Annual GIST Breakfast
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Transcript of Annual GIST Breakfast
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Annual GIST Breakfast
Heinrich & Corless LaboratoriesKnight Cancer Institute
Oregon Health & Science University
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• An review of projects and the people working on them
• Corless group:• Wild-type GIST project• Heinrich group:• Drug screening team • Combination therapy • Yeast model of SDH mutant GIST• Clinical research program
Topics
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Ion Torrent PGM
• Massively parallel (next-gen) sequencing
• Performed on a semi-conductor chip
www.iontorrent.com
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Cancer Gene PanelsBased on Semiconductor Sequencing
Panel # Genes
Availability
Non-small cell lung ca panel
23 Now available
GI stromal tumor panel 23 Now availableAML / MDS panel 42 Now availableGeneral solid tumor panel(Melanoma, colorectal ca, many others)
37 Now available
Lymphoma / myeloma panel
TBD Fall 2013
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AKT1 KRAS RB1AKT2 MAP2K1 SDHAAKT3 NF1 SDHAF1ATM NRAS SDHAF2BRAF PDGFRA SDHBCDKN2A PIK3CA SDHCHRAS PTEN SDHDKIT PTPN11 TP53
GIST Panel Using Next-Gen DNA Sequencing
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Cell Cycle and Wild-Type GIST Projects
• Cell cycle project • Collaboration with Jonathan Fletcher’s group, and others• Analyzing ~85 GISTs to determine the relationship between
malignant behavior and alterations in the following genes: TP53, RB1, CDKN2A
• Goal: be able to predict which GISTs are most likely to come back after initial surgery
• Wild-type GIST project• Collaboration with several groups in Europe• Analyzing ~40 WT GISTs to determine what genes are driving
their growth• Includes the SDH genes, which have recently been implicated in
Carney-Stratakis syndrome
Marina Pukay Dylan Nelson Tanaya Neff Rebecca O’Gara
Carol Beadling, Ph.D.
Nancy Collias, Ph.D.
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KIT Exon 1165%
KIT Exon 80.1%
KIT Exon 98%
KIT Exon 132%KIT Exon 17
1%PDGFRA Exon 12
2%
PDGFRA Exon 140.1%
PDGFRA Exon 18 other
3%
PDGFRA D842V
5%
SHDA/B/C/D Mutation (Carney-Stratakis)
6%Loss of SDHB ex-pression6%
BRAF2%
RAS gene mutation0.1%
NF10.2%
Molecular Subtypes of GIST
Imatinib
Crenolanib(?)
SunitinibSorafenib
Regorafenib
Vemurafenib
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Moving Forward
Ion Torrent ProtonIon Torrent PGM 4-8 samplesper chip
40-80 samplesper chip
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When is a WT GIST not a WT GIST?
Mutations Found using NGS Panel in 32 WT GIST Specimens from a Clinical Study
No mutation (n=19)KIT (n=4)NF1 (n=6)SDH (n=3)
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Comparison of Subgroups of KIT/PDGFRA WT GIST
RAS-P MUTANT GIST
NF-1 RAS-BRAF
SDHB+ SDHB+
IGF1R- IGF1R-
Young Adults/ Adults Adults
Equal sex Equal sex
Multifocal No multifocal
Small intestine Gastric/Small intestine
QUADRUPLE Negative GIST
No RAS-P/No SDH
SDHB+
To be defined
Any age?
To be defined
To be defined
Any site?
To be defined
SDH DEFICIENT GIST
SDH mutation NO SDH mutation
SDHB- SDHB-
IGF1R+ IGF1R+
Pediatric/Young Adults Adults
Prevalence of female Prevalence of female
Often Multifocal No multifocal (?)
Gastric Gastric (?)
