The histone chaperone HJURP is a new independent prognostic marker for luminal A breast carcinoma

Abstract

Background: Breast cancer is a heterogeneous disease with different molecular subtypes that have varying responses to therapy. An ongoing challenge in breast cancer research is to distinguish high-risk patients from good prognosis patients. This is particularly difficult in the low-grade, ER-positive luminal A tumors, where robust diagnostic tools to aid clinical treatment decisions are lacking. Recent data implicating chromatin regulators in cancer initiation and progression offers a promising avenue to develop new tools to help guide clinical decisions.

Methods: Here we exploit a published transcriptome dataset and an independent validation cohort to correlate the mRNA expression of selected chromatin regulators with respect to the four intrinsic breast cancer molecular subtypes. We then perform univariate and multivariate analyses to compare the prognostic value of a panel of chromatin regulators to Ki67, a currently utilized proliferation marker.

Results: Unsupervised hierarchical clustering revealed a gene cluster containing several histone chaperones and histone variants highly-expressed in the proliferative subtypes (basal-like, HER2-positive, luminal B) but not in the luminal A subtype. Several chromatin regulators, including the histone chaperones CAF-1 (subunits p150 and p60), ASF1b, and HJURP, and the centromeric histone variant CENP-A, associated with local and metastatic relapse and poor patient outcome. Importantly, we find that HJURP can discriminate favorable and unfavorable outcome within the luminal A subtype, outperforming the currently utilized proliferation marker Ki67, as an independent prognostic marker for luminal A patients.

Conclusions: The integration of chromatin regulators as clinical biomarkers, in particular the histone chaperone HJURP, will help guide patient substratification and treatment options for low-risk luminal A breast carcinoma patients.

Keywords: Biomarkers; CENP-A; Chromatin; Epigenetics; MKI67; Prognosis.

Figure 1

Hierarchical clustering of 1127 breast cancer samples according to the expression of select chromatin regulators. A) Summary of features for defined molecular subtypes of breast cancer based on (Mullan and Millikan, 2007; Reis‐Filho and Pusztai, 2011; Schnitt, 2010). B) Tumor specimens were divided into the four molecular subtypes (see methods). The cluster dendrogram (horizontal axis) shows the four subtypes of tumors colored as: basal‐like, red; HER2+, green; luminal B, purple; and luminal A, light blue. The dendrogram of the 58 classification probe sets corresponding to the chromatin regulators is shown on the vertical axis. Each column represents a single patient, and each row represents a single gene. Green squares, transcript levels below the median; black squares, transcript levels equal to the median; red squares, transcript levels greater than the median. Color saturation reflects the magnitude of the ratio relative to the median for each set of samples (see scale, top right). C) Enlargement of a gene cluster representing a putative CR “subtype gene signature”.

Figure 2

Significant associations between the mRNA expression of select chromatin regulators and breast cancer molecular subtypes. Box plots represent the mRNA expression levels (logarithmic) from our microarray data set (n = 1127) in different breast cancer subtypes. Boxes represent the 25th–75th percentile; brackets: range; black line: median; black dots: outliers. mRNA expression comparisons among different subtypes were done first by ANOVA test and then by Wilcoxon rank‐sum test. Significant p‐values (<0.05) were corrected for multiple testing by the Benjamini–Hochberg method and are indicated for each subtype pair. Basal‐Like (BLC; n = 214), HER2+ (n = 144), luminal B (Lum B; n = 257), and luminal A (Lum A; n = 512).

Figure 3

Significant associations between the mRNA expression of select chromatin regulators and breast cancer molecular subtypes. Box plots represent the expression levels (logarithmic) from our validation set (n = 71) in different breast cancer subtypes. Boxes represent the 25th–75th percentile; brackets: range; black line: median; black dots: outliers. Comparisons of mRNA expression between subtypes were done by a two‐sample Wilcoxon rank‐sum test. Significant p‐values from the test (<0.05) were corrected for multiple testing by the Bonferroni method and are indicated for each subtype pair. BLC (n = 11), HER2+ (n = 6), Lum B (n = 16) and Lum A (n = 38).

Figure 4

High HJURP and/or MCM2 expression significantly differentiates between good and poor outcome luminal A patients. Univariate Kaplan–Meier curves of metastasis‐free interval, disease‐free interval, and disease‐free survival in patients with low or high mRNA expression of the indicated gene using the validation set. A cut‐off value that divided the population into two was set according to median mRNA expression, as indicated. The blue line represents high mRNA expression while the red line represents low mRNA expression. The number of patients at risk per time point is shown below each plot. Only significant associations between a gene and a molecular subtype are shown, the p‐values (p < 0.05) were obtained from a log‐rank test and are in red. Expression of MKI67 is shown for comparison. BLC (n = 11), HER2+ (n = 6), Lum B (n = 16) and Lum A (n = 38).