Prevision Med & Molecular Testing

What does Peto’s Paradox explain

Why don’t whales get cancer - increased ratio of tumour suppressor genes to oncogenes

What’s p53

Guardian of the genome - tumour suppressor gene (TSG) - halt cell growth

Chemotherapy vs Refined chemotherapy vs Targeted MAB therapy

Chemotherapy kill every cell that divides

Refined chemo kills most rapidly dividing cells

Targeted MAB kill only cancer cells that have this target

Match the molecular target to each cancer: GI/Colorectal, Lung, Breast, Melanoma

ROS1, KRAS, EGFR, NRAS, BRAF, MSI/MMR, Oncotype, Her2, ER, PR, Kit, PDGFR, PIK3Ca, PDL1, NTRK, Alk, CKIT, BRCA, Ki67

GI/Colorectal: KRAS, NRAS, BRAF, MSI/MMR, Her2, Kit, PDGFR, PDL1, NTRK

Lung: EGFR, KRAS, NRAS, BRAF, MSI/MMR, Her2, kit, PDGFR,PDL1, Alk, ROS1, NTRK

Breast: ER, PR, Her2, PIK3Ca, PDL1, Oncotype, BRCA, Ki67, NTRK

Melanoma: BRAF, PDL1, NTRK, CKIT(mucosal melanoma)

In which molecular targets is the gene altered (e.g. insertion / deletion)

KRAS, NRAS, BRAF, EGFR, PDGFRa, CKIT, PIK3CA

In which molecular targets is the chromosome altered (e.g. oncogene is paired with another driver gene)

ALK, ROS1, NTRK

In which molecular targets is the gene important in protecting against cancer (e.g. oncogene is paired with another driver gene)

MSI/MMR

In which molecular targets does the gene hide the cancer from the immune system

PDL1

In which molecular targets does the gene have increased expression

HER2, ER, PR

What does PCR/Sequencing allow use to know

Looks at the genetic code in sequence

How does PCR work

• Amplify the target DNA with PCR

• For single gene tests can just use PCR product expansion to detect gene variants

• Or for multiple genes can do massive parallel sequencing AKA Next Generation Sequencing (NGS)

Explain the process of Next Generation Sequencing

• Tumour tissue sample

• Extract DNA

• Create a DNA (RNA sometimes) library

• Amplify the library on beads

• Sequence from the beads

2 options for sequencing methods

Ion detection(Ion torrent)

Colorimetric (Illumina)

EGFR sensitising mutation in lung cancer means it will respond to what treatment

Tyrosine kinase inhibitors (TKIs)

EGFR sensitising mutation in lung cancer means it will respond to Tyrosine kinase inhibitors (TKIs), except if they have what mutation

Unless there is a resistance mutation e.g T790M

What does ISH/Sequencing allow use to know

Looks at the structure of the chromosome - Detection of fusion oncoproteins which are constitutively activated by a translocation

Explain the process of FISH

• Fusion probe or break apart probe to detect these

• Two probes around the ALK gene

• Both fluoresce different colours

• When a fusion occurs they “break apart” and are separated

• If normal then they are overlapping

• Doesn’t tell you the partner gene but tells you there is a translocation present

If there is an ALK or ROS translocation in non-small cell lung cancer then the patient may respond to what treatment

Crizotinib

Neurotrophic tyrosine kinase receptor (NTKR) family is seen in lots of cancers. Where is it found & what does it do

Membrane bound receptor involved in cell differentiation

Cancers with the NTRK biomarker generally repsond well to what treatment

entrectinib

What does Immunohistochemistry allow use to know

Looks at the protein expression

How does IHC work

Use monoclonal antibodies to detect the proteins (antigens) expressed on tumour tissue on a glass slide

If a breast cancer expresses hormone receptors, (O)Estrogen or Progesterone, ER or PR then the patient will respond to what treatment

Anti-hormone therapy - tamoxifen

If a breast cancer overexpresses Her2 then the patient may receive what therapy

Herecptin - a monoclonal antibody therapy against the Her2 protein

Her2 is found where & does what

Surface receptor

Responsible for growth

Her2 is aka (2)

Her/neu, ERBB2

Her2 overexpression is seen in what 3 cancers mainly

breast cancer

gastric cancer

colorectal cancer

Her2 protein overexpressed on the tumour surface will score positive on IHC. But how can we test for it when it isn’t very strong?

In situ hybridisation (DDISH/FISH)

Most important 4 Mismatch repair proteins

• MLH1

• PMS2

• MSH2

• MSH6

(When working the four combine to repair mismatches in the DNA)

What would infer that the problem with the cancer is an issue with he MMR proteins

If errors are detected in microsatellite region then this infers problems with the protein expression

MMRs would usually fix these

How do we detect a lack of a functional MMR gene

By negative IHC

(as in if there’s no expression that’s considered the problem - different to a + IHC)

Can also be tested by DNA analysis of the microsatellite regions

2 possible causes of MMR deficiency

Lynch Syndrome

Muir Torre Syndrome

What does PDL1 stand for

Programmed death-ligand 1 (PD-L1)

Role of PD-L1

Aliases CD274 and B7-H1 → dampens down the immune response through decreased T cell proliferation

What can we find out from a liquid biopsy