Lymph nodes metastases
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Kinase Inhibitor Screening Team
• Goals• To characterize the activity of novel kinase inhibitors against
GIST-associated KIT mutations (or downstream signaling pathways) using cell lines expressing different KIT mutations
• help select promising agents to move into GIST clinical studies
• To collaborate with other GIST biologists to more rapidly evaluate promising agents and novel targets
• Academic labs (Fletcher, Debiec-Rychter, Druker, etc.)• Pharma companies (Novartis, Ariad, AROG, etc.)
Diana Griffith Arin McKinley Janice Patterson Ajia Town
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Kinase Inhibitor Screening Team:Major Accomplishments 2013-2014
• Profiling of regorafenib against GIST-associated mutations• Correlation with outcomes in patients treated as part
of phase 2 study• Study of post-regorafenib surgery or biopsy
specimens to identify mechanisms of regorafenib-resistance
• Profiling of ponatinib against GIST-associated mutations• Lead to phase 2 study that opened June 2013 (OHSU,
Dana Farber, FCCC)• Preliminary results to be presented ASCO 2014
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Combination Therapy
Alison Macleod Ph.D.Lilli Klug, future Ph.D.
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Imatinib Treatment of Metastatic GIST: How Long?
Le Cesne et al. Lancet Oncology. 2010;11:949.
Persistence
Resistance
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PrimaryMutations
Exon 13: 1%K642E
Exon 9 : 12%
Exon 11: 70%
Exon 17: 1%N822H/K, D820Y
ProteinDomain
Ligand binding
JM
ATP binding
Activation Loop
Exon 13 V654A
T670I
D816A/G/H/V
D820A/E/G/YN822H/KY823D
IM SU
A829P
Secondary Mutations
DrugSensitivity
Exon 14
Exon 17
Exon 18
Membrane
ResistantIntermediateSensitive
REG
NR
NR Not reported
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GIST Stem Cells
GIST Progenitors
Mature GIST
KIT-dependent, Imatinib-sensitive
KIT-independent, Imatinib-resistant
GIST Stem and Progenitor Cells are Resistant to Imatinib
Adapted from Heinrich et al. Lancet Oncology 2010
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Causing a “Traffic Jam”inside a Cancer Cell
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Finding Combination Treatments to kill KIT-mutant cells
24,000 different types of marbles = 24,000 different genes50 million marbles to be counted and sorted into 24,000 categoriesProblem: How to identify changes in expression induced by therapy
Analysis using RNASEQ (analogous to counting a mountain made up of 50 million marbles)
DNA RNA Protein
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How does combination therapy kill KIT-mutant cells: Analysis using RNASEQ
Blue 3/20Pink 4/20Gray 2/20Green 3/20Yellow 2/20
Blue 3/20Pink 8/20Gray 1/20Green 1/20Yellow 2/20
Combination therapy
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Analysis of RNA-Seq Data
KEGG Pathway analysis
4 target pathways
Removed targets not associated with the KIT/NFAT network49 targets
Removed targets with expression 0.5<x <2.0 or p-value >0.002378 targets
Removed uncharacterized and mimimally expressed genes9,164 targets
RNA-Seq Data20,207 targets
B.
Alison Macleod, Ph.D.Carol Beadling, Ph.D.Janice Patterson, Grad studentLilli Klug, future Ph.D.
