Breast Cancer Research and Treatment

, Volume 135, Issue 1, pp 153–165 | Cite as

Gene expression profiling of tumour epithelial and stromal compartments during breast cancer progression

  • Ana Cristina Vargas
  • Amy E. McCart Reed
  • Nic Waddell
  • Annette Lane
  • Lynne E. Reid
  • Chanel E. Smart
  • Sibylle Cocciardi
  • Leonard da Silva
  • Sarah Song
  • Georgia Chenevix-Trench
  • Peter T. Simpson
  • Sunil R. LakhaniEmail author
Preclinical Study


The progression of ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) marks a critical step in the evolution of breast cancer. There is some evidence to suggest that dynamic interactions between the neoplastic cells and the tumour microenvironment play an important role. Using the whole-genome cDNA-mediated annealing, selection, extension and ligation assay (WG-DASL, Illumina), we performed gene expression profiling on 87 formalin-fixed paraffin-embedded (FFPE) samples from 17 patients consisting of matched IDC, DCIS and three types of stroma: IDC-S (<3 mm from IDC), DCIS-S (<3 mm from DCIS) and breast cancer associated-normal stroma (BC-NS; >10 mm from IDC or DCIS). Differential gene expression analysis was validated by quantitative real time-PCR, immunohistochemistry and immunofluorescence. The expression of several genes was down-regulated in stroma from cancer patients relative to normal stroma from reduction mammoplasties. In contrast, neoplastic epithelium underwent more gene expression changes during progression, including down regulation of SFRP1. In particular, we observed that molecules related to extracellular matrix (ECM) remodelling (e.g. COL11A1, COL5A2 and MMP13) were differentially expressed between DCIS and IDC. COL11A1 was overexpressed in IDC relative to DCIS and was expressed by both the epithelial and stromal compartments but was enriched in invading neoplastic epithelial cells. The contributions of both the epithelial and stromal compartments to the clinically important scenario of progression from DCIS to IDC. Gene expression profiles, we identified differential expression of genes related to ECM remodelling, and specifically the elevated expression of genes such as COL11A1, COL5A2 and MMP13 in epithelial cells of IDC. We propose that these expression changes could be involved in facilitating the transition from in situ disease to invasive cancer and may thus mark a critical point in disease development.


Invasive ductal carcinoma Ductal carcinoma in situ Tumour stroma Formalin fixed paraffin embedded tissue Tumour progression Whole-genome DASL 



Breast cancer normal stroma


Ductal carcinoma in situ




Extracellular matrix


Fresh frozen


Formalin fixed paraffin embedded


Invasive ductal carcinoma








Invasive lobular carcinoma


Laser capture microdissection


Normal epithelium


Quantitative real time-PCR


Reduction mammoplasty


Reduction mammoplasty normal stroma


Whole-genome cDNA-mediated annealing, selection, extension and ligation assay



We thank all the patients and their families for the donation of samples for research. We thank Rebecca Johnston and Julie Johnson for excellent technical assistance. Ana Cristina Vargas was supported by a clinical fellowship from the Ludwig Institute for Cancer Research (LICR); Peter T Simpson is the recipient of a Fellowship from the National Breast Cancer Foundation, Australia. Georgia Chenevix-Trench is a Senior Principal Research Fellow of the National Health and Medical Research Council (NHMRC) of Australia. This work was funded in part by grants from the LICR, the NHMRC, the Australian Medical Association Queensland and the Queensland Health Pathology Service—Study, Education and Research Trust Fund.

Conflict of interest

PTS received funding from Illumina to present at a conference about the WG-DASL assay. The remaining authors declare that they have no conflict of interest.

Supplementary material

10549_2012_2123_MOESM1_ESM.doc (1.8 mb)
Supplementary material 1 (DOC 1826 kb)


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Copyright information

© Springer Science+Business Media, LLC. 2012

Authors and Affiliations

  • Ana Cristina Vargas
    • 1
  • Amy E. McCart Reed
    • 1
  • Nic Waddell
    • 2
  • Annette Lane
    • 1
  • Lynne E. Reid
    • 1
  • Chanel E. Smart
    • 1
  • Sibylle Cocciardi
    • 3
  • Leonard da Silva
    • 1
    • 6
  • Sarah Song
    • 1
    • 2
  • Georgia Chenevix-Trench
    • 3
  • Peter T. Simpson
    • 1
  • Sunil R. Lakhani
    • 1
    • 4
    • 5
    Email author
  1. 1.UQ Centre for Clinical ResearchThe University of QueenslandHerston, BrisbaneAustralia
  2. 2.Queensland Centre for Medical Genomics, Institute for Molecular BioscienceThe University of QueenslandSt Lucia, BrisbaneAustralia
  3. 3.Queensland Institute for Medical ResearchHerston, BrisbaneAustralia
  4. 4.School of MedicineThe University of QueenslandHerstonAustralia
  5. 5.Pathology Queensland, The Royal Brisbane and Women’s HospitalHerstonAustralia
  6. 6.São PauloBrazil

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