Cross-disease integration of single-cell RNA sequencing data from lung myeloid cells reveals TAM signature in in vitro model

Abstract

Advancements in single-cell RNA sequencing (scRNA-seq) have revealed the phenotypic and functional diversity of tumor-associated macrophages (TAMs), identifying specific populations that directly impact the antitumor response. However, despite the recognition of TAMs as promising therapeutic targets for cancer treatment, research is hindered by the lack of validated human preclinical models. Here, we applied scRNA-seq to a 3D human cell-based model comprising tumor cell line-derived spheroids, cancer-associated fibroblasts and primary monocytes, a setup widely used in immuno-oncology research. Integration of our in vitro data with publicly available patient-derived datasets showed that the macrophages in this model share phenotypic characteristics with the pro-angiogenic and pro-fibrotic SPP1⁺ TAM population recently found across multiple cancer types and inflammatory lung diseases. This population was linked to aspects of disease progression and associated with poor prognosis in several tumor indications, highlighting the need for relevant models enabling its study as an immunotherapy target. Our research validates the use of a 3D human cell-based culture as a more in vivo-relevant model and enables the preclinical testing of novel macrophage-targeting drugs in a human disease-relevant setup.

Keywords: 3D human cell-based model; Single-cell RNA sequencing; tumor-associated macrophages.

Figure 1.

Integration of in vitro- and patient-derived datasets.

Figure 2.

Integration of human scRNA-seq datasets identifies cross-disease macrophage subsets and finds that 3D cocultured macrophages share phenotypic characteristics with profibrotic TAM population found in vivo.

Figure 3.

3D cocultured macrophages comprise two subsets with similarities to TAMs, actively cycling macrophages and macrophages enriched in cholesterol and lipid metabolic pathways.

Figure 4.

3D macrophage population shares phenotypic characteristics with angiogenesis- and fibrosis-associated macrophages recently described across tumor indications and pulmonary fibrosis-related diseases.