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Updated: Jan 19, 2026

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Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations

Qian Zhu1, Xavier Tekpli2,3, Olga G Troyanskaya4,5,6

  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

Bioinformatics (Oxford, England)
|September 19, 2019
PubMed
Abstract

Insights

Breast cancer subtypes are driven by specific transcription factors (TFs) and their associated genetic/epigenetic changes. Understanding these lineage-specific TFs is key to deciphering breast cancer transcriptional profiles.

Area of Science:

  • Oncology
  • Genomics
  • Epigenetics

Background:

  • Breast cancer comprises diverse subtypes with distinct transcriptional profiles.
  • Transcriptional deregulation mechanisms underlying these subtypes are not fully understood.
  • Previous research on transcription factor networks has limitations.

Purpose of the Study:

  • To identify extended molecular signatures of distinct breast cancer subtypes.
  • To elucidate the role of transcription factors in driving subtype-specific transcriptional profiles.
  • To investigate the genetic and epigenetic alterations associated with these transcription factors.

Main Methods:

  • Computational analysis of thousands of gene expression datasets.
  • Utilized ENCODE ChIP-seq data and motif analysis.
  • Examined copy number and DNA methylation patterns of transcription factors and their targets.

Main Results:

  • Defined distinct molecular signatures for breast cancer subtypes.
  • Identified lineage-specific transcription factor repertoires determining these subtypes.
  • Observed specific patterns of genetic and epigenetic alterations at transcription factor loci.

Conclusions:

  • Distinct transcriptional profiles in breast cancer subtypes are linked to alterations in lineage-specific transcriptional regulators.
  • Genetic and epigenetic changes at transcription factors and their targets play a crucial role in breast cancer subtyping.
  • The findings provide insights into the molecular mechanisms driving breast cancer heterogeneity.

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