BRAF and Malignant Melanoma
From gene to cancer therapy
What is cancer?
• All cancers are genetic
diseases
• All cancers derive from
single cells that continually
divide in an unrestrained
manner
• Cancer cells behave in this
abnormal way because of
changes in the DNA
sequence of key genes,
which are known as cancer
genes
Human melanoma cell undergoing cell division
Image credit: Paul Smith & Rachel Errington, Wellcome Images
Key cancer facts
• 1 in 3 people will develop cancer
• 1 in 8 people will die from cancer
• There are approximately 200 types of cancer, each
with different causes, symptoms and treatments
• 309,527 people were newly diagnosed with cancer in
the UK (504 cases for every 100,000 people)
• An individual's risk of developing cancer depends on
many factors, including age, lifestyle and genetic
make-up
Cancer Research UK. Accessed April 2012
http://info.cancerresearchuk.org/cancerstats/incidence/?a=5441
Cancer incidence worldwide
Source: Cancer Research UK. Accessed April 2012
http://info.cancerresearchuk.org/cancerstats/world/the-global-picture/
The 20 most common causes of
death from cancer in the UK, 2009
Source: Cancer Research UK. Accessed April 2012
http://info.cancerresearchuk.org/cancerstats/mortality/cancerdeaths/
What is a mutation?
• Germline mutation
– A change in the DNA sequence that can be
inherited from either parent
• Somatic mutation
– A change in the DNA sequence in cells other than
sperm or egg
– The mutation is only present in the cancer cell and
its offspring (not in the patient’s healthy cells)
How do somatic mutations
cause cancer?
Somatic mutations in cancer
‘Passenger’ mutations
‘Driver’ mutations
(in Cancer Gene)
Types of cancer gene
• There are two main types of cancer genes:
– tumour suppressor genes
– oncogenes
• At present there are over 400 known somatic
cancer genes*
*Source: COSMIC. Accessed April 2012.
http://www.sanger.ac.uk/genetics/CGP/cosmic/
Tumour suppressor gene
These genes normally function to SUPPRESS cell
growth and division
TS
Cancer
Oncogene
Genes which normally function to PROMOTE cell
growth and division in a controlled manner
Ras
Cancer
Malignant melanoma
• Malignant melanoma
originates in
melanocytes, specialised
pigment cells found in the
skin
• Melanoma accounts for
4-5% of all skin cancers
but is responsible for 80%
of deaths
• New treatments are
needed
Advanced melanoma
Image credit: National Cancer Institute
Malignant melanoma in the UK
Source: Cancer Research UK. Accessed April 2012
http://info.cancerresearchuk.org/cancerstats/types/skin/incidence/uk-skin-cancer-incidence-statistics#Trends
Melanoma progression
The activity
• The BRAF gene codes for a signalling protein
• Mutations in BRAF are present in many types of
cancer, including malignant melanoma
• You will be looking for mutations by comparing
the DNA sequence from healthy tissue and
tumours
• Not all of you will find mutations
Part 1: Data analysis
Understanding the data
Ideogram: This represents
chromosome 7 on which the BRAF
gene is located. The red line shows
the region where BRAF is found.
Gene regions: This represents the
genes found in this region.
Sequence reads: This is the data
produced by the DNA sequencing
machine.
Red boxes indicate a change from
the reference BRAF sequence.
Completing the sheets
Consensus
CAC
TGT
AGC
TAG
ACC
AAA
ATC
ACC
TAT
Sense strand
3’
GTG
ACA
TCG
ATC
TGG
TTT
TAG
TGG
ATA
(GTG)
(ACA)
(GCT)
(CTA)
(GGT)
(TTT)
(GAT)
(GGT)
(ATA)
600
599
598
597
596
595
594
593
592
Amino acid
Codon no.
Read this way
5’
How to use the codon wheel
A
C
D
E
F
G
H
I
K
L
Alanine
Cysteine
Aspartic Acid
Glutamic Acid
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
M
N
P
Q
R
S
T
V
W
Y
Methionine
Asparagine
Proline
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophan
Tyrosine
Completing the sheets
Consensus
CAC
TGT
AGC
TAG
ACC
AAA
ATC
ACC
TAT
Sense strand
3’
GTG
ACA
TCG
ATC
TGG
TTT
TAG
TGG
ATA
(GTG)
(ACA)
(GCT)
(CTA)
(GGT)
(TTT)
(GAT)
(GGT)
(ATA)
V
T
A
L
G
F
D
G
I
600
599
598
597
596
595
594
593
Amino acid
Codon no.
592
Read this way
5’
Mark up your sequence
Part 2: Consult COSMIC
Source: COSMIC. Accessed September 2012.
http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/
Part 3: Data discussion
Answers
Sample
Sample 1
Sample 2
Sample 3
Sample 4
Sample 5
Sample 6
Sample 7
Sample 8
Sample 9
Sample 10
Mutation Codon
Yes/No number
Yes
No
Yes
No
Yes
No
Yes
No
Yes
No
600
600
600
600
600
-
Healthy
codon
sequence
GTG
GTG
GTG
GTG
GTG
-
Tumour Healthy
codon
amino
sequence
acid
GAG
V
GAG
V
GAG
V
GAG
V
GAG
V
-
Tumour
amino
acid
E
E
E
E
E
-
How common?
Source: COSMIC. Accessed September 2012.
Live page
How common?
Source: COSMIC. Accessed September 2012.
BRAF mutations
• In which tissues are BRAF mutations most
commonly found?
– thyroid
– large Intestine
– skin
– ovary
COSMIC is a live database, numbers are continually updated
Source: COSMIC. Accessed September 2012.
Live Page
BRAF and melanoma
Source: COSMIC. Accessed September 2012.
Live page
Understanding BRAF function
Understanding BRAF mutation
Part of a larger network
Why sequence melanomas?
Normal
• V600E mutation
discovered in 2002 at the
Sanger
Institute
and
the
Patient
Institute for Cancer
Research
• Identifying a commonly
occurring mutation in a
cancer gene can provide a
potential new drug target
BRAF V600E mutation
Image Credit: Wellcome Trust Cancer Genome Project
G T G = Val
G A G = Glu
Diagnosis and treatment
• How would you identify if an advanced
melanoma patient carried the BRAF
mutation? What treatment would you
prescribe and why?
• How would you treat an advanced melanoma
patient without the BRAF mutation?
Vemurafenib
Images courtesy of Grant McArthur, Jason Callahan, and Rod Hicks of the Peter MacCallum Cancer Centre.
McDermott, Downing and Stratton. N Engl J Med 2011;364:340-50.
Vemurafenib
A 38-year-old man with BRAF-mutant melanoma and miliary, subcutaneous metastatic deposits.
Wagle N et al. JCO 2011;29:3085-3096
©2011 by American Society of Clinical Oncology
Vemurafenib function
Challenges to treatment
Resistance mechanisms