Functional Genomics: Implications in Tissue Pathology
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Transcript of Functional Genomics: Implications in Tissue Pathology
René Bernards
Functional genomics:Implications in Tissue Pathology
The Netherlands Cancer InstituteAmsterdam
The Netherlands
Genotype-driven therapy of non-small cell lung cancer
Crizotinib
Kwak et al, N Engl J Med 2010
Erlotinib Gefitinib
Maemondo et al., N Engl J Med 2010
Endless two-way combinations of cancer drugs
1,000 x1,000 2
= 500,000 combinations
Test each combination in 1,000 patients:
500,000,000 patients needed
Three vignettes on the use of functional genetics to find effective combination therapies
• The case of BRAF mutant colon cancer• The case of KRAS mutant lung/colon cancer• The case of RTK mutant lung cancer
N Engl J Med. 2010 363:809-19Kopetz et al., ASCO 2010
Vemurafenib (PLX4032) - A selective BRAFV600E inhibitor
Differential response of BRAF inhibition in BRAF mutant melanoma versus colon cancer
BRAFV600E mutant CRC cell lines are also less responsive to PLX4032 than melanomas having the
same mutation
CRC
Melanoma
Short-term cell viability assay Long-term colony formation assay
Is feedback regulation responsible for the resistanceof CRC cells to BRAF inhibitors?
infect with shRNA kinome library
PCR amplify bar codes
WiDr(BRAFV600E)
Deep sequence Quantify shRNAs
vemurafenibculture to allow selection
control
Synthetic lethal shRNA screen: Inhibition of which kinase synergizes with PLX in BRAF mutant CRC?Synthetic lethal shRNA screen: Inhibition of which kinase synergizes with PLX in BRAF mutant CRC?
Inhibition of EGFR makes BRAF mutant CRC cellsvulnerable to BRAF inhibition
Inhibition of EGFR makes BRAF mutant CRC cellsvulnerable to BRAF inhibition
Grb
BRAF
EGFR
RAS
MEK
ERK
Cetuximab
MutantMutant
Synergistic response of BRAFV600E CRC to EGFR and BRAF inhibition
Synergistic response of BRAFV600E CRC to EGFR and BRAF inhibition
Cetuximab 1.25 g/mlGefitinib 0.125 MCetuximab 1.25 g/mlGefitinib 0.125 M
VACO (BRAFV600E)VACO (BRAFV600E)
Also seen in WiDr andKM20 (BRAFV600E)Also seen in WiDr andKM20 (BRAFV600E)
+Cetuximab
+Gefitinib
BRAFV600E inhibition causes feedback activationof EGFR
BRAFV600E inhibition causes feedback activationof EGFR
VACO (BRAFV600E)VACO (BRAFV600E)
Also seen in WiDr andKM20 (BRAFV600E)Also seen in WiDr andKM20 (BRAFV600E)
EGFR and BRAF inhibition synergize to induce apoptosis and suppress BRAFV600E CRC tumor growth
Also seen in WiDr (BRAFV600E)Also seen in WiDr (BRAFV600E)Prahallad et al, Nature 2012
Feedback regulation of EGFR by BRAF inhibition
Ligand
CDC25CCDC25C
PI3KPI3K
AKTAKT
VemurafenibVemurafenib
Cetuximab
Mechanism-based rational drug combinations: rapid translation to the clinic
8 months frompublication toclinical trial!
EGFR levels determine response to BRAFInhibition in multiple tumor types
EGFR levels determine response to BRAFInhibition in multiple tumor types
Control
Gefitinib
PLX4032
PLX4032+Gefitinib
Trametinib
Trametinib+Gefitinib
EGFR expression in melanoma is sufficient to confer resistance to BRAF and MEK inhibitors
BRAF mutant melanomas upregulate EGFR during the development of drug resistance
EGFR IHC in brown
Patient 7 Pre vemurafenib
Patient 9 Pre vemurafenib
Patient 7 Post vemurafenib
Patient 9 Post vemurafenib
Total:5/12 patients
became EGFR positive
(40%)
Three vignettes on combination therapies to fight resistance
• The case of BRAF mutant colon cancer• The case of KRAS mutant lung/colon cancer• The case of RTK mutant lung cancer
Nat Rev Cancer 3: 459–465. Nat. Rev. Clin. Oncol., 6 (2009) Cancer Research, 69 (10), 4286-4293 Clin Cancer Res 2012;18:2515-2525
Cell survival and proliferation
Inhibitor
Receptors
MEK inhibitorLow efficacy (PDX assay) for
KRAS mutant tumors
Targeting KRAS mutation with MEK inhibitor
Potential for clinic failure:
+Gefitinib (1uM)
Is the combination of MEK and EGFR inhibitors also effective in KRAS mutant cells?
