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Turkish Journal of Biology

Abstract

Background/aim: Breast cancer (BC) is the most frequently diagnosed malignancy among women and exhibits substantial molecular heterogeneity. Luminal tumors represent the largest molecular subtype and are primarily driven by estrogen receptor alpha (Erα), ahormone-dependent transcription factor (TF) that regulates gene expression programs controlling proliferation, differentiation, and endocrine response. Herein, the study aimed to identify functionally relevant TFs regulated by ERα as part of a complex regulatory program in luminal BC.

Materials and methods: An integrative transcriptomic approach was applied to identify TFs regulated by ERα in luminal BC. Differential gene expression analysis was integrated with RNA-seq data obtained from estrogen receptor 1 (ESR1) gene knockdown conditions. Network and enrichment analyses were conducted to reveal ERα-centered transcriptional programs. Key TFs acting as potential Erα-regulated mediators were evaluated for subtype-specific expression in BC patient cohorts and for associations with patient survival. MCF7 and T47D cells underwent a time course of hormone deprivation, and the gene expression patterns of two TF candidates were assessed. Clustered regularly interspaced short palindromic repeats–associated protein 9 (CRISPR–Cas9)-mediated gene knockout experiments were performed to interrogate the functional roles of the ERα-regulated candidate TFs.

Results: The integrative transcriptomic analysis identified 95 ERα-associated candidate genes. Network and enrichment analyses highlighted ERα-centered regulatory pathways with nine genes encoding TFs. Among these TFs, Msh homeobox 2 (MSX2) displayed a subtype-associated expression pattern in BC patients and was associated with favorable survival outcomes. Hormone deprivation significantly altered the expression of MSX2 in BC cell lines, which pinpoints the functional regulation by ERα. Time-course evaluation of MSX2 under hormone-deprived conditions confirmed that MSX2 may be regulated by ERα. Furthermore, functional interrogation using CRISPR-Cas9-mediated gene disruption demonstrated that the loss of MSX2 significantly impaired the proliferative capacity and viability of luminal BC cells.

Conclusion: These functional assessments identified MSX2 as an underexplored ERα-associated TF and suggest that the ERα–MSX2 regulatory relationship may contribute to transcriptional programs associated with luminal BC identity and cellular fitness.

Author ORCID Identifier

GAMZE TURAN: 0000-0003-4563-2792

ELİF KANSIZ: 0000-0003-1683-7377

GÖZDE KORKMAZ: 0000-0002-3574-1015

HANDE ÖZKAN: 0009-0007-1611-2268

DOI

10.55730/1300-0152.2982

Keywords

Luminal breast cancer, transcription factor, ESR1, MSX2, CRISPR

First Page

389

Last Page

403

Publisher

The Scientific and Technological Research Council of Türkiye (TÜBİTAK)

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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