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Transcriptomic Profiling of Paired Primary Tumors and CNS Metastases in Breast Cancer Reveals Immune Modulation
Ana Julia Aguiar de Freitas1, Muriele Bertagna Varuzza1, Stéphanie Calfa1
1Molecular Oncology Research Center, Teaching and Research Institute, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil.
International Journal of Molecular Sciences
|July 29, 2025
Summary
Molecular differences between primary breast tumors and brain metastases reveal immune suppression. Key genes like CXCL9 and CD79A may serve as biomarkers for improved outcomes in metastatic breast cancer.
Area of Science:
- Oncology
- Molecular Biology
- Immunology
Background:
- Breast cancer frequently metastasizes to the central nervous system (CNS), leading to poor prognosis.
- Molecular distinctions between primary tumors and CNS metastases are not well understood.
- Identifying these differences is crucial for developing targeted therapies.
Purpose of the Study:
- To compare transcriptomic profiles of primary breast tumors and matched CNS metastases.
- To identify immune-related biomarkers associated with CNS metastatic progression and patient survival.
- To understand the role of immune modulation in breast cancer brain colonization.
Main Methods:
- Analysis of 11 paired formalin-fixed paraffin-embedded (FFPE) samples from primary tumors and CNS metastases.
- Transcriptomic profiling using the NanoString nCounter platform and PanCancer IO 360 Gene Expression Panel.
- Differential gene expression analysis, survival analysis using TCGA and GEO datasets.
Main Results:
- Forty-five genes were significantly differentially expressed between primary tumors and CNS metastases.
- Immune genes CXCL9, IL7R, CD79A, and CTSW were consistently downregulated in CNS metastases.
- High CXCL9 and CD79A expression correlated with better overall survival (OS) and recurrence-free survival (RFS), while high IL7R and CTSW correlated with worse outcomes.
Conclusions:
- Immune suppression is a key feature of breast cancer CNS metastases.
- Transcriptional signatures highlight distinct molecular landscapes between primary and metastatic sites.
- Identified genes offer potential as prognostic biomarkers and therapeutic targets for CNS metastatic breast cancer.
