Distinguishing drivers and passengers Lecture 10

Question 1

Why are drivers difficult to distinguish?

Answer 1

Drivers are the intiating mutations that progress to cancer, passenger mutations are ones that occur as the cancer progresses that are not necessary for it to progress.

Difficult to tell the difference as a mutational change may have different effects in different tissues

Example:

• APC mutation in colon epithelial cell will initiate adenoma
• However in lung epithelial cell, no such change occurs

Question 2

What method can you use to distinguish a driver

Answer 2

• Take a cell type in question and introduce a mutation by CRISPR
• Then study the effect on the tissue in question
• However it is difficult to grow normal cells in culture without introducing another factor to keep them alive

(Is this a valid model given the manipulation of growth factors)

Can also use mouse models

Question 3

Give an example of driver and passenger mutations

Answer 3

• APC knockout mouse leads to intestinal polyposis phenotype (confirmed driver mutation)
• KRAS and BRAF mutations are also found in colorectal cancer but solo knockout does not develop polyps (hence they are passenger mutations) - they are however associated with poor prognosis so are drivers of progression

Question 4

What are the issues with using bioinformatics to identify drivers?

Answer 4

• Cancer has a background mutation rate
• This causes multiple mutations that are passengers, making it difficult to discern noise from genuine signals

Question 5

What methods can be used to discern drivers from background mutations?

Answer 5

1. Identify Genes mutated more frequently
   - Highly sensitive for mutations that are no obviously functionally relevant
2. Identify Genes with a functional impact
   - Done by SIFT and can predict what happens to a protein from a mutation. May not always be right however.
3. Identify mutations that cluster together
   - A gene may require a mutation in a particular protein domain in order to alter function. This is highly sensitive for picking drivers up, but not all tumours display this behaviour

Question 6

What are some mechanisms for loss of function of tumour suppressor genes

Answer 6

Deletion of chromosome region Whole chromosome loss Transcriptional silencing- aberrant methylation of promoter region Virus targeting

Question 7

Lists some other tumour suppressor genes involved in pathways controlling cell proliferation

Answer 7

NF1- Ras-GAP- associated with Neurofibromatosis type 1 and colon carcinoma, astrocytoma

AML APC- beta-catenin degradation- associated with familial adenomatous polyposis coli and colorectal, pancreatic, gastric and prostate carcinoma

PTEN- PIP3 phosphatase- associated with Cowden’s disease, breast and GI tumours and glioblastomas, breast, prostate, thyroid carcinomas

Question 8

List other tumour suppressor genes that are involved in maintaining the integrity of the genome

Answer 8

BRCA 1+2- DSB repair- associated with familial breast and ovarian cancers and breast, ovarian, prostate and pancreas

ATM- DSB repair- associated with ataxia Telangiectasia, leukaemias, lymphomas and breast cancers