Download Dia 1 - Circulating Tumor DNA (ctDNA)

Theradiagnostics
for cancer
Patrick Willems
GENDIA
Antwerp, Belgium
Treatment of cancer
• Surgery
• Radiation
• Chemotherapy
• Personalised treatment
Personalized cancer treatment
Immunotherapy
to modulate immune response :
–
–
–
–
Interferon (IFN) alfa-2b, IL2 (interleukin 2)
CTLA-4 inhibitors
PD-1 inhibitors
PD-L1 inhibitors
Targeted therapy with designer drugs
to target the genetic cause of the tumor
– EGFR inhibitors
– BRAF inhibitor
– MEK inhibitor
Bottlenecks in personalized cancer treatment
• Immunotherapy
Extremely expensive (100-300.000 Euro/year)
Few biomarkers (companion diagnostics)
• Targeted therapy with designer drugs
Very expensive (50-100.000 Euro/year)
Biomarkers (companion diagnostics)
Bottlenecks in personalized cancer treatment
The very high cost of personalised treatment makes
companion diagnostics (cancer biomarkers) necessary
These are referred to as Theradiagnostics
Theradiagnostics
Tumor DNA (FFPE - biopsy)
Circulating tumor DNA (ctDNA in liquid biopsy)
Market for theradiagnostics
TARGETS
DRUGS
SEQUENCING
Theradiagnostics market :
40 Billion USD per year
Current paradigm
PATIENT
general
visit
treatment
PHYSICIAN
Result
sample
Pathological studies
PATHOLOGIST
Lab
Future paradigm
PATIENT
Personalised
visit
treatment
PHYSICIAN
PHARMA
Result
sample
Molecular testing
Pathologist
LAB
The changing face of cancer diagnosis
Cancer Morbidity and Mortality
New cancers per year in Belgium
11 million inhabitants
• Lung :
7.100
• Colon :
6.500
• Prostate :
8.800
• Breast :
9.700
TOTAAL :
65.000
Treatment of cancer
• Surgery
• Radiation
• Chemotherapy
• Personalised treatment :
– Immunotherapy
– Targeted therapy with designer drugs
Immunotherapy for cancer
• CTLA-4 (cytotoxic T-lymphocyte–associated antigen 4) :
ipilimumab, tremelimumab
• PD-1 (programmed death-1) :
nivolumab, pembrolizumab, Lambrolizumab, pidilizumab
• PD-L1 (programmed death-1 ligand) :
BMS-935559, MEDI4736, MPDL3280A and MSB0010718C
• Other checkpoints : TIM3, LAG3, VISTA, KIR, OX40, CD40, CD137
Inhibition immune checkpoints
Biomarkers for immunotherapy
for Colorectal cancer
Few biomarkers for immunotherapy
First real biomarker : MicroSatellite Instability (MSI)
Response to pembrolizumab (PD-1 inhibitor) in CRC
MMR-proficient : 0 %
MMR-deficient : 40 %
NEJM : May 30, 2015 (Vogelstein group)
MSI as biomarker for immunotherapy
MMR deficiency
Genomic instability
Large mutation load in CRC
Many mutant proteins – neo antigens
Immune response with immunotherapy
MSI as biomarker for immunotherapy in CRC
MMR deficiency
Genomic instability
Large mutation load in CRC
Many mutant proteins – neo antigens
Immune response with immunotherapy
Treatment of cancer
• Surgery
• Radiation
• Chemotherapy
• Personalised treatment :
– Immunotherapy
– Targeted therapy with designer drugs
Targeted treatment for cancer
Personalised targeted treatment inhibits
specific mutations that cause cancer
These mutations are patient-specific
Mutations can be detected by molecular studies of :
. tumor material (biopsy) : FFPE, fresh or frozen
. blood (liquid biopsy)
Therapy is dependent upon the specific mutation
Personalised medicine
Which genetic anomalies cause cancer ?
