Molecular Biomarkers for Breast Cancer Prognosis


Introduction

A diagnosis of invasive breast carcinoma, usually made by mammography with pathologic assessment of a needle core biopsy, requires a series of decisions related to selection of most appropriate therapy. These decisions involve an assessment of traditional prognostic factors such as tumor size, grade, involvement of axillary lymph nodes by metastases, and breast cancer biomarker status including estrogen receptor-alpha (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) gene amplification status to aid in treatment decision-making. In addition, a number of commercially available genomic tests may be used to help inform these decisions for patients with early breast cancer (EBC). Several of these molecular assays have been validated in multicenter clinical trials and are recommended by the clinical guidelines to assist with decisions on systemic therapy for EBC patients. Genomic testing can provide important prognostic and, in some cases, predictive information that may help direct treatment decisions. These tests differ in the type of information they provide as well as in the patient populations in which they were conducted to validate them. Finally, in the past few years, liquid biopsy for breast cancer patients has been investigated with increasing interest for its diagnostic, prognostic, and predictive potential. Some of the liquid biopsy tests have been approved by US Food and Drug Administration (FDA) for clinical use in patients with breast cancer.

In this chapter, we briefly review the tissue-based molecular prognostic biomarkers and their application, including an update from the recent clinical trials ( Table 27.1 ). We will also discuss developments and progress being made with liquid biopsy–based molecular biomarkers in breast cancer.

Table 27.1
Breast Cancer Tissue Molecular Prognostic Biomarkers
Test Tissue Method Target Population Recommendation (ASCO)
Oncotype DX FFPE 21-gene RT-PCR ER/PR+, HER2−, LN− Strong
MammaPrint FF, FFPE 70-gene microarray ER/PR+, HER2−, LN− or 1–3 LN+ Strong
Prosigna (PAM50) FF, FFPE 50-gene RT-PCR ER/PR+, HER2−, LN− Strong
Breast Cancer Index FF, FFPE 11-gene RT-PCR ER/PR+, HER2−, LN− Moderate
EndoPredict FFPE 12-gene RT-PCR ER/PR+, HER2−, LN− Moderate
uPA and PAI-1 FF 2-protein ELISA ER/PR+, HER2−, LN− Weak
Mammostrat FFPE 5-protein IHC ER/PR+, HER2−, LN− No
IHC-4 FFPE 4-protein IHC ER/PR+, LN− or 1–3 LN+ No
Genomic Grade Index FF, FFPE 97-gene microarray ER/PR+, HER2−, LN− No
Rotterdam Signature FF 76-gene microarray ER/PR+ or −, LN− No
OncoMasTR FFPE 6-gene RT-PCR ER/PR+, HER2−, LN− or 1–3 LN+ No
Curebest 95GC FF, FFPE 95-gene microarray ER/PR+, LN− No
ASCO , American Society of Clinical Oncology; ELISA , enzyme-linked immunosorbent assay; ER , estrogen receptor-alpha; FF , fresh-frozen; FFPE , formalin-fixed paraffin-embedded; HER2 , human epidermal growth factor receptor 2; IHC , immunohistochemistry; LN , lymph node; PR , progesterone receptor; RT-PCR , reverse-transcriptase polymerase chain reaction.

Conventional (Tissue-Based) Molecular Prognostic Biomarkers

Over the last decade several commercially available genomic tests have been used to help define the natural history of this disease and, in some cases, the probability of response to specific treatments. Although these tests have used different methods and have been validated with different patient populations, they have become part of established breast cancer treatment guidelines.

Oncotype DX Recurrence Score Test

The Oncotype DX Recurrence Score test (Exact Sciences Laboratories LLC, Madison, WI) is based on a reverse-transcriptase polymerase chain reaction (RT-PCR) assay of 21 genes (16 breast cancer–related genes and 5 reference genes) on formalin-fixed, paraffin-embedded (FFPE) tissue. The genes analyzed include markers of proliferation, estrogen signaling genes, invasion, and HER2-related genes. Based on the gene expression profiles, an algorithm was developed to calculate a recurrence score (RS), with a higher score indicating an increased risk of distant recurrence at 10 years. The Oncotype DX Recurrence Score test provides prognostic as well as predictive information about the potential benefits of adjuvant chemotherapy in patients with ER/PR-positive and HER2-negative early-stage breast cancer.

