Comparison of breast cancer to healthy control tissue discovers novel markers with potential for prognosis and early detection

Abstract

This study was initiated to identify biomarkers with potential value for the early detection of poor-outcome breast cancer. Two sets of well-characterized tissues were utilized: one from breast cancer patients with favorable vs. poor outcome and the other from healthy women undergoing reduction mammaplasty. Over 46 differentially expressed genes were identified from a large list of potential targets by a) mining publicly available expression data (identifying 134 genes for quantitative PCR) and b) utilizing a commercial PCR array. Three genes show elevated expression in cancers with poor outcome and low expression in all other tissues, warranting further investigation as potential blood markers for early detection of cancers with poor outcome. Twelve genes showed lower expression in cancers with poor outcome than in cancers with favorable outcome but no differential expression between aggressive cancers and most healthy controls. These genes are more likely to be useful as prognostic tissue markers than as serum markers for early detection of aggressive disease. As a secondary finding was that, when histologically normal breast tissue was removed from a distant site in a breast with cancer, 7 of 38 specimens displayed a cancer-like expression profile, while the remaining 31 were genetically similar to the reduction mammaplasty control group. This finding suggests that some regions of ipsilateral histologically 'normal' breast tissue are predisposed to becoming malignant and that normal-appearing tissue with malignant signature might warrant treatment to prevent new primary tumors.

Figure 1. Unsupervised hierarchical clustering of 93 tissues and 67 genes.

Unsupervised hierarchical clustering of 93 tissues (24 invasive cancers, 38 ipsilateral normal, 3 contralateral normal, 28 normal tissues from reduction mammaplasty) from 64 patients and 67 genes that discriminate between invasive tissues and mammaplasty normal tissues (red and green dots: over- and under-expression by PCR). Columns: tissues form two distinct clusters (indicated below the figure). Rows: genes form a cancer and a normal cluster, the latter being divided in one with under-expression in all cancer tissues (left, green line) and one with mixed expression (orange-blue line). Luminal-like and basal-like clusters are indicated above the figure. The part of the heat map driving the luminal-like cluster is boxed (blue: luminal-like genes, turquoise: lobular tissues). Tissues from deceased or recurred patients have a black or orange dot above the tissue descriptor which has the following abbreviated components: PatientNo – Diagnosis (IDC = invasive ductal carcinoma, ILC = invasive lobular carcinoma, MET = metaplastic carcinoma, MUC = mucinous carcinoma, NML = normal) – Stage – Grade TissueNo – Description (CA = cancer, NM = normal mammaplasty, NI = normal ipsilateral, NC = normal contralateral) BI-RADS Density Subtype (LUM = luminal, BAS = basal HER2). The tissue descriptors are shaded as follows: orange = lobular cancers, pink = other cancers, green = ipsilateral normals, blue = contralateral normals, purple = mammaplasty normals. Heat map: Red = up-regulation, green = down-regulation, grey = missing or zero value. The lines below the heat map connect tissues from the same patient.