Nucleolar proteomics identifies S100A16 as a key nucleolar protein driving breast cancer metastasis

• Published in: Cell death & disease Vol. 16; no. 1; pp. 638 - 10
• Main Authors: Metge, Brandon J., Elbahoty, Mohamed H., Elhamamsy, Amr R., Popple, Anne E., Papineni, Bhavya, Samant, Rajeev S., Shevde, Lalita A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.08.2025; Springer Nature B.V; Nature Publishing Group
• Subjects: 13/1; 13/106; 13/21; 13/89; 14/63; 38/109; 38/77; 631/67/1347; 631/67/322; 631/80/642; 64/60; Animal models; Antibodies; Biochemistry; Biomedical and Life Sciences; Biosynthesis; Breast cancer; Cell Biology; Cell Culture; Cells; Cellular stress response; Chromatin; Datasets; DNA-directed RNA polymerase; Genes; Immunology; Immunoprecipitation; Life Sciences; Mass spectroscopy; Metastases; Metastasis; Nucleoli; Proteins; Proteomes; Proteomics; Ribonucleic acid; Ribosomal DNA; RNA; RNA polymerase; rRNA; Software; Solid tumors; Statistical analysis; Tumor cell lines; Tumor cells; Tumors
• ISSN: 2041-4889; 2041-4889
• DOI: 10.1038/s41419-025-07963-9

Metastasis is the leading cause of poor clinical outcomes in solid tumors; yet despite recent advances many of the driving factors of metastasis remain poorly understood. Tumor cells that successfully metastasize are subject to numerous stress points from intrinsic and extrinsic factors that the cell must overcome to survive and colonize a secondary site. The nucleolus, the site of ribosome biogenesis, serves as a central hub for sensing and responding to cellular stress and plays a crucial role in this process; furthermore, emerging evidence highlights the potential role of ribosome biogenesis in driving metastasis. To further elucidate the interplay between nucleolar function and metastasis, we performed a comprehensive analysis of nucleolar proteomes from primary and metastatic breast cancer cell lines and identified proteins differentially enriched in the nucleoli of metastatic cells, of which 48 showed statistically significant enrichment. Among these, S100A16 was the most significantly enriched nucleolar protein. Notably, chromatin immunoprecipitation mass spectrometry (ChIP-MS) revealed that S100A16 was associated at rDNA loci with RPA194, the catalytic subunit of RNA Polymerase I, indicating a role in rRNA biosynthesis. Functionally, loss of S100A16 disrupted RNA Polymerase I activation and subsequent rRNA synthesis, reversed epithelial-to-mesenchymal transition, inhibited invasion, and reduced metastatic incidence in animal models of breast cancer. Clinically, elevated S100A16 expression correlated with enrichment of ribosome biogenesis pathways and reduced relapse-free survival in metastatic breast cancer patients. In summary, we identified a critical role for S100A16 as a molecular modulator in the nucleolus that impinges upon breast cancer metastasis.