Oncotype DX Recurrence Score (RS) Test in Lymph Node–Negative Breast Cancer Patients

The prognostic significance of the RS test and its ability to predict benefit from adjuvant chemotherapy for the individual patient have been validated in ER/PR+, HER2-negative and axillary lymph node–negative breast cancer patients. In a retrospective analysis of the National Surgical Adjuvant Breast and Bowel Project (NSABP) B-14 trial, the RS test was performed in 668 breast cancer patients who were randomized to receive either tamoxifen or placebo. There were 51% (n = 338) in the low-risk (RS <18), 22% (n = 149) in the intermediate-risk (RS 18–30), and 27% (n = 181) in the high-risk (RS ≥31) groups ( Fig. 27.1 ). The 10-year rate of distant recurrence was significantly lower in the low-risk group (6.8%, 95% CI 4.0%–9.6%) than in the high-risk group (30.5%, 95% CI23.6%–37.4%) ( P < 0.001). When the distant recurrence-free intervals were stratified by RS, patients with a low- or intermediate-risk score had significant benefit from tamoxifen versus placebo, but the benefit of tamoxifen over placebo in the high-risk group was not significant. When distant recurrence-free intervals were compared according to quantitative ER expression (ER tertiles), quantitative ER expression in ER+, placebo-treated patients was not a prognostic factor ( P = 0.54). However, for patients treated with tamoxifen, those with ER expression in the lowest ER tertile had little benefit from tamoxifen, but there was a large benefit from tamoxifen in patients in the highest and mid-ER expression tertiles. These data established that RS was a prognostic factor for distant recurrence in node-negative ER+ patients. RS was also validated as being predictive of the magnitude of benefit for tamoxifen in individual patients.

Fig. 27.1, Oncotype DX low-risk, intermediate-risk, and high-risk groupings validated in the National Surgical Adjuvant Breast and Bowel Project (NSABP) B-14 trial. (A) Expression of genes known to play a role in breast cancer outcomes were selected for evaluation by reverse-transcriptase polymerase chain reaction (RT-PCR) of formalin-fixed, paraffin-embedded tissue samples. These genes play a role in cell proliferation (Ki67, STK15 , survivin, CCNB1 /cyclin B1, MYBL2 ), cell invasion (stromolysin 3 [ MMP11 ], cathepsin L2 [ CTSL2 ]), estrogen response (estrogen receptor-alpha [ ESR1 ], progesterone receptor [ PGR ], BCL2 , SCUBE2 ) and represent expression associated with the human epidermal growth factor receptor-2 amplicon ( HER2 / ERBB2 and GRB7 ), GSTM1 , CD68 , and BAG1 . Expression of these 16 genes as detected by RT-PCR was normalized against expression levels of five “house-keeping” genes (beta-actin [ACTB], GAPDH , RPLPO , GUS , and TFRC ). (B) A significant association was demonstrated between clinical outcomes of women enrolled in the NSABP B-14 trial and their assignment to the low-, intermediate-, or high-risk group based on the Recurrence Scores determined with this 21-gene expression assay. (C) A Recurrence Score of less than 18 was considered low-risk, 18 to 30 was intermediate-risk, and 31 or greater was high-risk.

The NSABP B-20 study was a multicenter trial to determine whether the addition of chemotherapy to tamoxifen for ER+, HER2-negative, node-negative breast cancer patients resulted in better survival compared with tamoxifen alone. The absolute benefit of chemotherapy at 10 years was 4.4%, which led to the widespread use of adjuvant cytotoxic therapy for this group of patients. In a retrospective study of a subgroup of the NSABP B-20 trial, the RS test was performed in 651 patients to determine the magnitude of benefit from chemotherapy as a function of the RS assay. Among these patients, 227 in the trial had received tamoxifen alone, while 424 had received tamoxifen plus chemotherapy. Patients with RS tests in the low (RS <18) or intermediate (RS 18–30) risk range derived no benefit from the addition of chemotherapy to tamoxifen. Only patients in the high-risk group (RS ≥31) significantly benefited from addition of chemotherapy to tamoxifen, with a relative risk of 10-year distant recurrence of 0.26 (95% CI 0.13–0.53, P < 0.001) compared with tamoxifen alone.

