Unravelling the cell-cell circuits underlying the functional reprogramming of KCs and TAMs during liver metastasis

Project Information

MetaMacNiche

Grant agreement ID: 101109361

DOI

10.3030/101109361

Project closed

EC signature date 3 March 2023

Start date 1 November 2023

End date 31 October 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 175 920,00

Coordinated by

VIB VZW
Belgium

Periodic Reporting for period 1 - MetaMacNiche (Unravelling the cell-cell circuits underlying the functional reprogramming of KCs and TAMs during liver metastasis)

Reporting period: 2023-11-01 to 2025-10-31

Summary of the context and overall objectives of the project

The liver is a highly vascularized organ due to its major role in filtering blood. Because of this, the liver is also one of the main site of metastatic dissemination for several cancers. The most common one is colorectal cancer, with up to 50% of patients developing liver metastases. The primary treatment for liver metastasis is surgery but, if metastases are too spread, surgery is not an option anymore. The 21st century has marked a boomed in immunotherapy, especially in cancer. However, previous research have highlighted that metastatic dissemination to the liver impairs systemic immune responses, making patients less responsive to immunotherapy.

Macrophages are the most abundant immune population in many cancers. Kupffer cells are the resident macrophages of the liver are the first cells to interact with metastatic cells due to their location in the liver sinusoids. Additionally, monocyte-derived macrophages are also rapidly recruited as metastatic cells are spreading to the liver, and will constitute the tumor-associated macrophages (TAMs). The distinct role of Kupffer cells and TAMs in metastatic spreading and anti-cancer immune response have been studied in the past but showed conflicting results. Macrophages in cancer do not form a homogenous cell populations and can be wired to perform various functions, either promoting or inhibiting anti-cancer immunity. Our group, and other have shown that macrophage function is dictated not only by intrinsic factor, but also by signals delivered by their surrounding cells (ie fibroblasts, endothelial cells, cancer cells…), defining the macrophage niche. Using unique tracking tools developed in our lab, as well as cutting-edge omics and spatial technologies, this project aims at deciphering the cross-talk between macrophages and their niche, the consequences on macrophage polarization and immunotherapy response, as well as identifying novel therapeutic targets that can modulate tumor macrophage activation.

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

This project first sought to characterize the cellular composition of each macrophage niche of the metastatic liver. Single-cell RNA-sequencing and VisiumHD technologies were used to obtain a whole transcriptomic map of liver metastases. Combined with transgenic mouse reporters, and high-throughput microscopy, several subsets of macrophages, either deriving from resident Kupffer cells or monocytes, exhibited different localization associated with distinct metastatic patterns (See picture). Those macrophage subsets resided in unique niches as rewired endothelial cells, and new subsets of cancer-associated fibroblast were arising, as new metastases were expanding. Interestingly, the accumulation of T cells in these niches was heterogeneous (see picture), suggesting different contribution to the overall anti-cancer immune response.
To get deeper insights regarding the contribution of the different macrophage subset to metastatic growth and the local immune response, depletion models were used to target specifically Kupffer cells or TAMs. Although no major effect was observed on tumor growth, different tumor organization were observed, underlying the facts that macrophages are a key player of the tumor micro-environment but their functional reprogramming rather than their deletion would efficiently improve tumor clearance. As a first step towards this direction, a novel in vivo CRISPR pipeline was used to knock-down specific receptors on Kupffer cells and TAMs.
Additionally, the effect of in vivo anti-PD1 treatment on the macrophage populations was also evaluated. Although there was no strong effect on tumor growth, as expected from the literature, the co-localization between macrophages and T cells appear to be changed.

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)

This project highlighted the complexity of the local cell-cell crosstalk between macrophages and their surrounding cells in liver metastases. Not only an important spatial diversity of macrophage subset was revealed but we also identified new cancer-associated fibroblast subsets which together could be major drivers of T cell recruitment and activation. This is crucial as it highlights the importance of focusing on the targeting of specific macrophage population to enhance their anti-tumor functions, while previous research sought to delete macrophage populations from the tumor microenvironment altogether.
The development of the in vivo CRISPR pipeline, and its optimization for cancer setting, already showed its feasibility and will prove valuable in the future to remove more receptors from the different macrophage populations and evaluate the impact on metastatic growth. Combining conventional immunotherapy, such as anti-PD1 blocking antibodies, with the in vivo CRISPR approach will allow us to remove the brakes hindering immunotherapy efficacy.
The extensive datasets generated thanks to this fellowship, including single-cell RNA sequencing, spatial transcriptomics and spatial proteomics are not only useful to this project but will also be useful to the host lab and the rest of the scientific community to address many more questions about the cells composing the metastatic niche.

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