studies. For example, research into checkpoint inhibitor therapies, such as anti-PD-1 treatments, revealed that they cause serine and glycine shortages in T-cells, underscoring the importance of the serine synthesis pathway for an effective immune response. This insight could lead to improvements in cancer immunotherapy strategies. The project shed light on how gene expression and metabolic processes contribute to tumor growth and metastasis. By identifying specific metabolic weaknesses in the interactions between cancer and stromal cells, new therapeutic targets could emerge.

Schematic diagram of dual ribosome profiling (Dual-RP). Ribosomes of two different cell types are ta