These retrospective analyses led to a prospective phase III noninferiority trial, Trial Assigning IndividuaLized Options for Treatment (TAILORx), randomizing patients between chemoendocrine therapy versus endocrine therapy alone in patients with ER+, HER2-negative, node-negative breast cancer and intermediate-risk RS test score. Women 18 to 75 years of age with T1–T2 cancers (or T1b and intermediate-high grade) were eligible, but they had to be willing to have chemotherapy assigned or randomized based on RS test results. There were 10,273 patients registered, divided into 1629 low-risk (RS 0–10), 6711 intermediate-risk (RS 11–25), and 1389 high-risk (RS 26–100) patients. Patients in the low-risk group received endocrine therapy alone, high-risk RS patients received endocrine therapy plus chemotherapy, and intermediate-risk patients were randomly assigned to endocrine therapy alone (3399 patients) or endocrine therapy plus chemotherapy (3312 patients). For the intent-to-treat population of patients with RS 11–25, there was not a significant difference in invasive disease-free survival (IDFS) between patients having chemoendocrine versus endocrine therapy (hazard ratio [HR] 1.08, 95% CI 0.94–1.24, P = 0.26). There was no benefit from chemotherapy for patients >50 years with RS result 11–25 or for patients ≤50 years with RS <16 ( Fig. 27.2 ). Patients who were ≤50 years with RS 16–20 had 1.6% greater freedom from distant recurrence at 9 years with chemoendocrine compared with endocrine therapy, whereas those with RS result 21–25 had 6.5% greater freedom from distant recurrence. Subsequent analysis of prespecified secondary objectives was done to determine whether clinical risk features added information for patients ≤50 years regarding prognosis for recurrence and prediction of chemotherapy benefit to that provided by the RS test. As defined by modified Adjuvant! Online criteria, low clinical risk features were: tumor size ≤3 cm and grade 1; tumor size ≤2 cm and grade 2; or tumor size ≤1 cm and grade 3. All other cases were defined as high clinical risk. For patients ≤50 years with RS results 16–20, there was no demonstrable benefit from chemotherapy for patients with low clinical risk, but there was 6.4% increase in freedom from distant recurrence at 9 years for patients with high clinical risk. For patients with RS results 21–25, there was 6.4% increase for patients with low clinical risk and 8.7% increase for patients with high clinical risk. Therefore the integration of clinical risk with genomic risk separated those with RS results 16–25 who had no demonstrable chemotherapy benefit from those who had absolute benefit ranging from 6.4% to 8.7%.

Fig. 27.2, The effect of age and menopausal status on chemotherapy benefit is demonstrated among women enrolled in the Trial Assigning IndividuaLized Options for Treatment (TAILORx) whose breast cancers had an intermediate Recurrence Score (18–25). Chemotherapy demonstrated little or no benefit for patients more than 50 years of age. Shown is the effect of age and menopausal status on chemotherapy benefit in 4338 women who had a recurrence score of 16 to 25 and were randomly assigned to endocrine therapy or chemoendocrine therapy. Estimated treatment hazard ratios (endocrine vs. chemoendocrine therapy) and 95% CIs for rate of distant recurrence at 9 years are shown (a hazard ratio >1 indicates that chemoendocrine therapy is better). Menopause was defined as an age of 60 years or older; age of 45 to 59 years with spontaneous cessation of menses for at least 12 months before registration; age of 45 to 59 years with cessation of menses for less than 12 months before registration and a follicle-stimulating hormone (FSH) level in the postmenopausal range (>34.4 IU per liter if the institutional range was not available); prior bilateral oophorectomy; or age younger than 60 years with prior hysterectomy without bilateral oophorectomy and an FSH level in the postmenopausal range (or >34.4 IU per liter if the institutional range was not available). The size of each square corresponds to the size of the subgroup; the horizontal lines represent the 95% CI.

