Single-cell profiling of bone metastasis ecosystems reveals pivotal role of INSR+AEC in clear cell renal cell carcinoma

Abstract

Background

Bone metastasis is a common and lethal complication of advanced clear cell renal cell carcinoma (ccRCC), yet the cellular and spatial architecture of the human bone metastatic niche remains incompletely defined, limiting identification of actionable targets.

Methods

We integrated matched single cell RNA sequencing with spatial transcriptomics and large scale bulk cohorts. Integrating multi computational pipelines to derive and validate an INSR⁺ artery endothelial relevant prognostic signature (IAERS). Functional consequences of COL4A1 were assessed with in vitro experiments.

Results

Single cell and spatial analyses uncovered pronounced malignant cell heterogeneity and a metastatic malignant programme enriched for extracellular matrix and adhesion pathways. Endothelial cells displayed the strongest inferred crosstalk with metastatic tumour cells; an INSR⁺ AEC subset was selectively enriched in bone metastases and spatially colocalized with metastatic foci. Ligand-receptor modelling identified a dominant COL4A1-SDC4 signalling axis linking INSR⁺ AEC to metastatic tumo ur cells, and GeneSwitches nominated TCF4 as a transcriptional switch sustaining the INSR⁺ AEC programme. COL4A1 knockdown impaired ccRCC proliferation, migration and invasion in vitro. A novel IAERS signature derived from INSR⁺ AEC programmes robustly stratified patient survival and metastatic status across independent cohorts.

Conclusions

These multi‑modal data define a prometastatic vascular niche in ccRCC centred on TCF4 associated INSR⁺ AEC and a COL4A1-SDC4 axis, providing candidate biomarkers and therapeutic avenues that target endothelial matrix interactions in bone metastatic disease.