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50 random genes whose expression was not affected by combination therapy
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• Identified abundance of JAK-STAT pathway targets
Alison Macleod
JAK-STAT pathway down regulated upon KIT inhibition
p value= 0.00097
KEGG Pathway Target
JAK-STAT MYC, BCL2L1, CCND2, OSM, CISH, SOCS1, IL2RA, IL21R, IL7R, CBLC
“Cancer” FOS, CCND1, VEGFA, MMP2, MYC, BCL2, BCL2L1, CBLC, PDGFRA
Wnt signaling pathway
NFAT1, NFAT2, NFAT3, NFAT4, FOSL, MYC, CCND1, CCND2
MAPK signaling pathway
NFAT1, NFAT3, FOS, TNF, MYC, DDIT3,MYC, PDGFRA, DUSP6
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Inhibiting the JAK-STAT Pathway Synergizes with KIT Kinase Inhibitors
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Yeast Model of SDH-deficient GIST:
Amber Bannon, future Ph.D.E Smith et al., Human Molecular Genetics 16:3136, 2007
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KIT Exon 1165%
KIT Exon 80.1%
KIT Exon 98%
KIT Exon 132%KIT Exon 17
1%PDGFRA Exon 12
2%
PDGFRA Exon 140.1%
PDGFRA Exon 18 other
3%
PDGFRA D842V
5%
SHDA/B/C/D Mutation (Carney-Stratakis)
6%Loss of SDHB ex-pression6%
BRAF2%
RAS gene mutation0.1%
NF10.2%
SDH Deficient GIST
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SDH Deficient GIST
Smith et al., Human Molecular Genetics, 2007
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SDH Deficient GIST
Yang H et al. Clin Cancer Res 2012;18:5562-5571
Methylated DNA: hypermethylation generally associated with gene silencing, can be inherited during cell division
Methylated histones: can activate or inhibit gene expression depending upon context
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SDH Deficient GIST:genome wide DNA hypermethylation
Killian et al., Cancer Discovery 2013
SDH deficient Kinase mutant
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Yeast Model of SDH-deficient GIST:Why use Yeast?
• There are no SDH deficient GIST cell lines• In contrast, there are established yeast strains with deficiency of
SDHA, SDHB, etc. • Yeast strains can be easily manipulated to:
• Study effects of gene replacement• Study effects of protein mutation on function including the
evaluation of 15+ novel SDHA/B mutations that we have seen in clinical specimens
NormalSDH deficientSevere mutationNormalSDH deficientModerately severe mutation
NormalSDH deficientNormal variantNormal variantNormal variant
Panizza E et al. Hum. Mol. Genet. 2013;22:804-815
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Yeast Model of SDH-deficient GIST:Why use Yeast?
• Yeast can be easily manipulated to study effects of reversible SDH protein loss/replacement on DNA and protein methylation
• Yeast provide a model system to evaluate potential therapies that might reverse the effects of SDH deficiency
• Your experiments will smell good, even if the results stink!
• Saccharomyces cerevisiae = Baker’s yeast = smells like bread
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Metabolic Consequences of SDH Deficiency in Yeast
0 50 100 150 200 250 300 350
-0.5
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
Cell Growth Assay
WT pRS416 sc-ura+Dextrose
ΔSDH1 pRS416 sc-ura+Dextrose
ΔSDH2 pRS416 sc-ura+Dextrose
ΔSDH1+ pRS416 SDH1 sc-ura+Dextrose
WT pRS416 sc-ura+Glycerol
ΔSDH1 pRS416 sc-ura+Glycerol
ΔSDH2 pRS416 sc-ura+Glycerol
ΔSDH1+ pRS416 SDH1 sc-ura+Glycerol
Hours
OD
at 6
00nm
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Metabolic Consequences of SDH Deficiency in Yeast
WT Δsdh1 Δsdh20
20
40
60
80
100
120
SDH Activity
Perc
ent o
f WT
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Clinical Study Team
Lindsay ChandlerResearch Coordinator
Wes WenzelResearch Assistant
Tracy WalkerResearch Nurse
Lindsay OvertonOncology Fellow
Tamara OlenyikResearch Coordinator
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Current and Upcoming Clinical Studies• Imatinib/sunitinib/regorafenib resistant GIST: ponatinib
phase 2 will re-open approximately July 1• Imatinib/sunitinib-resistant GIST: phase 1b combination
therapy with imatinib and BYL719 [PI3K inhibitor] is currently open
For more information: Tracy Walker (research nurse) [email protected]
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THANK YOU FOR YOUR GENEROUS SUPPORT!!