The use of the RS test for ER+, HER2-negative, node-negative breast cancer has also been supported by other clinical trials, including the Clalit Health Services (CHS) registry study and that using Surveillance, Epidemiology, and End Results (SEER) data.

Oncotype DX Recurrence Score (RS) Test in Lymph Node–Positive Breast Cancer Patients

For patients with ER/PR+, HER2-negative, and node-positive breast cancer, the prognostic utility of the RS test has been established by clinical trials and a retrospective study, including West German Study Group (WSG) Plan B (n = 3198, pN0-1), NSABP B-28 (n = 1065, pN+), PACS-01 (n = 530, pN+), and SEER (n = 6768, pN+). Southwest Oncology Group (SWOG) 8814 was a prospective randomized trial that demonstrated superior disease-free survival and overall survival (OS) at 10 years for postmenopausal patients receiving sequential Cytoxan, Adriamycin, 5-Fluorouracil (CAF) plus tamoxifen versus tamoxifen alone. A subanalysis of the RS test done on 367 patients from that trial demonstrated that the RS result was able to stratify the 10-year risk of disease-free and OS in patients receiving tamoxifen alone. These results confirmed that the RS test was a prognostic factor in node-positive patients. When disease-free survival was analyzed according to low risk (RS <18), intermediate risk (RS 18–30), or high risk (RS ≥31), only patients with high-risk RS results had survival benefit for the addition of chemotherapy to tamoxifen, suggesting a predictive role of the RS test for chemotherapy benefit in postmenopausal women with node-positive breast cancer.

The RxPONDER trials was a prospective phase III randomized clinical trial for patients with one to three positive axillary lymph nodes and hormone receptor–positive (HR+), HER2-negative breast cancer with RS ≤25, comparing IDFS for patients receiving adjuvant chemotherapy followed by endocrine therapy (2547 patients) to endocrine therapy alone (2536 patients). A prespecified interim analysis for IDFS was done after the disease site monitoring committee and the National Cancer Institute requested that the data be reported when 58% of expected events had occurred. At a median follow-up of 5.3 years there was 1.2% advantage in IDFS for patients receiving chemoendocrine therapy (92.2%) over endocrine therapy alone (91.0%) (HR 0.86, 95% CI 0.72–1.03, P = 0.10). There was no significant difference in IDFS for postmenopausal patients receiving chemoendocrine therapy (91.3%) versus endocrine therapy alone (91.9%), but there was a significant difference in IDFS for premenopausal patients receiving chemoendocrine therapy (93.9%) versus endocrine therapy alone (89.0%) (HR 0.60, 95% CI 0.43–0.83, P = 0.002). The significant differences in IDFS for premenopausal patients persisted regardless of whether RS was 0–13 versus 14–25 or whether patients had one versus two to three positive lymph nodes. From this interim analysis, it was concluded that postmenopausal patients with one to three positive lymph nodes and RS 0–25 can likely forego adjuvant chemotherapy without compromising IDFS, but premenopausal patients with one to three positive lymph nodes are likely to significantly benefit from adjuvant chemotherapy, even with a very low RS.

Other studies supporting the use of the RS test for lymph node–positive patients are the National Cancer Database study (NCDB; n = 13,163, pN1-2) and CHS trial (n = 709, pN1mi-1).

