This study evaluated the suitability of FFPE tissue for scRNAseq by comparing matched FFPE and fresh-frozen breast cancer samples from invasive ductal and invasive lobular carcinomas. Both approaches produced high-quality sequencing data, similar cellular heterogeneity, and concordant molecular profiles, with no cell populations detected exclusively by either method. The scRNAseq findings were consistent with IHC, FISH, and immune cell quantification results. Importantly, the study identified and validated a previously underrecognized subpopulation of neoplastic multiciliated cells (FOXJ1, ROPN1L), and analysis of 214 ER-positive tumors showed FOXJ1 expression in approximately one third of cases, suggesting that multiciliated differentiation is relatively frequent in breast cancer. These findings support the use of FFPE tissue for scRNAseq analyses and highlight a novel neoplastic cell subtype in breast cancer.

González-Martínez, S., Palacios, J., Carretero-Barrio, I., Lanza, V. F., García-Cosío Piqueras, M., Caniego-Casas, T., Hardisson, D., Esteban-Rodríguez, I., Cortés, J., & Pérez-Mies, B. (2025). Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer. Cells, 14(3), 197.