Developing novel single-cell technologies to model and perturb intra-tumor interactions and signaling – an innovation program for the next generation of immunotherapies

Project Information

TROJAN-Cell

Grant agreement ID: 101055341

DOI

10.3030/101055341

EC signature date 27 June 2022

Start date 1 October 2022

End date 30 September 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

WEIZMANN INSTITUTE OF SCIENCE
Israel

Periodic Reporting for period 1 - TROJAN-Cell (Developing novel single-cell technologies to model and perturb intra-tumor interactions and signaling – an innovation program for the next generation of immunotherapies)

Reporting period: 2022-10-01 to 2025-03-31

Summary of the context and overall objectives of the project

Single-cell genomic technologies have transformed many fields of research. We here seek to do just that in synthetic-immunology and immunotherapy. At present, our understanding of the complex crosstalk within the
tumor microenvironment (TME) is still limited, as is our ability to effectively engineer the immune system to attack tumor cells in spite of the robust immune-suppression signaling in most solid tumors. In line, current immunotherapies are effective only in a small subset of tumor types and patients, emphasizing the dire need to better understand immune-suppressive mechanisms within the TME and develop new immunotherapy
strategies.
What if we could develop technologies that reprogram the immune system to suit our therapeutic needs? In TROJAN-Cell, we are doing so by first uncovering fundamental principles of the immune-tumor niche using
advanced single-cell multiomics tools and modelling approaches. This will then serve to develop TROJAN- Cell—a novel synthetic immunology technology for engineering circuits capable of sensing inhibitory-
immune signals and generating a proportional self-regulated immune-activation response—thus using the tumor’s own pro-cancer signaling to eradicate it. We dissect the principles of the inhibitory crosstalk and signaling in the TME of diverse human tumors using diverse single-cell technologies and AI. We use this data to screen and develop models that recapitulate the human TME, which serve to define the function of checkpoints and immune circuits of interest which can reprogram the immune compartment. Using these toolsets we develop TROJAN-Cell, a novel toolset for transforming tumor inhibitory signals into potent, highly specific anti-tumor immunity.Our research will greatly expand our understanding of the immune-inhibitory crosstalk in the TME and give rise to novel immune engineering approaches and molecules, which may serve as the next generation of cancer immunotherapies.

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

During the first period of the proposal, we have made significant progress in measuring system-level molecular measurements of the immune-tumor crosstalk in the TME, which serves as a platform for the development of data-driven synthetic regulatory circuits and agents that reprogram the entire tumor-immune compartment and stimulate anti-tumor immunity in currently unresponsive tumors. First, we characterized the molecular and regulatory pathways of intra-tumoral immune cells and the cellular interactions of immune, stromal and tumor cells by developing novel single cell technologies (Zman-seq, PIC-seq, ATAC-seq and INs-seq) and applying them to human tumors samples (melanoma, NSCLC and breast cancer) and uncover the tissue-specific signaling networks and regulatory circuits between immune and non-immune cells in the TME. Second, we established reliable, reproducible mouse cancer models that reflect the heterogeneity of immune populations in these three major human tumor types, reflecting ICB responsive (melanoma), partially responsive (lung) and weakly responsive (breast) cancers. Third, we have used these data from the human samples and mouse model systems to identify candidate pathways, regulatory elements and genes that are exclusively activated by immune cells in the various TMEs and use this data to develop a novel TROJAN-Cell cell-therapy-based technology to radically modify the response of these models to ICB by engineering programable inter-cellular communication in the TME, using directed evolution of synthetic gene circuits coupled to powerful immune effector molecules. We have currently already gained significant progress in all objectives of the proposal and have successfully generated prototype TROJAN-Cell constructs which demonstrate very effective in vitro and in vivo activities. These are currently further developed and optimized.

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 development of the Zman-seq technology (Kirschenbaum et al., Cell 2024) which include development of a novel single cell technology which can measure single cell molecular data combined with time is beyond the state of the art, it is the first technology which has made it possible to track molecular data at single cell resolution in vivo and would not be possible without the ERC support. In addition, this unique data has enabled the development of a first of its kind next generation immunotherapy modality called Bispecific DC-T Cell Engager (BiCE)
which reprograms the tumor microenvironment by generating synthetic synapses between tumor specific T cells and conventional type 1 dendritic cells in the tumor environment. This is a molecule has never been generated before has significant advantages over any of current state of the art cancer immunotherapies as we have shown in our publication (Shapir et al Cell., 2024) in both in vitro and in vivo pre-clinical models and carries huge potential for development of more effective and less toxic immunotherapy which can make a huge impact on the society- this huge scientific and potentially clinical achievement would not be possible without the ERC support