Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing

Milan Radovich*, Susan E. Clare, Rutuja Atale, Ivanesa Pardo, Bradley A. Hancock, Jeffrey P. Solzak, Nawal Kassem, Theresa Mathieson, Anna Maria V Storniolo, Connie Rufenbarger, Heather A. Lillemoe, Rachel J. Blosser, Mi Ran Choi, Candice A. Sauder, Diane Doxey, Jill E. Henry, Eric E. Hilligoss, Onur Sakarya, Fiona C. Hyland, Matthew HickenbothamJin Zhu, Jarret Glasscock, Sunil Badve, Mircea Ivan, Yunlong Liu, George W. Sledge, Bryan P. Schneider

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)57-68
Number of pages12
JournalBreast Cancer Research and Treatment
Volume143
Issue number1
DOIs
StatePublished - Jan 2014

Funding

Acknowledgments We would like to thank Mark Mooney, James Elliott, Darryl Leon, and Ryan Richt for discussions of next-generation sequencing and analysis. We also like to thank Benjamin Haibe-Kains for assistance with PAM50 analysis and to thank Carla Bullitt, Stuart Tugendreich, Gordon Janaway, and Bryant Macy for assistance with Ingenuity Pathway Analysis. We also like to thank the IUSCC Tissue Procurement and Distribution Core for providing tissues for IHC and qPCR validations. Finally, we would like to thank and acknowledge the TCGA for the sample procurement, production of the TNBC RNA-seq data, and the clinical annotation of TCGA samples used in this publication. This work was supported by the Susan G. Komen for the Cure® (S.E.C., G.W.S., A.V.S., S.B., B.P.S.), Breast Cancer Research Foundation (S.E.C., A.V.S.) and the Catherine Peachey Fund (M.R., S.E.C., G.W.S., A.V.S., C.R., B.P.S.).. M.R. was supported by pre-doctoral fellowships from the National Institutes of Health, NRSA 1T32CA111198 Cancer Biology Training Program and 5TL1RR025759 Indiana Clinical and Translational Sciences Institute Career Development Award.

Keywords

  • Adjacent normal
  • Ductal epithelium
  • Normal breast
  • RNA-seq
  • TCGA
  • Triple-negative breast cancer

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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