Value Addition: BluePrint

BluePrint™: A Molecular Subtyping Profile for Breast Cancer

As our understanding of the biology of breast cancer has advanced, so too has our ability to enhance treatment and patient outcomes as demonstrated by the increased survival of women with breast cancer over the past decade.  While early detection and improved chemotherapy account for much of this progress, so also does a deeper understanding of the role of the estrogen and progesterone receptors and HER2 expression in our treatment strategies.  Inherent is the recognition of the critical role of gene and protein expression of the breast cancer cell and our ability to characterize this in a way that clinicians can use to make treatment decisions.  Routine immunohistochemistry has given way to ER, PR and HER2 measurement by single gene expression such as Target Print ® and multi-gene expression assays such as MammaPrint® have evolved so that they have become part of routine decision-making for prognosis and prediction in the clinic worldwide.  An additional level of understanding comes from recognition of the molecular subtypes of breast cancer, which further characterize tumors as Basal, Luminal or ERBB2 (HER2+) intrinsic subtypes.

 

Agendia developed BluePrint, a multi-gene profile, for the classification of breast cancer into Basal-type, Luminal-type and ERBB2-type (HER2/neu positive) molecular subclasses. Following risk assessment with a MammaPrint 'low risk' or 'high risk' result, additional stratification into a molecular subtype provides the next level of genomic breast cancer analysis.

 

  • The BluePrint Molecular Subtyping Profile combined with the patient's MammaPrint test result, provides a greater level of clinical information to assist in therapeutic decision-making.
  • BluePrint is an 80-gene expression signature which classifies breast cancer into Basal-type, Luminal-type and ERBB2-type cancers.
  • An increasing body of evidence in the medical community suggests that breast cancer patients within these molecular subgroups have different prognoses with varied responses to specific therapies

 

Development

 

The BluePrint signature determines the RNA levels of 80 genes that best discriminate among these three distinctive subtypes. Tumors from an initial cohort of 295 patients(1,2) were used for the development of gene expression profiles specific for the Basal-type, Luminal-type and ERBB2-type breast cancers.

 

Using state-of-the-art bioinformatics tools, Agendia identified genes whose expression ratios best discriminate between the three subgroups. Subtype specific gene expression profiles were identified in a 3-fold cross-validation procedure. Optimal classification of the training samples in the corresponding Basal-type, Luminal-type and ERBB2-type subgroups was reached with a set of 80 genes. Next, a nearest-centroid classification procedure utilizing the 80-gene profile was developed that most accurately classified the breast cancer molecular subtypes on all samples.(3)


Validation

 

The BluePrint molecular subtyping profile was subsequently validated on 374 independent samples hybridized to 44k Agilent arrays resulting in 90% concordance between the molecular subtyping profile and the classification based on ER, PR and HER2/neu status.  Additionally, the profile was further validated using publicly available datasets (n=251 (4) and n=159 (5)) generated using Affymetrix arrays with concordance of 79% between the BluePrint profile and classification using ER, PR and HER2/neu receptor status.(3) 
 

 

When combined, BluePrint characterized a total of 13% (116) of the breast tumors as Basal-type, 66% (603) as Luminal-type and 22% (198) as ERBB2-type. Compared to single-marker readout for the presence of ER, PR and HER2, 13% of the samples that were scored positive for the presence of ER/PR did not express a luminal-type gene profile.(3-6)

Figure 1. On the left scatterplot of samples from the first validation samples (n=374) and on the right of samples from the second vali­dation set (n=410) with the classifier indices for the Basal-type shown on the x-axis, Luminal-type on the z-axis and ERBB2-type on the y-axis.(6

 

Outcome

 

MammaPrint risk-classification, followed by the 80-gene, BluePrint molecular subtyping profile, can help identify specific groups of breast cancer patients who are at increased risk of distant recurrence. Moreover, groups with low risk of recurrence are recognized, thereby, aiding in treatment planning. Implementation of this knowledge can improve the clinical management of breast cancer patients.

 

MammaPrint risk-classification, followed by the 80-gene, BluePrint molecular subtyping profile, can help identify specific groups of breast cancer patients who are at increased risk of distant recurrence. Moreover, groups with low risk of recurrence are recognized, thereby, aiding in treatment planning. Implementation of this knowledge can improve the clinical management of breast cancer patients.

 

Result Description

Basal-type

Basal-type breast cancers are characterized by gene expression of the basal-myoepithelial cell origin. The Basal-type cancers are typically triple-negative for ER, PR and HER2/neu (basal-like) with a specific gene expression profile. Hormone therapy and anti-HER2 therapies, such as trastuzumab and lapatinib, are not believed  to be effective against these cancers, although chemotherapy is thought to be helpful.  A Basal-type molecular subtyping result means that the tumor most closely resembles the Basal-type intrinsic subtype.

 

Luminal-type

Luminal-type breast cancers are characterized by gene expression of luminal epithelial cells that line the breast ducts and glands. The Luminal-type cancers are typically hormone receptor positive tumors and therefore responsive to hormonal therapy. A Luminal-type molecular subtyping result means that the tumor most closely resembles the Luminal-type intrinsic subtype. Patients classified as MammaPrint 70-gene signature 'low risk' and Luminal-type can be expected to have a clinical course similar to luminal A, usually treated with hormonal therapy. Patients classified as MammaPrint 'high risk' and Luminal-type can be expected to have a clinical course similar to luminal B patients who usually benefit from more aggressive treatment which may include chemotherapy.

 

ERBB2-type

The ERBB2-type breast cancers are characterized by amplification or over-expression of the HER2 locus. The ERBB2-type cancers are typically HER2-positive tumors (HER2/neu positive). ERRB2-type cancers tend to grow more quickly and may recur, although they can often be treated with targeted therapies such as trastuzumab and lapatinib. An ERBB2-type molecular subtyping result means that the tumor most closely resembles the ERBB2-type intrinsic subtype.

 

Reference

  1. van de Vijver MJ, et al., N Engl J Med 2002, 347:1999-2009
  2. Fan C et al., N Engl J Med. 2006, 355(6):560-9
  3. Stork-Sloots et al., Abstract #1083, ASCO 2009
  4. Miller LD, et al., Proc Natl Acad Sci U S A 2005, 102:13550-13555
  5. Pawitan Y, et al., Breast Cancer Res 2005, 7:R953-964
  6. de Snoo et al., Abstract #6131, SABCS 2009

Information extracted from Agendia.com