Assessing the Tumor Suppressive Impact and Regulatory Mechanisms of SPDEF Expression in Breast Cancer

TL;DR

Low SPDEF gene expression is linked to worse breast cancer survival, especially in aggressive Basal tumors and younger or Black patients, suggesting it could be a new biomarker for treatment.

Contribution

This study identifies SPDEF as a tumor suppressor in breast cancer and reveals its epigenetic regulation through DNA methylation.

Findings

Low SPDEF expression correlates with worse survival in breast cancer patients, particularly in Basal subtypes and younger or Black patients.

Promoter methylation and DNMT overexpression are linked to reduced SPDEF expression and poor prognosis.

SPDEF downregulation is associated with aggressive molecular features like EMT, DNA repair, and immune pathway changes.

Abstract

Breast cancer is a highly diverse disease, and some tumor types, such as the Basal subtype, are particularly aggressive and insusceptible to treatment modalities. Our study investigated the SAM Pointed Domain ETS Factor (SPDEF) gene, which has been proposed to be involved in breast cell growth and differentiation. Through analysis of tumor samples from over 1200 patients, we demonstrated that low SPDEF levels were linked with worse survival across breast cancers, with the most profound changes seen in Basal tumors, younger patients, and Black or African American patients. We then determined a significant role of epigenetic DNA modification in SPDEF regulation, implicating enhanced promoter methylation underlying gene silencing. Loss of SPDEF also coincided with changes in other important pathways, including DNA repair and immune regulation. These findings suggest that SPDEF and its epigenetic regulation could serve as important clinical biomarkers and offer novel avenues for targeted therapies in breast cancer.

Background/Objectives: Breast cancer is a heterogeneous disease, and the role of the transcription factor SPDEF remains controversial. We aimed to clarify the prognostic value of SPDEF, explore demographic and molecular correlates of its expression, and investigate potential regulatory mechanisms underlying its dysregulation. Methods: Genomic and clinical data for 1218 breast cancer tumors were obtained from The Cancer Genome Atlas (TCGA). SPDEF mRNA expression was compared across intrinsic subtypes, age, and race, and prognostic significance was evaluated by Kaplan–Meier analysis. Promoter methylation patterns and DNA methyltransferase (DNMT) expression were examined as potential regulatory drivers. Co-expression analysis was performed using gene panels representing luminal differentiation, basal identity, EMT, proliferation, DNA repair, and immune signaling. Results: Low SPDEF expression was significantly associated with worse overall, relapse-free, and metastasis-free survival across all breast cancers. Expression was lowest in Basal tumors, as well as among younger and Black or African American patients. Promoter methylation at six CpG islands correlated with both reduced SPDEF expression and inferior survival, and DNMT1, DNMT3A, and DNMT3B overexpression also aligned with poor prognosis and Basal enrichment. Co-expression analysis revealed that SPDEF downregulation coincided with loss of luminal markers and increased EMT, proliferation, DNA repair, and immune pathways. Conclusions: SPDEF functions as a tumor suppressor in breast cancer, with reduced expression linked to poor outcomes, aggressive molecular features, and epigenetic regulation. These findings highlight SPDEF and DNMT-driven methylation as potential prognostic biomarkers for enhanced risk stratification and targets for novel therapies, particularly in Basal breast cancers.

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