DNA diagnosis in malignant melanoma Patrick Willems GENDIA Antwerp, Belgium
Jan 04, 2016
DNA diagnosis in malignant melanoma
Patrick Willems
GENDIA
Antwerp, Belgium
Personalized cancer treatment
• Immunotherapy to stimulate immune response to cancer
PD-1 inhibitors
PD-L1 inhibitors
CTLA-4 inhibitors
• Targeted therapy with designer drugs that target the genetic cause of the tumor
mAB: Herceptin
TKI: Gleevec
Treatment of Malignant melanoma
• surgery• radiation• Chemotherapy• Targeted treatment
– BRAF inhibitor (Vemurafenib)– MEK inhibitor
• Immunotherapy – Interferon (IFN) alfa-2b, IL2 (interleukin 2) – CTLA-4 inhibitors (Ipilimumab)– PD-1 inhibitors (Pembrolizumab and nivolumab)
Problems in personalized cancer treatment
• Immunotherapy
Very Expensive (100-300.000 Euro/year
Few biomarkers (companion diagnostics)
• Designer drugs
Expensive (50-100.000 Euro/year)
Biomarkers (companion diagnostics)
Problems in personalized cancer treatment
The very high cost of personalised treatment makes
companion diagnostics (cancer biomarkers) necessary
Cancer biomarkers
tumor material (biopsy)
blood (liquid biopsy)
Market for tumor biomarkers in Liquid biopsies
TARGETS DRUGS SEQUENCING
Liquid biopsy market
for tumor biomarkers:
40 Billion USD per year
(Illumina estimate)
PHYSICIAN
Current paradigm
sampleResult
Pathological studies
PATIENT
PATHOLOGIST
general
treatmentvisit
Lab
PHYSICIAN
Future paradigm
sampleResult
Molecular testing
PHARMA
PATIENT
LAB
Personalised
treatmentvisit
Pathologist
Cancer Morbidity and Mortality
Melanoma : 1-8 %
New cancers per year in Belgium
• Lung : 7.100
• Colon : 6.500
• Prostate : 8.800
• Breast : 9.700
• MM : 1.500
TOTAAL : 65.000
Incidence MM
• Higher in sunny countries
• Higher in light skin people
• Increasing everywhere
Skin cancer
• Basal cell carcinoma :75 %
• Spinocellular epithelioma: 5%
• Melanoma : 10 %
• Other : 10 %
Malignant melanoma
• Melanoma is a malignant tumor of melanocytes.
• Fifth most common cancer in men and the seventh in women
• 76.100 new cases in 2014 in the US
• 9.710 deaths in 2014 in the US
• Five-year survival rates for patients with metastatic disease < 10%
Personalised targeted treatment of MM
Personalised targeted treatment
inhibits specific somatic mutations
that cause MM
These mutations are patient-specific
These mutations can be detected
by molecular studies of
tumor material (biopsy)
blood (liquid biopsy)
Why liquid biopsies for MM ?
• Common cancer
• High mortality
• High load of driver oncogenic mutations
• Druggable targets
Inheritance of cancer
• Breast Cancer : 10 %• Colon cancer : 5-10 %• Prostate cancer : low• Lung cancer : very low
• Melanoma : 10 %
Majority of cancers are caused by genetic anomalies in the tumor
(somatic mutations)
Minority of cancers is inherited (germline mutations) :
Germline mutations in MM
P
Gene/Locus Protein Function
CDKN2A
(cyclin-dependent kinase inhibitor 2)
AD
20 -40 %
p16 (INK4)
p14 (ARF)
p16 : CDK inhibitor
p14 : binds MDM2- p53
CDK4
(cyclin-dependent kinase 4)
AD
<10 fam
control of cell proliferation
MC1R melanocortin-1 receptorXRCC3 Risk factor
X-ray repair cross-complementing protein 3
DNA repair protein
MITF Risk factor microphthalmia-associated
transcription factortranscription factor
TERT Risk factor
telomerase reverse transcriptase
Telomerase integrity
POT1 Risk factor Telomerase integrity
ACD Risk factor POT1-interacting protein 1 Telomerase integrity
TERF2IPRisk factor
TERF2-interacting protein Telomerase integrity
BAP1 AD Breast cancer associated prtotein
Inheritance of MM
10 % germline mutations
MANY somatic mutations
Cancer genes and mutations
