Comparative measures of proliferation using Ki-67 Labeling Index and a 14-gene prognostic expression signature in breast cancer
Authors: Alice Wang, Charles Rowland, Karen Chew, Sheng-Yung Chang, Steve Anderson, Joe Gray, Sam Broder, James Bennington, John Sninsky, Fred Waldman
Journal: Clinical Cancer Research (2008)

A32    Background:  Measures of tumor cell proliferation may prove valuable in predicting response to cytotoxic chemotherapeutic drugs since they arrest dividing cells. We previously identified a 14-gene metastasis expression signature not dependent on hormone expression levels and enriched in proliferation genes that can predict a woman’s risk for metastasis in early-stage breast cancer. How molecular expression signatures compare to routinely used assays is critical to an evaluation of their independent clinical utility. Tumor cell proliferation as assessed by Ki-67 labeling index (LI) has been show to yield prognostic information in breast cancer in some but not all studies. In this study, we examined the agreement between the expression signature and the Ki-67 LI.   Methods : FFPE tissue samples from a cohort of 282 N-, ER+ untreated breast cancer were tested. The expression of Ki-67 and the genes in the signature were measured by immunostaining and real-time RT-PCR, respectively. The Metastasis Scores (MS) from the equally-weighted 14-gene signature using 3 normalization genes were calculated. Both median cut point and two cut point comparisons for these two proliferation markers were used. The single cut point chosen was the median for both assays. Classification into low, intermediate, and high risk categories used the commonly accepted  20% for Ki-67 LI. Analogous classification into three categorized risk groups used pre-specified cut points developed in a separate sample set for the expression signature. The kappa statistic was used to assess agreement between risk classifications of the two measures. Exact binomial confidence limits were calculated for estimates of the percent of concordance between the two measures.   Results:  We compared the agreement of high and low risk designations for subjects based on the median values of either KI-67 LI or the MS. There was moderate agreement between these two measures as suggested by the kappa coefficient of 0.44 (95% CI: 0.33 to 0.54) and 72% (95% CI: 66% to 77%) of subjects concordantly classified as either low or high risk for both measures. When considering two cutoffs per measure such that subjects are classified as high, intermediate, or low risk, we found the agreement to be only fair with a weighted kappa coefficient of 0.22 (95% CI: 0.15 to 0.28) and 38% (95% CI: 33% to 44%) concordantly classified in the identical category. In addition, the correlation coefficient, R 2 ,  between  Ki-67 LI and MS was 0.37. We did not find a strong correlation (R 2  = 0.27) between Li-67LI and the mRNA level of this gene.   Conclusions:  Classification into two risk categories led to moderate agreement between the Ki-67 LI and 14-gene expression signature. Classification into three risk categories resulted in only fair concordance of these two proliferation assays. The Ki-67 expression levels measured by immunostaing and real-time PCR were weakly concordant. Outcome studies are required to determine the comparative prognostic performance of these assays. The limited number of genes in the signature will facilitate mechanistic studies and may serve as targets for future therapies.