Gefitinib (1uM)
0.25 0.5 1
Selumetinib (uM)
CRC: SW620(KRASG12V)
NSCLC: H358 (KRASG12C)
0.25 0.5 1
Selumetinib (uM)
0 0.125 0.25 0.5 1
Selumetinib(μM)
H747
SW480
SW620
SW837
CRC
H358
H23
H2030
H2122
NSCLC
RNAi screen for enhancers of MEK inhibitors
ERBB3 activation is mostly dependent on heterodimerization
ERBB3 binding partners
ERBB family
shERBB3
shERBB3
H358 (KRASG12C)
Also seen in H2030, H2122,SW837, SW480 and SW620
Targeting EGFR and ERBB2 sensitizes KRAS mutant cells to MEK inhibitor
+Dacometinib (0.5uM)
+Afatinib (0.5uM)
+Gefitinib (0.5uM)
+Pertuzumab (2.5ug/ml)
0.25 0.5 1
Selumetinib (uM)
• Gefitinib: EGFR inhibitor
• Pertuzumab: ERBB2-targeting monoclonal antibody
• Afatinib: EGFR and ERBB2 inhibitor
• Dacometinib: EGFR, ERBB2 and ERBB4 inhibitor
MEK inhibition induces ERBB2 and ERBB3 transcription
EGFR+ERBB2 inhibitor synergizes with MEK inhibitor to induce apoptosis in KRAS mutant cells
Selumetinib
Afatinib
+-+ +
+-- -
Clev. PARP
p-BAD (S112)
p-BAD(S136)
BAD
p-ERK
ERK1/2
p-p90RSK
p90RSK
p-AKT
AKT
H358
p-BIM(S69)
BIM
Targeting EGFR and ERBB2 sensitizes KRAS mutant cells to MEK inhibitor in a xenograft model
25
0%
34
3%
30
6%
H2122 xenografts
BRAF BRAF
Melanoma
Colon cancer
BRAFi/MEKi
BRAFi/MEKi+
EGFRi
Genotype Tissue type Effective therapy
KRAS KRASColon cancerLung cancer
MEKi+
EGFRi+HER2i
Three vignettes on combination therapies to fight resistance
• The case of BRAF mutant colon cancer• The case of KRAS mutant lung/colon cancer• The case of RTK mutant lung cancer
Resistance to TKIs is a frequent problem in the clinic
Crizotinib
GefitinibErlotinib
Acquired resistance to EGFR inhibitors
Sequist et al., Sci Transl Med 2011 Choi et al., NEJM 2010
* L1196M in EML4-ALK
* Other unknown mechanisms
T790M(49%)
Cell line models matching NSCLC genotypes
PC9 (EGFRDelE746A750)H3255 (EGFRL858R)
Erlotinib Gefitinib
TKI-sensitive NSCLC cell lines
H3122(EML4-ALK)
Finding genes that can cause resistance tocrizotinib in EML4-ALK positive NSCLC
culture to allow selection
crizotinibcontrol
infect with shRNA library
PCR amplify bar codes
H3122(EML4-ALK)
Suppression of MED12 causes crizotinib resistance
shMED12#1shMED12#2
MED12
Transcription Mediator complex
CDK8
L1224F, recurrent in Prostate cancer (5%)
Uterine Leiomyomas (70%)
Exon 2
Mäkinen et al., Science Express 2011; Barbieri et al. Nat Genet. 2012
Exon 26
MED12 mutations in cancers
PC9 (EGFRDelE746A750)
MED12 knockdown causes MEK and ERK activation
ERK
MED12
p-ERK
pLKO
shM
ED12#3
shM
ED12#5
pLKO
shM
ED12#3
shM
ED12i#
5
Gefitinib: - - - + + +
p-MEK
MEK
infect with TRC shRNA kinome library MED12KD
(EML4-ALK)
+ Crizotinibculture to allow selection
control
Resistant
Re-sensitization screen: Which kinase to inhibit to restore the crizotinib sensitivity in MED12KD cells?
infect with TRC shRNA kinome library
PCR amplify bar codes
MED12KD
(EML4-ALK)
Deep sequence Quantify shRNAs
+ Crizotinibculture to allow selection
control
Depleted by Crizotinib
Resistant
Re-sensitization screen: Which kinase to inhibit to restore the crizotinib sensitivity in MED12KD cells?
Suppression of TGFR2 restores the crizotinib sensitivity in MED12KD cells
I
II
TGF activation is sufficient to drive drug resistance
H3122(EML4-ALK)
Downregulation of MED12 leads to elevated TGFR signaling in different tumor types
PC9 (EGFRDelE746A750)
H3122(EML4-ALK)
PC9 A375(BARFV6700E)
Melanoma
PC9 SKCO-1(KRASV12)
ColonNSCLCNSCLC
TGF activates the RAS-RAF-MEK-ERK pathway
Zhang, Y. Cell Research 2009:19 p128
MED12KD also causes resistance to chemotherapies through TGF signaling
Generation of a “MED12KD signature”
H3122; NSCLCPC9; NSCLCSKCO1; colon cancerA375; melanomaHuh7; HCC
Wild type+
MED12KD
Differentially expressed genesin 3 out of 5 cell lines (>2-fold);237 genes
MED12 loss induces an EMT-like phenotype
A MED12KD signature predicts resistance to chemotherapy in stage III colon cancer
Three gene profiles specific for intrinsic subtypes
• A-type profile of 32 genes• B-type profile of 53 genes• C-type profile of 102 genes
Three gene profiles specific for intrinsic subtypes
• A-type profile of 32 genes• B-type profile of 53 genes• C-type profile of 102 genes
Colon cancer also has “intrinsic subtypes”
44
Colon cancer subtypes differ in biology and in response to chemotherapy
TGFR2 inhibitor restores the crizotinib sensitivity in MED12KD cells
And by other means?EMT by MED12 loss
TGFsignaling
response to targeted drugs
TGFR inhibitors
potential treatment strategy:
(also true for EGFR inhibitors)
H3122(EML4-ALK)
Precision medicinePrecision medicine
Alterations in pathwaysAlterations in pathways
Cancer genome analysesCancer genome analyses
Cross talk between pathways Cross talk between pathways
Functional genetic analysesFunctional genetic analyses
Acknowledgements
The people involved:Chong SunSid HuangAnirudh PrahalladWipawadee GrernrumLorenza MitempergherFloris GroenendijkTheo KnijnenburgAndy SchlickerLodewijk WesselsWouter NijkampRoderick Beijersbergen
Collaborators:Federica Di NicolantonioAlberto BardelliPaul RoepmanPeter ten Dijke
Our funding sources:Our funding sources: