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Updated: May 5, 2026
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and
Milan Radovich1, Susan E Clare, Rutuja Atale
1Division of General Surgery, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA, mradovic@iupui.edu.
Abstract:
Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. Komen for the Cure Tissue Bank, and 10 histologically normal tissues adjacent to tumor. Pathway analysis comparing TNBCs to optimized normal controls of microdissected normal epithelium versus classic controls composed of adjacent normal tissue revealed distinct molecular signatures. Differential gene expression of TNBC compared with normal comparators demonstrated important findings for TNBC-specific clinical trials testing targeted agents; lack of over-expression for negative studies and over-expression in studies with drug activity. Next, by comparing each individual TNBC to the set of microdissected normals, we demonstrate that TNBC heterogeneity is attributable to transcriptional chaos, is associated with non-silent DNA mutational load, and explains transcriptional heterogeneity in addition to known molecular subtypes. Finally, chaos analysis identified 146 core genes dysregulated in >90 % of TNBCs revealing an over-expressed central network. In conclusion, use of microdissected normal ductal epithelium from healthy volunteers enables an optimized approach for studying TNBC and uncovers biological heterogeneity mediated by transcriptional chaos.
Insights
Triple-negative breast cancers (TNBCs) exhibit significant heterogeneity. Using normal ductal epithelium, researchers identified transcriptional chaos as a key driver, revealing novel therapeutic targets for TNBC drug development.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Triple-negative breast cancers (TNBCs) lack standard therapeutic targets (ER, PR, HER-2), presenting a significant clinical challenge.
- TNBCs are highly heterogeneous, complicating treatment strategies and drug development.
- Novel comparators are needed to understand TNBC biology and identify new therapeutic avenues.
Purpose of the Study:
- To investigate TNBC heterogeneity using microdissected normal ductal epithelium as a novel comparator.
- To identify molecular signatures and potential therapeutic targets in TNBC.
- To explore the role of transcriptional chaos in TNBC development and heterogeneity.
Main Methods:
- RNA sequencing of 94 TNBCs, 20 microdissected normal breast tissues, and 10 adjacent normal tissues.
- Comparative transcriptome analysis between TNBCs and normal controls.
- Pathway analysis and differential gene expression analysis.
- Chaos analysis to identify core dysregulated genes in TNBC.
Main Results:
- Distinct molecular signatures were revealed when comparing TNBCs to microdissected normal epithelium versus adjacent normal tissue.
- Differential gene expression patterns in TNBCs correlated with findings in clinical trials of targeted agents.
- TNBC heterogeneity is significantly linked to transcriptional chaos and non-silent DNA mutational load.
- Chaos analysis identified 146 core genes dysregulated in over 90% of TNBCs, forming an over-expressed central network.
Conclusions:
- Microdissected normal ductal epithelium from healthy volunteers provides an optimized model for studying TNBC.
- Transcriptional chaos is a major contributor to TNBC biological heterogeneity.
- This approach uncovers potential therapeutic targets and informs the development of targeted agents for TNBC.
