A Five-Gene Molecular Grade Index and HOXB13:IL17BR Are Complementary Prognostic Factors in Early Stage Breast Cancer

Abstract

Purpose: Histologic tumor grade is a well-established prognostic factor for breast cancer, and tumor grade^associated genes are the common denominator of many prognostic gene signatures. The objectives of this study are as follows: (a) to develop a simple gene expression index for tumor grade (molecular grade index or MGI), and (b) to determine whether MGI and our previously described HOXB13:IL17BR index together provide improved prognostic information. Experimental Design: From our previously published list of genes whose expression correlates with both tumor grade and tumor stage progression, we selected five cell cycle^related genes to build MGI and evaluated MGI in two publicly available microarray data sets totaling 410 patients. Using two additional cohorts (n = 323), we developed a real-time reverse transcription PCR assay for MGI, validated its prognostic utility, and examined its interaction with HOXB13:IL17BR. Results: MGI performed consistently as a strong prognostic factor and was comparable with a more complex 97-gene genomic grade index in multiple data sets. In patients treated with endocrine therapy, MGI and HOXB13:IL17BR modified each other's prognostic performance. High MGI was associated with significantly worse outcome only in combination with high HOXB13:IL17BR, and likewise, high HOXB13:IL17BR was significantly associated with poor outcome only in combination with high MGI. Conclusions: We developed and validated a five-gene reverse transcription PCR assay for MGI suitable for analyzing routine formalin-fixed paraffin-embedded clinical samples. The combination of MGI and HOXB13:IL17BR outperforms either alone and identifies a subgroup (f30%) of early stage estrogen receptor^positive breast cancer patients with very poor outcome despite endocrine therapy.The most recent (2005) St. Gallen consensus guidelines for treatment selection for early stage breast cancer consider both risk of recurrence and endocrine responsiveness to better balance risk and benefit of systemic adjuvant therapies (1). To better define risk stratification, genome-wide expression profiling studies have created multiple prognostic gene signatures for breast cancer (2, 3). An important issue is whether these signatures overlap in their prognostic information and whether combining several of these signatures would provide more accurate prognosis. In one comparative study, four signatures (the intrinsic subtypes, 70-gene signature, wound response signature, and Recurrence Score) were found to be highly concordant in classifying patients into low and high-risk groups (4). Notably, combining these signatures did not yield significant improvement in predictive accuracy, suggesting that the prognostic information provided by these signatures is largely overlapping (4). Sotiriou et al. (5) showed that a 97-gene tumor grade signature was comparable with the 70-gene signature and the Recurrence Score algorithm (6) in independent cohorts, and they hypothesized that most of the prognostic power of these signatures comes f...

MIB1/Ki-67 labelling index can classify grade 2 breast cancer into two clinically distinct subgroups

“…For instance, a recent meta-analysis of publicly available BC gene expression studies showed that the key biological drivers in nine prognostic signatures were proliferation related genes, in addition to ER signalling and ERBB2 amp lification [14]; results which have been reinforced by other authors [15]. As a consequence, attempts, such as genomic grade index (GGI) and mo lecular grade index (M GI), have been made to stratify grade 2 BC into lo w and high risk subgroups to imp rove clin ical relevance [16,17]. In their study, Sotiriou et al concluded that the gene signature characteristics displayed by grade 2 BC appears to be a mixture of signatures displayed by grade 1 and 3, rather than being independent or intermediate between t he two.…”

“…In their study, Sotiriou et al concluded that the gene signature characteristics displayed by grade 2 BC appears to be a mixture of signatures displayed by grade 1 and 3, rather than being independent or intermediate between t he two. Moreover, the M GI appears to be as powerful prognostically as the GGI and relies only on five genes; all involved in different cell cycle phases, evaluated using quantitative PCR [17]. Ho wever, the co mplexity, quality assurance requirements and interpretation issues of expression array-based profiling and assays using nucleic acids (RNA and DNA) extracted fro m formalin-fixed paraffin embedded samples, coupled with its cost, potentially limit the use of this technology in the routine clin ical setting [18,19].…”

Transcriptional Profiles of Peripheral Blood Leukocytes Identify Patients with Cholangiocarcinoma and Predict Outcome

“…Recently, a small set of genes from differential expression profiles of several cancers has been used as a molecular signature for tumor diagnosis and prognosis in patients with urinary bladder cancer, breast cancer (Osman et al, 2006;de Reynies et al, 2009;Ma et al, 2008), adrenocortical tumor, colorectal cancer (Xu, et al, 2013) and intrahepatic CCA (Nishino et al, 2008;Kraiklang, et al, 2014). From the typical expression profile found in PBLs of CCA patients, we identified a set of three proteolytic related genes (PLAU, SERPINB2, CTSL) that when computed into "prognostic index", had significant power to predict the prognosis of CCA patients.…”

A Novel Breast Cancer Index for Prediction of Distant Recurrence in HR+ Early-Stage Breast Cancer with One to Three Positive Nodes

“…For each case, three 10-mm tissue sections were cut, and an H&E slide was used to confirm 40% content of invasive cancer before manual macrodissection to enrich tumor content for RNA extraction. Total RNA was reverse transcribed and the resulting cDNA was preamplified using the PreAmp Master Mix Kit per the manufacturer's instructions (Applied Biosystems), followed by TaqMan RT-PCR as previously described (17). H/I, MGI, and BCI were calculated as described previously, blinded to all other variables (9,17,18).…”

“…Total RNA was reverse transcribed and the resulting cDNA was preamplified using the PreAmp Master Mix Kit per the manufacturer's instructions (Applied Biosystems), followed by TaqMan RT-PCR as previously described (17). H/I, MGI, and BCI were calculated as described previously, blinded to all other variables (9,17,18). Precision/reproducibility of the BCI assay was completed under quality system regulation (QSR) as part of the clinical laboratory (CLIA) quality management process and has been reported previously (9).…”