Molecular Signatures

Molecular signatures represent what info

distinct patterns of gene expression, mutations, epigenetic alterations, or proteomic changes that characterize a specific cancer type or tumour behaviour

Criteria for Molecular Signature to be clinically useful

They must diagnose a particular cancer, prognosticate the patient’s journey or predict response to treatment

Chronic myeloid leukemia (CML), BCR::ABL1 positive, is a myeloproliferative neoplasm (MPN) characterized by

clonal granulocytic proliferation

What mutation leads to the formation of the chimeric fusion gene BCR::ABL1, which is responsible for production of the oncoprotein BCR::ABL1

Reciprocal translocation t(9;22)

Problem with BCR::ABL1 protein in CML

It has uncontrolled tyrosine kinase activity, causing abnormal pluripotent hematopoietic progenitor cells to initiate excessive production of all myeloid lineage cells

CML treatment (mechanism & drug)

Target with a general tyrosine kinase inhibitor (TKI)

Imatinib(Gleevec)

When did molecular signature research begin

1960 - sequencing of 1 gene at a time

When was p53 discovered

1980s

Why can’t p53 be used in specific cancer predictions

It’s too common - Found in more then 50% of all cancers

p53 can be used to prognosticate what

Aggressiveness

p53 can be used to diagnose what disease

LiFraumenni disease

Expression of Her2 helps predict what

response to traztuzumab

Treatment for ALK fusion protein

Crizontinib

True/False Immunohistochemistry can only test for one protein per tissue slide

True

What proteins does immunohistochemistry test for

ER, PR, HER2, MMR

Method of immunohistochemistry

Antigen retrieval followed by use of monoclonal antibodies to detect antigens

Fish mechanism & info gained

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

(mechanism in pic)

What do these have in common:

• KRAS

• NRAS

• BRAF

• EGFR

• PIK3CA

They are forms of single gene testing

Does proteomics test 1 gene or multiple

Multiple

What 2 things can proteomics be used for

Predict Breast Cancer Molecular Subtypes - Luminal A,B, Her2+,TNBC(Basal)

Predict Colorectal Cancer Molecular Subtypes - Mismatch repair proteins (MMR)

Why is genome sequencing better than Sanger/NGS

Faster

5 steps to NGS

What info does Profiling Comprehensive Genomic Profiling provide

What types of cancers have a high tumour mutational burden

Tumour mutational burden is higher in the tissues that are in constant contact with the mutagen

Effect of increased TMB on a tumour

• More mutations

• More Neoantigens

• More chance of being identified as non-self

• More chance of the tumour being ”seen” by the immune system

• More chance of the cell being eliminated right!

What defines the Premalignant Phase in Breast Cancer

Still has Basement Membrane

PDL1 stands for what

Programmed death-ligand 1

What does PDL1 do & what is the effect of that

Transmembrane protein which binds to PD1 a receptor on T cells which dampens down the immune response through decreased T cell proliferation

True/False TMB is a good biomarker for immunotherapy

No - Not really, patients with high TMB do not respond to therapy

Changes depending on Cancer, e.g. works very well in Melanoma

In what cancers is PDL1 found

Currently indicated in lung cancer, triple negative breast cancer (See Her2), melanoma

Why doesn’t immunotherapy not always work

Not all tumours express PD1 & tumours are built to outsmart the immune system

Is MSI being high a good/bad thing? Why?

Bad - Becomes Tumor-Agnostic

HRD scores assesses DNA damage across a broad section of genes, particularly around BRCA

HRD Scores & Genomic Instability Signatures are used in what cancers

ovarian, prostate, breast, and pancreatic cancers

Oncotype DX is used in what cancer

Gene signature profile Used in Breast Cancer

Oncotype Dx tests DNA, RNA or protein

mRNA is quantified and results applied to a nomogram

What oncotype Dx score would mean someone doesn’t get chemo

Up to about 20-25 you wouldn’t usually get chemo

Name the 7 Clinically Useful Molecular Signatures we have at present

What is Spatial biology used for

Spatial biology looks at stroma changes - can detect if cancer will stay as dysplasia or start to spread

Test tumours microenvironment

What do Single cell transcriptomics do

What are 2 important Cell Markers to test Neighbourhood Expression

CD44

EpCAM

How do we use these advanced diagnostics/prognos tics/predictive biomarkers?

What info/work is done in molecular tumour boards

• Collect tumor & molecular data

• Annotate variants

• Review in MTB meeting

• Generate personalized treatment plan

• Follow up on outcomes

Benefits of molecular tumour boards

• More actionable targets

• Enables precision therapy & trial access

• Encourages multidisciplinary collaboration

• Standardizes molecular interpretation

Challenges of molecular tumour boards

• Variants of unknown significance (VUS)

• Limited therapy/trial access

• Resource & time intensive

High TMB suggests potential benefit from what treatment

immune checkpoint inhibitors (ICIs)

KRAS G12C mutation opens the possibility of what treatment

KRAS-targeted therapy