MammaPrint

The MammaPrint assay (Agendia, Irvine, CA) is a microarray test of 70 genes that are implicated in breast cancer development. Initially the prognostic value of MammaPrint was established and validated in small cohorts. The initial expression array study that defined the 70-gene expression signature used frozen tumor tissue from 117 node-negative breast cancer patients, 34 from women who experienced distant metastatic disease within 5 years of diagnosis (poor prognosis signature) and 44 from patients who continued to be disease-free after a period of at least 5 years. Rapid metastases were associated with upregulation of a subset of cell cycle, invasion and metastasis, angiogenesis, and signal transduction genes in the poor prognosis subgroup ( Fig. 27.3 ). The current test uses RT-PCR to characterize gene expression and, therefore, can be used in either fresh-frozen tumor samples or FFPE tissues. The patients are separated into low-risk and high-risk groups for distant metastasis in 10 years based on the MammaPrint Index (i.e., score). Recently its predictive significance related to chemotherapy benefit has been validated in a large prospective randomized trial—Microarray in Node negative and 1-3 positive lymph node Disease may Avoid ChemoTherapy (MINDACT). This trial enrolled 6693 patients across nine countries. The patients had EBC with either uninvolved lymph nodes or one to three involved axillary lymph nodes. The majority had ER/PR+, HER2-negative disease. The results demonstrated that patients identified as being at high risk according to clinicopathologic criteria but low risk of recurrence (ROR) based on the MammaPrint score had an excellent prognosis with a 5-year metastasis-free survival of 94.7%. The trial also showed that using MammaPrint would result in a 46% reduction in the administration of chemotherapy to high-risk patients per clinicopathologic criteria. The study found no added value for MammaPrint in patients who were classified as clinically low-risk but had a high MammaPrint result.

Fig. 27.3, MammaPrint: expression array–supervised classification based on prognosis signatures. (A) Use of prognostic reporter genes to identify optimally two types of disease outcome from 78 sporadic breast carcinomas into a poor prognosis and good prognosis group. (B) Expression matrix of 70 prognostic marker genes from tumors of 78 breast cancer patients ( left panel ). Each row represents a tumor and each column a gene, whose name is labeled between (B) and (C). Genes are ordered according to their correlation coefficient with the two prognostic groups. Tumors are ordered by the correlation to the average profile of the good prognosis group (middle panel) . Solid line , Prognostic classifier with optimal accuracy; dashed line , with optimized sensitivity. Above the dashed line patients have a good prognosis signature, below the dashed line the prognosis signature is poor. The metastasis status for each patient is shown in the right panel ; white indicates patients who developed distant metastases within 5 years after the primary diagnosis; black indicates patients who continued to be disease-free for at least 5 years. (C) Same as for (B), but the expression data matrix is for tumors of 19 additional breast cancer patients using the same 70 optimal prognostic marker genes. Thresholds in the classifier (solid and dashed line) are the same as (B). Rapid metastases were associated with upregulation of a subset of cell cycle, invasion and metastasis, angiogenesis, and signal transduction genes in the poor prognosis subgroup.

Prosigna (PAM50)

Prosigna PAM50 (NanoString Technologies, Seattle, WA) measures the expression of 50 genes by RT-PCR in either fresh-frozen samples or FFPE tissue. Based on the gene expression profile, the breast tumors are classified into one of four intrinsic subtypes: luminal A, luminal B, HER2-enriched, and basal-like. This assay provides an ROR score to predict the risk of relapse at 5 years, and it has been validated in patients with node-negative and node-positive breast cancer. Recently, the PAM50 assay was validated on the probe-based nCounter Analysis System. The workflow was simplified, and a local pathology laboratory was able to perform the test. The measurement result from nCounter was highly concordant with that from RT-PCR. For FFPE, mRNA expression measured by nCounter was more precise and accurate compared to RT-PCR.

The ROR score takes into account intrinsic subtypes, proliferation score, and tumor size, and classifies patients into low-, intermediate-, and high-risk groups ( Fig. 27.4 ). The prognostic and predictive value of PAM50 has been validated in several clinical trials, including the National Cancer Institute of Canada Clinical Trials Group (NCIC CTG MA.12), the translational arm of the ATAC (anastrozole or tamoxifen alone or combined) trial (TransATAC), and the Austrian Breast and Colorectal Cancer Study Group 8 (ABCSG-8).

Fig. 27.4, Comparison of Prosigna (PAM50) risk of recurrence (ROR) with Oncotype DX recurrence score (RS) stratified by low-, intermediate-, and high-risk groups using breast cancers from women enrolled in the ATAC trial evaluating treatment with anastrozole or tamoxifen. Distant recurrence over 10 years for axillary lymph node–negative populations predicted to be at low (<10%), intermediate (10%–20%), or high risk (>20%) by risk of recurrence (no tumor size; ROR ; solid lines ) or recurrence score ( RS ; dashed lines ) in (A) the absence of clinical treatment scores (CTS) and (B) combination with CTS.