• 140 driver genes • 60 % TSG• 40 % oncogenes
• > 1000 driver gene mutations(Most tumors 2-10 driver gene mutations)
• Millions (?) passenger gene mutations(Most tumors 10-100 passenger gene mutations)
Driver and passenger gene mutations
Tumors with high mutation load
due to Mutagens or genomic instability
form many neoantigens
and are candidates for immunotherapy
TUMOR MUTATIONS EXPLANATION
HNPCC 1782 Genomic instability
Lung 150 Mutagen (smoke)
Melanoma 80 Mutagen (sun)
Somatic mutations in cancer
P
Melanoma Breast Lung Colon Prostate
TP53 10 23 34 48 16
KRAS Few < 10 19 35 5
NRAS 13-25
BRAF 10-50 Few 1-4 8-15 Few
PIK3CA Few 26 4 22 2
EGFR Few < 10 34 < 10 4
MLL3 Few 7 10 12 5
CTNNB1 2-3 < 10 < 10 < 10 4
Somatic mutations in MM
P
Gene % Mutations Targeted therapy
BRAF Activating point mutations 10-50 Dabrafenib, vemurafenib
NRAS Activating point mutations 13-25 MEK162
KIT Activating point mutations 2-6 Dasatinib, imatinib
MEK1 Activating point mutations 6 Trametinib, MEK162
CTNNB1 Activating point mutations 2-3 Cyclin D1 inhibitor
CDKN2A Deletions 50
CDK4 Activating point mutations 10 LY2835219
GNA11 Activating point mutations 2
PTEN Deletions 20-40
p53 Activating point mutations 10
GNAQ Activating point mutations 1
PIC3CA Activating point mutations 5
Overall 60-70
Somatic mutations in MM
P
Gene % Mutations
SkinNormal
Sun
SkinMuch sun
Mucosa Acra Eye
BRAF + 50-60 10 5-10 15-25 < 1
NRAS + 20 10-15 5-15 10-15 <1
KIT + < 1 2 20 15 <1
CDK4CCND1
+ Low Low High High Low
CDKN2A _ Low Low High High Low
CNV MANY MANY
Other BAP1GNAQGNA11
Somatic mutations in uvual MM
P
Gene % Mutationsin MM
% Mutationsin uveal MM
BRAF 50 % < 1 %
NRAS 13-25 % < 1 %
MEK1 6 % < 1 %
KIT 2-6 % < 1 %
CTNNB1 2-3 % < 1 %
GNA11 2 % 32 %
GNAQ 1 % 50 %
BAP1 < 1 %
Cell growth and survival pathway
Cell growth pathway
• Ligands
• Receptors : KIT (EGFR, HER2, MET)
• Secondary messengers : 2 pathways :
1. MAPK pathway : RAS, BRAF, MEK, ERK, Cyclins, CDK4/6
2. PI3K / AKT pathway : PI3K, PTEN, AKT, mTOR
Designer molecules
DNA testing to orient personalised treatment
P
Gene
% Mutations Targeted therapy
BRAF 10-50 Dabrafenib, vemurafenib
NRAS 13-25 MEK162
MEK1 6 Trametinib, MEK162
KIT 2-6 Dasatinib, imatinib
CTNNB1 2-3 Cyclin D1 inhibitor
CDK4 10 LY2835219
DNA testing to follow treatment and detect metastasis and resistance
P
Gene
% Mutations Targeted therapy Respons ResistanceRelaps
BRAF 10-50 Dabrafenib, vemurafenib
50 % Most
NRAS 13-25 MEK162
Resistance to BRAF inhibitors with reactivation opf MAPK pathway
P
Gene Mechanism
BRAF Amplification Splice variants
NRAS Activating point mutation
MEK1 Activating point mutation
MEK2 Activating point mutation
PTEN loss Activating PI3K/AKT pathway
PI3CA Activating PI3K/AKT pathway
Cell growth and survival pathway
Combination therapy BRAF en MEK inhibitors
P
BRAF MEK
Dabrafenib Trametinib
Vemurafenib Cobimetinib
Resistance to BRAF-MEK inhibitors combi with reactivation of MAPK pathway or PI
P
Gene Mutation Mechanism
BRAF Amplification Splice variants
Activation MAPK pathway
NRAS Activating point mutation Activation MAPK pathway
MEK1 Activating point mutation
Activation MAPK pathway
MEK2 Activating point mutation
Activation MAPK pathway
PTEN loss Activating PI3K/AKT pathway
PI3CA Activating PI3K/AKT pathway Activating PI3K/AKT pathway
Cell growth and survival pathway
Resistance to BRAF-MEK inhibitors combi with reactivation of MAPK or PI3K pathway
P
Mechanism Therapy
Re-Activation MAPK pathway
Inhibition distal MAPK pathway
ERK inhibitors
Activating PI3K/AKT pathway
Inhibition PI3K/AKT pathway
PI3K inhibitorsAKT inhibitorsmTOR inhibitors
Why perform genetic studies on tumor DNA ?
