Biomarkers

Many tumours are heterogeneous. This means all the cells are not the same. Instead, some cells, or groups of cells, throughout the tumour will have different genetic mutations (changes in the genes) or a different molecular make-up.

If a sample is taken from a part of a tumour that’s different to the rest of the tumour, it may show different results to a sample taken from elsewhere in the same tumour.

This means that the results of the biomarker test may not truly reflect the tumour and its likely behaviour.

What is the 1p/19q test?

The 1p/19q test may predict long-term survival in people who have some types of brain tumour. 

The test can also be useful in diagnosing certain types of brain tumours and, therefore, in making decisions about the most appropriate treatment for you.

Is the 1p/19q test suitable for me?

The type of brain tumour that may be suitable for 1p/19q testing is oligodendroglioma.

How does the test work and what does it show?

Our bodies are made up of cells. Each cell has 23 pairs of chromosomes, which carry your genes (DNA). One chromosome of each pair is inherited from your mother, and the other from your father. Each pair of chromosomes are numbered 1 to 22, then XX or XY.

The 1p/19q test looks at genetic changes to chromosomes 1 and 19 to see whether they have a section missing. If the sections called the p section of chromosome 1 and the q section of chromosome 19 are missing, this means that the genes carried in those sections are also missing. 

These genes seem to be involved in resistance to chemotherapy drugs. So if you’re found to be missing both those sections, you’re more likely to have a better response to chemotherapy and longer overall survival.

What is the histone H3.3 K27M test?

The histone H3.3 K27M test may predict response to treatment for certain types of tumour.

Is the histone H3.3 K27M test suitable for me?

The histone H3.3 K 27M test is suitable for:

· Paediatric diffuse midline gliomas (previously called DIPG)

How does the test work and what does it show?

Up to 80% of paediatric diffuse midline gliomas have a mutation of the histone H3. A histone is a group of proteins that your DNA wraps around in your chromosomes.

What is the IDH1/IDH2 test?

The IDH1/IDH2 test may predict long-term survival in people who have certain types of brain tumour. It may also be useful in predicting how effective a particular treatment is likely to be.

Is the IDH1/IDH2 test suitable for me?

If you have a glioma, you may be suitable for IDH1/IDH2 testing, but speak to your neuro-oncologist for information and advice.

Gliomas that may be suitable include:

· Astocytomas (grade 2)

· Astrocytomas (grade 3)

· Oligodendrogliomas

· Glioblastomas, in particular secondary glioblastomas (tumours that evolved from lower grade gliomas)

How does the test work and what does it show?

IDH1 and IDH2 are genes. A change (mutation) in the IDH1/IDH2 genes has been found in about 80% of astrocytomas, oligodendrogliomas and secondary glioblastomas.

Tumours that have the change are known as IDH–mutant, and those without the change are known as IDH-wildtype.

For people with high grade types of these glioma, those whose tumours are IDH-mutant tend to have better long-term survival rates than those who are IDH-wildtype.

It’s not yet clear how mutations of the IDH1/IDH2 genes link to outcomes for people with low grade brain tumours – both in terms of long-term survival and also treatment outcomes. However, there’s some evidence that, similar to high grade gliomas, people whose tumours are IDH-mutant have better long-term survival rates than those who are IDH-wildtype.

Further research needs to be carried out before clear conclusions can be drawn, but it may be that chemoradiotherapy (a combination of chemotherapy and radiotherapy) is more effective for some people with grade 2 gliomas who have the IDH1/IDH2 mutation, than those who don’t. (See TP53/ATRX mutations section further on.)

It’s important to be aware that people with gliomas that have the IDH1/IDH2 mutation tend to be younger adults and older children, which may partially account for their longer survival.

What is the MGMT methylation test?

For people with certain tumour types, the MGMT methylation test helps to predict how effective chemotherapy treatment is likely to be, although there are many other factors that also affect response to treatment. This can be used to help plan a suitable, individualised treatment plan.

Is the MGMT methylation test suitable for me?

NICE (National Institute for Health and Care Excellence) recommends that all high grade glioma tumours should be tested for MGMT promoter methylation to inform prognosis and guide treatment.

The types of brain tumour suitable for MGMT biomarker testing include:

• Glioblastoma. It can only predict your response to the chemotherapy drug, temozolomide (TMZ).

• Anaplastic gliomas (grade 3). Grade 3 astrocytoma and anaplastic oligodendroglioma

You may have heard of recent research that suggested that the MGMT test may also be useful for predicting prognosis in grade 2 gliomas. This research is in very early stages and is not evidence-based. More research is needed to confirm if this is the case.

What does the test show?

In summary, the test looks at the amount (percentage) of something called methylation. If your tumour is found to be:

• MGMT methylated, you’re more likely to respond well to TMZ chemotherapy.
• MGMT unmethylated, you’re less likely to respond to TMZ chemotherapy.

This helps your healthcare team decide on the best course of treatment for you. For example, if your tumour is unmethlyated, giving you high doses of chemotherapy may give you lots of unpleasant side-effects, but with little benefit in terms of reducing your tumour.

If you do decide to have the test, you need to be aware that it may be found to be unmethylated. Speak to your healthcare team about what would happen next if this turned out to be the case.

There are other factors that influence the effectiveness of chemotherapy, so there’ll always be ‘good’ and ‘poor’ responders in both the methylated and unmethylated groups.