Breast Cancer Index

The Breast Cancer Index (bioTheranostics, San Diego, CA) is an RT-PCR–based test combining two independent biomarkers, the HOXB13:IL17BR ratio (H:I) and the Molecular Grade Index (MGI), which measures expression of five cell cycle-related genes. The specimen can be fresh-frozen or FFPE tissue. This assay predicts the risk of overall (0–10 years) and late (5–10 years) distant recurrence, and the benefit of extended endocrine therapy in ER/PR+, HER2-negative, node-negative breast cancer patients. The prognostic value for BCI for detecting early and late recurrences has been validated in several prospective and retrospective trials including ER/PR+, HER2-negative, and lymph node–negative patients treated with adjuvant endocrine therapy. The BCI test was found to be a better biomarker in predicting late recurrence than Oncotype DX or immunohistochemical (IHC)-4 when all three tests were compared for long-term follow-up in the same trial-TransATAC study ( Fig. 27.5 ). Clinically BCI helps to identify patients who may benefit from extending (5–10 years) hormonal therapy.

Fig. 27.5, Comparison of recurrences in the TransATAC Clinical Trial according to the breast cancer index ( BCI ), Recurrence Score, and IHC4 prognostic assays. Prognostic value of the prespecified risk groups of BCI and 21-gene recurrence score and the post hoc–determined categorical risk groups of IHC4 for overall 10-year distant recurrence in patients with estrogen receptor–positive, node-negative breast cancer. The graphs are presented for all patients assigned to either anastrozole or tamoxifen for (A) BCI, (B) 21-gene recurrence score, and (C) IHC4; for patients assigned to anastrozole in the ATAC trial for (D) BCI, (E) 21-gene recurrence score, and (F) IHC4; and for patients assigned to tamoxifen in the ATAC trial for (G) BCI, (H) 21-gene recurrence score, and (I) IHC4.

EndoPredict (EP)

EndoPredict (Sividon Diagnostics GmbH, Germany) is an 11-gene RT-PCR assay that includes eight cancer-related genes ( BIRC5 , UBE2C , DHCR7 , RBBP8 , IL6ST , AZGP1 , MGP , and STC2 ) and three reference genes ( CALM2 , OAZ1 , and RPL37A ) to normalize comparison of the products. The test is performed on FFPE tissue and can predict the likelihood of distant recurrence in ER/PR+, HER2-negative EBC patients. The EndoPredict score (EP) is calculated from the expression levels of these eight genes. EP has been combined with tumor size and lymph node status to generate a comprehensive risk score-EPclin score. Patients are then classified into low- and high-risk groups using both the EP and EPclin scores. The prognostic value of EndoPredict has been validated in two large randomized phase III trials, ABCSG 6 (n = 378) and ABCSG 8 (n = 1324), which recruited postmenopausal patients with ER+, lymph node–negative (LN−) and LN+ EBC treated with endocrine therapy. Both EP and EPclin scores correlate with the risk of distant recurrence at 5 and 10 years. Later, the GEICAM 9906 trial found that EP was an independent prognostic biomarker in ER+, HER2-negative, and LN+ breast cancer patients treated with adjuvant chemotherapy followed by endocrine therapy. This trial also found that EPclin provided independent prognostic information beyond PAM50 ROR score. In the TransATAC study, EPclin outperformed EP and seemed superior to Oncotype DX in predicting the risk of late (>5 years) recurrence ( Fig. 27.6 ).

Fig. 27.6, Comparison of distant recurrence-free survival by EndoPredict, EPclin, and Oncotype DX recurrence score. The Kaplan-Meier estimates for 10-year distant recurrence according to EP, EPclin, and recurrence score, split into tertiles in all patients, were determined for EP, EPclin, and RS and tested for equality using the log-rank test. The numbers of patients at risk in each group at various time points are given below each graph. Statistical tests were two-sided. CI , Confidence interval; EP , EndoPredict; HR , hazard ratio; RS , recurrence score.

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