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

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Abstract

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.

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Abbreviations

BC-NS:

Breast cancer normal stroma

DCIS:

Ductal carcinoma in situ

DCIS-S:

DCIS-stroma

ECM:

Extracellular matrix

FF:

Fresh frozen

FFPE:

Formalin fixed paraffin embedded

IDC:

Invasive ductal carcinoma

IDC-S:

IDC-stroma

IF:

Immunofluorescence

IHC:

Immunohistochemistry

ILC:

Invasive lobular carcinoma

LCM:

Laser capture microdissection

NE:

Normal epithelium

qRT-PCR:

Quantitative real time-PCR

RM:

Reduction mammoplasty

RM-NS:

Reduction mammoplasty normal stroma

WG-DASL:

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

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Acknowledgments

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.

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Author notes

  1. Leonard da Silva

    Present address: , Avenida Divino Salvador, 876, São Paulo, Brazil

Authors and Affiliations

  1. UQ Centre for Clinical Research, The University of Queensland, Herston, Brisbane, QLD, Australia

    Ana Cristina Vargas, Amy E. McCart Reed, Annette Lane, Lynne E. Reid, Chanel E. Smart, Leonard da Silva, Sarah Song, Peter T. Simpson & Sunil R. Lakhani

  2. Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia

    Nic Waddell & Sarah Song

  3. Queensland Institute for Medical Research, Herston, Brisbane, QLD, Australia

    Sibylle Cocciardi & Georgia Chenevix-Trench

  4. School of Medicine, The University of Queensland, Herston, QLD, Australia

    Sunil R. Lakhani

  5. Pathology Queensland, The Royal Brisbane and Women’s Hospital, Herston, QLD, Australia

    Sunil R. Lakhani

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  1. Ana Cristina Vargas
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Corresponding author

Correspondence to Sunil R. Lakhani.

Additional information

Ana Cristina Vargas and Amy E McCart Reed, and Peter T Simpson and Sunil R Lakhani contributed equally to this study.

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Vargas, A.C., Reed, A.E.M., Waddell, N. et al. Gene expression profiling of tumour epithelial and stromal compartments during breast cancer progression. Breast Cancer Res Treat 135, 153–165 (2012). https://doi.org/10.1007/s10549-012-2123-4

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