How does the test work?

If you’d like to understand the test more:

• MGMT is a protein in cells, including tumour cells, that repairs damage to the cell’s DNA. For example, the damage caused by chemotherapy drugs to tumour cells.
• The more MGMT protein that the tumour produces, the less effective the chemotherapy drug is expected to be, as the protein will repair the damage to the tumour.
• The production of the MGMT protein is controlled by the MGMT gene.
• Some tumour cells have a change in their MGMT gene. This change is called methylation.
• If the MGMT gene is methylated, it effectively turns the gene off.
• If the MGMT gene is turned off, less MGMT protein is produced in that cell.
• If there’s less MGMT protein to repair the tumour cell,
  a chemotherapy drug is more likely to be effective.
• The more cells in the tumour that are methylated, the more cells will be damaged by the chemotherapy drug.
• The MGMT test estimates how much of the MGMT protein is likely to be produced in the tumour cells and states it as the amount (percentage) of methylation.

There’s some debate about what percentage marks a tumour as methylated and what as unmethylated. As a result, the test isn’t 100% accurate.

TERT promoter mutation test

When found with 1p/19q co-deletion and IDH-mutant biomarkers, the TERT promoter mutation suggests a diagnosis of oligodendroglioma, and predicts greater benefit from chemotherapy and radiotherapy and longer survival, particularly in grade 2 and 3 gliomas.

However, when the TERT mutation is found on its own in grade 2 and 3 gliomas, it predicts poorer survival. This suggests the need for early, more aggressive treatment.

When the TERT mutation is found with IDH-wildtype, this suggests a diagnosis of glioblastoma. In higher grade gliomas, such as glioblastoma, the TERT mutation is associated with poor overall survival.

It’s thought that the TERT mutation may also worsen the poor response to treatment (temozolomide and radiotherapy) in MGMT unmethylated glioblastomas.

Frequently found in adult diffuse gliomas (grades 2 and 3) and often in astroctyomas with IDH1/2 mutations, these biomarkers are useful in confirming the diagnosis of these tumours.

Tumours that are IDH-mutated and have mutations in ATRX and TP53 grow more slowly than tumours without the IDH-mutation, but have also been found to be resistant to radiotherapy.

This means radiotherapy is less likely to kill these tumour cells, and so is less effective in tumours with these mutations.

However, in low grade gliomas, if the radiotherapy is combined with chemotherapy drugs that block the repair of DNA, this can result in longer survival than receiving radiotherapy alone.

TP53 has also been found to help predict prognosis in the sub-type of medulloblastomas known as SHH (sonic hedgehog) type. SHH types of medulloblastoma with a mutation in TP53 tend to have a worse prognosis.

There are 2 different mutations in the BRAF gene that may be of interest. These are the KIAA1549-BRAF fusion gene in childhood brain tumours and the BRAF V600E mutation in adult brain tumours.

What is the BRAF test?

The BRAF test (along with other investigations) can sometimes help determine whether a tumour is an astrocytoma (grade 1 tumour) rather than another type of astrocytoma, if there’s uncertainty. These tumours are more common in children than adults.

There is some evidence that a mutation in the KIAA1549-BRAF fusion gene can cause poorer outcomes in low grade gliomas in children.

The BRAF V600E mutation in adults may increase the growth and spread of tumour cells. This is being investigated as a target for various drugs.

Is the BRAF test suitable for me?

BRAF testing is only clinically useful in a few selected tumour types and is most commonly used to determine whether a tumour is a grade 1 astrocytoma.

If you’re interested in BRAF testing, please speak to your neuro-oncologist for information and advice.

How does the test work and what does it show?

BRAF is a gene that makes a protein called B-raf. The B-raf protein is important because it sends signals to direct the growth of cells within our body. This is known as the MAPK pathway inside the cell.

Research has found that some brain tumours (types of grade 1 and 2 astrocytoma, including grade 1 pilocytic astrocytoma) may have a fault with their BRAF gene.

The fault leads to the BRAF gene permanently sending signals that make cells divide and create copies of themselves. This uncontrolled growth of cells contributes to tumour formation.

A mutation in the EGFRvlll gene is found in about 20-30% of glioblastomas, and is tumour-specific. This means it’s not found in normal brain tissue.

As a result, its presence can confirm a diagnosis of glioblastoma. Although it’s important to note that its absence doesn’t mean it’s not a glioblastoma.

As it only appears in tumour cells, it could also be used as a target for treatments, as well as predicting prognosis. Research is underway and this test isn’t routinely offered.

Recent research has identified markers, which can predict prognosis, in particular sub-types of childhood medulloblastomas – the sub-types known as SHH (with TP53 wildtype), Group 3 and Group 4.

A pattern of chromosome gains and losses was found that could separate these sub-types, normally classified as standard-risk, into favourable-risk and high-risk categories.

Those in the favourable-risk group would need less intensive, aggressive chemotherapy, and so have fewer side-effects.

Sometimes when a cell is dividing, a mistake can be made and 2 separate genes can fuse together. These fusion genes can make fusion proteins.

It’s been found that children with certain types of brain tumour and fusions of the YAP1 protein had better prognoses than children without the fusion, known as YAP1-wildtype. These include childhood supratentorial subependymomas and ependymomas.