CORDIS - EU research results

Exploiting the hypoxia response in T cells for Next-Generation Immuno-Oncology

Periodic Reporting for period 2 - NextGen IO (Exploiting the hypoxia response in T cells for Next-Generation Immuno-Oncology)

Reporting period: 2020-08-01 to 2022-01-31

NextGen_IO has a core focus on immuno-oncology, specifically on target discovery and drug development, with the aim of exploiting several opportunities that the hypoxia pathway in T cells offers for the treatment of cancer. It is well recognised that the clinical response of immunotherapies depends on the ability of T-cells to mount an effective effector response, persist in
treated patients and avoid exhaustion and toxicities. Several approaches to immunotherapy have shown promise in clinical trials, especially the use of immune checkpoint inhibitors and, more recently, autologous adoptive T-cell therapies.
However, current state-of-the-art immunotherapies are only effective in a small fraction of patients, offering a medical need to be addressed in several cancer types. Importantly, the tumor microenvironment has specific features that impact the immune response, including decreased oxygenation, aberrant vascularization and altered nutrient availability; all these influence the success of immunotherapies. The current project aims to exploit this pathway with a multi-disciplinary strategy, to deliver several early-stage drug discovery outputs.
The main overall objectives are:

1. Development of a novel small molecule inhibitor to modulate the hypoxic response in T cells.
2. Therapeutic target discovery in T cells, focused on hypoxia-driven epigenetic modifications.
3. Development of T cell therapies for the treatment of solid hypoxic tumors.

The relevance for the society has different perspectives (wider impacts): an indirect impact on health as a result of advancing the understanding of the biology of new targets, an economic impact resulting from patent applications, technology transfer and potential spin-out creation; and finally promoting the biotechnology/pharma industry at the regional level as a result of ongoing collaborations, employment and technology transfer activities.
The majority of work is progressing as expected, with only some activities being affected/delayed by the lockdown periods during 2020 (mostly activities associated with in vivo methodologies).

1. Development of a novel small molecule inhibitor to modulate the hypoxic response in T cells.

With the main objective of developing a first in class inhibitor of Factor Inhibiting HIF (FIH), we have generated several tools to study the biology of the target and we have performed several screenings leading to 3 series of chemical compounds that are hits. These hits are entering into a hit to lead campaign characterised by an iterative process consisting of medicinal chemistry, structural biology, and biology. The initial screening was virtual (performed by Domainex Ltd.) followed by a microscale thermopheresis selection of the binders. Then, a library of analogues was designed, purchased, and screened with the aim of broadening the chemical diversity. These hits are now entering a hit to lead campaign. We have also performed structural biology activities on FIH, confirming the previously described 3D structure and this will greatly support future medicinal chemistry activities. Regarding the biology of FIH, we have used CRISPR to delete the target on several tumor cell lines resulting in reduced proliferation and growth of lung tumors in vitro and in vivo. We have characterised the immune infiltrate of FIH deficient tumors demonstrating an increased immune infiltrate. We expect to publish this work in 2022 and recently (late 2021) an ERC PoC grant has been submitted to support future drug discovery and technology transfer activities.

2. Therapeutic target discovery in T cells, focused on hypoxia-driven epigenetic modifications.

We have performed RNAseq and proteomic approaches on different cell populations with the aim of identifying new therapeutic targets in the tumor microenvironment. This approach has resulted on the identification of several molecules with therapeutic potential, such as Syndecan-3 (Prieto-Fernández et al), several epigenetic enzymes, and components of the proteasome. In order to validate the real utility of these targets, we have developed tools based on T cell exhaustion and rescue of the cytotoxicity under hypoxia. Following this line of research, we have established international collaborations and we are planning to submit at least 2 additional research articles before the end of the project.

3. Development of T cell therapies for the treatment of solid hypoxic tumors.

The development of cell therapies to treat solid tumors is strongly emerging as a priority in the scientific community. We are working on methods of exploiting hypoxia, a common feature of solid tumors, in order to develop more effective cell therapies. One line of work is focused on fine tuning the expansion methods of CAR-T cells ex vivo with the aim of increasing the persistence of CAR-T cells once infused into the patient. This new methodology has been submitted for protection in the form of a patent application (2021) and a manuscript is being prepared. Other project is focused on developing CAR-T cells that bind to hypoxia-induced targets. A new monoclonal antibody has been generated and a second patent application has been drafted, we expect to file this application on the coming weeks.
The main differentiation factor of this project is to leverage hypoxia in solid tumors in order to develop new therapies. The state of the art in cancer therapy research is rapidly moving into advanced therapies, and cell therapy is a central theme in this approach. We are now in a privileged situation to capitalise on the ongoing work on CAR-T cells, especially in the context of technology transfer and high profile collaborations and publications. We are working on the pillars of a new cell therapy spin-off from the Host Institution.

The Covid situation has been a shocker at the start of the project, but we have been able to adapt to the new situation without major deviations or delays by:
- Increasing our capability on bioinformatics and performing decentralised work including subcontracting parts of the drug discovery campaign as planned.
- Contributing to several SARS-CoV-2 research projects leading to new lines of research and funding for our laboratory.

Our expectation before the end of the project includes: at least 3 total patent applications covering new therapies and technology transfer in the form of a new company or licensing, reinforcing our interactions/collaborations with pharma industry, continue training of early career researchers with at least 6 PhD projects completed, publication of results (10 articles as corresponding authors in the period), and contribute to dissemination by classic and alternative approaches.
Asis Palazon, Principal Investigator, CIC bioGUNE, Basque Country