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González-Martínez S, Palacios J, Carretero-Barrio I, Lanza VF, García-Cosío Piqueras M, Caniego-Casas T, Hardisson D, Esteban-Rodríguez I, Cortés J, Pérez-Mies B. Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer. Cells 2025; 14:197. [PMID: 39936988 PMCID: PMC11816443 DOI: 10.3390/cells14030197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 01/18/2025] [Accepted: 01/26/2025] [Indexed: 02/13/2025] Open
Abstract
The purpose of this study was to evaluate the suitability of formalin-fixed and paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA sequencing (scRNAseq). To this end, we compared single-cell profiles from FFPE and matched FF tissue samples of one invasive carcinoma of no special type carcinoma (invasive ductal carcinoma-IDC) and one invasive lobular carcinoma (ILC) to assess consistency in cell type distribution and molecular profiles. The results were validated using immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and electron microscopy. Additionally, immune cell proportions identified by IHC were quantified using QuPath and compared to the scRNAseq results. FFPE- and FF-derived libraries demonstrated high-quality sequencing metrics, and cellular heterogeneity was similar. No exclusive cell populations were identified by either approach. The four samples analysis identified six types of epithelial cells, as well as tumoral microenvironment populations. The scRNAseq results from epithelial neoplastic cells were concordant with common IHC markers. The proportion of immune cells identified by IHC in FFPE sections were similar to those obtained by scRNAseq. We identified and validated a previously poorly recognized subpopulation of neoplastic multi-ciliated cells (MCCs) (FOXJ1, ROPN1L). Analysis of FOXJ1 in 214 ER-positive invasive carcinomas demonstrated protein expression in one third of tumors, suggesting frequent focal MCC differentiation. Our results support the suitability of scRNAseq analysis using FFPE tissue, and identified a subpopulation of neoplastic MCC in breast cancer.
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Affiliation(s)
- Silvia González-Martínez
- “Contigo Contra el Cáncer de la Mujer” Foundation, 28010 Madrid, Spain; (S.G.-M.); (J.C.)
- Molecular Pathology of Cancer Group, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain; (I.C.-B.); (M.G.-C.P.); (T.C.-C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
| | - José Palacios
- Molecular Pathology of Cancer Group, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain; (I.C.-B.); (M.G.-C.P.); (T.C.-C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
- Department of Pathology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
- Faculty of Medicine, University of Alcalá, 28801 Madrid, Spain
| | - Irene Carretero-Barrio
- Molecular Pathology of Cancer Group, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain; (I.C.-B.); (M.G.-C.P.); (T.C.-C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
- Department of Pathology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Val F. Lanza
- Centre for Biomedical Research in Infectious Diseases Networks (CIBERINFEC), Carlos III Health Institute, 28029 Madrid, Spain;
- UCA-GTB Unit, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - Mónica García-Cosío Piqueras
- Molecular Pathology of Cancer Group, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain; (I.C.-B.); (M.G.-C.P.); (T.C.-C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
- Department of Pathology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Tamara Caniego-Casas
- Molecular Pathology of Cancer Group, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain; (I.C.-B.); (M.G.-C.P.); (T.C.-C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
| | - David Hardisson
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
- Department of Pathology, Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain;
- Faculty of Medicine, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Isabel Esteban-Rodríguez
- Department of Pathology, Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain;
- Faculty of Medicine, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Javier Cortés
- “Contigo Contra el Cáncer de la Mujer” Foundation, 28010 Madrid, Spain; (S.G.-M.); (J.C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron-Salud Group, 08017 Barcelona, Spain
- Medica Scientia Innovation Research, 08007 Barcelona, Spain
- Medica Scientia Innovation Research, Ridgewood, NJ 07450, USA
- Department of Medicine, Faculty of Biomedical and Health Sciences, European University of Madrid, 28670 Madrid, Spain
- IOB Institute of Oncology Madrid, Hospital Beata María Ana de Jesús, 28007 Madrid, Spain
| | - Belén Pérez-Mies
- Molecular Pathology of Cancer Group, Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain; (I.C.-B.); (M.G.-C.P.); (T.C.-C.)
- Centre for Biomedical Research in Cancer Networks (CIBERONC), Carlos III Health Institute, 28029 Madrid, Spain;
- Department of Pathology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
- Faculty of Medicine, University of Alcalá, 28801 Madrid, Spain
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Wu Q, Tao X, Luo Y, Zheng S, Lin N, Xie X. A novel super-enhancer-related gene signature predicts prognosis and immune microenvironment for breast cancer. BMC Cancer 2023; 23:776. [PMID: 37596527 PMCID: PMC10439574 DOI: 10.1186/s12885-023-11241-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND This study targeted at developing a robust, prognostic signature based on super-enhancer-related genes (SERGs) to reveal survival prognosis and immune microenvironment of breast cancer. METHODS RNA-sequencing data of breast cancer were retrieved from The Cancer Genome Atlas (TCGA), 1069 patients of which were randomly assigned into training or testing set in 1:1 ratio. SERGs were downloaded from Super-Enhancer Database (SEdb). After which, a SERGs signature was established based on the training set, with its prognostic value further validated in the testing set. Subsequently, we identified the potential function enrichment and tumor immune infiltration of the model. Moreover, in vitro experiments were completed to further explore the biological functions of ZIC2 gene (one of the risk genes in the prognostic model) in breast cancer. RESULTS A risk score system of prognostic value was constructed with 6 SERGs (ZIC2, NFE2, FOXJ1, KLF15, POU3F2 and SPIB) to find patients in high-risk group with significantly worse prognosis in both training and testing sets. In addition, a multivariate regression was established via integrating the 6 genes with age and N stage, indicating well performance by calibration, time-dependent receiver operating characteristic (ROC) analysis and decision curve analysis (DCA). Further analysis demonstrated that tumor-associated pathological processes and pathways were significantly enriched in the high-risk group. In general, the novel SERGs signature could be applied to screen breast cancer with immunosuppressive microenvironment for the risk score was negatively correlated with ESTIMATE score, tumor-infiltration lymphocytes (such as CD4 + and CD8 + T cell), immune checkpoints and chemotactic factors. Furthermore, down-regulation of ZIC2 gene expression inhibited the cell viability, cellular migration and cell cycle of breast cancer cells. CONCLUSIONS The novel SERGs signature could predict the prognosis of breast cancer; and SERGs might serve as potential therapeutic targets for breast cancer.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xuan Tao
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yang Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China
| | - Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, Fujian, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
- Department of Gastrointestinal Surgery, The 900th Hospital of Joint Logistics Support Forces of Chinese PLA, Fuzhou, Fujian, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, China.
- Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
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