• Initial diagnosis and prognosis
• Monitoring recurrence – metastasis
On which tissue should genetic studies be performed ?
• If melanoma occurs in different family members :
Genetic studies on DNA from blood to identify a germline mutation :
CDKN2A - CDK4 (melanoma)
BAP1 (uveal melanoma, mesothelioma)
• If melanoma is sporadic :
Genetic studies on Tumor DNA or liquid biopsy to identify a somatic mutation
BRAF
NRAS
KIT
.
Genetic studies to identify somatic mutations
• FFPE material of the tumor
Analysis of DNA
from Formaldehyde Fixed-Paraffin Embedded
Melanoma tissue
• Liquid biopsy
Analysis of DNA from circulating tumor cells in blood (ctDNA)
Ct DNA
cell-free DNA (cfDNA) is released from healthy, inflamed or cancerous tissue undergoing apoptosis or necrosis
circulating tumor (ctDNA) is only a small fraction of cfDNA in blood
cell-free DNA (cfDNA)
• Cell-free DNA (cfDNA) in plasma of healthy individuals : Mandel and Métais (1948)
• A proportion of cfDNA in pregnant women is fetus-derived (cffDNA) : Lo et al. (1997)
• Non-Invasive Prenatal testing (NIPT) : 2012 : start
2015 : > 1 million tests
Market : 4 billion USD
• Increased concentrations of cfDNA in the circulation of cancer patients : Leon et al. (1977)
• A proportion of cfDNA is tumor-derived : Stroun et al. (1987)
• Circulating tumor DNA (ctDNA) testing (liquid biopsy) : 2015 : start
Market : 40 billion USD
Advantages of liquid biopsies vs FFPE
• No biopsy needed
• Better representation of :
• Total mutation load• Mutations in metastatic cells• Reaction to therapy• Development of resistance
ctDNA
circulating tumor DNA
testing in blood
for detection of cancer
www.circulatingtumorDNA.net
Technology to detect mutations in ctDNA
Next gen sequencing (NGS) + specific technology
• Digital PCR (dilution over many wells)
• Epcam selection for epithelial tumors
• Selection of mutant sequence
Mutant Allele - specific PCR
Companies focusing on ctDNA
• Pangaea Biotech• Cynvenio• BGI• Agena Bioscience • Boreal Genomics • Chronix Biomedical • Genomic Health • Guardant Health• Inivata• Molecular MD • Myriad Genetics• Natera • Personal Genome Diagnostics• Sysmex Inostics• Trovagene
Liquid biopsy market
for tumor biomarkers:
40 Billion USD per year
ct DNA testing on liquid biopsy for malignant melanoma
1. DESCRIPTION : ct DNA testing on liquid biopsies :
• BRAF: 10-50 %– V600E : 80–90% – V600K : 5-12% – V600R or V600D : 5%
• NRAS : 13-25 %– positions 12, 13, or 61
2. SAMPLE : blood in specific test kits with Streck tubes provided by GENDIA
3. TURNAROUND TIME : 3 weeks
4. PRICE : < 1000 Euro
How offer ctDNA testing to your patients ?
1. Refer to our consultation :
Email [email protected] to ask for an appointment
2. Take blood yourself :
Email [email protected] to ask for kits
www.circulatingtumorDNA.net
www.circulatingtumorDNA.net