Genetics of cancer
Majority of cancers are caused by genetic anomalies in the tumor
(somatic mutations)
Minority of cancers is inherited (germline mutations)
• Breast Cancer :
10 %
• Colon cancer :
3-5%
• Prostate cancer :
low
• Lung cancer :
very low
Cancer gene mutations
Genes
Mutations
Germline
Somatic
Wellknown genes
Still largely unknown
Limited number of genes
Large number of genes
Cancer-specific genes
Cancer-specific (APC) and aspecific
(BRAF, EGFR, KRAS) genes
1 or 2 mutations per patient
Many mutations in each patient
Large number of different mutations
Limited number
Unknown (novel-private) mutations
Recurrent mutations
Inactivating sequence mutations
Few inactivating sequence mutations
Inactivating hypermethylation (MLH1)
Activating sequence variants
Amplification of genes (HER2)
Deletions of genes (PTEN)
Two step cancer theory
(Knudson)
Retinoblastoma (RB1 gene)
Mesothelioma
Uveal melanoma (BAP1 gene)
Two step cancer theory
(Knudson)
Inherited cancer :
1. Germline mutation in all cells
2. Somatic mutation in cancer cell
Sporadic cancer :
1. No germline mutation
2. Somatic mutations in the 2 gene copies in cancer cell
Multistep cancer theory
(Vogelstein)
Vogelstein et al, Science Aug 22, 2013
Cancer genes and mutations
• 140 driver genes
• 60 % Tumor suppressor genes
• 40 % Oncogenes
• > 1000 driver gene mutations
(Most tumors 2-10 driver gene mutations)
• Millions of passenger gene mutations
(Most tumors 10-100 passenger gene mutations)
Mutations in cancer
• Gate keeper mutations : transforms normal cell into tumor cell
Rb in retinoblastoma
APC in colon cancer
• Driver mutations : confers growth advantage to tumor cell
HER2 in breast cancer
KRAS in colon cancer
• Passenger mutations : accidental mutation not conferring
growth advantage to tumor cell
Any gene
Also driver gene
Driver and passenger gene mutations
TUMOR
MUTATIONS
EXPLANATION
HNPCC
1782
Genomic instability
Lung
150
Mutagen (smoke)
Melanoma
80
Mutagen (sun)
Tumors with high mutation load
due to Mutagens or genomic instability
form many neoantigens
and are candidates for immunotherapy
Somatic mutations
GENE
MECHANISM
TARGETED THERAPY
APC
Inactivating mutation
-----------
TP53
Inactivating mutation
-----------
EGFR
KRAS
Activating point mutations
Gene Amplification
Overexpression ligands
Overexpression nuclear EGFR
Activating point mutations
Cetuximab,
panitumumab
erlotinib, gefitinib,
afatinib
Tipifarnib, lonafarnib
BRAF
Activating point mutations
Dabrafenib,
sorafenib,vemurafenib,
NRAS
Activating point mutations
MEK162
PIK3CA
Activating point mutations
Inactivating somatic mutations in cancer
Cancer-specific
gene
TP53
Breast
Lung
Colon
Prostate
BRCA
---
APC
MLH1
---
23
34
48
16
Activating somatic mutations in cancer
Melanoma
Breast
KRAS
NRAS
13-25
BRAF
10-50
PIK3CA
CTNNB1
2-3
CRC
Prostate
17
35
5
3-5
26
EGFR
Lung
1-4
8-15
4
22
2
34
??
4
48
4
Cell growth and survival pathway
Cell growth pathway
• Ligands
• Receptors : EGFR
• Secondary messengers : 2 pathways :
1. MAPK / RAS pathway : RAS, BRAF, MEK, ERK, Cyclins, CDK4/6
2. mTOR / AKT pathway : PIK3CA, PTEN, AKT, mTOR
Classical treatment in colon cancer
• Surgery
• Chemotherapy
• In case of EGFR mutation or overexpression
Start anti EGFR therapy :
• mAB : cetuximab, panitumumab
• TKI : erlotinib, gefitinib, afatinib
EGFR mutations
• Lung Ca : activating mutations in TK domain
• Glioblastoma : activating mutations in Extracellular domain
• Colorectal ca : unclear :
Overexpression membrane EGFR (mEGFR)
Overexpression nuclear EGFR (nEGFR)
Gene Amplification
Overexpression ligands
Activating point mutations
EGFR status
Anti-EGFR therapy
mAB : cetuximab, panitumumab
TKI : erlotinib, gefitinib, afatinib
EGFR Resistance : T790M mutation
Inhibitors of EGFR with the T790M mutation :
AZD9291
CO-1831
EGFR resistance : KRAS and BRAF mutations
TREATMENT
E
G
F
R
K
R
A
S
W
I
L
D
RELAPSE
EGFR resistance in CRC: KRAS and BRAF mutations
Resistance against EGFR therapy
– KRAS mutation : 40 %
– BRAF mutation : 8-15 %
– NRAS mutation : 1-6 %
• Mostly pre-existent – selection due to anti-EGFR treatment
• Also new due to ongoing mutagenesis ?
