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Development of an eight gene expression profile implicating human breast tumours of all grade

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Abstract

The goal of improving systemic treatment of breast cancers is to evolve from treating every patient with non-specific cytotoxic chemotherapy/hormonal therapy, to a more individually-tailored direct treatment. Although anatomic staging and histological grade are important prognostic factors, they often fail to predict the clinical course of this disease. This study aimed to develop a gene expression profile associated with breast cancers of differing grades. We extracted mRNA from FFPE archival breast IDC tissue samples (Grades I–III), including benign tumours. Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays were used to determine gene expression profiles and validated by Q-PCR. IHC was used to detect the AXIN2 protein in all tissues. From the array data, an independent group t-test revealed that 178 genes were significantly (P ≤ 0.01) differentially expressed between three grades of malignant breast tumours when compared to benign tissues. From these results, eight genes were significantly differentially expressed in more than one comparison group and are involved in processes implicated in breast cancer development and/or progression. The two most implicated candidates genes were CLD10 and ESPTI1 as their gene expression profile from the microarray analysis was replicated in Q-PCR analyses of the original tumour samples as well as in an extended population. The IHC revealed a significant association between AXIN2 protein expression and ER status. It is readily acknowledged and established that significant differences exist in gene expression between different cancer grades. Expansion of this approach may lead to an improved ability to discriminate between cancer grade and other pathological factors.

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Abbreviations

AGRF:

Australian Genome Research Facility

ANOVA:

Analysis of variance

APC :

Adenomatosis Polyposis Coli Gene

AXIN2 :

Axin 2 Gene

Bp :

Base pair

CDC42EP3 :

CDC42 effector protein 3

CLD10 :

Claudin 10

CXCL16 :

Chemokine ligand 16

DNA:

Deoxyribonucleic acid

dNTPs:

Deoxynucleotide triphosphate

EPSTI1 :

Epithelial stromal interaction 1

ER:

Estrogen receptor

FFPE:

Formalin-fixed paraffin-embedded

GAPDH :

Glyceraldehyde 3-phosphate dehydrogenase gene

H&E:

Haematoxylin and eosin

IDC:

Invasive ductal carcinoma

mRNA:

Messenger ribonucleic acid

PALMD :

Palmdelphin

Q-PCR:

Quantitative real time polymerase chain reaction

RNA:

Ribonucleic acid

RPL13A :

Ribosomal Protein Ligand 13A Gene

SRW:

Stephen R. Weinstein

TCEA3 :

Transcription elongation factor 3

ZAN :

Zonadhesin

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Acknowledgments

P.N.G. was funded by a Griffith University Postgraduate Research Scholarship. The authors thank the Gold Coast Hospital Department of Pathology, and the patients from whom samples were obtained.

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Authors and Affiliations

  1. Genomics Research Centre, Griffith Health Institute, Griffith University, Gold Coast Campus, Parklands Drive, Southport, QLD, 4222, Australia

    P. N. Gabrovska, R. A. Smith, T. Tiang, L. M. Haupt & L. R. Griffiths

  2. Department of Pathology, Gold Coast Hospital, Queensland Health, Southport, QLD, Australia

    S. R. Weinstein

Authors
  1. P. N. Gabrovska
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  2. R. A. Smith
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  3. T. Tiang
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  4. S. R. Weinstein
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  5. L. M. Haupt
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  6. L. R. Griffiths
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Corresponding author

Correspondence to L. R. Griffiths.

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Gabrovska, P.N., Smith, R.A., Tiang, T. et al. Development of an eight gene expression profile implicating human breast tumours of all grade. Mol Biol Rep 39, 3879–3892 (2012). https://doi.org/10.1007/s11033-011-1167-6

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  • DOI: https://doi.org/10.1007/s11033-011-1167-6

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