Gene expression profiling in primary breast cancer distinguishes patients developing local recurrence after breast-conservation surgery, with or without postoperative radiotherapy

Emma Niméus-Malmström, Morten Krogh, Per Malmström, Carina Strand, Irma Fredriksson, Per Karlsson, Bo Nordenskjöld, Olle Stål, Görel Ostberg, Carsten Peterson, Mårten Fernö, Emma Niméus-Malmström, Morten Krogh, Per Malmström, Carina Strand, Irma Fredriksson, Per Karlsson, Bo Nordenskjöld, Olle Stål, Görel Ostberg, Carsten Peterson, Mårten Fernö

Abstract

Introduction: Some patients with breast cancer develop local recurrence after breast-conservation surgery despite postoperative radiotherapy, whereas others remain free of local recurrence even in the absence of radiotherapy. As clinical parameters are insufficient for identifying these two groups of patients, we investigated whether gene expression profiling would add further information.

Methods: We performed gene expression analysis (oligonucleotide arrays, 26,824 reporters) on 143 patients with lymph node-negative disease and tumor-free margins. A support vector machine was employed to build classifiers using leave-one-out cross-validation.

Results: Within the estrogen receptor-positive (ER+) subgroup, the gene expression profile clearly distinguished patients with local recurrence after radiotherapy (n = 20) from those without local recurrence (n = 80 with or without radiotherapy). The receiver operating characteristic (ROC) area was 0.91, and 5,237 of 26,824 reporters had a P value of less than 0.001 (false discovery rate = 0.005). This gene expression profile provides substantially added value to conventional clinical markers (for example, age, histological grade, and tumor size) in predicting local recurrence despite radiotherapy. Within the ER- subgroup, a weaker, but still significant, signal was found (ROC area = 0.74). The ROC area for distinguishing patients who develop local recurrence from those who remain local recurrence-free in the absence of radiotherapy was 0.66 (combined ER+/ER-).

Conclusion: A highly distinct gene expression profile for patients developing local recurrence after breast-conservation surgery despite radiotherapy has been identified. If verified in further studies, this profile might be a most important tool in the decision making for surgery and adjuvant therapy.

Figures

Figure 1
Figure 1
A hypothetical clinical routine scheme for the choice of surgery and radiotherapy after preoperative gene expression analysis.
Figure 2
Figure 2
A Sammon map of the 100 estrogen receptor-positive patients within the LR+RT+ group (red dots, 20 patients) and the LR-RT+/LR-RT- group (blue dots, 80 patients). The Sammon map was performed with all 26,824 reporters. Euclidean distance in log2 expression values was used as the distance measure. LR-RT- = no local recurrence, no radiotherapy given; LR-RT+ = no local recurrence after radiotherapy; LR+RT+ = local recurrence developed after radiotherapy.
Figure 3
Figure 3
Receiver operating characteristic (ROC) curves for the support vector machine classification of LR+RT+ versus LR-RT+/LR-RT- groups within the estrogen receptor-positive (ER+) group (left part) and estrogen receptor-negative (ER-) group (right part). The specificity is defined as the fraction of the LR-RT+/LR-RT- patients correctly classified, and the sensitivity as the fraction of the LR+RT+ patients correctly classified. LR-RT- = no local recurrence, no radiotherapy given; LR-RT+ = no local recurrence after radiotherapy; LR+RT+ = local recurrence developed after radiotherapy.
Figure 4
Figure 4
The 81 most important genes. A heatmap of 81 genes (rows) and 100 patients (columns) with patients ordered according to their leave-one-out support vector machine classification value: estrogen receptor-positive patients within LR+RT+ (red, n = 20) and LR-RT+/LR-RT- (blue, n = 80) groups. The gene selection and ordering are described in the text. Expression values are logarithmically transformed, centered around zero, and normalized to unit standard deviation. LR-RT- = no local recurrence, no radiotherapy given; LR-RT+ = no local recurrence after radiotherapy; LR+RT+ = local recurrence developed after radiotherapy.

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