Addition of BRAF or MEK inhibitor
EGFR resistance in CRC : PIK3CA mutation
Resistance against EGFR therapy
PIK3CA mutation : 10-30 %
PTEN loss
Addition of mTOR inhibitor
PIK3CA
• PIK3CA encodes p110 subunit of Phosphatidylinositol 3-kinase
PIK3 phosphorylates PI
PI is central in AKT/mTOR pathway
• PIK3CA driver mutations in :
–
–
–
–
Breast cancer (26 %)
Endometrium (23 %)
Colon (22 %)
Non-tumor : somatic overgrowth syndromes
(Cowden and Clove syndrome)
• Therapy : PIK3, AKT, mTOR inhibitors
Why genetic studies on tumor DNA ?
• Initial diagnosis and prognosis
• Monitoring recurrence – metastasis
Genetic studies in cancer
• Blood DNA
If CRC occurs in different family members :
Genetic studies on DNA from blood to identify a germline mutation (BRCA)
• Tumor
• MSI : in order to determine sensitivity for immunotherapy
• Mutations in EGFR, KRAS, BRAF, NRAS, PIK3CA
to determine sensitivity for targeted therapy
• Liquid biopsy
• Initial theradiagnostics if tumor material is unavailable
• Follow up during cancer treatment
• Screening of high risk patients (HNPCC carriers, BRCA carriers)
Genetic studies of somatic mutations
• DNA studies on tumor material
Analysis of DNA from tumor (FFPE, fresh, frozen)
• Circulating tumor DNA (ctDNA) in Liquid biopsy
Analysis of circulating tumor DNA (ctDNA) in blood
Circulating tumor DNA (ctDNA)
ctDNA
ctDNA from tumor tissue is released
through secretion, necrosis and apoptosis,
but mainly through apoptosis.
cell-free DNA (cfDNA) testing
•
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 liquid biopsies
•
No tissue biopsy needed
•
No FFPE fixation
•
Profiling the overall genotype of cancer
• primary cancer
• circulating cells
• metastases
•
Better evaluation of :
• reaction to therapy
• development of resistance
Tissue biopsy
TISSUE BIOPSY
EGFR TREATMENT
E
G
F
R
K
R
A
S
W
I
L
D
RELAPSE
Liquid biopsy
LIQUID BIOPSY
TREATMENT
E
G
F
R
K
R
A
S
B
R
A
F
W
I
L
D
Companies focusing on Theradiagnostics
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Cynvenio
BGI
Agena Bioscience
Boreal Genomics
Chronix Biomedical
Genomic Health
Guardant Health
Inivata
Molecular MD
Pangaea Biotech
Myriad Genetics
Pathway Genomics
Natera
Personal Genome Diagnostics
Sysmex Inostics
Trovagene
ETC
Theradiagnostics market :
40 Billion USD per year
ct DNA testing on liquid biopsy for CRC
1. DESCRIPTION : ct DNA testing on liquid biopsies :
90 mutations in 9 cancer genes :
•
•
•
•
•
EGFR
TP53
KRAS
BRAF
PIK3CA
•
•
•
•
NRAS
CTNNB1
GNAS
FOXL2
2. SAMPLE : blood in specific test kits with Streck tubes (GENDIA)
3. TURNAROUND TIME : 3 weeks
4. PRICE : 650 Euro
How offer ctDNA testing to your patients ?
1. Take blood yourself :
Email [email protected] to ask for kits
2. Refer to our consultation :
Email [email protected] to ask for an appointment
www.circulatingtumorDNA.net
www.circulatingtumorDNA.net