Molecular tumour profiles for early breast cancer

Breast cancer is the most common cancer in the UK, with 1 in 7 women receiving a diagnosis at some point in their lifetime. It is now understood that breast cancer is made up of a range of distinct biological diseases and this information can be used to risk-stratify patients, allowing for personalised treatment. In early breast cancer, this information can help to select who might benefit from adjuvant chemotherapy and spare those who will derive little or no benefit.

Previously, decisions regarding adjuvant therapies for early breast cancer were based on pathological factors, such as tumour size, histological grade, number of involved lymph nodes, hormone receptor status and HER2 status. These factors can be fed into prognostic models such as Predict and the Nottingham Prognostic Index.

There are currently several different commercial gene expression assays available. These tests analyse the expression of sets of genes as a surrogate marker for metastatic potential and identify tumours with more aggressive biology. The genes selected vary between tests, although there is some overlap. All of the assays currently in routine use analyse RNA extracted from formalin-fixed, paraffin-embedded (FFPE) breast tumour samples.

Algorithms are used to present the relative expression of the cancer-related genes compared to control genes as a score, indicative of risk of future disease recurrence. Higher expression levels of genes associated with favourable outcomes result in a lower recurrence score; higher expression of genes associated with a poor prognosis result in a higher recurrence score. 

The following molecular profiling tests have been recommended by NICE to guide decision-making regarding the use of adjuvant chemotherapy in hormone receptor positive, HER2-negative and lymph node-negative early breast cancer. The NICE criteria for use of these tests require that patients: 

• have an estimated intermediate risk of distant recurrence based on the analysis of tumour pathological features by a validated tool such as Predict or the Nottingham Prognostic Index; or
• would benefit from the information provided by the test in terms of helping them to choose, with their clinician, whether or not to have adjuvant chemotherapy.

Oncotype DX

• A 21-gene recurrence score assay comprising 16 cancer-related genes and five reference genes.  
• Uses reverse transcription-qualitative polymerase chain reaction (RT-qPCR) technology. 
• Validated in pre- and post-menopausal women with hormone receptor positive, HER2-negative breast cancer which is either lymph node-negative or with one to three lymph nodes involved. 
• Gene expression is used to calculate a recurrence score (RS) between 0 and 100 which indicates the 10-year risk of distant recurrence when treated with hormonal therapy alone for five years. 
• Oncotype DX additionally presents the group average absolute chemotherapy benefit; it is currently the only molecular profiling test validated to predict benefit from chemotherapy treatment. 
• Predicted chemotherapy benefit depends on the recurrence score and age as summarised in the table below:

• Data from the RxPONDER trial which investigated Oncotype DX use in patients with between one and three positive lymph nodes and a recurrence score of less than 25 showed no improvement in invasive disease-free survival at five years for postmenopausal patients receiving chemotherapy in addition to endocrine therapy, whereas premenopausal women seemed to benefit from chemotherapy regardless of their recurrence score.
• Some hospital trusts have gained permission to use this test in node-positive patients during the Covid-19 pandemic. 

Prosigna

• An assay designed to predict likelihood of metastases developing within 10 years of initial cancer diagnosis and to provide information on the breast cancer subtype (luminal A versus luminal B). 
• Uses direct mRNA counting using fluorescent probes.
• Measures the expression of 50 genes involved in intrinsic subtype classification of breast cancer and generates a score between 0 and 100.    
• Validated in post-menopausal women with hormone receptor positive, HER2-negative and lymph node-negative or positive early-stage breast cancer.
• Risk stratification is dependent on lymph node status: 
  • Lymph node negative disease: low risk (0 to 40), intermediate risk (41 to 60) or high risk (61 to 100). 
  • Lymph node positive disease (up to three positive nodes): low risk (0 to 15), intermediate risk (16 to 40), or high risk (41 to 100).  
• NICE approval is only for use in lymph node negative disease at present. Some NHS hospital trusts have gained permission to use this in node-positive patients during the Covid-19 pandemic. 

EndoPredict

• An assay designed to predict likelihood of metastases developing within 10 years of initial cancer diagnosis.
• Can be used in pre- or post-menopausal women with hormone receptor positive, HER2-negative and lymph node-negative or positive (up to three nodes) breast cancer.   
• Measures RNA expression of 12 genes to generate a score between 0 and 15. A score of 0–5 indicates low risk of distant disease recurrence and a score of 5–15 indicates high risk.
• EndoPredict Clinical (EPClin) is a refined system of EndoPredict that is combined with tumour size and nodal status. An EPClin score of less than 3.3 indicates low risk and greater than 3.3 indicates high risk of metastases in the next 10 years (more than 10%).

Other assays

• There are a number of other assays that are not currently recommended by NICE, including MammaPrint (cost effectiveness) and IHC4+C (concerns regarding analytical validity).

• These tests require a FFPE tumour sample, typically from a tumour resection specimen.
  • Molecular tumour profiles cannot be performed on a surgically resected tissue sample if the patient has received neo-adjuvant endocrine therapy or chemotherapy.
  • Core biopsy samples may not be representative of tumour biology due to intratumoural heterogeneity, however they may be the only tumour sample available in some cases.
  • Some studies have looked at concordance of recurrence scores between resection specimens and core biopsies with high concordance typically seen.
• Liaise with your local cellular pathology department to confirm local contract and request arrangements. 

• Molecular tumour profiling tests assess gene expression patterns to inform prognosis and treatment.
• There are three different ways of obtaining profiles –RT-qPCR, direct mRNA counting using fluorescent probes and measuring RNA expression.
• Molecular tumour profiling tests are carried out on FFPE tumour tissue.

For clinicians

• NICE: Guidance on tumour profiling tests to guide adjuvant chemotherapy decisions in early breast cancer 

References:

• Sestak I, Buus R, Cuzick and others. ‘Comparison of the Performance of 6 Prognostic Signatures for Estrogen Receptor–Positive Breast Cancer: A Secondary Analysis of a Randomized Clinical Trial’. JAMA Oncology, 2018: issue 4, page 545. DOI: 10.1001/jamaoncol.2017.5524 
• Sparano J, Gray R, Makower D and others. ‘Adjuvant Chemotherapy Guided by a 21-Gene Expression Assay in Breast Cancer’. New England Journal of Medicine, 2018: issue 379, pages 111–121. DOI: 10.1056/NEJMoa1804710

For patients

• Breast Cancer Now: Breast cancer prognosis information